bioRxiv Channel: Francis Crick Institute
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This feed contains articles for bioRxiv Channel "Francis Crick Institute"
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https://biorxiv.org
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Myosin II controls junction fluctuations to guide epithelial tissue ordering
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https://biorxiv.org/cgi/content/short/078204v1?rss=1"
Scott CurranCharlotte StrandkvistJasper BathmannMarc de GennesAlexandre KablaGuillaume SalbreuxBuzz Baum2016-09-29doi:10.1101/078204Cold Spring Harbor Laboratory Press2016-09-29
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The FACT complex and cell cycle progression are essential to maintain asymmetric transcription factor partitioning during cell division
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https://biorxiv.org/cgi/content/short/075135v1?rss=1"
Eva HerreroSonia StinusEleanor BellowsPeter H Thorpe2016-09-19doi:10.1101/075135Cold Spring Harbor Laboratory Press2016-09-19
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Protein Kinase C and the stress response pathways are required for kinetochore homeostasis.
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https://biorxiv.org/cgi/content/short/078196v1?rss=1"
Elena Ledesma-FernándezEva HerreroGuđjón ÓlafssonPeter Thorpe2016-09-28doi:10.1101/078196Cold Spring Harbor Laboratory Press2016-09-28
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Free ISG15 as a dimer generates IL-1β-producing CD8α+ dendritic cells at the site of infection
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https://biorxiv.org/cgi/content/short/111658v1?rss=1"
Napolitano, A.van der Veen, A. G.Bunyan, M.Borg, A.Kjaer, S.Beling, A.Knobeloch, K.-P.Frickel, E.2017-02-27doi:10.1101/111658Cold Spring Harbor Laboratory Press2017-02-27
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A simple analytical formula to compute the residual Mutual Information between pairs of data vectors
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https://biorxiv.org/cgi/content/short/041988v1?rss=1"
Jens KleinjungAnthony C.C. Coolen2016-03-01doi:10.1101/041988Cold Spring Harbor Laboratory Press2016-03-01
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Activity-Dependent Control Of Inhibitory Interneuron Number In The Mammalian Cortex
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https://biorxiv.org/cgi/content/short/134916v1?rss=1"
Denaxa, M.Neves, G.Rabinowitz, A.Kemlo, S.Liodis, P.Burrone, J.Pachnis, V.2017-05-17doi:10.1101/134916Cold Spring Harbor Laboratory Press2017-05-17
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Pairwise Hybrid Incompatibilities Dominate During Allopatric Speciation For A Simple Genotype-Phenotype Map Of Embryonic Spatial Patterning
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https://biorxiv.org/cgi/content/short/123265v1?rss=1"
Khatri, B. S.Goldstein, R.2017-04-02doi:10.1101/123265Cold Spring Harbor Laboratory Press2017-04-02
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Rate Of Fixation Of Rare Variants In A Population
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https://biorxiv.org/cgi/content/short/123232v1?rss=1"
Khatri, B. S.2017-04-02doi:10.1101/123232Cold Spring Harbor Laboratory Press2017-04-02
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Genome sequence of a diabetes-prone desert rodent reveals a mutation hotspot around the ParaHox gene cluster
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https://biorxiv.org/cgi/content/short/093401v1?rss=1"
Hargreaves, A. D.Zhou, L.Christensen, J.Marletaz, F.Liu, S.Li, F.Jansen, P. G.Spiga, E.Hansen, M. T.Horn Pedersen, S. V.Biswas, S.Serikawa, K.Fox, B. A.Taylor, W. R.Mulley, J. F.Zhang, G.Heller, R. S.Holland, P. W. H.2016-12-17doi:10.1101/093401Cold Spring Harbor Laboratory Press2016-12-17
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Combinatorial Regulation Of The Balance Between Dynein Microtubule End Accumulation And Initiation Of Directed Motility
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https://biorxiv.org/cgi/content/short/126508v1?rss=1"
Jha, R.Roostalu, J.Trokter, M.Surrey, T.2017-04-11doi:10.1101/126508Cold Spring Harbor Laboratory Press2017-04-11
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Mutational signatures associated with tobacco smoking in human cancer
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https://biorxiv.org/cgi/content/short/051417v1?rss=1"
Ludmil B AlexandrovYoung Seok JuKerstin HaasePeter Van LooInigo MartincorenaSerena Nik-ZainalYasushi TotokiAkihiro FujimotoHidewaki NakagawaTatsuhiro ShibataPeter J CampbellPaolo VineisDavid H PhillipsMichael R Stratton2016-05-03doi:10.1101/051417Cold Spring Harbor Laboratory Press2016-05-03
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Universal Patterns Of Selection In Cancer And Somatic Tissues
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https://biorxiv.org/cgi/content/short/132324v1?rss=1"
10/tumor in endometrial and colorectal cancers. Half of driver substitutions occur in yet-to-be-discovered cancer genes. With increasing mutation burden, numbers of driver mutations increase, but not linearly. We identify novel cancer genes and show that genes vary extensively in what proportion of mutations are drivers versus passengers.nnHIGHLIGHTSO_LIUnlike the germline, somatic cells evolve predominantly by positive selectionnC_LIO_LINearly all ([~]99%) coding mutations are tolerated and escape negative selectionnC_LIO_LIFirst exome-wide estimates of the total number of driver coding mutations per tumornC_LIO_LI1-10 coding driver mutations per tumor; half occurring outside known cancer genesnC_LI
]]>Martincorena, I.Raine, K. M.Gerstung, M.Dawson, K. J.Haase, K.Van Loo, P.Davies, H.Stratton, M. R.Campbell, P. J.2017-04-29doi:10.1101/132324Cold Spring Harbor Laboratory Press2017-04-29
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GOTHiC, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C data
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https://biorxiv.org/cgi/content/short/023317v1?rss=1"
Borbala MifsudInigo MartincorenaElodie DarboRobert SugarStefan SchoenfelderPeter FraserNicholas Luscombe2015-07-27doi:10.1101/023317Cold Spring Harbor Laboratory Press2015-07-27
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Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers
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https://biorxiv.org/cgi/content/short/117291v1?rss=1"
Blakely, C. M.Watkins, T. B. K.Wu, W.Gini, B.Chabon, J. J.McCoach, C. E.McGranahan, N.Wilson, G. A.Birkbak, N. J.Olivas, V.Rotow, J.Maynard, A.Wang, V.Gubens, M.Banks, K.Lanman, R.Caulin, A.St. John, J.Cordero, A.Giannikopoulos, P.Mack, P.Gandara, D.Husain, H.Doebele, R.Riess, J.Diehn, M.Swanton, C.Bivona, T. G.2017-03-16doi:10.1101/117291Cold Spring Harbor Laboratory Press2017-03-16
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Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition
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https://biorxiv.org/cgi/content/short/073478v1?rss=1"
Jakob VowinckelAleksej ZelezniakArtur KiblerRoland BrudererMichael MuellederLukas ReiterMarkus Ralser2016-09-05doi:10.1101/073478Cold Spring Harbor Laboratory Press2016-09-05
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FAM83G/PAWS1 controls cytoskeletal dynamics and cell migration through association with the SH3 adaptor CD2AP
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https://biorxiv.org/cgi/content/short/106971v1?rss=1"
Sapkota, G. P.Cummins, T. D.Wu, K. Z. L.Bozatzi, P.Dingwell, K. S.Macartney, T. J.Wood, N. T.Varghese, J.Gourlay, R.Campbell, D. G.Prescott, A.Griffis, E.Smith, J. C.2017-02-08doi:10.1101/106971Cold Spring Harbor Laboratory Press2017-02-08
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Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics
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https://biorxiv.org/cgi/content/short/104307v1?rss=1"
Sagner, A.Gaber, Z.Delile, J.Kong, J. H.Rousso, D. L.Pearson, C. A.Weicksel, S. E.Mousavy Gharavy, N.Briscoe, J.Novitch, B.2017-01-30doi:10.1101/104307Cold Spring Harbor Laboratory Press2017-01-30
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Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells
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https://biorxiv.org/cgi/content/short/152637v1?rss=1"
Ghahramani, A.Donati, G.Luscombe, N. M.Watt, F. M.2017-06-20doi:10.1101/152637Cold Spring Harbor Laboratory Press2017-06-20
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Neutral tumor evolution?
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https://biorxiv.org/cgi/content/short/158006v1?rss=1"
Tarabichi, M.Martincorena, I.Gerstung, M.Markowetz, F.Spellman, P. T.Morris, Q. D.Lingjaerde, O. C.Wedge, D. C.Van Loo, P.- PCAWG Evolution and Heterogeneity Working Group,2017-06-30doi:10.1101/158006Cold Spring Harbor Laboratory Press2017-06-30
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Allele-specific multi-sample copy number segmentation
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https://biorxiv.org/cgi/content/short/166017v1?rss=1"
Ross, E. M.Haase, K.Van Loo, P.Markowetz, F.2017-07-20doi:10.1101/166017Cold Spring Harbor Laboratory Press2017-07-20
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Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis
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https://biorxiv.org/cgi/content/short/168153v1?rss=1"
Poetsch, A. R.Boulton, S. J.Luscombe, N.2017-07-25doi:10.1101/168153Cold Spring Harbor Laboratory Press2017-07-25
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3’UTR Remodelling of Axonal Transcripts in Sympathetic Neurons
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https://biorxiv.org/cgi/content/short/170100v1?rss=1"
Andreassi, C.Luisier, R.Crerar, H.Franke, S.Luscombe, N. M.Cuda, G.Gaspari, M.Riccio, A.2017-07-30doi:10.1101/170100Cold Spring Harbor Laboratory Press2017-07-30
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The evolutionary history of 2,658 cancers
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https://biorxiv.org/cgi/content/short/161562v1?rss=1"
Gerstung, M.Jolly, C.Leshchiner, I.Dentro, S. C.Gonzalez, S.Mitchell, T. J.Rubanova, Y.Anur, P.Rosebrock, D.Yu, K.Tarabichi, M.Deshwar, A.Wintersinger, J.Kleinheinz, K.Vazquez-Garcia, I.Haase, K.Sengupta, S.Macintyre, G.Malikic, S.Donmez, N.Livitz, D. G.Cmero, M.Demeulemeester, J.Schumacher, S.Fan, Y.Yao, X.Lee, J.Schlesner, M.Boutros, P. C.Bowtell, D. D.Zhu, H.Getz, G.Imielinski, M.Beroukhim, R.Sahinalp, S. C.Ji, Y.Peifer, M.Markowetz, F.Mustonen, V.Yuan, K.Wang, W.Morris, Q. D.Spellman, P. T.Wedge, D. C.V2017-07-11doi:10.1101/161562Cold Spring Harbor Laboratory Press2017-07-11
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Probing tissue-scale deformation by in vivo force application reveals a fast tissue softening during early embryogenesis
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https://biorxiv.org/cgi/content/short/167155v1?rss=1"
D'Angelo, A.Dierkes, K.Carolis, C.Salbreux, G.Solon, J.2017-07-21doi:10.1101/167155Cold Spring Harbor Laboratory Press2017-07-21
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Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments
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https://biorxiv.org/cgi/content/short/161638v1?rss=1"
Yung, C. K.O'Connor, B. D.Yakneen, S.Zhang, J.Ellrott, K.Kleinheinz, K.Miyoshi, N.Raine, K. M.Royo, R.Saksena, G. B.Schlesner, M.Shorser, S. I.Vazquez, M.Weischenfeldt, J.Yuen, D.Butler, A. P.Davis-Dusenbery, B. N.Eils, R.Ferretti, V.Grossman, R. L.Harismendy, O.Kim, Y.Nakagawa, H.Newhouse, S. J.Torrents, D.Stein, L. D.- PCAWG Technical Working Group,2017-07-10doi:10.1101/161638Cold Spring Harbor Laboratory Press2017-07-10
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Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours
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https://biorxiv.org/cgi/content/short/179705v1?rss=1"
Rodriguez-Martin, B.Alvarez, E. G.Baez-Ortega, A.Demeulemeester, J.Ju, Y. S.Zamora, J.Detering, H.Li, Y.Contino, G.Dentro, S. C.Bruzos, A. L.Dueso-Barroso, A.Ardeljan, D.Tojo, M.Roberts, N. D.Blanco, M. G.Edwards, P. A. W.Weischenfeldt, J.Santamarina, M.Puiggros, M.Chong, Z.Chen, K.Lee, E. A.Wala, J. A.Raine, K.Butler, A.Waszak, S. M.Navarro, F. C. P.Schumacher, S. E.Monlong, J.Maura, F.Bolli, N.Bourque, G.Gerstein, M.Park, P. J.Berroukhim, R.Torrents, D.Korbel, J. O.Martincorena, I.Fitzgerald, R. C.Van Loo, P.Ka2017-08-24doi:10.1101/179705Cold Spring Harbor Laboratory Press2017-08-24
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Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models
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https://biorxiv.org/cgi/content/short/180372v1?rss=1"
Luisier, R.Tyzack, G. E.Hall, C. E.Ule, J.Luscombe, N. M.Patani, R.2017-08-24doi:10.1101/180372Cold Spring Harbor Laboratory Press2017-08-24
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Systematic mapping of the free energy landscapes of a growing immunoglobulin domain identifies a kinetic intermediate associated with co-translational proline isomerization
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https://biorxiv.org/cgi/content/short/189050v1?rss=1"
Waudby, C. A.Karyadi, M.-E.Wlodarski, T.Cassaignau, A. M. E.Chan, S.Schmidt-Engler, J. M.Wentink, A. S.Camilloni, C.Vendruscolo, M.Cabrita, L. D.Christodoulou, J.2017-09-14doi:10.1101/189050Cold Spring Harbor Laboratory Press2017-09-14
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ATR is a multifunctional regulator of male mouse meiosis
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https://biorxiv.org/cgi/content/short/172106v1?rss=1"
Widger, A.Mahadevaiah, S. K.Lange, J.ElInati, E.Zohren, J.Hirota, T.Stanzione, M.Ojarikre, O.Maciulyte, V.de Rooij, D.Toth, A.Keeney, S.Turner, J. M.2017-09-15doi:10.1101/172106Cold Spring Harbor Laboratory Press2017-09-15
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A Yeast Global Genetic Screen Reveals that Metformin Induces an Iron Deficiency-Like State
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https://biorxiv.org/cgi/content/short/190389v1?rss=1"
Stynen, B.Abd-Rabbo, D.Kowarzyk, J.Miller-Fleming, L.Ralser, M.Michnick, S.2017-09-18doi:10.1101/190389Cold Spring Harbor Laboratory Press2017-09-18
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Non-canonical circadian oscillations in Drosophila S2 cells drive gene-expression cycles coupled to metabolic oscillations
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https://biorxiv.org/cgi/content/short/191338v1?rss=1"
Rey, G.Milev, N. B.Valekunja, U. K.Ch, R.Ray, S.Silva Dos Santos, M.Nagy, A. D.Antrobus, R.MacRae, J. I.Reddy, A. B.2017-09-20doi:10.1101/191338Cold Spring Harbor Laboratory Press2017-09-20
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Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
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https://biorxiv.org/cgi/content/short/192757v1?rss=1"
Li, C.Lenhard, B.Luscombe, N. M.2017-09-22doi:10.1101/192757Cold Spring Harbor Laboratory Press2017-09-22
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Identifying developmentally important genes with single-cell RNA-seq from an embryo
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https://biorxiv.org/cgi/content/short/197699v1?rss=1"
Ilsley, G. R.Suyama, R.Noda, T.Satoh, N.Luscombe, N. M.2017-10-03doi:10.1101/197699Cold Spring Harbor Laboratory Press2017-10-03
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Actin and Src-family kinases regulate nuclear YAP1 and its export
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https://biorxiv.org/cgi/content/short/201004v1?rss=1"
Ege, N.Dowbaj, A. M.Jiang, M.Howell, M.Jenkins, R. P.Sahai, E.2017-10-11doi:10.1101/201004Cold Spring Harbor Laboratory Press2017-10-11
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WDR11-mediated Hedgehog signalling defects underlie a new ciliopathy related to Kallmann syndrome
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https://biorxiv.org/cgi/content/short/200154v1?rss=1"
Kim, Y.-J.Osborn, D.Lee, J.-Y.Araki, M.Araki, K.Mohun, T.Kansakoski, J. E. M.Brandstack, N.Kim, H.-T.Miralles, F.Kim, C.-H.Brown, N. A.Kim, H.-G.Martinez-Barbera, J. P.Ataliotis, P.Raivio, T.Layman, L. C.Kim, S.-H.2017-10-10doi:10.1101/200154Cold Spring Harbor Laboratory Press2017-10-10
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Plasmodium falciparum dipeptidyl aminopeptidase 3 activity is important for efficient erythrocyte invasion.
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https://biorxiv.org/cgi/content/short/202812v1?rss=1"
Lehmann, C.Tan, M. S. Y.de Vries, L. E.Russo, I.Sanchez, M. I.Goldberg, D. A.Deu, E.2017-10-13doi:10.1101/202812Cold Spring Harbor Laboratory Press2017-10-13
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Data Science Issues in Understanding Protein-RNA Interactions
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https://biorxiv.org/cgi/content/short/208124v1?rss=1"
Chakrabarti, A. M.Haberman, N.Praznik, A.Luscombe, N. M.Ule, J.2017-10-25doi:10.1101/208124Cold Spring Harbor Laboratory Press2017-10-25
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Detection of cytosolic Shigella flexneri via a C-terminal triple-arginine motif of GBP1 inhibits actin-based motility
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https://biorxiv.org/cgi/content/short/212175v1?rss=1"
Piro, A.Hernandez, D.Luoma, S.Feeley, E.Finethy, R.Yirga, A.Frickel, E.Lesser, C.Coers, J.2017-11-01doi:10.1101/212175Cold Spring Harbor Laboratory Press2017-11-01
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Coherent olfactory bulb gamma oscillations arise from coupling independent columnar oscillators
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https://biorxiv.org/cgi/content/short/213827v1?rss=1"
Peace, S. T.Johnson, B. C.Li, G.Kaiser, M. E.Fukunaga, I.Schaefer, A. T.Molnar, A. C.Cleland, T. A.2017-11-03doi:10.1101/213827Cold Spring Harbor Laboratory Press2017-11-03
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A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection
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https://biorxiv.org/cgi/content/short/216879v1?rss=1"
Singhania, A.Verma, R.Graham, C. M.Lee, J.Trang, T.Richarsdon, M.Lecine, P.Leissner, P.Berry, M. P. R.Wilkinson, R. J.Kaiser, K.Rodrigue, M.Woltmann, G.Haldar, P.O'Garra, A.2017-11-09doi:10.1101/216879Cold Spring Harbor Laboratory Press2017-11-09
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Active sampling state dynamically enhances olfactory bulb odor representation
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https://biorxiv.org/cgi/content/short/222588v1?rss=1"
Jordan, R.Fukunaga, I.Kollo, M.Schaefer, A. T.2017-11-21doi:10.1101/222588Cold Spring Harbor Laboratory Press2017-11-21
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BCL11A interacts with SOX2 to control the expression of epigenetic regulators in lung squamous cell carcinoma
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https://biorxiv.org/cgi/content/short/223776v1?rss=1"
Lazarus, K. A.Hadi, F.Zambon, E.Bach, K.Santolla, M.-F.Watson, J. K.Correia, L. L.Das, M.Ugur, R.Pensa, S.Becker, L.Campos, L. S.Ladds, G.Liu, P.Evan, G.McCaughan, F.Le Quesne, J.Lee, J.-H.Calado, D.Khaled, W. T.2017-11-22doi:10.1101/223776Cold Spring Harbor Laboratory Press2017-11-22
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A hidden Markov model approach to characterizing the photo-switching behavior of fluorophores
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https://biorxiv.org/cgi/content/short/223875v1?rss=1"
Patel, L.Gustafsson, N.Lin, Y.Ober, R.Henriques, R.Cohen, E.2017-11-22doi:10.1101/223875Cold Spring Harbor Laboratory Press2017-11-22
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A single cycle influenza virus coated in H7 hemagglutinin provides heterotypic protection and neutralising antibody responses to both glycoproteins.
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https://biorxiv.org/cgi/content/short/224550v1?rss=1"
Powell, T. J.Rijal, P.McEwen-Smith, R. M.Byun, H.Hardwick, M.Schimanski, L. M.Huang, K.-Y. A.Daniels, R. S.Townsend, A. R. M.2017-11-27doi:10.1101/224550Cold Spring Harbor Laboratory Press2017-11-27
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CYRI (FAM49) proteins are local inhibitors of Scar/WAVE induced lamellipodia that bind directly to active Rac1
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https://biorxiv.org/cgi/content/short/164905v1?rss=1"
Fort, L.Batista, J.Thomason, P. A.Spence, H. J.Greaves, J.Martin, K. J.Anderson, K. I.Brown, P.Lilla, S.Neilson, M. P.Tafelmeyer, P.Zanivan, S.Ismail, S.Tomkinson, N. C. O.Chamberlain, L. H.Insall, R. H.Machesky, L. M.2017-11-29doi:10.1101/164905Cold Spring Harbor Laboratory Press2017-11-29
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Sniff-invariant intensity perception using olfactory bulb coding of inhalation dynamics
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https://biorxiv.org/cgi/content/short/226969v1?rss=1"
Jordan, R.Kollo, M.Schaefer, A. T.2017-11-29doi:10.1101/226969Cold Spring Harbor Laboratory Press2017-11-29
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Regionalization of the nervous system requires axial allocation prior to neural lineage commitment
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https://biorxiv.org/cgi/content/short/229203v1?rss=1"
Metzis, V.Steinhauser, S.Pakanavicius, E.Gouti, M.Stamataki, D.Lovell-Badge, R.Luscombe, N. M.Briscoe, J.2017-12-04doi:10.1101/229203Cold Spring Harbor Laboratory Press2017-12-04
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AP-4 mediated ATG9A sorting underlies axonal and autophagosome biogenesis defects in a mouse model of AP-4 deficiency syndrome
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https://biorxiv.org/cgi/content/short/235101v1?rss=1"
Ivankovic, D.Lopez-Domenech, G.Drew, J.Tooze, S. A.Kittler, J. T.2017-12-16doi:10.1101/235101Cold Spring Harbor Laboratory Press2017-12-16
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PolNet Analysis: a software tool for the quantification of network-level endothelial cell polarity and blood flow during vascular remodelling
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https://biorxiv.org/cgi/content/short/237602v1?rss=1"
Bernabeu, M. O.Jones, M. L.Nash, R. W.Pezzarossa, A.Coveney, P. V.Gerhardt, H.Franco, C. A.2017-12-22doi:10.1101/237602Cold Spring Harbor Laboratory Press2017-12-22
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The Homeostatic Logic of Reward
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https://biorxiv.org/cgi/content/short/242974v1?rss=1"
Morville, T.Friston, K.Burdakov, D.Siebner, H. R.Hulme, O. J.2018-01-05doi:10.1101/242974Cold Spring Harbor Laboratory Press2018-01-05
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Characterization of P. falciparum dipeptidyl aminopeptidase 3 specificity identifies different amino acid preferences between peptide-based substrates and inhibitors.
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https://biorxiv.org/cgi/content/short/246124v1?rss=1"
Deu, E.de Vries, L. E.Sanchez, M. I.Groborz, K.Kuppens, L.Poreba, M.Lehmann, C.Yuan, F.Arastu-Kapur, S.Bogyo, M.Drag, M.2018-01-11doi:10.1101/246124Cold Spring Harbor Laboratory Press2018-01-11
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A role for a conserved kinase in the transcriptional control of methionine biosynthesis in Escherichia coli experiencing sustained nitrogen starvation
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https://biorxiv.org/cgi/content/short/254623v1?rss=1"
Switzer, A.Evangelopoulos, D.Figueira, R.de Carvalho, L.Brown, D.Wigneshweraraj, S.2018-01-27doi:10.1101/254623Cold Spring Harbor Laboratory Press2018-01-27
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Predicting Human Protein Function with Multi-task Deep Neural Networks
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https://biorxiv.org/cgi/content/short/256420v1?rss=1"
Fa, R.Cozzetto, D.Wan, C.Jones, D. T.2018-01-30doi:10.1101/256420Cold Spring Harbor Laboratory Press2018-01-30
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Machine learning models in electronic health records can outperform conventional survival models for predicting patient mortality in coronary artery disease
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https://biorxiv.org/cgi/content/short/256008v1?rss=1"
Steele, A. J.Cakiroglu, S. A.Shah, A. D.Denaxas, S. C.Hemingway, H.Luscombe, N. M.2018-01-30doi:10.1101/256008Cold Spring Harbor Laboratory Press2018-01-30
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ANIMA: Association Network Integration for Multiscale Analysis
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https://biorxiv.org/cgi/content/short/257642v1?rss=1"
Deffur, A.Wilkinson, R. J.Mayosi, B. M.Mulder, N. M.2018-01-31doi:10.1101/257642Cold Spring Harbor Laboratory Press2018-01-31
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Generative adversarial networks uncover epidermal regulators and predict single cell perturbations
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https://biorxiv.org/cgi/content/short/262501v1?rss=1"
Ghahramani, A.Watt, F. M.Luscombe, N. M.2018-02-08doi:10.1101/262501Cold Spring Harbor Laboratory Press2018-02-08
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TCR-MHC Interaction Strength Defines Trafficking and Resident Memory Status of CD8 T cells in the Brain
]]>
https://biorxiv.org/cgi/content/short/263152v1?rss=1"
Sanecka, A.Yoshida, N.Kolawole, E. M.Patel, H.Evavold, B. D.Frickel, E.2018-02-09doi:10.1101/263152Cold Spring Harbor Laboratory Press2018-02-09
<![CDATA[
Spatio-temporal relays control layer specificity of motion-direction sensitive neurons in Drosophila
]]>
https://biorxiv.org/cgi/content/short/262451v1?rss=1"
Apitz, H.Salecker, I.2018-02-10doi:10.1101/262451Cold Spring Harbor Laboratory Press2018-02-10
<![CDATA[
Population Turnover in Remote Oceania Shortly After Initial Settlement
]]>
https://biorxiv.org/cgi/content/short/268037v1?rss=1"
Lipson, M.Skoglund, P.Spriggs, M.Valentin, F.Bedford, S.Shing, R.Buckley, H.Phillip, I.Ward, G. K.Mallick, S.Rohland, N.Broomandkhoshbacht, N.Cheronet, O.Ferry, M.Harper, T. K.Michel, M.Oppenheimer, J.Sirak, K.Stewardson, K.Auckland, K.Hill, A. V. S.Maitland, K.Oppenheimer, S. J.Parks, T.Robson, K.Williams, T. N.Kennett, D. J.Mentzer, A. J.Pinhasi, R.Reich, D.2018-02-19doi:10.1101/268037Cold Spring Harbor Laboratory Press2018-02-19
<![CDATA[
Differential expression of an alternative splice variant of IL-12Rβ1 impacts early dissemination in the mouse and associates with disease outcome in both mouse and humans exposed to tuberculosis
]]>
https://biorxiv.org/cgi/content/short/271627v1?rss=1"
Das, M. K.Ray, A. A.Cai, Y.Singhania, A.Graham, C.Liao, M.Fountain, J. J.Pearl, J. E.Pareek, M.Haldar, P.O'Garra, A.Chen, X.Cooper, A. M.2018-02-26doi:10.1101/271627Cold Spring Harbor Laboratory Press2018-02-26
<![CDATA[
Human axial progenitors generate trunk neural crest cells
]]>
https://biorxiv.org/cgi/content/short/272591v1?rss=1"
Frith, T. J. R.Granata, I.Stout, E.Wind, M.Thompson, O.Neumann, K.Stavish, D.Heath, P. R.Hackland, J. O. S.Anastassiadis, K.Gouti, M.Briscoe, J.Wilson, V.Guarracino, M. R.Andrews, P. W.Tsakiridis, A.2018-02-27doi:10.1101/272591Cold Spring Harbor Laboratory Press2018-02-27
<![CDATA[
Predicting improved protein conformations with a temporal deep recurrent neural network
]]>
https://biorxiv.org/cgi/content/short/275008v1?rss=1"
Pfeiffenberger, E.Bates, P. A.2018-03-03doi:10.1101/275008Cold Spring Harbor Laboratory Press2018-03-03
<![CDATA[
A strategy to study intrinsically mixed folded proteins: The structure in solution of ataxin-3
]]>
https://biorxiv.org/cgi/content/short/275131v1?rss=1"
Sicorello, A.Kelly, G.Oregioni, A.Novacek, J.sklenar, v.Pastore, A.2018-03-09doi:10.1101/275131Cold Spring Harbor Laboratory Press2018-03-09
<![CDATA[
Neurofilament light as a blood biomarker for neurodegeneration in Down syndrome
]]>
https://biorxiv.org/cgi/content/short/281139v1?rss=1"
Strydom, A.Heslegrave, A.Startin, C. M.Mok, K. Y.Hardy, J.Groet, J.Nizetic, D.The LonDownS consortium,Zetterberg, H.2018-03-13doi:10.1101/281139Cold Spring Harbor Laboratory Press2018-03-13
<![CDATA[
Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency
]]>
https://biorxiv.org/cgi/content/short/281519v1?rss=1"
Mulholland, C. B.Traube, F. R.Parsa, E.Eckl, E.-M.Schoenung, M.Modic, M.Bartoschek, M. D.Stolz, P.Ryan, J.Carell, T.Leonhardt, H.Bultmann, S.2018-03-13doi:10.1101/281519Cold Spring Harbor Laboratory Press2018-03-13
<![CDATA[
DIA-NN: Deep neural networks substantially improve the identification performance of Data-independent acquisition (DIA) in proteomics
]]>
https://biorxiv.org/cgi/content/short/282699v1?rss=1"
Demichev, V.Messner, C. B.Lilley, K. S.Ralser, M.2018-03-15doi:10.1101/282699Cold Spring Harbor Laboratory Press2018-03-15
<![CDATA[
Identifying the genetic basis of variation in cell behaviour in human iPS cell lines from healthy donors
]]>
https://biorxiv.org/cgi/content/short/285627v1?rss=1"
Vigilante, A.Laddach, A.Moens, N.Meleckyte, R.Leha, A.Ghahramani, A.Culley, O. J.Kathuria, A.Hurling, C.Vickers, A.Tewary, M.Zandstra, P.HipSci Consortium,Durbin, R.Fraternali, F.Stegle, O.Birney, E.Luscombe, N. M.Danovi, D.Watt, F. M.2018-03-20doi:10.1101/285627Cold Spring Harbor Laboratory Press2018-03-20
<![CDATA[
Glycosylation-dependent modulation of the lL-2 signaling axis determines Th17 differentiation and IL-10 production
]]>
https://biorxiv.org/cgi/content/short/287920v1?rss=1"
Gabrysova, L.Mann, E. H.Bradley, L.MacRae, J. I.Whicher, C.Hawrylowicz, C. M.Anastasiou, D.O'Garra, A.2018-03-23doi:10.1101/287920Cold Spring Harbor Laboratory Press2018-03-23
<![CDATA[
AutonoMouse: High throughput automated operant conditioning shows progressive behavioural impairment with graded olfactory bulb lesions.
]]>
https://biorxiv.org/cgi/content/short/291815v1?rss=1"
10^6 trials. We validate this "AutonoMouse" system in a series of olfactory behavioural tasks and show that acquired data is comparable to previous semi-manual approaches. Furthermore, we use AutonoMouse to systematically probe the impact of graded olfactory bulb lesions on olfactory behaviour and resolve the long-standing conundrum about the apparent lack of impact of lesions on olfactory abilities. The modular nature and open-source design of AutonoMouse should allow for similar robust and systematic assessments across neuroscience research areas.
]]>Erskine, A.Bus, T.Herb, J. T.Schaefer, A. T.2018-03-29doi:10.1101/291815Cold Spring Harbor Laboratory Press2018-03-29
<![CDATA[
Comparable affinity of RabGDIα for GTP- and GDP-bound forms of Rab7 supports a four-state transition model for Rab7 subcellular localization
]]>
https://biorxiv.org/cgi/content/short/287516v1?rss=1"
Kanemitsu, A. F.Morishita, S.Kjaer, S.Fukuda, M.Schiavo, G.Nakamura, T.2018-03-27doi:10.1101/287516Cold Spring Harbor Laboratory Press2018-03-27
<![CDATA[
A non-cell autonomous actin redistribution enables isotropic retinal growth
]]>
https://biorxiv.org/cgi/content/short/293951v1?rss=1"
Matejcic, M.Salbreux, G.Norden, C.2018-04-03doi:10.1101/293951Cold Spring Harbor Laboratory Press2018-04-03
<![CDATA[
Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing
]]>
https://biorxiv.org/cgi/content/short/297853v1?rss=1"
Attig, J.Agostini, F.Gooding, C.Singh, A.Chakrabarti, A. M.Haberman, N.Emmett, W.Smith, C. W.Luscombe, N. M.Ule, J.2018-04-09doi:10.1101/297853Cold Spring Harbor Laboratory Press2018-04-09
<![CDATA[
Maternal pluripotency factors prime the zygotic genome to respond to intercellular signals
]]>
https://biorxiv.org/cgi/content/short/306803v1?rss=1"
Gentsch, G. E.Spruce, T.Owens, N. D. L.Smith, J. C.2018-04-23doi:10.1101/306803Cold Spring Harbor Laboratory Press2018-04-23
<![CDATA[
Creating Standards for Evaluating Tumour Subclonal Reconstruction
]]>
https://biorxiv.org/cgi/content/short/310425v1?rss=1"
Boutros, P. C.Salcedo, A.Tarabichi, M.Espiritu, S. M. G.Deshwar, A. G.David, M.Wilson, N. M.Dentro, S.Wintersinger, J. A.Liu, L. Y.Ko, M.Sivanandan, S.Zhang, H.Zhu, K.Yang, T.-H.Chilton, J. M.Buchanan, A.Lalansingh, C. M.P'ng, C.Anghel, C. V.Umar, I.Lo, B.Simpson, J. T.Stuart, J. M.Anastassiou, D.Guan, Y.Ewing, A.Ellrott, K.Wedge, D. C.Morris, Q. D.Van Loo, P.DREAM SMC-Het Participants,2018-04-28doi:10.1101/310425Cold Spring Harbor Laboratory Press2018-04-28
<![CDATA[
Modelling mitosis with multiple phenotypes: relation to Haeckels biogenetic recapitulation law
]]>
https://biorxiv.org/cgi/content/short/253203v1?rss=1"
Alexandrov, Y.2018-01-24doi:10.1101/253203Cold Spring Harbor Laboratory Press2018-01-24
<![CDATA[
Genomic determinants of sympatric speciation of the Mycobacterium tuberculosis complex across evolutionary timescales.
]]>
https://biorxiv.org/cgi/content/short/314559v1?rss=1"
Chiner-Oms, A.Sanchez-Buso, L.Corander, J.Gagneux, S.Harris, S.Young, D.Gonzalez-Candelas, F.Comas, I.2018-05-04doi:10.1101/314559Cold Spring Harbor Laboratory Press2018-05-04
<![CDATA[
Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types
]]>
https://biorxiv.org/cgi/content/short/312041v1?rss=1"
Dentro, S. C.Leshchiner, I.Haase, K.Tarabichi, M.Wintersinger, J.Deshwar, A. G.Yu, K.Rubanova, Y.Mcintyre, G.Vazquez-Garcia, I.Kleinheinz, K.Livitz, D. G.Malikic, S.Donmez, N.Sengupta, S.Demeulemeester, J.Anur, P.Jolly, C.Cmero, M.Rosebrock, D.Schumacher, S.Fan, Y.Fittall, M.Drews, R. M.Yao, X.Lee, J.Schlesner, M.Adams, D. J.Getz, G.Boutros, P. C.Imielinski, M.Beroukhim, R.Sahinalp, S. C.Ji, Y.Peifer, M.Martincorena, I.Markowetz, F.Mustonen, V.Yuan, K.Gerstung, M.Spellman, P. T.Wang, W.Morris, Q. D.Wedge, D.2018-05-05doi:10.1101/312041Cold Spring Harbor Laboratory Press2018-05-05
<![CDATA[
Automating multimodal microscopy with NanoJ-Fluidics
]]>
https://biorxiv.org/cgi/content/short/320416v1?rss=1"
Almada, P.Pereira, P.Culley, S.Caillol, G.Boroni-Rueda, F.Dix, C. L.Laine, R. F.Charras, G.Baum, B.Leterrier, C.Henriques, R.2018-05-14doi:10.1101/320416Cold Spring Harbor Laboratory Press2018-05-14
<![CDATA[
Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma
]]>
https://biorxiv.org/cgi/content/short/321612v1?rss=1"
Mourikis, T.Benedetti, L.Foxall, E.Perner, J.Cereda, M.Lagergren, J.Howell, M.Yau, C.Fitzgerald, R.Scaffidi, P.Ciccarelli, F. D.2018-05-14doi:10.1101/321612Cold Spring Harbor Laboratory Press2018-05-14
<![CDATA[
Mechanics of CaMKII-actin networks
]]>
https://biorxiv.org/cgi/content/short/308353v1?rss=1"
Khan, S. M.Molloy, J. E.Downing, K. H.2018-05-14doi:10.1101/308353Cold Spring Harbor Laboratory Press2018-05-14
<![CDATA[
Discovery of a novel stereospecific β-hydroxyacyl-CoA lyase/thioesterase shared by three metabolic pathways in Mycobacterium tuberculosis
]]>
https://biorxiv.org/cgi/content/short/322404v1?rss=1"
Wang, H.Fedorov, A. A.Fedorov, E. V.Hunt, D. M.Rodgers, A.Garza-Garcia, A.Bonanno, J. B.Almo, S. C.Carvalho, L. P.2018-05-15doi:10.1101/322404Cold Spring Harbor Laboratory Press2018-05-15
<![CDATA[
TET1 drives global DNA demethylation via DPPA3-mediated inhibition of maintenance methylation
]]>
https://biorxiv.org/cgi/content/short/321604v1?rss=1"
Mulholland, C. B.Ryan, J.Qin, W.Bartoschek, M. D.Traube, F. R.Parsa, E.Modic, M.Nixdorf, D.Ziegenhain, C.Carell, T.Enard, W.Bultmann, S.Leonhardt, H.2018-05-15doi:10.1101/321604Cold Spring Harbor Laboratory Press2018-05-15
<![CDATA[
Repression of divergent noncoding transcription by a sequence-specific transcription factor
]]>
https://biorxiv.org/cgi/content/short/314310v1?rss=1"
Wu, A. C.Patel, H.Chia, M.Moretto, F.Frith, D.Snijders, A. P.van Werven, F. J.2018-05-17doi:10.1101/314310Cold Spring Harbor Laboratory Press2018-05-17
<![CDATA[
Phosphorylation of a Toxoplasma gondii tyrosine transporter by calcium-dependent kinase 3 is important for parasite fitness
]]>
https://biorxiv.org/cgi/content/short/339671v1?rss=1"
Wallbank, B. A.Dominicus, C. S.Broncel, M.Legrave, N.MacRae, J. I.Staines, H. M.Treeck, M.2018-06-05doi:10.1101/339671Cold Spring Harbor Laboratory Press2018-06-05
<![CDATA[
Modelling the nuclear envelope of HeLa cells
]]>
https://biorxiv.org/cgi/content/short/344986v1?rss=1"
Karabag, C.Jones, M. L.Peddie, C. J.Weston, A. E.Collinson, L. M.Reyes-Aldasoro, C. C.2018-06-12doi:10.1101/344986Cold Spring Harbor Laboratory Press2018-06-12
<![CDATA[
Plasmodium-specific atypical memory B cells are not part of the long-lived memory response
]]>
https://biorxiv.org/cgi/content/short/350819v1?rss=1"
Perez-Mazliah, D.Gardner, P. J.Schweighoffer, E.McLaughlin, S.Hosking, C.Tumwine, I.Davis, R. S.Potocnik, A. J.Tybulewicz, V.langhorne, j.2018-06-22doi:10.1101/350819Cold Spring Harbor Laboratory Press2018-06-22
<![CDATA[
Dual RNAseq of human leprosy lesions identifies bacterial determinants linked to host immune response
]]>
https://biorxiv.org/cgi/content/short/354407v1?rss=1"
Montoya, D.Andrade, P. R.Silva, B. J. A.Teles, R. M. B.Bryson, B.Sadanand, S.Noel, T.Lu, J.Sarno, E.Arnvig, K. B.Young, D.Lahiri, R.Williams, D. L.Fortune, S.Bloom, B. R.Pellegrini, M.Modlin, R. L.2018-06-22doi:10.1101/354407Cold Spring Harbor Laboratory Press2018-06-22
<![CDATA[
Transcriptome-wide profiling of mammalian spliceosome and branchpoints with iCLIP
]]>
https://biorxiv.org/cgi/content/short/353599v1?rss=1"
Briese, M.Haberman, N.Sibley, C.Chakrabarti, A.Wang, Z.Konig, J.Perera, D.Wickramasinghe, V.Venkitaraman, A.Luscombe, N.Smith, C.Curk, T.Ule, J.2018-06-22doi:10.1101/353599Cold Spring Harbor Laboratory Press2018-06-22
<![CDATA[
Nanoscale Polarization of the Vaccinia Virus Entry Fusion Complex Drives Efficient Fusion
]]>
https://biorxiv.org/cgi/content/short/360073v1?rss=1"
Gray, R.Albrecht, D.Beerli, C.Cohen, G.Henriques, R.Mercer, J.2018-07-01doi:10.1101/360073Cold Spring Harbor Laboratory Press2018-07-01
<![CDATA[
γ-proteobacteria eject their polar flagella under nutrient depletion, retaining flagellar motor relic structures
]]>
https://biorxiv.org/cgi/content/short/367458v1?rss=1"
Ferreira, J. L.Gao, F. Z.Rossmann, F. M.Nans, A.Brenzinger, S.Hosseini, R.Briegel, A.Thormann, K. M.Rosenthal, P. B.Beeby, M.2018-07-18doi:10.1101/367458Cold Spring Harbor Laboratory Press2018-07-18
<![CDATA[
Bcl6 promotes neurogenic conversion through transcriptional repression of multiple self-renewal-promoting extrinsic pathways.
]]>
https://biorxiv.org/cgi/content/short/370999v1?rss=1"
Bonnefont, J.Tiberi, L.van den Ameele, J.Potier, D.Gaber, Z.Lin, X.Bilheu, A.Herpoel, A.Velez Bravo, F.Guillemot, F.Aerts, S.Vanderhaeghen, P.2018-07-18doi:10.1101/370999Cold Spring Harbor Laboratory Press2018-07-18
<![CDATA[
Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries
]]>
https://biorxiv.org/cgi/content/short/370056v1?rss=1"
Zuercher, K.Ballif, M.Fenner, L.Borrell, S.Keller, P. M.Gnokoro, J.Marcy, O.Yotebieng, M.Diero, L.Carter, E. J.Rockwood, N.Wilkinson, R. J.Cox, H.Ezati, N.Abimiku, A. l. G.Collantes, J.Avihingsanon, A.Kawkitinarong, K.Reinhard, M.Hoemke, R.Huebner, R.Gagneux, S.Boettger, E. C.Egger, M.on behalf of the International Epidemiology Databases to Evaluate AIDS (IeDEA),2018-07-18doi:10.1101/370056Cold Spring Harbor Laboratory Press2018-07-18
<![CDATA[
Antibiotic resistance evasion is explained by rare mutation frequency and not by lack of compensatory mechanisms
]]>
https://biorxiv.org/cgi/content/short/374215v1?rss=1"
Carvalho, L. P.Evangelopoulos, D.Prosser, G.Rodgers, A.Dagg, B.Khatri, B.Ho, M. M.Gutierrez, M.Cortes, T.2018-07-23doi:10.1101/374215Cold Spring Harbor Laboratory Press2018-07-23
<![CDATA[
Survival of the frequent at finite population size and mutation rate: filing the gap between quasispecies and monomorphic regimes
]]>
https://biorxiv.org/cgi/content/short/375147v1?rss=1"
Khatri, B. S.2018-07-23doi:10.1101/375147Cold Spring Harbor Laboratory Press2018-07-23
<![CDATA[
A Ubiquitin-Binding Domain that Does Not Bind Ubiquitin
]]>
https://biorxiv.org/cgi/content/short/375832v1?rss=1"
Lim, M.Newman, J. A.Williams, H. L.Aitkenhead, H.Gileadi, O.Svejstrup, J.2018-07-24doi:10.1101/375832Cold Spring Harbor Laboratory Press2018-07-24
<![CDATA[
Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation
]]>
https://biorxiv.org/cgi/content/short/378133v1?rss=1"
Macpherson, J. A.Theisen, A.Masino, L.Fets, L.Driscoll, P. C.Encheva, V.Snijders, A. P.Martin, S. R.Kleinjung, J.Barran, P. E.Fraternali, F.Anastasiou, D.2018-07-26doi:10.1101/378133Cold Spring Harbor Laboratory Press2018-07-26
<![CDATA[
Nitrogen utilisation by the metabolic generalist pathogen Mycobacterium tuberculosis
]]>
https://biorxiv.org/cgi/content/short/385278v1?rss=1"
Agapova, A.Hunt, D. M.Petridis, M.Garza-Garcia, A.Sohaskey, C. D.Carvalho, L. P.2018-08-05doi:10.1101/385278Cold Spring Harbor Laboratory Press2018-08-05
<![CDATA[
Mapping the human kinome in response to DNA damage
]]>
https://biorxiv.org/cgi/content/short/385344v1?rss=1"
Owusu, M.Bannauer, P.Mourikis, A.Jones, A.Ferreira da Silva, J.Caldera, M.Wiedner, M.Lardeau, C.-H.Menche, J.Kubicek, S.Ciccarelli, F.Loizou, J.2018-08-06doi:10.1101/385344Cold Spring Harbor Laboratory Press2018-08-06
<![CDATA[
Target-specific precision of CRISPR-mediated genome editing
]]>
https://biorxiv.org/cgi/content/short/387027v1?rss=1"
Chakrabarti, A. M.Henser-Brownhill, T.Monserrat, J.Poetsch, A. R.Luscombe, N. M.Scaffidi, P.2018-08-09doi:10.1101/387027Cold Spring Harbor Laboratory Press2018-08-09
<![CDATA[
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens.
]]>
https://biorxiv.org/cgi/content/short/389858v1?rss=1"
Ciccarelli, F. D.Kuppili Venkata, S.Repana, D.Nulsen, J.Dressler, L.Bortolomeazzi, M.Tourna, A.Yakovleva, A.Palmieri, T.2018-08-11doi:10.1101/389858Cold Spring Harbor Laboratory Press2018-08-11
<![CDATA[
P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress
]]>
https://biorxiv.org/cgi/content/short/394239v1?rss=1"
Bugai, A.Quaresma, A. J.Friedel, C. C.Lenasi, V.Sibley, C. R.Kukanja, P.Fujinaga, K.Blasius, M.Hennig, T.Ule, J.Doelken, L.Barboric, M.2018-08-17doi:10.1101/394239Cold Spring Harbor Laboratory Press2018-08-17
<![CDATA[
Genome-Wide Reconstitution of Chromatin Transactions: RSC Preferentially disrupts H2A.Z-Containing Nucleosomes
]]>
https://biorxiv.org/cgi/content/short/394692v1?rss=1"
Cakiroglu, A.Clapier, C.Ehrensberger, A.Darbo, E.Cairns, B.Luscombe, N.Svejstrup, J.2018-08-17doi:10.1101/394692Cold Spring Harbor Laboratory Press2018-08-17
<![CDATA[
CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage
]]>
https://biorxiv.org/cgi/content/short/397000v1?rss=1"
Soczek, K. M.Grant, T.Rosenthal, P. B.Mondragon, A.2018-08-21doi:10.1101/397000Cold Spring Harbor Laboratory Press2018-08-21
<![CDATA[
A divergent kinase lacking the glycine-rich loop regulates membrane ultrastructure of the Toxoplasma parasitophorous vacuole
]]>
https://biorxiv.org/cgi/content/short/397489v1?rss=1"
Beraki, T.Hu, X.Broncel, M.Young, J. C.O'Shaughnessy, W. J.Borek, D. M.Treeck, M.Reese, M. L.2018-08-22doi:10.1101/397489Cold Spring Harbor Laboratory Press2018-08-22
<![CDATA[
EGFR SIGNALING COORDINATES PATTERNING WITH CELL SURVIVAL DURING DROSOPHILA EPIDERMAL DEVELOPMENT
]]>
https://biorxiv.org/cgi/content/short/399865v1?rss=1"
Crossman, S. H.Streichan, S.vincent, J.-P.2018-08-24doi:10.1101/399865Cold Spring Harbor Laboratory Press2018-08-24
<![CDATA[
An Artificial Intelligence Workflow for Defining Host-Pathogen Interactions
]]>
https://biorxiv.org/cgi/content/short/408450v1?rss=1"
Fisch, D. H.Yakimovich, A.Clough, B.Wright, J.Bunyan, M.Howell, M.Mercer, J.Frickel, E.-M.2018-09-05doi:10.1101/408450Cold Spring Harbor Laboratory Press2018-09-05
<![CDATA[
Function and essentiality of Plasmodium falciparum Plasmepsin V
]]>
https://biorxiv.org/cgi/content/short/404798v1?rss=1"
Boonyalai, N.Collins, C. R.Hackett, F.Withers-Martinez, C.Blackman, M. J.2018-09-06doi:10.1101/404798Cold Spring Harbor Laboratory Press2018-09-06
<![CDATA[
Apical caspase reporters uncover unknown stages of apoptosis and enable ready visualization of undead cells
]]>
https://biorxiv.org/cgi/content/short/419630v1?rss=1"
Baena-Lopez, L. A.Arthurton, L.Bischoff, M.Vincent, J.-P.Alexandre, C.McGregor, R.2018-09-17doi:10.1101/419630Cold Spring Harbor Laboratory Press2018-09-17
<![CDATA[
Id4 eliminates the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells
]]>
https://biorxiv.org/cgi/content/short/426015v1?rss=1"
Blomfield, I. M.Rocamonde, B.Masdeu, M. D. M.Mulugeta, E.Vaga, S.van den Berg, D. L. C.Huillard, E.Guillemot, F.Urban, N.2018-09-25doi:10.1101/426015Cold Spring Harbor Laboratory Press2018-09-25
<![CDATA[
Temporal control of cortico-thalamic neuron specification by regulation of Neurogenin activity and Polycomb repressive complexes
]]>
https://biorxiv.org/cgi/content/short/431684v1?rss=1"
Oishi, K.van den Berg, D. L. C.Guillemot, F.2018-10-01doi:10.1101/431684Cold Spring Harbor Laboratory Press2018-10-01
<![CDATA[
NanoJ: a high-performance open-source super-resolution microscopy toolbox
]]>
https://biorxiv.org/cgi/content/short/432674v1?rss=1"
Laine, R.Tosheva, K.Gustafsson, N.Gray, R. D. M.Almada, P.Albrecht, D.Risa, G. T.Hurtig, F.Lindas, A.-C.Baum, B.Mercer, J.Leterrier, C.Pereira, P. M.Culley, S.Henriques, R.2018-10-01doi:10.1101/432674Cold Spring Harbor Laboratory Press2018-10-01
<![CDATA[
Mitochondria form cholesterol-rich contact sites with the nucleus during retrograde response
]]>
https://biorxiv.org/cgi/content/short/445411v1?rss=1"
Desai, R.East, D. A.Hardy, L.Crosby, J.Faccenda, D.Alvarex, M. S.Mainenti, M.Hussey, L. K.Bentham, R.Szabadkai, G.Zappulli, V.Dhoot, G.Fleck, R. A.Vizcay-Barrena, G.Smith, K.Campanella, M.2018-10-17doi:10.1101/445411Cold Spring Harbor Laboratory Press2018-10-17
<![CDATA[
Fix your membrane receptor imaging: Actin cytoskeleton and CD4 membrane organization disruption by chemical fixation
]]>
https://biorxiv.org/cgi/content/short/450635v1?rss=1"
Pereira, P. M.Albrecht, D.Jacobs, C.Marsh, M.Mercer, J.Henriques, R.2018-10-23doi:10.1101/450635Cold Spring Harbor Laboratory Press2018-10-23
<![CDATA[
Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord
]]>
https://biorxiv.org/cgi/content/short/472415v1?rss=1"
Delile, J.Rayon, T.Melchionda, M.Edwards, A.Briscoe, J.Sagner, A.2018-11-16doi:10.1101/472415Cold Spring Harbor Laboratory Press2018-11-16
<![CDATA[
Robust estimation of recent effective population size from number of independent origins in soft sweeps
]]>
https://biorxiv.org/cgi/content/short/472266v1?rss=1"
Khatri, B. S.Burt, A.2018-11-19doi:10.1101/472266Cold Spring Harbor Laboratory Press2018-11-19
<![CDATA[
The Spatio-Temporal Control of Zygotic Genome Activation
]]>
https://biorxiv.org/cgi/content/short/488056v1?rss=1"
1,000 zygotic genes disregard the N/C timer for their activation, and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal and BMP signaling together generate most of the spatio-temporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.
]]>Gentsch, G.Owens, N. D. L.Smith, J. C.2018-12-06doi:10.1101/488056Cold Spring Harbor Laboratory Press2018-12-06
<![CDATA[
Nucleosome positioning stability is a significant modulator of germline mutation rate variation across the human genome
]]>
https://biorxiv.org/cgi/content/short/494914v1?rss=1"
300,000 de novo mutations from whole-genome trio sequencing and high-resolution nucleosome maps in human. We found that de novo mutation rates are elevated around strong, translationally stable nucleosomes, a previously under-appreciated aspect. We confirmed this observation having controlled for local sequence context and other potential confounding factors. Analysis of the underlying mutational processes suggests that the increased mutation rates around strong nucleosomes are shaped by a combination of low-fidelity replication, frequent DNA damage and insufficient/error-prone repair in these regions. Interestingly, strong nucleosomes are preferentially located in young SINE/LINE elements, implying frequent nucleosome re-positioning (i.e. shifting of dyad position) and their contribution to hypermutation at new retrotransposons during evolution. These findings provide novel insights into how chromatin organization affects germline mutation rates and have important implications in human genetics and genome evolution.
]]>Li, C.Luscombe, N. M.2018-12-13doi:10.1101/494914Cold Spring Harbor Laboratory Press2018-12-13
<![CDATA[
Interleukin-36 promotes systemic Type-I IFN responses in severe psoriasis.
]]>
https://biorxiv.org/cgi/content/short/496851v1?rss=1"
Catapano, M.Vergnano, M.Romano, M.Mahil, S. K.Choon, S.-E.Burden, D. A.Young, H. S.Carr, I. M.Lachmann, H. J.Lombardi, G.Smith, C.Ciccarelli, F. D.Barker, J. N.Capon, F.2018-12-14doi:10.1101/496851Cold Spring Harbor Laboratory Press2018-12-14
<![CDATA[
Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks
]]>
https://biorxiv.org/cgi/content/short/499244v1?rss=1"
Wan, C.Cozzetto, D.Fa, R.Jones, D. T.2018-12-17doi:10.1101/499244Cold Spring Harbor Laboratory Press2018-12-17
<![CDATA[
TorC2 dependent phosphorylation modulates calcium regulation of fission yeast myosin.
]]>
https://biorxiv.org/cgi/content/short/498865v1?rss=1"
Baker, K. B.Gyamfi, I. A.Mashanov, G. I.Molloy, J. E.Geeves, M. A.Mulvihill, D. P.2018-12-18doi:10.1101/498865Cold Spring Harbor Laboratory Press2018-12-18
<![CDATA[
CSynth: A Dynamic Modelling and Visualisation Tool for 3D Chromatin Structure
]]>
https://biorxiv.org/cgi/content/short/499806v1?rss=1"
Todd, S.Todd, P.McGowan, S. J.Hughes, J. R.Kakui, Y.Leymarie, F. F.Latham, W.Taylor, S.2019-01-03doi:10.1101/499806Cold Spring Harbor Laboratory Press2019-01-03
<![CDATA[
Whole Genome Doubling mitigates Muller’s Ratchet in Cancer Evolution
]]>
https://biorxiv.org/cgi/content/short/513457v1?rss=1"
Lopez, S.Lim, E.Huebner, A.Dietzen, M.Mourikis, T.Watkins, T. B.Rowan, A.Dewhurst, S. M.Birkbak, N. J.Wilson, G. A.Jamal-Hanjani, M.Swanton, C.TRACERx Consortium,McGranahan, N.2019-01-07doi:10.1101/513457Cold Spring Harbor Laboratory Press2019-01-07
<![CDATA[
Comparative analysis of Synthetic Physical Interactions with the yeast centrosome
]]>
https://biorxiv.org/cgi/content/short/514166v1?rss=1"
Howell, R. S.Csikasz-Nagy, A.Thorpe, P. H.2019-01-07doi:10.1101/514166Cold Spring Harbor Laboratory Press2019-01-07
<![CDATA[
Genomic approaches reveal an endemic sub-population of gray wolves in Southern China
]]>
https://biorxiv.org/cgi/content/short/512921v1?rss=1"
Wang, G.-D.Zhang, M.Wang, X.Yang, M. A.Cao, P.Liu, F.Lu, H.Feng, X.Skoglund, P.Wang, L.Fu, Q.Zhang, Y.-P.2019-01-08doi:10.1101/512921Cold Spring Harbor Laboratory Press2019-01-08
<![CDATA[
Missense variants in health and disease target distinct functional pathways and proteomics features
]]>
https://biorxiv.org/cgi/content/short/512764v1?rss=1"
Laddach, A.Ng, J. C.-F.Fraternali, F.2019-01-09doi:10.1101/512764Cold Spring Harbor Laboratory Press2019-01-09
<![CDATA[
A Novel Repertoire of Blood Transcriptome Modules Based on Co-expression Patterns Across Sixteen Disease and Physiological States
]]>
https://biorxiv.org/cgi/content/short/525709v1?rss=1"
Altman, M. C.Rinchai, D.Baldwin, N.Whalen, E.Garand, M.Kabeer, B. A.Toufiq, M.Presnell, S.Chiche, L.Jourde-Chiche, N.Phillips, T.Klintmalm, G.O'Garra, A.Berry, M.Bloom, C.Wilkinson, R. J.Graham, C. M.Lipman, M.Lertmemongkolchai, G.Bedognetti, D.Kheradmand, F.Mejias, A.Ramilo, O.Palucka, K.Pascual, V.Banchereau, J.Chaussabel, D.2019-01-23doi:10.1101/525709Cold Spring Harbor Laboratory Press2019-01-23
<![CDATA[
The visual system of the genetically tractable crustacean Parhyale hawaiensis: diversification of eyes and visual circuits associated with low-resolution vision
]]>
https://biorxiv.org/cgi/content/short/527564v1?rss=1"
Ramos, A. P.Gustafsson, O.Labert, N.Salecker, I.Nilsson, D. E.Averof, M.2019-01-23doi:10.1101/527564Cold Spring Harbor Laboratory Press2019-01-23
<![CDATA[
Neuronal differentiation affects tissue mechanics and progenitor arrangement in the vertebrate neuroepithelium
]]>
https://biorxiv.org/cgi/content/short/536342v1?rss=1"
Guerrero, P.Perez-Carrasco, R.Zagorski, M.Page, D.Kicheva, A.Briscoe, J.Page, K.2019-01-31doi:10.1101/536342Cold Spring Harbor Laboratory Press2019-01-31
<![CDATA[
Simultaneous tracking of cell motility in liquid and at the solid-liquid interface
]]>
https://biorxiv.org/cgi/content/short/541615v1?rss=1"
Hook, A. L.Flewellen, J. L.Zaid, I. M.Berry, R. M.Dubern, J.-F.Carabelli, A.Wildman, R.Russell, N.Williams, P.Alexander, M. R.2019-02-05doi:10.1101/541615Cold Spring Harbor Laboratory Press2019-02-05
<![CDATA[
Segment 2 from influenza A(H1N1)pdm09 viruses confers temperature sensitive HA yield on candidate vaccine virus growth in eggs that is complemented by PB2 701D
]]>
https://biorxiv.org/cgi/content/short/541235v1?rss=1"
Hussain, S.Turnbull, M. L.Pinto, R. M.McCauley, J. W.Engelhardt, O. G.Digard, P.2019-02-08doi:10.1101/541235Cold Spring Harbor Laboratory Press2019-02-08
<![CDATA[
Perturbation of the gut microbiota by antibiotics results in accelerated breast tumour growth and metabolic dysregulation
]]>
https://biorxiv.org/cgi/content/short/553602v1?rss=1"
Kirkup, B.McKee, A.Makin, K.Paveley, J.Caim, S.Alcon-Giner, C.Leclaire, C.Dalby, M.Le Gall, G.Andrusaite, A.Kreuzaler, P.Driscoll, P.MacRae, J.Calvani, E.Ghanate, A.Milling, S.Yuneva, M.Weilbaecher, K.Korcsmaros, T.Hall, L. J.Robinson, S. D.2019-02-19doi:10.1101/553602Cold Spring Harbor Laboratory Press2019-02-19
<![CDATA[
Improving diagnosis and monitoring of treatment response in pulmonary tuberculosis using the molecular bacterial load assay (MBLA)
]]>
https://biorxiv.org/cgi/content/short/555995v1?rss=1"
Sabiiti, W.Azam, K.Kuchaka, D.Mtafya, B.Bowness, R. E.Oravcova, K.Farmer, E.Honeyborne, I.Evangelopoulos, D.McHugh, T. D.Xiao, H.Khosa, C.Rachow, A.Heinrich, N.Kampira, E.Davies, G.Bhatt, N.Ntinginya, N.Viegas, S.Jani, I.Kamdolozi, M.Mdolo, a.Khonga, M.Boeree, M. J.Philips, P. P.Sloan, D. J.Hoelscher, M.Kibiki, G.Gillespie, S. H.2019-02-28doi:10.1101/555995Cold Spring Harbor Laboratory Press2019-02-28
<![CDATA[
TGF-β family ligands exhibit distinct signaling dynamics that are driven by receptor localization
]]>
https://biorxiv.org/cgi/content/short/565416v1?rss=1"
Miller, D. S. J.Schmierer, B.Hill, C. S.2019-03-01doi:10.1101/565416Cold Spring Harbor Laboratory Press2019-03-01
<![CDATA[
A Complex Interplay of Anionic Phospholipid Binding Regulates 3-Phosphoinositide-Dependent-Kinase-1 Homodimer Activation
]]>
https://biorxiv.org/cgi/content/short/566430v1?rss=1"
De Las Heras, G.Calleja, V.Bailly, R.Dessolin, J.Requejo-Isidro, J.Larijani, B.2019-03-03doi:10.1101/566430Cold Spring Harbor Laboratory Press2019-03-03
<![CDATA[
The Personal Genome Project-UK: an open access resource of human multi-omics data
]]>
https://biorxiv.org/cgi/content/short/566711v1?rss=1"
Chervova, O.Conde, L.Guerra-Assuncao, J. A.Moghul, I.Webster, A. P.Berner, A.Larose Cadieux, E.Tian, Y.Voloshin, V.Hamoudi, R. A.Herrero, J.Beck, S.2019-03-04doi:10.1101/566711Cold Spring Harbor Laboratory Press2019-03-04
<![CDATA[
Identification of RBPMS as a smooth muscle master splicing regulator via proximity of its gene with super-enhancers
]]>
https://biorxiv.org/cgi/content/short/563304v1?rss=1"
Nakagaki-Silva, E. E.Gooding, C.Llorian, M.Jacob, A. G.Richards, F.Buckroyd, A.Sinha, S.Smith, C. W.2019-02-28doi:10.1101/563304Cold Spring Harbor Laboratory Press2019-02-28
<![CDATA[
An Integrated Chemical Proteomics Approach for Quantitative Profiling of Intracellular ADP-Ribosylation
]]>
https://biorxiv.org/cgi/content/short/568527v1?rss=1"
Kalesh, K.Lukauskas, S.Borg, A. J.Snijders, A. P.Leung, A. K. L.Haskard, D. O.DiMaggio, P. A.2019-03-05doi:10.1101/568527Cold Spring Harbor Laboratory Press2019-03-05
<![CDATA[
In the chick embryo, estrogen can induce chromosomally male ZZ left gonad epithelial cells to form an ovarian cortex which supports oogenesis
]]>
https://biorxiv.org/cgi/content/short/568691v1?rss=1"
Guioli, S.Zhao, D.Nandi, S.Clinton, M.Lovell-Badge, R.2019-03-05doi:10.1101/568691Cold Spring Harbor Laboratory Press2019-03-05
<![CDATA[
Differential requirements of cyclase associated protein (CAP) for actin turnover during the lytic cycle of Toxoplasma gondii
]]>
https://biorxiv.org/cgi/content/short/569368v1?rss=1"
Hunt, A.Wagener, J.Kent, R.Carmeille, R.Russell, M.Peddie, C.Collinson, L.Heaslip, A.Ward, G. E.Treeck, M.2019-03-06doi:10.1101/569368Cold Spring Harbor Laboratory Press2019-03-06
<![CDATA[
CHIME: CMOS-hosted in-vivo microelectrodes for massively scalable neuronal recordings
]]>
https://biorxiv.org/cgi/content/short/570069v1?rss=1"
Kollo, M.Racz, R. R.Hanna, M.Obaid, A.Angle, M. R.Wray, W.Kong, Y.Hierlemann, A.Muller, J.Melosh, N. A.Schaefer, A. T.2019-03-08doi:10.1101/570069Cold Spring Harbor Laboratory Press2019-03-08
<![CDATA[
Oncogenic signaling alters cell shape and mechanics to facilitate cell division under confinement.
]]>
https://biorxiv.org/cgi/content/short/571885v1?rss=1"
Matthews, H. K.Ganguli, S.Plak, K.Taubenberger, A. V.Piel, M.Guck, J.Baum, B.2019-03-09doi:10.1101/571885Cold Spring Harbor Laboratory Press2019-03-09
<![CDATA[
Mammalian olfaction is a high temporal bandwidth sense
]]>
https://biorxiv.org/cgi/content/short/570689v1?rss=1"
300 Hz bandwidth to simultaneously determine odour concentrations of two odours in air. We show that temporal correlation of odour concentrations reliably predicts whether odorants emerge from the same or different sources in normal turbulent environments outside and in laboratory conditions. To replicate natural odour dynamics in a reproducible manner we developed a multichannel odour delivery device allowing presentation of several odours with 10 ms temporal resolution. Integrating this device in an automated operant conditioning system we demonstrate that mice can reliably discriminate the correlation structure of odours at frequencies of up to 40 Hz. Consistent with this finding, output neurons in the olfactory bulb show segregated responses depending on the correlation of odour stimuli with populations of 10s of neurons sufficient to reach behavioural performance. Our work thus demonstrates that mammals can perceive temporal structure in odour stimuli at surprisingly fast timescales. This in turn might be useful for key behavioural challenges (Jacobs, 2012) such as odour source separation (Hopfield, 1991), figure-ground separation (Rokni et al., 2014) or odour localisation (Vergassola et al., 2007; Vickers, 2000).
]]>Erskine, A.Ackels, T.Dasgupta, D.Fukunaga, I.Schaefer, A. T.2019-03-09doi:10.1101/570689Cold Spring Harbor Laboratory Press2019-03-09
<![CDATA[
Lactate potentiates differentiation and expansion of cytotoxic T cells
]]>
https://biorxiv.org/cgi/content/short/571745v1?rss=1"
Rundqvist, H.Velica, P.Barbieri, L.Gameiro, P.Cunha, P.Gojkovic, M.Mijwel, S.Ahlstedt, E.Foskolou, I. P.Ruiz-Perez, M.Arsenian-Henriksson, M.Ule, J.Ostman, A.Johnson, R.2019-03-09doi:10.1101/571745Cold Spring Harbor Laboratory Press2019-03-09
<![CDATA[
Massively Parallel Microwire Arrays Integrated with CMOS chips for Neural Recording
]]>
https://biorxiv.org/cgi/content/short/573295v1?rss=1"
Obaid, A. M.Hanna, M.-E. S.Wu, Y.-W.Kollo, M.Racz, R. R.Angle, M. R.Muller, J.Brackbill, N.Wray, W.Franke, F.Chichilnisky, E. J.Hierlemann, A.Ding, J. B.Schaefer, A. T.Melosh, N. A.2019-03-11doi:10.1101/573295Cold Spring Harbor Laboratory Press2019-03-11
<![CDATA[
Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis.
]]>
https://biorxiv.org/cgi/content/short/576660v1?rss=1"
Phillips, H. M.Stothard, C. A.Shaikh Qureshi, W. M.Kousa, A. I.Briones-Leon, A.Khasawneh, R.Sanders, R.Mazotta, S.Dodds, R.Seidel, K.Bates, T.Nakatomi, M.Cockell, S.Schneider, J. E.Mohun, T. J.Maehr, R.Kist, R.Peters, H.Bamforth, S. D.2019-03-14doi:10.1101/576660Cold Spring Harbor Laboratory Press2019-03-14
<![CDATA[
Neuronal programming by microbiota enables environmental regulation of intestinal motility
]]>
https://biorxiv.org/cgi/content/short/579250v1?rss=1"
Obata, Y.Boeing, S.Castano, A.Carina Bon-Frauches, A.Gomez de Aguero, M.Boesmans, W.Yilmaz, B.Lopes, R.Huseynova, A.Maradana, M. R.Vanden Berghe, P.Murray, A. J.Stockinger, B.Macpherson, A. J.Pachnis, V.2019-03-15doi:10.1101/579250Cold Spring Harbor Laboratory Press2019-03-15
<![CDATA[
ESCRT-III/Vps4 controls heterochromatin-nuclear envelope attachments
]]>
https://biorxiv.org/cgi/content/short/579805v1?rss=1"
Pieper, G. H.Sprenger, S.Teis, D.Oliferenko, S.2019-03-15doi:10.1101/579805Cold Spring Harbor Laboratory Press2019-03-15
<![CDATA[
Protein structure without structure determination: direct coupling analysis based on in vitro evolution
]]>
https://biorxiv.org/cgi/content/short/582056v1?rss=1"
Fantini, M.Lisi, S.de los Rios, P.Cattaneo, A.Pastore, A.2019-03-20doi:10.1101/582056Cold Spring Harbor Laboratory Press2019-03-20
<![CDATA[
Identification of reduced host transcriptomic signatures for tuberculosis and digital PCR-based validation and quantification
]]>
https://biorxiv.org/cgi/content/short/583674v1?rss=1"
Gliddon, H. D.Kaforou, M.Alikian, M.Habgood-Coote, D.Zhou, C.Oni, T.Anderson, S. T.Brent, A. J.Crampin, A. C.Eley, B.Heyderman, R. S.Kern, F.Langford, P. R.Ottenhoff, T. H.French, N.Hibberd, M. L.Wright, V. J.Dockrell, H. M.Coin, L. J.Wilkinson, R. J.Levin, M.2019-03-21doi:10.1101/583674Cold Spring Harbor Laboratory Press2019-03-21
<![CDATA[
ERK1/2 signalling dynamics promote neural differentiation by regulating the polycomb repressive complex
]]>
https://biorxiv.org/cgi/content/short/586719v1?rss=1"
Semprich, C. I.Metzis, V.Patel, H.Briscoe, J.Storey, K. G.2019-03-22doi:10.1101/586719Cold Spring Harbor Laboratory Press2019-03-22
<![CDATA[
Prediction of inter-residue contacts with DeepMetaPSICOV in CASP13
]]>
https://biorxiv.org/cgi/content/short/586800v1?rss=1"
Kandathil, S. M.Greener, J. G.Jones, D. T.2019-03-24doi:10.1101/586800Cold Spring Harbor Laboratory Press2019-03-24
<![CDATA[
A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring
]]>
https://biorxiv.org/cgi/content/short/587295v1?rss=1"
Altman, M. C.Baldwin, N.Whalen, E.Al-Shaikhly, T.Presnell, S.Khaenam, P.Gersuk, V. H.Chiche, L.Jourde-Chiche, N.Phillips, T.Klintmalm, G.O'Garra, A.Berry, M.Bloom, C.Wilkinson, R. J.Graham, C. M.Lipman, M.Lertmemongkolchai, G.Kheradmand, F.Mejias, A.Ramilo, O.Palucka, K.Pascual, V.Banchereau, J.Chaussabel, D.2019-03-24doi:10.1101/587295Cold Spring Harbor Laboratory Press2019-03-24
<![CDATA[
Apical transport of Crumbs maintains epithelial cell polarity
]]>
https://biorxiv.org/cgi/content/short/592311v1?rss=1"
Aguilar-Aragon, M.Fletcher, G.Thompson, B. J.2019-03-28doi:10.1101/592311Cold Spring Harbor Laboratory Press2019-03-28
<![CDATA[
Mycobacterium tuberculosis cording in the cytosol of live lymphatic endothelial cells
]]>
https://biorxiv.org/cgi/content/short/595173v1?rss=1"
Lerner, T. R.Queval, C. J.Lai, R. P.Russell, M. R. G.Fearns, A.Greenwood, D. J.Collinson, L.Wilkinson, R. J.Gutierrez, M. G.2019-04-01doi:10.1101/595173Cold Spring Harbor Laboratory Press2019-04-01
<![CDATA[
Mask family proteins ANKHD1 and ANKRD17 regulate YAP nuclear import, stability and phase separation.
]]>
https://biorxiv.org/cgi/content/short/595439v1?rss=1"
Sidor, C.Borreguero-Munoz, N.Fletcher, G.Elbediwy, A.Vanyai, H.Guillermin, O.Thompson, B. J.2019-04-01doi:10.1101/595439Cold Spring Harbor Laboratory Press2019-04-01
<![CDATA[
Elevated LRRK2 and α-synuclein levels in CSF of infectious meningitis patients
]]>
https://biorxiv.org/cgi/content/short/599381v1?rss=1"
Herbst, S.Marais, S.Gutierrez, M. G.Waddell, S. J.Wilkinson, R. J.Lai, R. P.2019-04-04doi:10.1101/599381Cold Spring Harbor Laboratory Press2019-04-04
<![CDATA[
Canonical NOTCH signaling controls the early progenitor state and emergence of the medullary epithelial lineage in fetal thymus development.
]]>
https://biorxiv.org/cgi/content/short/600833v1?rss=1"
Liu, D.Kousa, A.O'Neill, K.Guillemot, F.Popis, M.Farley, A. M.Tomlinson, S. R.Ulyanchenko, S.Seymour, P. A.Serup, P.Koch, U.Radtke, F.Blackburn, C. C.2019-04-05doi:10.1101/600833Cold Spring Harbor Laboratory Press2019-04-05
<![CDATA[
Widespread FUS mislocalization is a molecular hallmark of ALS
]]>
https://biorxiv.org/cgi/content/short/491787v1?rss=1"
Tyzack, G. E.Luisier, R.Taha, D. M.Neeves, J.Modic, M.Mitchell, J. S.Meyer, I.Greensmith, L.Newcombe, J.Ule, J.Luscombe, N. M.Patani, R.2019-04-09doi:10.1101/491787Cold Spring Harbor Laboratory Press2019-04-09
<![CDATA[
A fence function for adherens junctions in epithelial cell polarity
]]>
https://biorxiv.org/cgi/content/short/605808v1?rss=1"
Aguilar-Aragon, M.Tournier, A.Thompson, B. J.2019-04-11doi:10.1101/605808Cold Spring Harbor Laboratory Press2019-04-11
<![CDATA[
Natural hypothalamic circuit dynamics underlying object memorization
]]>
https://biorxiv.org/cgi/content/short/603936v1?rss=1"
Kosse, C.Burdakov, D.2019-04-11doi:10.1101/603936Cold Spring Harbor Laboratory Press2019-04-11
<![CDATA[
nf-core: Community curated bioinformatics pipelines
]]>
https://biorxiv.org/cgi/content/short/610741v1?rss=1"
Ewels, P.Peltzer, A.Fillinger, S.Alneberg, J.Patel, H.Wilm, A.Garcia, M.Di Tommaso, P.Nahnsen, S.2019-04-16doi:10.1101/610741Cold Spring Harbor Laboratory Press2019-04-16
<![CDATA[
Epigenetic regulation of unique genes and repetitive elements by the KRAB zinc finger protein ZFP57
]]>
https://biorxiv.org/cgi/content/short/611400v1?rss=1"
Shi, H.Strogantsev, R.Takahashi, N.Kazachenka, A.Lorincz, M.Hemberger, M.Ferguson-Smith, A.2019-04-18doi:10.1101/611400Cold Spring Harbor Laboratory Press2019-04-18
<![CDATA[
Rapid sensory integration in orexin neurons governs probability of future movements
]]>
https://biorxiv.org/cgi/content/short/620096v1?rss=1"
Karnani, M. M.Schöne, C.Bracey, E. F.Gonzalez, J. A.Viskaitis, P.Adamantidis, A.Burdakov, D.2019-04-26doi:10.1101/620096Cold Spring Harbor Laboratory Press2019-04-26
<![CDATA[
Altered Hippocampal-Prefrontal Neural Dynamics in Mouse Models of Down Syndrome
]]>
https://biorxiv.org/cgi/content/short/644849v1?rss=1"
Chang, P.Bush, D.Schorge, S.Good, M.Canonica, T.Shing, N.Noy, S.Wiseman, F. K.Burgess, N.Tybulewicz, V. L.Walker, M. C.Fisher, E. M.2019-05-23doi:10.1101/644849Cold Spring Harbor Laboratory Press2019-05-23
<![CDATA[
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
]]>
https://biorxiv.org/cgi/content/short/653105v1?rss=1"
Zhou, N.Jiang, Y.Bergquist, T. R.Lee, A. J.Kacsoh, B. Z.Crocker, A. W.Lewis, K. A.Georghiou, G.Nguyen, H. N.Hamid, M. N.Davis, L.The Critical Assessment of Function Annotation,Rost, B.Brenner, S. E.Orengo, C. A.Jeffery, C. J.Bosco, G. D.Hogan, D. A.Martin, M. J.O'Donovan, C.Mooney, S. D.Greene, C. S.Radivojac, P.Friedberg, I.2019-05-29doi:10.1101/653105Cold Spring Harbor Laboratory Press2019-05-29
<![CDATA[
ScanningSWATH enables ultra-fast proteomics using high-flow chromatography and minute-scale gradients
]]>
https://biorxiv.org/cgi/content/short/656793v1?rss=1"
Messner, C.Demichev, V.Bloomfield, N.Ivosev, G.Wasim, F.Zelezniak, A.Lilley, K.Tate, S.Ralser, M.2019-05-31doi:10.1101/656793Cold Spring Harbor Laboratory Press2019-05-31
<![CDATA[
Single-Cell Signalling Analysis of Heterocellular Organoids
]]>
https://biorxiv.org/cgi/content/short/659896v1?rss=1"
1 million single small intestinal organoid cells by mass cytometry reveals cell-type and cell-state specific signalling networks in stem, Paneth, enteroendocrine, tuft, goblet cells, and enterocytes. Integrating single-cell PTM analysis with Thiol-reactive Organoid Barcoding in situ (TOBis) enables high-throughput comparison of signalling networks between organoid cultures. Multivariate cell-type specific PTM analysis of colorectal cancer tumour microenvironment organoids reveals that shApc, KrasG12D, and Trp53R172H cell-autonomously mimic signalling states normally induced by stromal fibroblasts and macrophages. These results demonstrate how standard mass cytometry workflows can be modified to perform high-throughput multivariate cell-type specific signalling analysis of healthy and cancerous organoids.
]]>Qin, X.Sufi, J.Vlckova, P.Kyriakidou, P.Acton, S. E.Li, V. S. W.Nitz, M.Tape, C. J.2019-06-06doi:10.1101/659896Cold Spring Harbor Laboratory Press2019-06-06
<![CDATA[
Retroviral integration into nucleosomes throughDNA looping and sliding along the histone octamer
]]>
https://biorxiv.org/cgi/content/short/663336v1?rss=1"
Wilson, M. D.Renault, L.Maskell, D. P.Ghoneim, M.Pye, V. E.Nans, A.Rueda, D. S.Cherepanov, P.Costa, A.2019-06-07doi:10.1101/663336Cold Spring Harbor Laboratory Press2019-06-07
<![CDATA[
Plasmodium Kinesin-8X associates with mitotic spindles and is essential for oocyst development during parasite proliferation and transmission
]]>
https://biorxiv.org/cgi/content/short/665836v1?rss=1"
Zeeshan, M.Shilliday, F.Liu, T.Abel, S.Mourier, T.Ferguson, D. J. P.Rea, E.Stanway, R. R.Roques, M.Williams, D.Daniel, E.Brady, D.Roberts, A. J.Sinden, R. E.Holder, A. A.Pain, A.Le Roch, K. G.Moores, C. A.Tewari, R.2019-06-10doi:10.1101/665836Cold Spring Harbor Laboratory Press2019-06-10
<![CDATA[
Systematic analysis of Plasmodium myosins reveals differential expression, localization and function in invasive and proliferative parasite stages
]]>
https://biorxiv.org/cgi/content/short/671578v1?rss=1"
Wall, R. J.ZEESHAN, M.Katris, N. J.Limenitakis, R.Rea, E.Stock, J.Brady, D.Waller, R. F.Holder, A. A.Tewari, R.2019-06-14doi:10.1101/671578Cold Spring Harbor Laboratory Press2019-06-14
<![CDATA[
Inherited duplications of PPP2R3B promote naevi and melanoma via a novel C21orf91-driven proliferative phenotype
]]>
https://biorxiv.org/cgi/content/short/672576v1?rss=1"
Polubothu, S.Al-Olabi, L.Lionarons, D. A.Harland, M.Thomas, A.Horswell, S.Hunt, L.Wlodarchak, N.Aguilera, P.Brand, S.Bryant, D.Beales, P.Carrera, C.Chen, H.Elgar, G.Harwood, C. A.Howell, M.Jenkins, D.Larue, L.Loughlin, S.MacDonald, J.Malvehy, J.Barberan Martin, S.Martins da Silva, V.Molina, M.Morrogh, D.Moulding, D.Nsengimana, J.Pittman, A.Puig-Butille, J.-A.Parmar, K.Sebire, N. J.Scherer, S.Stadnik, P.Stanier, P.Tell-Marti, G.Waelchli, R.Zarrei, M.Zecchin, D.Puig, S.Bataille, V.Xing, Y.Healey, E.Moore, G. E.2019-06-15doi:10.1101/672576Cold Spring Harbor Laboratory Press2019-06-15
<![CDATA[
Plasmodium condensin core subunits (SMC2/SMC4) mediate atypical mitosis and are essential for parasite proliferation and transmission
]]>
https://biorxiv.org/cgi/content/short/674028v1?rss=1"
Pandey, R.Abel, S.Boucher, M.Wall, R. J.Zeeshan, M.Rea, E.Freville, A.Lu, X. M.Brady, D.Daniel, E.Stanway, R. R.Wheatley, S.Batugedara, G.Hollin, T.Bottrill, A. R.Gupta, D.Holder, A. A.Le Roch, K. G.Tewari, R.2019-06-17doi:10.1101/674028Cold Spring Harbor Laboratory Press2019-06-17
<![CDATA[
PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy
]]>
https://biorxiv.org/cgi/content/short/680561v1?rss=1"
Akpinar, B.Bell, N.Pyne, A.Hoogenboom, B.2019-06-24doi:10.1101/680561Cold Spring Harbor Laboratory Press2019-06-24
<![CDATA[
Broadly inhibiting anti-neuraminidase monoclonal antibodies induced by trivalent influenza vaccine and H7N9 infection in humans
]]>
https://biorxiv.org/cgi/content/short/682450v1?rss=1"
Rijal, P.Wang, B. B.Tan, T. K.Schimanski, L.Janesch, P.Dong, T.McCauley, J. M.Daniels, R. S.Townsend, A.Huang, K.-Y. A.2019-06-26doi:10.1101/682450Cold Spring Harbor Laboratory Press2019-06-26
<![CDATA[
RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
]]>
https://biorxiv.org/cgi/content/short/681924v1?rss=1"
Bonetti, A.Agostini, F.Suzuki, A. M.Hashimoto, K.Pascarella, G.Gimenez, J.Roos, L.Nash, A. J.Ghilotti, M.Cameron, C. J.Valentine, M.Medvedeva, Y. A.Noguchi, S.Agirre, E.Kashi, K.Samudyata, S.Luginbuehl, J.Cazzoli, R.Agrawal, S.Luscombe, N. M.Blanchette, M.Kasukawa, T.De Hoon, M.Arner, E.Lenhard, B.Plessy, C.Castelo-Branco, G.Orlando, V.Carninci, P.2019-06-27doi:10.1101/681924Cold Spring Harbor Laboratory Press2019-06-27
<![CDATA[
Insights into human genetic variation and population history from 929 diverse genomes
]]>
https://biorxiv.org/cgi/content/short/674986v1?rss=1"
Bergström, A.McCarthy, S. A.Hui, R.Almarri, M. A.Ayub, Q.Danecek, P.Chen, Y.Felkel, S.Hallast, P.Kamm, J.Blanche, H.Deleuze, J.-F.Cann, H.Mallick, S.Reich, D.Sandhu, M. S.Skoglund, P.Scally, A.Xue, Y.Durbin, R.Tyler-Smith, C.2019-06-27doi:10.1101/674986Cold Spring Harbor Laboratory Press2019-06-27
<![CDATA[
Actomyosin regulation by Eph receptor signaling couples boundary cell formation to border sharpness
]]>
https://biorxiv.org/cgi/content/short/683631v1?rss=1"
Cayuso, J.Xu, Q.Addison, M.Wilkinson, D.2019-06-27doi:10.1101/683631Cold Spring Harbor Laboratory Press2019-06-27
<![CDATA[
Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy
]]>
https://biorxiv.org/cgi/content/short/686626v1?rss=1"
Prahst, C.Ashrafzadeh, P.Harrington, K.Venkatraman, L.Richards, M.Russo, A. M.Cho, K.-S.Chang, K.Mead, T.Chen, D. F.Richardson, D.Claesson-Welsh, L.Franco, C.Bentley, K.2019-06-28doi:10.1101/686626Cold Spring Harbor Laboratory Press2019-06-28
<![CDATA[
Kinesin-8B controls basal body function and flagellum formation and is key to malaria parasite transmission
]]>
https://biorxiv.org/cgi/content/short/686568v1?rss=1"
Zeeshan, M.Ferguson, D. J. P.Abel, S.Burrrell, A.Rea, E.Brady, D.Daniel, E.Delves, M.Vaughan, S.Holder, A. A.Le Roch, K. G.Moores, C. A.Tewari, R.2019-06-28doi:10.1101/686568Cold Spring Harbor Laboratory Press2019-06-28
<![CDATA[
High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation
]]>
https://biorxiv.org/cgi/content/short/688010v1?rss=1"
25%), most of which had never hitherto been implicated in immunology. Furthermore, they were conspicuously enriched in genes for which humans show poor tolerance to loss-of-function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with one another and with specific physiologic traits. By limiting the freedom of individual immune parameters, such linkages impose genetically regulated "immunological structures", whose integrity was found to be associated with immunocompetence. Hence, our findings provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.
]]>Abeler-Dörner, L.Laing, A.Lorenc, A.Ushakov, D. S.Clare, S.Speak, A.Duque, M.White, J. K.Ramirez-Solis, R.Saran, N.Bull, K. R.Moron, B.Iwasaki, J.Barton, P. R.Caetano, S.Hng, K. I.Cambridge, E.Forman, S.Crockford, T. L.Griffiths, M.Kane, L.Harcourt, K.Brandt, C.Notley, G.Babalola, K. O.Warren, J.Mason, J. C.Meeniga, A.Karp, N. A.Melvin, D.Cawthorne, E.Weinrick, B.Rahim, A.Drissler, S.Meskas, J.Yue, A.Lux, M.Song-Zhao, G.Chan, A.Ballesteros Reviriego, C.Abeler, J.Wilson, H.Przemska-Kosicka, A.Edmans, M.Stre2019-07-02doi:10.1101/688010Cold Spring Harbor Laboratory Press2019-07-02
<![CDATA[
Cyclin-dependent-like kinase 5 is required for pain signalling in both human neurons and mouse models
]]>
https://biorxiv.org/cgi/content/short/690172v1?rss=1"
La Montanara, P.Hervera Abad, A.Baltussen, L.Palmisano, I.De Virgiliis, F.Gao, Y.Qasim, K.Gorgoraptis, N.Wong, K.Downs, J.Di Lazzaro, V.Pizzorusso, T.Ultanir, S.Leonard, H.Nagy, I.Mazarakis, N.Di Giovanni, S.2019-07-02doi:10.1101/690172Cold Spring Harbor Laboratory Press2019-07-02
<![CDATA[
Greb1 is required for axial elongation and segmentation in vertebrate embryos.
]]>
https://biorxiv.org/cgi/content/short/692095v1?rss=1"
Prajapati, R. S.Mitter, R.Vezzaro, A.Ish-Horowicz, D.2019-07-06doi:10.1101/692095Cold Spring Harbor Laboratory Press2019-07-06
<![CDATA[
Perifornical Area Urocortin-3 Neurons Promote Infant-directed Neglect and Aggression
]]>
https://biorxiv.org/cgi/content/short/697334v1?rss=1"
Autry, A. E.Wu, Z.Kohl, J.Bambah-Mukku, D.Rubinstein, N. D.Marin-Rodriguez, B.Carta, I.Sedwick, V.Dulac, C.2019-07-09doi:10.1101/697334Cold Spring Harbor Laboratory Press2019-07-09
<![CDATA[
TRF1 prevents permissive DNA damage response, recombination and Break Induced Replication at telomeres
]]>
https://biorxiv.org/cgi/content/short/697979v1?rss=1"
Vannier, J.-B.Porreca, R. M.Law, P. P.Herrera-Moyano, E.Gonzalez Franco, R.Montoya, A.Faull, P.Kramer, H.2019-07-10doi:10.1101/697979Cold Spring Harbor Laboratory Press2019-07-10
<![CDATA[
Structure of D. melanogaster ARC1 reveals a repurposed molecule with characteristics of retroviral Gag
]]>
https://biorxiv.org/cgi/content/short/691972v1?rss=1"
Cottee, M. A.Letham, S. C.Young, G. R.Stoye, J. P.Taylor, I. A.2019-07-10doi:10.1101/691972Cold Spring Harbor Laboratory Press2019-07-10
<![CDATA[
Lessons in genome engineering: opportunities, tools and pitfalls
]]>
https://biorxiv.org/cgi/content/short/710871v1?rss=1"
Poernbacher, I.Crossman, S.Kurth, J.Nojima, H.Baena-Lopez, A.Alexandre, C.vincent, J.-P.2019-07-22doi:10.1101/710871Cold Spring Harbor Laboratory Press2019-07-22
<![CDATA[
A landmark-free morphometric pipeline: Application to characterise a Down syndrome model skull phenotype
]]>
https://biorxiv.org/cgi/content/short/711259v1?rss=1"
Toussaint, N.Redhead, Y.Liu, W.Fisher, E.Hallgrimsson, B.Tybulewicz, V.Green, J. B. A.Schnabel, J.2019-07-22doi:10.1101/711259Cold Spring Harbor Laboratory Press2019-07-22
<![CDATA[
O-linked mucin-type glycosylation regulates the transcriptional programme downstream of EGFR in breast cancer
]]>
https://biorxiv.org/cgi/content/short/714675v1?rss=1"
Tajadura-Ortega, V.Gambardella, G.Skinner, A.Ter-Borch Gram Schjoldager, K.Beatson, R.Graham, R.Achkova, D.Taylor-Papadimitriou, J.Ciccarelli, F. D.Burchell, J.2019-07-25doi:10.1101/714675Cold Spring Harbor Laboratory Press2019-07-25
<![CDATA[
Chemical precision glyco-mutagenesis by glycosyltransferase engineering in living cells
]]>
https://biorxiv.org/cgi/content/short/669861v1?rss=1"
Schumann, B.Malaker, S. A.Wisnovsky, S. P.Debets, M. F.Agbay, A. J.Fernandez, D.Wagner, L. J. S.Lin, L.Choi, J.Fox, D. M.Peh, J.Gray, M. A.Pedram, K.Kohler, J. J.Mrksich, M.Bertozzi, C. R.2019-06-13doi:10.1101/669861Cold Spring Harbor Laboratory Press2019-06-13
<![CDATA[
Global profiling of myristoylation in Toxoplasma gondii reveals key roles for lipidation in CDPK1 and MIC7 function
]]>
https://biorxiv.org/cgi/content/short/719062v1?rss=1"
Broncel, M.Dominicus, C.Hunt, A.Wallbank, B. A.Federico, S.Young, J. C.Treeck, M.2019-07-30doi:10.1101/719062Cold Spring Harbor Laboratory Press2019-07-30
<![CDATA[
Precision of Tissue Patterning is Controlled by Dynamical Properties of Gene Regulatory Networks
]]>
https://biorxiv.org/cgi/content/short/721043v1?rss=1"
Exelby, K.Herrera-Delgado, E.Garcia Perez, L.Perez-Carrasco, R.Sagner, A.Metzis, V.Sollich, P.Briscoe, J.2019-07-31doi:10.1101/721043Cold Spring Harbor Laboratory Press2019-07-31
<![CDATA[
jULIEs: extracellular probes for recordings and stimulation in the structurally and functionally intact mouse brain
]]>
https://biorxiv.org/cgi/content/short/721548v1?rss=1"
Racz, R. R.Kollo, M.Racz, G.Bulz, C.Ackels, T.Warner, T.Wray, W. A.Kiskin, N.Chen, C.Ye, Z.de Hoz, L.Rancz, E. A.Schaefer, A. T.2019-08-01doi:10.1101/721548Cold Spring Harbor Laboratory Press2019-08-01
<![CDATA[
Improving protein function prediction with synthetic feature samples created by generative adversarial networks
]]>
https://biorxiv.org/cgi/content/short/730143v1?rss=1"
Wan, C.Jones, D. T.2019-08-08doi:10.1101/730143Cold Spring Harbor Laboratory Press2019-08-08
<![CDATA[
Th22 cells are a major contributor to the mycobacterial CD4+ T cell response and are depleted during HIV infection
]]>
https://biorxiv.org/cgi/content/short/732263v1?rss=1"
Bunjun, R.Omondi, F. M. A.Makatsa, M. S.Muller, T. L.Prentice, C.Wilkinson, R. J.Riou, C.Burgers, W. A.2019-08-13doi:10.1101/732263Cold Spring Harbor Laboratory Press2019-08-13
<![CDATA[
Lysine acetylation promotes PALB2 chromatin association to maintain genome stability
]]>
https://biorxiv.org/cgi/content/short/735811v1?rss=1"
Esashi, F.Fournier, M.Bleuyard, J.-Y.Couturier, A. M.Ellins, J.Hester, S.Smerdon, S. J.Tora, L.2019-08-15doi:10.1101/735811Cold Spring Harbor Laboratory Press2019-08-15
<![CDATA[
A single cell transcriptome atlas of the developing zebrafish hindbrain
]]>
https://biorxiv.org/cgi/content/short/745141v1?rss=1"
Tambalo, M.Mitter, R.Wilkinson, D.2019-08-23doi:10.1101/745141Cold Spring Harbor Laboratory Press2019-08-23
<![CDATA[
Elongations of epithelial colony in vitro: symmetry breaking through collective effects
]]>
https://biorxiv.org/cgi/content/short/755181v1?rss=1"
Comelles, J.Soumya, S. S.Anvitha, S.Salbreux, G.Jülicher, F.Inamdar, M. M.Riveline, D.2019-09-04doi:10.1101/755181Cold Spring Harbor Laboratory Press2019-09-04
<![CDATA[
Apical length modulates dendritic excitability in L5 pyramidal neurons
]]>
https://biorxiv.org/cgi/content/short/754499v1?rss=1"
Galloni, A. R.Laffere, A.Rancz, E. A.2019-09-04doi:10.1101/754499Cold Spring Harbor Laboratory Press2019-09-04
<![CDATA[
Protein ubiquitylation is essential for the schizont to merozoite transition in Plasmodium falciparum blood-stage development
]]>
https://biorxiv.org/cgi/content/short/755439v1?rss=1"
Wu, Y.Encheva, V.Green, J. L.Lasonder, E.Prommaban, A.Kunzelmann, S.Christodoulou, E.Grainger, M.Truongvan, N.Bothe, S.Sharma, V.Song, W.Pinzuti, I.Uthaipibull, C.Srichairatanakool, S.Barault, V.Langsley, G.Schindelin, H.Stieglitz, B.Snijders, A. P.Holder, A. A.2019-09-04doi:10.1101/755439Cold Spring Harbor Laboratory Press2019-09-04
<![CDATA[
The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection
]]>
https://biorxiv.org/cgi/content/short/758318v1?rss=1"
Giraud-Gatineau, A.Coya, J. M.Maure, A.Biton, A.Thomson, M.Bernard, E. M.Gutierrez, M. G.Larrouy-Maumus, G.Brosch, R.Gicquel, B.Tailleux, L.2019-09-06doi:10.1101/758318Cold Spring Harbor Laboratory Press2019-09-06
<![CDATA[
Delineating the rules for structural adaptation of membrane-associated proteins to evolutionary changes in membrane lipidome
]]>
https://biorxiv.org/cgi/content/short/762146v1?rss=1"
Makarova, M.Peter, M.Balogh, G.Glatz, A.MacRae, J. I.Mora, N. L.Booth, P.Makeyev, E.Vigh, L.Oliferenko, S.2019-09-09doi:10.1101/762146Cold Spring Harbor Laboratory Press2019-09-09
<![CDATA[
Homeostatic maintenance and age-related functional decline in the Drosophila ear
]]>
https://biorxiv.org/cgi/content/short/764670v1?rss=1"
Keder, A.Tardieu, C.Malong, L.Filia, A.Kashkenbayeva, A.Gale, J. E.Lovett, M.Jarman, A. P.Albert, J. T.2019-09-10doi:10.1101/764670Cold Spring Harbor Laboratory Press2019-09-10
<![CDATA[
Real-time dynamics of Plasmodium NDC80 as a marker for the kinetochore during atypical mitosis and meiosis
]]>
https://biorxiv.org/cgi/content/short/767830v1?rss=1"
Pandey, R.Zeeshan, M.Ferguson, D. J. P.Markus, R.Brady, D.Daniel, E.Stanway, R. R.Holder, A. A.Guttery, D. S.Tewari, R.2019-09-13doi:10.1101/767830Cold Spring Harbor Laboratory Press2019-09-13
<![CDATA[
Copy number motifs expose genome instability type and predict driver events and disease outcome in breast cancer
]]>
https://biorxiv.org/cgi/content/short/769356v1?rss=1"
Pladsen, A. V.Nilsen, G.Rueda, O. M.Aure, M. R.Borgan, O.Liestol, K.Vitelli, V.Frigessi, A.Langerod, A.OSBREAC,Mathelier, A.Engebraten, O.Wedge, D.Van Loo, P.Caldas, C.Borresen-Dale, A.-L.Russnes, H. G.Lingjaerde, O. C.2019-09-14doi:10.1101/769356Cold Spring Harbor Laboratory Press2019-09-14
<![CDATA[
A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth
]]>
https://biorxiv.org/cgi/content/short/770768v1?rss=1"
Kamrad, S.Grossbach, J.Rodriguez-Lopez, M.Townsend, S.Mulleder, M.Cappelletti, V.Stojanovski, G.Picotti, P.Beyer, A.Ralser, M.Bahler, J.2019-09-16doi:10.1101/770768Cold Spring Harbor Laboratory Press2019-09-16
<![CDATA[
Fluctuation-based Super-Resolution Traction Force Microscopy
]]>
https://biorxiv.org/cgi/content/short/772947v1?rss=1"
Stubb, A.Laine, R. F.Guzman, C.Henriques, R.Jacquemet, G.Ivaska, J.2019-09-18doi:10.1101/772947Cold Spring Harbor Laboratory Press2019-09-18
<![CDATA[
Proteasome-mediated protein degradation resets the cell division cycle and triggers ESCRT-III-mediated cytokinesis in an archaeon
]]>
https://biorxiv.org/cgi/content/short/774273v1?rss=1"
Tarrason Risa, G.Hurtig, F.Bray, S.Hafner, A.Harker-Kirschneck, L.Faull, P.Davis, C.Papatziamou, D.Mutavchiev, D. R.Fan, C.Meneguello, L.Arashiro Pulschen, A.Dey, G.Culley, S.Kilkenny, M. L.Pellegrini, L.de Bruin, R. A. M.Henriques, R.Snijders, A. P.Saric, A.Lindas, A.-C.Robinson, N.Baum, B.2019-09-18doi:10.1101/774273Cold Spring Harbor Laboratory Press2019-09-18
<![CDATA[
Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation
]]>
https://biorxiv.org/cgi/content/short/777326v1?rss=1"
Dimchev, G.Amiri, B.Humphries, A. C.Schaks, M.Dimchev, V.Stradal, T. E. B.Faix, J.Krause, M.Way, M.Falcke, M.Rottner, K.2019-09-20doi:10.1101/777326Cold Spring Harbor Laboratory Press2019-09-20
<![CDATA[
The speed of GTP hydrolysis determines GTP cap size and controls microtubule stability
]]>
https://biorxiv.org/cgi/content/short/779108v1?rss=1"
Roostalu, J.Thomas, C.Cade, N. I.Kunzelmann, S.Taylor, I. A.Surrey, T.2019-09-23doi:10.1101/779108Cold Spring Harbor Laboratory Press2019-09-23
<![CDATA[
Closed mitosis requires local disassembly of the nuclear envelope
]]>
https://biorxiv.org/cgi/content/short/779769v1?rss=1"
Dey, G.Culley, S.Curran, S. A.Henriques, R.Kukulski, W.Baum, B.2019-09-23doi:10.1101/779769Cold Spring Harbor Laboratory Press2019-09-23
<![CDATA[
Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication
]]>
https://biorxiv.org/cgi/content/short/789578v1?rss=1"
Gruszka, D. T.Xie, S.Kimura, H.Yardimci, H.2019-10-01doi:10.1101/789578Cold Spring Harbor Laboratory Press2019-10-01
<![CDATA[
B cells extract antigens using Arp2/3-generated actin foci interspersed with linear filaments
]]>
https://biorxiv.org/cgi/content/short/792481v1?rss=1"
Roper, S. I.Wasim, L.Malinova, D.Way, M.Cox, S.Tolar, P.2019-10-04doi:10.1101/792481Cold Spring Harbor Laboratory Press2019-10-04
<![CDATA[
Differential spatiotemporal targeting of Toxoplasma and Salmonella by GBP1 assembles caspase signalling platforms
]]>
https://biorxiv.org/cgi/content/short/792804v1?rss=1"
Fisch, D.Clough, B.Domart, M.-C.Bando, H.Masonou, T.Collinson, L. M.Yamamoto, M.Shenoy, A.Frickel, E.-M.2019-10-05doi:10.1101/792804Cold Spring Harbor Laboratory Press2019-10-05
<![CDATA[
Mechanism of RPA-Facilitated Processive DNA Unwinding by the Eukaryotic CMG Helicase
]]>
https://biorxiv.org/cgi/content/short/796003v1?rss=1"
Kose, H. B.Xie, S.Cameron, G.Strycharska, M. S.Yardimci, H.2019-10-07doi:10.1101/796003Cold Spring Harbor Laboratory Press2019-10-07
<![CDATA[
Cryo-EM Structures of the XPF-ERCC1 Endonuclease Reveal an Auto-Inhibited Conformation and the Basis for Activation
]]>
https://biorxiv.org/cgi/content/short/796524v1?rss=1"
Jones, M. L.Beuron, F.Borg, A.Nans, A.Earl, C.Briggs, D. C.Bowles, M.Morris, E. P.Linch, M.McDonald, N. Q.2019-10-07doi:10.1101/796524Cold Spring Harbor Laboratory Press2019-10-07
<![CDATA[
Three-dimensional super-resolution fluorescence imaging of DNA
]]>
https://biorxiv.org/cgi/content/short/796151v1?rss=1"
Yardimci, S.Burnham, D. R.Terry, S. Y. A.Yardimci, H.2019-10-07doi:10.1101/796151Cold Spring Harbor Laboratory Press2019-10-07
<![CDATA[
Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli mice allows protection from multiple retroviruses
]]>
https://biorxiv.org/cgi/content/short/802363v1?rss=1"
Yap, M. W.Young, G. R.Varnaite, R.Morand, S.Stoye, J. P.2019-10-11doi:10.1101/802363Cold Spring Harbor Laboratory Press2019-10-11
<![CDATA[
Salt-inducible kinases (SIKs) regulate TGFβ-mediated transcriptional and apoptotic responses
]]>
https://biorxiv.org/cgi/content/short/809228v1?rss=1"
Hutchinson, L. D.Darling, N. J.Nicolaou, S.Gori, I.Squair, D. R.Cohen, P.Hill, C. S.Sapkota, G. P.2019-10-17doi:10.1101/809228Cold Spring Harbor Laboratory Press2019-10-17
<![CDATA[
Divergent excitation two photon microscopy for 3D random access mesoscale imaging at single cell resolution
]]>
https://biorxiv.org/cgi/content/short/821405v1?rss=1"
Janiak, F. K.Bartel, P.Bale, M.T, Y.Komulainen, E. H.Zhou, M.Staras, K.Prieto-Godino, L. L.Euler, T.Maravall, M.Baden, T.2019-10-29doi:10.1101/821405Cold Spring Harbor Laboratory Press2019-10-29
<![CDATA[
Mimicry embedding for advanced neuralnetwork training of 3D biomedical micrographs
]]>
https://biorxiv.org/cgi/content/short/820076v1?rss=1"
Yakimovich, A.Huttunen, M.Samolej, J.Clough, B.Yoshida, N.Mostowy, S.Frickel, E.Mercer, J.2019-10-28doi:10.1101/820076Cold Spring Harbor Laboratory Press2019-10-28
<![CDATA[
In vivo control of Toxoplasma gondii by zebrafish macrophages
]]>
https://biorxiv.org/cgi/content/short/828624v1?rss=1"
Yoshida, N.Domart, M.-C.Yakimovich, A.Mazon-Moya, M. J.Collinson, L.Mercer, J.Frickel, E.Mostowy, S.2019-11-02doi:10.1101/828624Cold Spring Harbor Laboratory Press2019-11-02
<![CDATA[
Subcellular mRNA localization regulates ribosome biogenesis in migrating cells
]]>
https://biorxiv.org/cgi/content/short/829739v1?rss=1"
Dermit, M.Dodel, M.Lee, F. C. Y.Azman, M. S.Schwenzer, H.Jones, J. L.Blagden, S. P.Ule, J.Mardakheh, F. K.2019-11-04doi:10.1101/829739Cold Spring Harbor Laboratory Press2019-11-04
<![CDATA[
Escape from nonsense mediated decay associates with anti-tumor immunogenicity
]]>
https://biorxiv.org/cgi/content/short/823716v1?rss=1"
Litchfield, K.Reading, J.Lim, E.Xu, H.Liu, P.Al-Bakir, M.Wong, S.Rowan, A.Funt, S.Merghoub, T.Lauss, M.Svane, I. M.Jonsson, G.Herrero, J.Larkin, J.Quezada, S. A.Hellmann, M. D.Turajlic, S.Swanton, C.2019-11-07doi:10.1101/823716Cold Spring Harbor Laboratory Press2019-11-07
<![CDATA[
Functional characterisation of gut microbiota and metabolism in Type 2 diabetes indicates that Clostridiales and Enterococcus could play a key role in the disease
]]>
https://biorxiv.org/cgi/content/short/836114v1?rss=1"
Mora-Ortiz, M.Oregioni, A.Claus, S. P.2019-11-09doi:10.1101/836114Cold Spring Harbor Laboratory Press2019-11-09
<![CDATA[
Immune surveillance in clinical regression of pre-invasive squamous cell lung cancer
]]>
https://biorxiv.org/cgi/content/short/833004v1?rss=1"
Pennycuick, A.Teixeira, V. H.AbdulJabbar, K.Raza, S. E. A.Lund, T.Akarca, A.Rosenthal, R.Pipinikas, C. P.Lee-Six, H.Chandrasekharan, D. P.Hynds, R. E.Gowers, K. H. C.Henry, J. Y.Denais, C.Falzon, M.Antoniou, S.Durrenberger, P. F.Furness, A.Carroll, B.Thakrar, R. M.George, P. J.Marafioti, T.Swanton, C.Thirlwell, C.Campbell, P. J.Yuan, Y.Quezada, S. A.McGranahan, N.Janes, S. M.2019-11-10doi:10.1101/833004Cold Spring Harbor Laboratory Press2019-11-10
<![CDATA[
RNA modifications detection by comparative Nanopore direct RNA sequencing
]]>
https://biorxiv.org/cgi/content/short/843136v1?rss=1"
Leger, A.Amaral, P. P.Pandolfini, L.Capitanchik, C.Capraro, F.Barbieri, I.Migliori, V.Luscombe, N. M.Enright, A. J.Tzelepis, K.Ule, J.Fitzgerald, T.Birney, E.Leonardi, T.Kouzarides, T.2019-11-15doi:10.1101/843136Cold Spring Harbor Laboratory Press2019-11-15
<![CDATA[
Integrated Genomic Analysis Reveals Key Features of Long Undecoded Transcript Isoform (LUTI)-based Gene Repression
]]>
https://biorxiv.org/cgi/content/short/843458v1?rss=1"
Tresenrider, A.Jorgensen, V.Chia, M.Liao, H.van Werven, F.Unal, E.2019-11-15doi:10.1101/843458Cold Spring Harbor Laboratory Press2019-11-15
<![CDATA[
FUS gene is dual-coding with both proteins united in molecular hallmarks of amyotrophic lateral sclerosis
]]>
https://biorxiv.org/cgi/content/short/848580v1?rss=1"
Brunet, M. A.Jacques, J.-F.Nassari, S.Tyzack, G. E.McGoldrick, P.Zinman, L.Jean, S.Robertson, J.Patani, R.Roucou, X.2019-11-20doi:10.1101/848580Cold Spring Harbor Laboratory Press2019-11-20
<![CDATA[
Cyclic peptides can engage a single binding pocket through multiple, entirely divergent modes
]]>
https://biorxiv.org/cgi/content/short/850321v1?rss=1"
Patel, K.Walport, L. J.Walshe, J. L.Solomon, P.Low, J. K. K.Tran, D. H.Mouradian, K. S.Silva, A. P. G.Wilkinson-White, L.Matthews, J. M.Guss, J. M.Payne, R. J.Passioura, T.Suga, H.Mackay, J. P.2019-11-21doi:10.1101/850321Cold Spring Harbor Laboratory Press2019-11-21
<![CDATA[
Microtubule Nucleation by Single Human γTuRC in a Partly Open Asymmetric Conformation
]]>
https://biorxiv.org/cgi/content/short/853218v1?rss=1"
Consolati, T.Locke, J.Roostalu, J.Asthana, J.Lim, W. M.Gannon, J.Martino, F.Costa, A.Surrey, T.2019-11-23doi:10.1101/853218Cold Spring Harbor Laboratory Press2019-11-23
<![CDATA[
Engineering transplantable jejunal mucosal grafts using primary patient-derived organoids from children with intestinal failure
]]>
https://biorxiv.org/cgi/content/short/854083v1?rss=1"
Meran, L.Massie, I.Weston, A.Gaifulina, R.Faull, P.Orford, M.Kucharska, A.Baulies, A.Hirst, E.Konig, J.Tedeschi, A. M.Pellegata, A. F.Eli, S.Snijders, A. P.Collinson, L.Thapar, N.Thomas, G.Eaton, S.Bonfanti, P.De Coppi, P.Li, V. S. W.2019-11-25doi:10.1101/854083Cold Spring Harbor Laboratory Press2019-11-25
<![CDATA[
The breast cancer oncogene IKKε coordinates mitochondrial function and serine metabolism
]]>
https://biorxiv.org/cgi/content/short/855361v1?rss=1"
Xu, R.Jones, W.Wilcz-Villega, E.Costa, S.Rajeeve, V.Bentham, R. B.Bryson, K.Nagano, A.Yaman, B.Olendo Barasa, S.Wang, Y.Chelala, C.Cutillas, P.Szabadkai, G.Frezza, C.Bianchi, K.2019-11-26doi:10.1101/855361Cold Spring Harbor Laboratory Press2019-11-26
<![CDATA[
Cryogenic OrbiSIMS Localizes Semi-Volatile Molecules in Biological Tissues
]]>
https://biorxiv.org/cgi/content/short/862391v1?rss=1"
Newell, C. L.Vorng, J.-L.MacRae, J. I.Gilmore, I.Gould, A. P.2019-12-02doi:10.1101/862391Cold Spring Harbor Laboratory Press2019-12-02
<![CDATA[
The apparent requirement for protein synthesis during G2 phase is due to checkpoint activation
]]>
https://biorxiv.org/cgi/content/short/863548v1?rss=1"
Lockhead, S.Moskaleva, A.Kamenz, J.Chen, Y.Kang, M.Reddy, A. R. K.Santos, S.Ferrell, J. E.2019-12-03doi:10.1101/863548Cold Spring Harbor Laboratory Press2019-12-03
<![CDATA[
Widespread use of the "ascidian" mitochondrial genetic code in tunicates
]]>
https://biorxiv.org/cgi/content/short/865725v1?rss=1"
Pichon, J.Luscombe, N. M.Plessy, C.2019-12-05doi:10.1101/865725Cold Spring Harbor Laboratory Press2019-12-05
<![CDATA[
A FIJI Macro for quantifying pattern in extracellular matrix
]]>
https://biorxiv.org/cgi/content/short/867507v1?rss=1"
Wershof, E.Barry, D. J.Jenkins, R. P.Rullan, A.Wilkins, A.Roxanis, I.Anderson, K. I.Park, D.Bates, P. A.Sahai, E.2019-12-06doi:10.1101/867507Cold Spring Harbor Laboratory Press2019-12-06
<![CDATA[
Role of SHIP2 in cell repulsion regulated by Eph receptor and ephrin signaling
]]>
https://biorxiv.org/cgi/content/short/872846v1?rss=1"
Ashlin, T. G.Wu, Z.Xu, Q.Wilkinson, D.2019-12-11doi:10.1101/872846Cold Spring Harbor Laboratory Press2019-12-11
<![CDATA[
A switch in cilia-mediated Hedgehog signaling controls muscle stem cell quiescence and cell cycle progression
]]>
https://biorxiv.org/cgi/content/short/2019.12.21.884601v1?rss=1"
View larger version (31K):
org.highwire.dtl.DTLVardef@1cbaa81org.highwire.dtl.DTLVardef@273898org.highwire.dtl.DTLVardef@f4b26corg.highwire.dtl.DTLVardef@edda2c_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Cruz-Migoni, S. B.Mohd Imran, K.Wahid, A.Rahman, O.Briscoe, J.Borycki, A.-G.2019-12-22doi:10.1101/2019.12.21.884601Cold Spring Harbor Laboratory Press2019-12-22
<![CDATA[
Transcription levels of a long noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast
]]>
https://biorxiv.org/cgi/content/short/2019.12.24.887935v1?rss=1"
Moretto, F.Wood, N. E.Chia, M.Li, C.Luscombe, N.van Werven, F.2019-12-27doi:10.1101/2019.12.24.887935Cold Spring Harbor Laboratory Press2019-12-27
<![CDATA[
Species-specific developmental timing is associated with global differences in protein stability in mouse and human
]]>
https://biorxiv.org/cgi/content/short/2019.12.29.889543v1?rss=1"
Rayon, T.Stamataki, D.Perez-Carrasco, R.Garcia-Perez, L.Barrington, C.Melchionda, M.Exelby, K.Tybulewicz, V.Fisher, E. M. C.Briscoe, J.2019-12-31doi:10.1101/2019.12.29.889543Cold Spring Harbor Laboratory Press2019-12-31
<![CDATA[
Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson's disease at Chr16q11.2 and on the MAPT H1 allele.
]]>
https://biorxiv.org/cgi/content/short/2020.01.06.896241v1?rss=1"
Soutar, M.Melandri, D.Annuario, E.Monaghan, A.Welsh, N.D'Sa, K.Guelfi, S.Zhang, D.Pittman, A.Trabzuni, D.Pan, K.Kia, D. A.Bictash, M.Gandhi, S.Houlden, H.Cookson, M. R.Wood, N.Singleton, A.Hardy, J.Whiting, P.Blauwendraat, C.Whitworth, A.Manzoni, C.Ryten, M.Lewis, P.Plun-Favreau, H.2020-01-07doi:10.1101/2020.01.06.896241Cold Spring Harbor Laboratory Press2020-01-07
<![CDATA[
Local retinoic acid directs emergence of the extraocular muscle functional unit
]]>
https://biorxiv.org/cgi/content/short/2020.01.07.897694v1?rss=1"
Comai, G. E.Tesarova, M.Dupe, V.Rhinn, M.Vallecillo Garcia, P.da Silva, F.Feret, B.Exelby, K.Dolle, P.Carlsson, L.Pryce, B.Spitz, F.Stricker, S.Zikmund, T.Kaiser, J.Briscoe, J.Schedl, A.Ghyselinck, N. B.Schweitzer, R.Tajbakhsh, S.2020-01-07doi:10.1101/2020.01.07.897694Cold Spring Harbor Laboratory Press2020-01-07
<![CDATA[
Identifying strategies to target the metabolic flexibility of tumours.
]]>
https://biorxiv.org/cgi/content/short/2020.01.06.896571v1?rss=1"
Yuneva, M.Mendez-Lucas, A.Lin, W.Driscoll, P. C.Legrave, N.Novellasdemunt Vilaseca, L.Xie, C.Charles, M.Wilson, Z.Jones, N. P.Rayport, S. G.Rodriguez-Justo, M.Li, V. S. W.MacRae, J. I.Hay, N.Chen, X.2020-01-07doi:10.1101/2020.01.06.896571Cold Spring Harbor Laboratory Press2020-01-07
<![CDATA[
Intergenic RNA mainly derives from nascent transcripts of known genes
]]>
https://biorxiv.org/cgi/content/short/2020.01.08.898478v1?rss=1"
2.5 billion publicly available RNA-seq reads across 5 human cell lines and multiple cellular compartments to annotate transcriptional units in the human genome. About 80% of transcripts from unannotated intergenic regions can be attributed to the fuzzy transcription of existing genes; the remaining transcripts originate mainly from putative long non-coding RNA loci that are rarely spliced. We validated the transcriptional activity of these intergenic RNA using independent measurements, including transcriptional start sites, chromatin signatures, and genomic occupancies of RNA polymerase II in various phosphorylation states. We also analysed the nuclear localisation and sensitivities of intergenic transcripts to nucleases to illustrate that they tend to be rapidly degraded either on-chromatin by XRN2 or off-chromatin by the exosome.
ConclusionsWe provide a curated atlas of intergenic RNAs that distinguishes between alternative processing of well annotated genes from independent transcriptional units based on the combined analysis of chromatin signatures, nuclear RNA localisation and degradation pathways.
]]>Agostini, F.Zagalak, J. A.Attig, J.Ule, J.Luscombe, N. M.2020-01-09doi:10.1101/2020.01.08.898478Cold Spring Harbor Laboratory Press2020-01-09
<![CDATA[
ARID2 deficiency promotes tumor progression and is associated with higher sensitivity to PARP inhibition in lung cancer
]]>
https://biorxiv.org/cgi/content/short/2020.01.10.898726v1?rss=1"
Moreno, T.Gonzalez-Silva, L.Monterde, B.Betancor-Fernandez, I.Revilla, C.Agraz-Doblas, A.Freire, J.Isidro, P.Quevedo, L.Montes-Moreno, S.Cereceda, L.Astudillo, A.Casar, B.Crespo, P.Morales Torres, C.Scaffidi, P.Gomez-Roman, J.Salido, E.Varela, I.2020-01-10doi:10.1101/2020.01.10.898726Cold Spring Harbor Laboratory Press2020-01-10
<![CDATA[
Regulated repression, and not activation, governs the cell fate promoter controlling yeast meiosis
]]>
https://biorxiv.org/cgi/content/short/2020.01.13.904912v1?rss=1"
Tam, J.van Werven, F.2020-01-14doi:10.1101/2020.01.13.904912Cold Spring Harbor Laboratory Press2020-01-14
<![CDATA[
Super-Beacons: open-source probes with spontaneous tunable blinking compatible with live-cell super-resolution microscopy
]]>
https://biorxiv.org/cgi/content/short/2020.01.20.912311v1?rss=1"
Pereira, P. M.Gustafsson, N.Marsh, M.Mhlanga, M. M.Henriques, R.2020-01-20doi:10.1101/2020.01.20.912311Cold Spring Harbor Laboratory Press2020-01-20
<![CDATA[
Human AKTIP interacts with ESCRT proteins and functions at the midbody in cytokinesis
]]>
https://biorxiv.org/cgi/content/short/2020.01.19.911891v1?rss=1"
Merigliano, C.Burla, R.La Torre, M.Del Giudice, S.Teo, H. L.Liew, C. W.Goh, W. I.Chojnowski, A.Olmos, Y.Chiolo, I. E.Carlton, J. G.Raimondo, D.Stewart, C. L.Rhodes, D.Wright, G. D.Burke, B.Saggio, I.2020-01-20doi:10.1101/2020.01.19.911891Cold Spring Harbor Laboratory Press2020-01-20
<![CDATA[
Pyphe: A python toolbox for assessing microbial growth and cell viability in high-throughput colony screens
]]>
https://biorxiv.org/cgi/content/short/2020.01.22.915363v1?rss=1"
Kamrad, S.Rodriguez-Lopez, M.Cotobal, C.Correia-Melo, C.Ralser, M.Bahler, J.2020-01-23doi:10.1101/2020.01.22.915363Cold Spring Harbor Laboratory Press2020-01-23
<![CDATA[
Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism
]]>
https://biorxiv.org/cgi/content/short/2020.02.09.940536v1?rss=1"
Fedoryshchak, R. O.Ocasio, C. A.Strutton, B.Mattocks, J.Corran, A. J.Tate, E. W.2020-02-10doi:10.1101/2020.02.09.940536Cold Spring Harbor Laboratory Press2020-02-10
<![CDATA[
A divergent cyclin/cyclin-dependent kinase complex controls the atypical replication of Plasmodium berghei during gametogony and parasite transmission.
]]>
https://biorxiv.org/cgi/content/short/2020.02.14.928432v1?rss=1"
Balestra, A. C.Zeeshan, M.Rea, E.Pasquarello, C.Klages, N.Mourier, T.Subudhi, A. K.Arboit, P.Brusini, L. A.Pandey, R.Brady, D.Vaughan, S.Holder, A. A.Pain, A.Ferguson, D.Hainard, A.Tewari, R.Brochet, M.2020-02-14doi:10.1101/2020.02.14.928432Cold Spring Harbor Laboratory Press2020-02-14
<![CDATA[
Defective heart chamber growth and myofibrillogenesis after knockout of adprhl1 gene function by targeted disruption of the ancestral catalytic active site.
]]>
https://biorxiv.org/cgi/content/short/2020.02.13.947424v1?rss=1"
Smith, S. J.Towers, N.Demetriou, K.Mohun, T. J.2020-02-14doi:10.1101/2020.02.13.947424Cold Spring Harbor Laboratory Press2020-02-14
<![CDATA[
Enteric glia as a source of neural progenitors in adult zebrafish
]]>
https://biorxiv.org/cgi/content/short/2020.02.14.949859v1?rss=1"
McCallum, S.Obata, Y.Fourli, E.Boeing, S.Peddie, C. J.Xu, Q.Horswell, S.Kelsh, R.Collinson, L.Wilkinson, D.Pin, C.Pachnis, V.Heanue, T.2020-02-15doi:10.1101/2020.02.14.949859Cold Spring Harbor Laboratory Press2020-02-15
<![CDATA[
A lipocalin mediates unidirectional haem biomineralization in malaria parasites
]]>
https://biorxiv.org/cgi/content/short/2020.02.18.954289v1?rss=1"
Matz, J. M.Drepper, B.Blum, T. B.van Genderen, E.Burrell, A.Martin, P.Stach, T.Collinson, L.Abrahams, J. P.Matuschewski, K.Blackman, M. J.2020-02-19doi:10.1101/2020.02.18.954289Cold Spring Harbor Laboratory Press2020-02-19
<![CDATA[
Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene-dose-sensitive AD-suppressor in human brain
]]>
https://biorxiv.org/cgi/content/short/2020.01.29.918037v1?rss=1"
6 million people worldwide at high risk of Alzheimers disease (AD) are those with Down Syndrome (DS, caused by trisomy 21 (T21)), 70% of whom develop dementia during lifetime, caused by an extra copy of {beta}-amyloid-(A{beta})-precursor-protein gene. We report AD-like pathology in cerebral organoids grown in vitro from non-invasively sampled strands of hair from 71% of DS donors. The pathology consisted of extracellular diffuse and fibrillar A{beta} deposits, hyperphosphorylated/pathologically conformed Tau, and premature neuronal loss.
Presence/absence of AD-like pathology was donor-specific (reproducible between individual organoids/iPSC lines/experiments). Pathology could be triggered in pathology-negative T21 organoids by CRISPR/Cas9-mediated elimination of the third copy of chromosome-21-gene BACE2, but prevented by combined chemical {beta} and {gamma}-secretase inhibition. We found that T21-organoids secrete increased proportions of A{beta}-preventing (A{beta}1-19) and A{beta}-degradation products (A{beta}1-20 and A{beta}1-34). We show these profiles mirror in cerebrospinal fluid of people with DS. We demonstrate that this protective mechanism is mediated by BACE2-trisomy and cross-inhibited by clinically trialled BACE1-inhibitors. Combined, our data prove the physiological role of BACE2 as a dose-sensitive AD-suppressor gene, potentially explaining the dementia delay in [~]30% of people with DS. We also show that DS cerebral organoids could be explored as pre-morbid AD-risk population detector and a system for hypothesis-free drug screens as well as identification of natural suppressor genes for neurodegenerative diseases.
]]>Alic, I.Goh, P. A.Murray, A.Portelius, E.Gkanatsiou, E.Gough, G.Mok, K. Y.Koschut, D.Brunmeir, R.Yeap, Y. J.O'Brien, N. L.Groet, J.Shao, X.Havlicek, S.Dunn, N. R.Kvartsberg, H.Brinkmalm, G.Hithersay, R.Startin, C.Hamburg, S.Phillips, M.Pervushin, K.Turmaine, M.Wallon, D.Rovelet-Lecrux, A.Soininen, H.Volpi, E.Martin, J. E.Foo, J. N.Becker, D. L.Rostagno, A.Ghiso, J.Krsnik, Z.Simic, G.Kostovic, I.Mitrecic, D.LonDownS Consortium,Francis, P. T.Blennow, K.Strydom, A.Hardy, J.Zetterberg, H.Nizetic, D.2020-01-31doi:10.1101/2020.01.29.918037Cold Spring Harbor Laboratory Press2020-01-31
<![CDATA[
Visual Biochemistry: modular microfluidics enables kinetic insight from time-resolved cryo-EM
]]>
https://biorxiv.org/cgi/content/short/2020.03.04.972604v1?rss=1"
Maeots, M.-E.Lee, B.Nans, A.Jeong, S.-G.Esfahani, M. M. N.Smith, D. J.Lee, C.-S.Lee, S. S.Peter, M.Enchev, R. I.2020-03-05doi:10.1101/2020.03.04.972604Cold Spring Harbor Laboratory Press2020-03-05
<![CDATA[
Semantic Segmentation of HeLa Cells: An Objective Comparison between one Traditional Algorithm and Three Deep-Learning Architectures
]]>
https://biorxiv.org/cgi/content/short/2020.03.05.978478v1?rss=1"
Karabag, C.Jones, M. L.Peddie, C. J.Weston, A. E.Collinson, L. M.Reyes-Aldasoro, C. C.2020-03-05doi:10.1101/2020.03.05.978478Cold Spring Harbor Laboratory Press2020-03-05
<![CDATA[
Transcriptomic characterization of tuberculous sputum reveals a host Warburg effect and microbial cholesterol catabolism
]]>
https://biorxiv.org/cgi/content/short/2020.03.09.983163v1?rss=1"
Lai, R. P.Cortes, T.Marais, S.Rockwood, N.Burke, M. L.Garza-Garcia, A.Horswell, S.O'Garra, A.Young, D. B.Wilkinson, R. J.2020-03-09doi:10.1101/2020.03.09.983163Cold Spring Harbor Laboratory Press2020-03-09
<![CDATA[
Identification of Conserved Evolutionary Trajectories in Tumors
]]>
https://biorxiv.org/cgi/content/short/2020.03.09.967257v1?rss=1"
Hodzic, E.Shrestha, R.Malikic, S.Collins, C. C.Litchfield, K.Turajlic, S.Sahinalp, C.2020-03-09doi:10.1101/2020.03.09.967257Cold Spring Harbor Laboratory Press2020-03-09
<![CDATA[
LED Zappelin': An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging.
]]>
https://biorxiv.org/cgi/content/short/2020.03.10.986000v1?rss=1"
Zimmermann, M. J.Chagas, A. M.Bartel, P.Pop, S.Prieto-Godino, L. L.Baden, T.2020-03-11doi:10.1101/2020.03.10.986000Cold Spring Harbor Laboratory Press2020-03-11
<![CDATA[
Progressive changes in hippocampal stem cell properties ensure lifelong neurogenesis
]]>
https://biorxiv.org/cgi/content/short/2020.03.12.987107v1?rss=1"
Harris, L.Rigo, P.Stiehl, T.Gaber, Z.Austin, S. H. L.Masdeu, M. d. M.Edwards, A.Urban, N.Marciniak-Czochra, A.Guillemot, F.2020-03-12doi:10.1101/2020.03.12.987107Cold Spring Harbor Laboratory Press2020-03-12
<![CDATA[
A high-coverage Neandertal genome from Chagyrskaya Cave
]]>
https://biorxiv.org/cgi/content/short/2020.03.12.988956v1?rss=1"
Mafessoni, F.Grote, S.de Filippo, C.Slon, V.Kolobova, K. A.Viola, B.Markin, S.Chintalapati, M.Peyregne, S.Skov, L.Skoglund, P.Krivoshapkin, A. I.Derevianko, A. P.Meyer, M.Kelso, J.Peter, B.Prüfer, K.Pääbo, S.2020-03-13doi:10.1101/2020.03.12.988956Cold Spring Harbor Laboratory Press2020-03-13
<![CDATA[
psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation
]]>
https://biorxiv.org/cgi/content/short/2020.03.15.992701v1?rss=1"
Strittmatter, L. M.Capitanchik, C.Newman, A. J.Hallegger, M.Norman, C. M.Fica, S. M.Oubridge, C.Luscombe, N. M.Ule, J.Nagai, K.2020-03-15doi:10.1101/2020.03.15.992701Cold Spring Harbor Laboratory Press2020-03-15
<![CDATA[
A Novel Machine Learning Approach Uncovers New and Distinctive Inhibitors for Cyclin-Dependent Kinase 9
]]>
https://biorxiv.org/cgi/content/short/2020.03.18.996538v1?rss=1"
Assmann, M.Bal, M.Craig, M.D'Oyley, J.Phillips, L.Triendl, H.Bates, P. A.Bashir, U.Ruprah, P.Shaker, N.Stojevic, V.2020-03-19doi:10.1101/2020.03.18.996538Cold Spring Harbor Laboratory Press2020-03-19
<![CDATA[
ZeroCostDL4Mic: an open platform to simplify access and use of Deep-Learning in Microscopy
]]>
https://biorxiv.org/cgi/content/short/2020.03.20.000133v1?rss=1"
Chamier, L. v.Jukkala, J.Spahn, C.Lerche, M.Hernandez-perez, S.Mattila, P.Karinou, E.Holden, S.Can Solak, A.Krull, A.Buchholz, T.-O.Jug, F.Royer, L. A.Heilemann, M.Laine, R. F.Jacquemet, G.Henriques, R.2020-03-20doi:10.1101/2020.03.20.000133Cold Spring Harbor Laboratory Press2020-03-20
<![CDATA[
Geometric differences between nuclear envelopes of Wild-type and Chlamydia trachomatis-infected HeLa cells
]]>
https://biorxiv.org/cgi/content/short/2020.04.02.021733v1?rss=1"
Karabag, C.Jones, M. L.Peddie, C. J.Weston, A. E.Collinson, L. M.Reyes-Aldasoro, C. C.2020-04-02doi:10.1101/2020.04.02.021733Cold Spring Harbor Laboratory Press2020-04-02
<![CDATA[
Differential protein phosphorylation affects the localisation of two secreted Toxoplasma proteins and is widespread during stage conversion
]]>
https://biorxiv.org/cgi/content/short/2020.04.09.035279v1?rss=1"
Young, J.Broncel, M.Teague, H.Russell, M. R.McGovern, O.Renshaw, M.Frith, D.Snijders, A. P.Collinson, L. M.Carruthers, V. B.Ewald, S. E.Treeck, M.2020-04-10doi:10.1101/2020.04.09.035279Cold Spring Harbor Laboratory Press2020-04-10
<![CDATA[
Co-activation of NF-κB and MYC renders cancer cells addicted to IL6 for survival and phenotypic stability
]]>
https://biorxiv.org/cgi/content/short/2020.04.12.038414v1?rss=1"
Barbosa, R.Xu, A. Q.D'Andrea, D.Copley, F.Patel, H.Chakravarty, P.Clear, A.Calaminici, M.Janz, M.Zhang, B.Schmidt-Supprian, M.Wang, J.Gribben, J.Tooze, R.Fitzgibbon, J.Franzoso, G.Rajewsky, K.Calado, D. P.2020-04-13doi:10.1101/2020.04.12.038414Cold Spring Harbor Laboratory Press2020-04-13
<![CDATA[
Jchain-driven cre enables specific genetic manipulation and timestamping of plasma cell in their niche.
]]>
https://biorxiv.org/cgi/content/short/2020.04.12.038380v1?rss=1"
Xu, A. Q.Barbosa, R.Calado, D. P.2020-04-13doi:10.1101/2020.04.12.038380Cold Spring Harbor Laboratory Press2020-04-13
<![CDATA[
A pan-cancer landscape of somatic substitutions in non-unique regions of the human genome
]]>
https://biorxiv.org/cgi/content/short/2020.04.14.040634v1?rss=1"
Tarabichi, M.Demeulemeester, J.Verfaillie, A.Flanagan, A. M.Van Loo, P.Konopka, T.2020-04-15doi:10.1101/2020.04.14.040634Cold Spring Harbor Laboratory Press2020-04-15
<![CDATA[
The deubiquitylase USP9X controls ribosomal stalling
]]>
https://biorxiv.org/cgi/content/short/2020.04.15.042291v1?rss=1"
Clancy, A.Heride, C.Pinto-Fernandez, A.Kallinos, A.Kayser-Bricker, K.Wang, W.Smith, V.Elcocks, H.Davis, S.Fessler, S.McKinnon, C.Katz, M.Hammonds, T.Jones, N. P.O'Connell, J.Follows, B.Mischke, S.Caravella, J. A.Ioannidis, S.Dinsmore, C.Kim, S.Behrens, A.Komander, D.Kessler, B. M.Urbe, S.Clague, M. J.2020-04-16doi:10.1101/2020.04.15.042291Cold Spring Harbor Laboratory Press2020-04-16
<![CDATA[
Endophilin A2 regulates B cell protein trafficking and humoral responses
]]>
https://biorxiv.org/cgi/content/short/2020.04.20.050419v1?rss=1"
Malinova, D.Wasim, L.Tolar, P.2020-04-20doi:10.1101/2020.04.20.050419Cold Spring Harbor Laboratory Press2020-04-20
<![CDATA[
A Structure-Based Mechanism for DNA Entry into the Cohesin Ring
]]>
https://biorxiv.org/cgi/content/short/2020.04.21.052944v1?rss=1"
Higashi, T. L.Eickhoff, P.Simoes, J. S.Locke, J.Nans, A.Flynn, H. R.Snijders, A. P.Papageorgiou, G.O'Reilly, N.Chen, Z. A.O'Reilly, F. J.Rappsilber, J.Costa, A.Uhlmann, F.2020-04-21doi:10.1101/2020.04.21.052944Cold Spring Harbor Laboratory Press2020-04-21
<![CDATA[
Unifying the mechanism of mitotic exit control in a spatio-temporal logical model
]]>
https://biorxiv.org/cgi/content/short/2020.04.22.054791v1?rss=1"
Howell, R. S.Klemm, C.Thorpe, P. H.Csikasz-Nagy, A.2020-04-23doi:10.1101/2020.04.22.054791Cold Spring Harbor Laboratory Press2020-04-23
<![CDATA[
Ribosome profiling reveals ribosome stalling on tryptophan codons upon oxidative stress in fission yeast
]]>
https://biorxiv.org/cgi/content/short/2020.04.23.054833v1?rss=1"
Rubio, A.Ghosh, S.Mulleder, M.Ralser, M.Mata, J.2020-04-24doi:10.1101/2020.04.23.054833Cold Spring Harbor Laboratory Press2020-04-24
<![CDATA[
Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation
]]>
https://biorxiv.org/cgi/content/short/2020.04.23.057208v1?rss=1"
Debets, M. F.Tastan, O. Y.Wisnovsky, S. P.Malaker, S. A.Angelis, N.Moeckl, L. K. R.Choi, J.Flynn, H.Wagner, L. J. S.Bineva-Todd, G.Antononopoulos, A.Cioce, A.Browne, W. M.Li, Z.Briggs, D. C.Douglas, H. L.Hess, G. T.Agbay, A. J.Roustan, C.Kjaer, S.Haslam, S. M.Snijders, A. P.Bassik, M. C.Moerner, W. E.Li, V. S. W.Bertozzi, C. R.Schumann, B.2020-04-25doi:10.1101/2020.04.23.057208Cold Spring Harbor Laboratory Press2020-04-25
<![CDATA[
Ultra-sparse connectivity within the lateral hypothalamus
]]>
https://biorxiv.org/cgi/content/short/2020.04.25.061564v1?rss=1"
Burdakov, D.Karnani, M. M.2020-04-27doi:10.1101/2020.04.25.061564Cold Spring Harbor Laboratory Press2020-04-27
<![CDATA[
Extensive transcriptional and chromatin changes underlie astrocyte maturation in vivo and in culture
]]>
https://biorxiv.org/cgi/content/short/2020.04.28.066043v1?rss=1"
Lattke, M.Goldstone, R.Guillemot, F.2020-04-30doi:10.1101/2020.04.28.066043Cold Spring Harbor Laboratory Press2020-04-30
<![CDATA[
Cryo-EM of human Arp2/3 complexes provides structural insights into actin nucleation modulation by ARPC5 isoforms
]]>
https://biorxiv.org/cgi/content/short/2020.05.01.071704v1?rss=1"
von Loeffelholz, O.Purkiss, A.Cao, L.Kjaer, S.Kogata, N.Romet-Lemonne, G.Way, M.Moores, C. A.2020-05-01doi:10.1101/2020.05.01.071704Cold Spring Harbor Laboratory Press2020-05-01
<![CDATA[
Gliding motility of Plasmodium merozoites
]]>
https://biorxiv.org/cgi/content/short/2020.05.01.072637v1?rss=1"
Yahata, K.Hart, M. N.Davies, H.Asada, M.Templeton, T. J.Treeck, M.Moon, R. W.Kaneko, O.2020-05-03doi:10.1101/2020.05.01.072637Cold Spring Harbor Laboratory Press2020-05-03
<![CDATA[
RNA binding regulates TRIM25-mediated RIG-I ubiquitylation
]]>
https://biorxiv.org/cgi/content/short/2020.05.04.070177v1?rss=1"
Haubrich, K.Augsten, S.Simon, B.Masiewicz, P.Perez, K.Lethier, M.Rittinger, K.Gabel, F.Cusack, S.Hennig, J.2020-05-05doi:10.1101/2020.05.04.070177Cold Spring Harbor Laboratory Press2020-05-05
<![CDATA[
Type I and III interferons disrupt lung epithelial repair during recovery from viral infection
]]>
https://biorxiv.org/cgi/content/short/2020.05.05.078360v1?rss=1"
Major, J.Crotta, S.Llorian, M.McCabe, T. M.Gad, H. H.Hartmann, R.Wack, A.2020-05-05doi:10.1101/2020.05.05.078360Cold Spring Harbor Laboratory Press2020-05-05
<![CDATA[
Lack of adaptation to centriolar defects leads to p53-independent microcephaly in the absence of Cep135
]]>
https://biorxiv.org/cgi/content/short/2020.05.07.082032v1?rss=1"
Malumbres, M.Gonzalez-Martinez, J.Cwersch, A.Martinez-Alonso, D.Lopez, L. R.Almagro, J.Megias, D.Boskovic, J.Gilabert, J.Grana Castro, O.Pierani, A.Behrens, A.Ortega, S.2020-05-08doi:10.1101/2020.05.07.082032Cold Spring Harbor Laboratory Press2020-05-08
<![CDATA[
Genetic determinants of receptor-binding preference and zoonotic potential of H9N2 avian influenza viruses
]]>
https://biorxiv.org/cgi/content/short/2020.05.11.088203v1?rss=1"
Peacock, T. P.Sealy, J. E.Harvey, W. T.Benton, D. J.Reeve, R.Iqbal, M.2020-05-12doi:10.1101/2020.05.11.088203Cold Spring Harbor Laboratory Press2020-05-12
<![CDATA[
Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans
]]>
https://biorxiv.org/cgi/content/short/2020.05.14.095414v1?rss=1"
Ng, K.Faulkner, N.Cornish, G.Rosa, A.Earl, C.Wrobel, A.Benton, D.Roustan, C.Bolland, W.Thompson, R.Agua-Doce, A.Hobson, P.Heaney, J.Rickman, H.Paraskevopoulou, S.Houlihan, C. F.Thomson, K.Sanchez, E.Shin, G. Y.Spyer, M. J.Walker, P. A.Kjaer, S.Riddell, A.Beale, R.Swanton, C.Gandhi, S.Stockinger, B.Gamblin, S.McCoy, L. E.Cherepanov, P.Nastouli, E.Kassiotis, G.2020-05-15doi:10.1101/2020.05.14.095414Cold Spring Harbor Laboratory Press2020-05-15
<![CDATA[
Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine
]]>
https://biorxiv.org/cgi/content/short/2020.05.14.096115v1?rss=1"
Durgan, J.Lystad, A. H.Sloan, K.Carlsson, S. R.Wilson, M. I.Marcassa, E.Ulferts, R.Webster, J.Lopez-Clavijo, A. F.Wakelam, M. J.Beale, R.Simonsen, A.Oxley, D.Florey, O.2020-05-15doi:10.1101/2020.05.14.096115Cold Spring Harbor Laboratory Press2020-05-15
<![CDATA[
The PAXFOXO1s trigger fast trans-differentiation of chick embryonic neural cells into alveolar rhabdomyosarcoma with tissue invasive properties limited by S phase entry inhibition
]]>
https://biorxiv.org/cgi/content/short/2020.05.18.097618v1?rss=1"
GONZALEZ CURTO, G.Der Vartanian, A.FRARMA, Y.Manceau, L.Baldi, L.Prisco, S.ELAROUCI, N.Causeret, F.RIGOLET, M.AURADE, F.DE REYNIES, A.CONTREMOULINS, V.RELAIX, F.FAKLARIS, O.BRISCOE, J.GILARDI-HEBENSTREIT, P.RIBES, V.2020-05-20doi:10.1101/2020.05.18.097618Cold Spring Harbor Laboratory Press2020-05-20
<![CDATA[
Frizzled-dependent Planar Cell Polarity without Wnt Ligands
]]>
https://biorxiv.org/cgi/content/short/2020.05.23.108977v1?rss=1"
Yu, J. J. S.Maugarny-Cales, A.Pelletier, S.Alexandre, C.Bellaiche, Y.Vincent, J.-P.McGough, I. J.2020-05-24doi:10.1101/2020.05.23.108977Cold Spring Harbor Laboratory Press2020-05-24
<![CDATA[
FAM83F regulates canonical Wnt signalling through an interaction with CK1α
]]>
https://biorxiv.org/cgi/content/short/2020.05.25.114504v1?rss=1"
Dunbar, K.Jones, R. A.Dingwell, K. S.Macartney, T.Smith, J. C.Sapkota, G. P.2020-05-26doi:10.1101/2020.05.25.114504Cold Spring Harbor Laboratory Press2020-05-26
<![CDATA[
CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals
]]>
https://biorxiv.org/cgi/content/short/2020.05.29.123513v1?rss=1"
Ganier, C.Du-Harpur, X.Harun, N.Wan, B.Arthurs, C.Luscombe, N.Watt, F.Lynch, M.2020-05-31doi:10.1101/2020.05.29.123513Cold Spring Harbor Laboratory Press2020-05-31
<![CDATA[
20 years of African Neuroscience: Waking a sleeping giant
]]>
https://biorxiv.org/cgi/content/short/2020.06.03.131391v1?rss=1"
Maina, M. B.Ahmad, U.Harun, I. A.Kwairanga, H. S.Nasr, F. E.Salihu, A. T.Abushouk, A. I.Muhammad, A.Awadelkareem, M. A.Amin, A.Imam, A.Akinrinade, I. D.Yakubu, A. H.Azeez, I. A.Mohammed, Y. G.Adamu, A. A.Ibrahim, B. H.Bukar, A. M.Yaro, A. U.Prieto-Godino, L. L.Baden, T.2020-06-04doi:10.1101/2020.06.03.131391Cold Spring Harbor Laboratory Press2020-06-04
<![CDATA[
Systematic analysis of mutational spectra associated with DNA repair deficiency in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2020.06.04.133306v1?rss=1"
2-fold increased mutagenesis with a broad spectrum of mutational outcomes including changes in single or multiple types of base substitutions induced by defects in base excision or nucleotide excision repair, or elevated levels of 50-400 bp deletions in translesion polymerase mutants rev-3(pol {zeta}) and polh-1(pol {eta}). Mutational signatures associated with defective homologous recombination fall into two classes: 1) mutants lacking brc-1/BRCA1 or rad-51/RAD51 paralogs show elevated base substitutions, indels and structural variants, while 2) deficiency for MUS-81/MUS81 and SLX-1/SLX1 nucleases, and HIM-6/BLM, HELQ-1/HELQ and RTEL-1/RTEL1 helicases primarily cause structural variants. Genome-wide investigation of mutagenesis patterns identified elevated rates of tandem duplications often associated with inverted repeats in helq-1 mutants, and a unique pattern of translocation events involving homeologous sequences in rip-1 paralog mutants. atm-1/ATM DNA damage checkpoint mutants harboured complex structural variants enriched in subtelomeric regions, and chromosome end-to-end fusions. Finally, while inactivation of the p53-like gene cep-1 did not affect mutagenesis, combined brc-1 cep-1 deficiency displayed increased, locally clustered mutagenesis. In summary, we provide a global view of how DNA repair pathways prevent germ cell mutagenesis.
]]>Meier, B.Volkova, N. N.Hong, Y.Bertolini, S.Gonzalez-Huici, V.Petrova, T.Boulton, S.Campbell, P. J.Gerstung, M.Gartner, A.2020-06-04doi:10.1101/2020.06.04.133306Cold Spring Harbor Laboratory Press2020-06-04
<![CDATA[
Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos
]]>
https://biorxiv.org/cgi/content/short/2020.06.05.135913v1?rss=1"
Alanis-Lobato, G.Zohren, J.McCarthy, A.Fogarty, N. M. E.Kubikova, N.Hardman, E.Greco, M.Wells, D.Turner, J. M. A.Niakan, K.2020-06-05doi:10.1101/2020.06.05.135913Cold Spring Harbor Laboratory Press2020-06-05
<![CDATA[
Repurposing the orphan drug nitisinone to control the transmission of African trypanosomiasis
]]>
https://biorxiv.org/cgi/content/short/2020.06.08.139808v1?rss=1"
Acosta-Serrano, A.Sterkel, M.Haines, L.Casas-Sanchez, A.Owino, V.Vionette-Amaral, R.Quek, S.Rose, C.Silva dos Santos, M.Garcia Escude, N.Ismail, H.Paine, M. I.Barribeau, S. M.Wagstaff, S.MacRae, J. I.Masiga, D.Yakob, L.Oliveira, P. L.2020-06-08doi:10.1101/2020.06.08.139808Cold Spring Harbor Laboratory Press2020-06-08
<![CDATA[
An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling
]]>
https://biorxiv.org/cgi/content/short/2020.06.08.140228v1?rss=1"
Dowbaj, A. M.Jenkins, R. P.Hahn, K.Montagner, M.Sahai, E. M.2020-06-09doi:10.1101/2020.06.08.140228Cold Spring Harbor Laboratory Press2020-06-09
<![CDATA[
SOX2 is required independently in both stem and differentiated cells for pituitary tumour genesis in p27 null mice.
]]>
https://biorxiv.org/cgi/content/short/2020.06.09.142638v1?rss=1"
Moncho-Amor, V.Chakravarty, P.Galichet, C.Matheu, A.Lovell-Badge, R.Rizzoti, K.2020-06-10doi:10.1101/2020.06.09.142638Cold Spring Harbor Laboratory Press2020-06-10
<![CDATA[
Critical role of WNK1 in MYC-dependent early thymocyte development
]]>
https://biorxiv.org/cgi/content/short/2020.06.11.147017v1?rss=1"
Köchl, R.Vanes, L.Llorian Sopena, M.Chakravarty, P.Hartweger, H.Fountain, K.White, A.Cowan, J.Anderson, G.Tybulewicz, V.2020-06-12doi:10.1101/2020.06.11.147017Cold Spring Harbor Laboratory Press2020-06-12
<![CDATA[
Dentate gyrus development requires a cortical hem-derived astrocytic scaffold.
]]>
https://biorxiv.org/cgi/content/short/2020.06.11.145672v1?rss=1"
Caramello, A.Galichet, C.Lovell-Badge, R.Rizzoti, K.2020-06-12doi:10.1101/2020.06.11.145672Cold Spring Harbor Laboratory Press2020-06-12
<![CDATA[
Pan-cancer detection of driver genes at the single-patient resolution
]]>
https://biorxiv.org/cgi/content/short/2020.06.12.147983v1?rss=1"
Nulsen, J.Misetic, H.Yau, C.Ciccarelli, F. D.2020-06-12doi:10.1101/2020.06.12.147983Cold Spring Harbor Laboratory Press2020-06-12
<![CDATA[
Structure of the cysteine-rich domain of Plasmodium falciparum P113 identifies the location of the RH5 binding site
]]>
https://biorxiv.org/cgi/content/short/2020.06.12.149534v1?rss=1"
Campeotto, I.Galaway, F.Mehmood, S.Barfod, L.Quinkert, D.Kotraiah, V.Phares, T. W.Wright, K. E.Snijders, A. P.Draper, S. J.Higgins, M.Wright, G. J.2020-06-13doi:10.1101/2020.06.12.149534Cold Spring Harbor Laboratory Press2020-06-13
<![CDATA[
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
]]>
https://biorxiv.org/cgi/content/short/2020.06.12.145151v1?rss=1"
Huddleston, J.Barnes, J. R.Rowe, T.Kondor, R.Wentworth, D. E.Whittaker, L.Ermetal, B.Daniels, R. S.McCauley, J. W.Fujisaki, S.Nakamura, K.Kishida, N.Watanabe, S.Hasegawa, H.Barr, I.Subbarao, K.Neher, R.Bedford, T.2020-06-13doi:10.1101/2020.06.12.145151Cold Spring Harbor Laboratory Press2020-06-13
<![CDATA[
Phase separation induced by cohesin SMC protein complexes
]]>
https://biorxiv.org/cgi/content/short/2020.06.13.149716v1?rss=1"
Ryu, J.-K.Bouchoux, C.Liu, H. W.Kim, E.Minamino, M.de Groot, R.Katan, A. J.Bonato, A.Marenduzzo, D.Michieletto, D.Uhlmann, F.Dekker, C.2020-06-14doi:10.1101/2020.06.13.149716Cold Spring Harbor Laboratory Press2020-06-14
<![CDATA[
Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution
]]>
https://biorxiv.org/cgi/content/short/2020.06.12.147033v1?rss=1"
Lawson, C. L.Kryshtafovych, A.Adams, P. D.Afonine, P.Baker, M. L.Barad, B. A.Bond, P.Burnley, T.Cao, R.Cheng, J.Chojnowski, G.Cowtan, K.Dill, K. A.DiMaio, F.Farrell, D.Fraser, J. S.Herzik, M. A.Hoh, S. W.Hou, J.Hung, L.-W.Igaev, M.Joseph, A. P.Kihara, D.Kumar, D.Mittal, S.Monastyrskyy, B.Olek, M.Palmer, C.Patwardhan, A.Perez, A.Pfab, J.Pintilie, G. D.Richardson, J. S.Rosenthal, P. B.Sarkar, D.Schaefer, L. U.Schmid, M. F.Schroeder, G. F.Shekhar, M.Si, D.Singharoy, A.Terashi, G.Terwilliger, T. C.Vaiana, A.Wan2020-06-15doi:10.1101/2020.06.12.147033Cold Spring Harbor Laboratory Press2020-06-15
<![CDATA[
Rostrocaudal Patterning and Neural Crest Differentiation of Human Pre-Neural Spinal Cord Progenitors in vitro
]]>
https://biorxiv.org/cgi/content/short/2020.06.16.155564v1?rss=1"
Cooper, F.Gentsch, G. E.Mitter, R.Bouissou, C.Healy, L.Hernandez-Rodriguez, A.Smith, J. C.Bernardo, A. S.2020-06-16doi:10.1101/2020.06.16.155564Cold Spring Harbor Laboratory Press2020-06-16
<![CDATA[
Human Whole Genome Sequencing in South Africa
]]>
https://biorxiv.org/cgi/content/short/2020.06.10.144402v1?rss=1"
Glanzmann, B.Jooste, T.Ghoor, S.Gordon, R.Mia, R.Mao, R.Li, H.Charls, P.Douman, C.Kotze, M.Peeters, A.Loots, G.Esser, M.Tiemessen, C.Wilkinson, R.Louw, J.Gray, G.Warren, R.Moller Moller, M.Kinnear, C.2020-06-10doi:10.1101/2020.06.10.144402Cold Spring Harbor Laboratory Press2020-06-10
<![CDATA[
Maladaptive nutrient signalling sustains the m.3243A>G mtDNA mutation
]]>
https://biorxiv.org/cgi/content/short/2020.06.18.159103v1?rss=1"
G. These studies reveal that the mutation promotes changes in metabolites which is associated with the upregulation of the PI3K-Akt-mTORC1 axis in patient-derived cells and tissues. Remarkably, pharmacological inhibition of PI3K, Akt, or mTORC1 activated mitophagy, reduced mtDNA mutant load and rescued cellular bioenergetic function. The rescue was prevented by inhibition of mitophagy. The PI3K-Akt-mTORC1 axis thus represents a potential therapeutic target that may benefit people suffering from the consequences of the m.3243A>G mutation.
]]>Chung, C.-Y.Singh, K.Kotiadis, V. N.Ahn, J. H.Kabir, L.Topley, E.Tan, J.Andrews, W. D.Plotegher, N.Guella, G.Pitceathly, R. D. S.Szabadkai, G.Yuneva, M.Duchen, M. R.2020-06-19doi:10.1101/2020.06.18.159103G mtDNA mutation]]>Cold Spring Harbor Laboratory Press2020-06-19
<![CDATA[
Genetic dissection of Down syndrome-associated alterations in APP/amyloid-β biology using mouse models
]]>
https://biorxiv.org/cgi/content/short/2020.06.19.162115v1?rss=1"
Tosh, J. L.Rhymes, E.Mumford, P.Whittaker, H. T.Pulford, L. J.Noy, S. J.Cleverley, K.Walker, M. L.Tybulewicz, V. L. J.Wykes, R. C.Fisher, E. M. C.Wiseman, F. K.2020-06-20doi:10.1101/2020.06.19.162115Cold Spring Harbor Laboratory Press2020-06-20
<![CDATA[
CRYO-EM STRUCTURE OF THE DELTA-RETROVIRAL INTASOME IN COMPLEX WITH THE PP2A REGULATORY SUBUNIT B56gamma
]]>
https://biorxiv.org/cgi/content/short/2020.06.19.161513v1?rss=1"
Barski, M. S.Minnell, J. J.Hodakova, Z.Pye, V.Nans, A.Cherepanov, P.Maertens, G. N.2020-06-20doi:10.1101/2020.06.19.161513Cold Spring Harbor Laboratory Press2020-06-20
<![CDATA[
From local resynchronization to global pattern recovery in the zebrafish segmentation clock
]]>
https://biorxiv.org/cgi/content/short/2020.06.22.166215v1?rss=1"
Uriu, K.Liao, B.-K.Oates, A.Morelli, L.2020-06-23doi:10.1101/2020.06.22.166215Cold Spring Harbor Laboratory Press2020-06-23
<![CDATA[
The native structure of the full-length, assembled influenza A virus matrix protein, M1.
]]>
https://biorxiv.org/cgi/content/short/2020.06.24.168567v1?rss=1"
Peukes, J.Xiong, X.Erlendsson, S.Qu, K.Wan, W.Calder, L. J.Schraidt, O.Kummer, S.Freund, S. M. V.Kräusslich, H.-G.Briggs, J. A. G.2020-06-24doi:10.1101/2020.06.24.168567Cold Spring Harbor Laboratory Press2020-06-24
<![CDATA[
The phosphatidylinositol 3-phosphate binding protein SNX4 controls ATG9A recycling and autophagy
]]>
https://biorxiv.org/cgi/content/short/2020.06.24.169193v1?rss=1"
Stenmark, H.Ravussin, A.Tooze, S.2020-06-24doi:10.1101/2020.06.24.169193Cold Spring Harbor Laboratory Press2020-06-24
<![CDATA[
Centromere-specific antibody-mediated karyotyping of Okinawan Oikopleura dioica suggests the presence of three chromosomes.
]]>
https://biorxiv.org/cgi/content/short/2020.06.23.166173v1?rss=1"
Liu, A. W.Tan, Y.Masunaga, A.Plessy, C.Luscombe, N. M.2020-06-24doi:10.1101/2020.06.23.166173Cold Spring Harbor Laboratory Press2020-06-24
<![CDATA[
SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids
]]>
https://biorxiv.org/cgi/content/short/2020.06.24.167049v1?rss=1"
Giobbe, G. G.Bonfante, F.Zambaiti, E.Gagliano, O.Jones, B. C.Luni, C.Laterza, C.Perin, S.Stuart, H. T.Pagliari, M.Bortolami, A.Mazzetto, E.Manfredi, A.Colantuono, C.Di Filippo, L.Pellegata, A. F.Li, V. S. W.Eaton, S.Thapar, N.Cacchiarelli, D.Elvassore, N.De Coppi, P.2020-06-24doi:10.1101/2020.06.24.167049Cold Spring Harbor Laboratory Press2020-06-24
<![CDATA[
A thermostable, closed, SARS-CoV-2 spike protein trimer.
]]>
https://biorxiv.org/cgi/content/short/2020.06.15.152835v1?rss=1"
Xiong, X.Qu, K.Ciazynska, K. A.Hosmillo, M.Carter, A. P.Ebrahimi, S.Ke, Z.Scheres, S. H. W.Bergamaschi, L.Grice, G. L.Zhang, Y.The CITIID-NIHR COVID-19 BioResource Collaboration,Nathan, J. A.Baker, S.James, L. C.Baxendale, H. E.Goodfellow, I.Doffinger, R.Briggs, J. A. G.2020-06-17doi:10.1101/2020.06.15.152835Cold Spring Harbor Laboratory Press2020-06-17
<![CDATA[
Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme
]]>
https://biorxiv.org/cgi/content/short/2020.06.28.176040v1?rss=1"
Fedoryshchak, R. O.Prechova, M.Butler, A.Lee, R.O'Reilly, N.Flynn, H.Snijders, A. P.Eder, N.Ultanir, S.Mouilleron, S.Treisman, R.2020-06-28doi:10.1101/2020.06.28.176040Cold Spring Harbor Laboratory Press2020-06-28
<![CDATA[
Age-related degeneration leads to gliosis but not regeneration in the zebrafish retina
]]>
https://biorxiv.org/cgi/content/short/2020.06.28.174821v1?rss=1"
View larger version (41K):
org.highwire.dtl.DTLVardef@1a184daorg.highwire.dtl.DTLVardef@1193750org.highwire.dtl.DTLVardef@7e65c0org.highwire.dtl.DTLVardef@4a2fe3_HPS_FORMAT_FIGEXP M_FIG C_FIG Our data suggest there are key differences between mechanisms driving regeneration in response to acute damage versus age-related chronic damage. It may be that either the number of cells dying in natural ageing is not enough to stimulate MG to proliferate, or the low number of microglia and respective signals released are not sufficient to trigger MG proliferation. Importantly, we show that gliotic MG cells can be stimulated to repair damaged neurons in old zebrafish retina.
]]>Martins, R. R.Zamzam, M.Moosajee, M.Thummel, R. B.Henriques, C. M.MacDonald, R. B.2020-06-29doi:10.1101/2020.06.28.174821Cold Spring Harbor Laboratory Press2020-06-29
<![CDATA[
Genetic architecture of host proteins interacting with SARS-CoV-2
]]>
https://biorxiv.org/cgi/content/short/2020.07.01.182709v1?rss=1"
Pietzner, M.Wheeler, E.Carrasco-Zanini, J.Raffler, J.Kerrison, N. D.Oerton, E.Auyeung, V. P. W.Luan, J.Finan, C.Casas, J. P.Ostroff, R.Williams, S. A.Kastenmüller, G.Ralser, M.Gamazon, E. G.Wareham, N. J.Hingorani, A. D.Langenberg, C.2020-07-01doi:10.1101/2020.07.01.182709Cold Spring Harbor Laboratory Press2020-07-01
<![CDATA[
A 3-hydroxyacyl-CoA dehydratase (DEH) involved in very long chain fatty acid synthesis is crucial for oocyst mitotic division but not cell size during parasite transmission in Plasmodium
]]>
https://biorxiv.org/cgi/content/short/2020.07.01.182774v1?rss=1"
Guttery, D. S.Pandey, R.Ferguson, D.Wall, R.Brady, D.Gupta, D.Holder, A. A.Tewari, R.2020-07-02doi:10.1101/2020.07.01.182774Cold Spring Harbor Laboratory Press2020-07-02
<![CDATA[
High-resolution structures of malaria parasite actomyosin and actin filaments
]]>
https://biorxiv.org/cgi/content/short/2020.07.02.183871v1?rss=1"
Vahokoski, J.Calder, L. J.Lopez, A. J.Molloy, J. E.Rosenthal, P. B.Kursula, I.2020-07-02doi:10.1101/2020.07.02.183871Cold Spring Harbor Laboratory Press2020-07-02
<![CDATA[
Plasmodium berghei kinesin-5 associates with the spindle apparatus during cell division but is dispensable for parasite proliferation
]]>
https://biorxiv.org/cgi/content/short/2020.07.03.186031v1?rss=1"
Zeeshan, M.Brady, D.Stanway, R. R.Moores, C.Holder, A. A.Tewari, R.2020-07-03doi:10.1101/2020.07.03.186031Cold Spring Harbor Laboratory Press2020-07-03
<![CDATA[
Macrophage-specific responses to human- and animal-adapted tubercle bacilli reveal pathogen and host factors driving multinucleated cell formation
]]>
https://biorxiv.org/cgi/content/short/2020.07.02.185744v1?rss=1"
Queval, C. J.Fearns, A.Botella, L.Smyth, A.Schnettger, L.Mitermite, M.Wooff, E.Villareal-Ramos, B.Garcia-Gimenez, W.Heunis, T.Trost, M.Werling, D.Salguero, F. J.Gordon, S. V.Gutierrez, M.2020-07-03doi:10.1101/2020.07.02.185744Cold Spring Harbor Laboratory Press2020-07-03
<![CDATA[
PRC1 and EB1 Binding Dynamics Reveal a Solidifying Central Spindle during Anaphase Compaction in Human Cells
]]>
https://biorxiv.org/cgi/content/short/2020.07.09.195347v1?rss=1"
Jayant AsthanaNicholas I. CadeWei Ming LimThomas Surrey2020-07-09doi:10.1101/2020.07.09.195347Cold Spring Harbor Laboratory Press2020-07-09
<![CDATA[
Ventricular, atrial and outflow tract heart progenitors arise from spatially and molecularly distinct regions of the primitive streak.
]]>
https://biorxiv.org/cgi/content/short/2020.07.12.198994v1?rss=1"
Kenzo IvanovitchPablo Soro-BarrioProbir ChakravartyRebecca A JonesS. Neda Mousavy GharavyDespina StamatakiJulien DelileJames C SmithJames Briscoe2020-07-12doi:10.1101/2020.07.12.198994Cold Spring Harbor Laboratory Press2020-07-12
<![CDATA[
SPACE exploration of chromatin proteome to reveal associated RNA-binding proteins
]]>
https://biorxiv.org/cgi/content/short/2020.07.13.200212v1?rss=1"
Rafiee, M.-r.Zagalak, J.Tyzack, G.Patani, R.Ule, J.Luscombe, N. M.2020-07-13doi:10.1101/2020.07.13.200212Cold Spring Harbor Laboratory Press2020-07-13
<![CDATA[
Resolving phylogeny and polyploid parentage using genus-wide genome-wide sequence data from birch trees
]]>
https://biorxiv.org/cgi/content/short/2020.07.13.200444v1?rss=1"
Wang, N.Kelly, L.McAllister, H. A.Zohren, J.Buggs, R.2020-07-13doi:10.1101/2020.07.13.200444Cold Spring Harbor Laboratory Press2020-07-13
<![CDATA[
Semi-Supervised Learning of Protein Secondary Structure from Single Sequences
]]>
https://biorxiv.org/cgi/content/short/2020.07.13.201459v1?rss=1"
Moffat, L.Jones, D. T.2020-07-14doi:10.1101/2020.07.13.201459Cold Spring Harbor Laboratory Press2020-07-14
<![CDATA[
The Mycobacterium tuberculosis sRNA F6 regulates expression of groEL/S
]]>
https://biorxiv.org/cgi/content/short/2020.07.15.204107v1?rss=1"
Houghton, J.Rodgers, A.Rose, G.Arnvig, K. B.2020-07-15doi:10.1101/2020.07.15.204107Cold Spring Harbor Laboratory Press2020-07-15
<![CDATA[
Quantifying the monomer-dimer equilibrium of tubulin with mass photometry
]]>
https://biorxiv.org/cgi/content/short/2020.07.16.199083v1?rss=1"
10-2 s-1. Our results demonstrate the capabilities of mass photometry for quantifying protein-protein interactions and clarify the energetics and kinetics of tubulin heterodimerisation.
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/199083v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@3edeb3org.highwire.dtl.DTLVardef@18ee80eorg.highwire.dtl.DTLVardef@1251b04org.highwire.dtl.DTLVardef@110b081_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Fineberg, A.Surrey, T.Kukura, P.2020-07-16doi:10.1101/2020.07.16.199083Cold Spring Harbor Laboratory Press2020-07-16
<![CDATA[
The malaria parasite sheddase SUB2 governs host red blood cell membrane sealing at invasion
]]>
https://biorxiv.org/cgi/content/short/2020.07.15.205732v1?rss=1"
Collins, C. R.Hackett, F.Howell, S. A.Snijders, A. P.Russell, M. R.Collinson, L. M.Blackman, M. J.2020-07-17doi:10.1101/2020.07.15.205732Cold Spring Harbor Laboratory Press2020-07-17
<![CDATA[
A multipass membrane protein interacts with the cGMP-dependent protein kinase to regulate critical calcium signals in malaria parasites
]]>
https://biorxiv.org/cgi/content/short/2020.07.18.209973v1?rss=1"
Balestra, A. C.Koussis, K.Klages, N.Howell, S. A.Flynn, H. R.Bantscheff, M.Pasquarello, C.Perrin, A. J.Brusini, L.Arboit, P.Sanz, O.Peces-Barba Castano, L.Withers-Martinez, C.Hainard, A.Ghidelli-Disse, S.Snijders, A. P.Baker, D. A.Blackman, M. J.Brochet, M.2020-07-18doi:10.1101/2020.07.18.209973Cold Spring Harbor Laboratory Press2020-07-18
<![CDATA[
An aberrant cytoplasmic intron retention programme is a blueprint for ALS-related RBP mislocalization
]]>
https://biorxiv.org/cgi/content/short/2020.07.20.211557v1?rss=1"
100 IRTs with increased cytoplasmic (but not nuclear) abundance in ALS samples. Furthermore, these aberrant cytoplasmic IRTs possess sequence-specific attributes and differential predicted binding affinity to RNA binding proteins (RBPs). Remarkably, TDP-43, SFPQ and FUS - RBPs known for nuclear-to-cytoplasmic mislocalization in ALS - avidly and specifically bind to this aberrant cytoplasmic pool of IRTs, as opposed to any individual IRT. Our data are therefore consistent with a novel role for cytoplasmic IRTs in regulating compartment-specific protein abundance. This study provides new molecular insight into potential pathomechanisms underlying ALS and highlights aberrant cytoplasmic IRTs as potential therapeutic targets.
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/211557v2_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@153fc1eorg.highwire.dtl.DTLVardef@cd3506org.highwire.dtl.DTLVardef@544868org.highwire.dtl.DTLVardef@15ddb68_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Tyzack, G. E.Neeves, J.Klein, P.Crerar, H.Ziff, O.Taha, D. M.Luisier, R.Luscombe, N. M.Patani, R.2020-07-21doi:10.1101/2020.07.20.211557Cold Spring Harbor Laboratory Press2020-07-21
<![CDATA[
HIV coinfection is associated with low fitness rpoB variants in rifampicin-resistant Mycobacterium tuberculosis
]]>
https://biorxiv.org/cgi/content/short/2020.07.20.208835v1?rss=1"
Loiseau, C.Brites, D.Reinhard, M.Zuercher, K.Borrell, S.Ballif, M.Fenner, L.Cox, H.Rutaihwa, L. K.Wilkinson, R. J.Yotebieng, M.Carter, E. J.Abimiku, A.Marcy, O.Gotuzzo, E.Avihingsanon, A.Zetola, N.Doulla, B.Boettger, E. C.Egger, M.Gagneux, S.2020-07-22doi:10.1101/2020.07.20.208835Cold Spring Harbor Laboratory Press2020-07-22
<![CDATA[
Protective porcine influenza virus-specific monoclonal antibodies recognize similar haemagglutinin epitopes as humans
]]>
https://biorxiv.org/cgi/content/short/2020.07.21.213470v1?rss=1"
Holzer, B.Rijal, P.McNee, A.Paudyal, B.Clark, B.Manjegowda, T.Salguero, F. J.Bessell, E.Schwartz, J. C.Moffat, K.Pedrera, M.Graham, S. P.Placido, M. B.-D.La Ragione, R. M.Mwangi, W.Beverley, P.McCauley, J. W.Daniels, R. S.Hammond, J.Townsend, A. R.Tchilian, E.2020-07-22doi:10.1101/2020.07.21.213470Cold Spring Harbor Laboratory Press2020-07-22
<![CDATA[
Phase Unwrapping with a Rapid Opensource Minimum Spanning TreE AlgOrithm (ROMEO)
]]>
https://biorxiv.org/cgi/content/short/2020.07.24.214551v1?rss=1"
Dymerska, B.Eckstein, K.Bachrata, B.Siow, B.Trattnig, S.Shmueli, K.Robinson, S. D.2020-07-24doi:10.1101/2020.07.24.214551Cold Spring Harbor Laboratory Press2020-07-24
<![CDATA[
Tissue-specific and interferon-inducible expression of non-functional ACE2 through endogenous retrovirus co-option
]]>
https://biorxiv.org/cgi/content/short/2020.07.24.219139v1?rss=1"
Ng, K.Attig, J.Bolland, W.Young, G.Major, J.Wack, A.Kassiotis, G.2020-07-24doi:10.1101/2020.07.24.219139Cold Spring Harbor Laboratory Press2020-07-24
<![CDATA[
Citizen science, cells and CNNs - deep learning for automatic segmentation of the nuclear envelope in electron microscopy data, trained with volunteer segmentations
]]>
https://biorxiv.org/cgi/content/short/2020.07.28.223024v1?rss=1"
Spiers, H.Songhurst, H.Nightingale, L.de Folter, J.Hutchings, R.Peddie, C. J.Weston, A.Strange, A.Hindmarsh, S.Lintott, C.Collinson, L. M.Jones, M. L.2020-07-29doi:10.1101/2020.07.28.223024Cold Spring Harbor Laboratory Press2020-07-29
<![CDATA[
Control and mechanisms of pulsatile flows in epithelial monolayers
]]>
https://biorxiv.org/cgi/content/short/2020.07.29.226357v1?rss=1"
Thiagarajan, R.Bhat, A.Salbreux, G.Inamdar, M. M.Riveline, D.2020-07-30doi:10.1101/2020.07.29.226357Cold Spring Harbor Laboratory Press2020-07-30
<![CDATA[
Maternal iron deficiency perturbs embryonic cardiovascular development
]]>
https://biorxiv.org/cgi/content/short/2020.08.03.230615v1?rss=1"
Kalisch-Smith, J. I.Ved, N.Szumska, D.Munro, J.Troup, M.Harris, S. E.Jacquemot, A.Miller, J. J.Stuart, E. M.Wolna, M.Hardman, E.Prin, F.Lana-Elola, E.Aoidi, R.Fisher, E. M. C.Tybulewicz, V. L. J.Mohun, T. J.Lakhal-Littleton, S.Giannoulatou, E.Sparrow, D. B.2020-08-03doi:10.1101/2020.08.03.230615Cold Spring Harbor Laboratory Press2020-08-03
<![CDATA[
Correlative Light Electron Ion Microscopy reveal in vivo localisation of bedaquiline in Mycobacterium tuberculosis infected lungs
]]>
https://biorxiv.org/cgi/content/short/2020.08.05.237537v1?rss=1"
Fearns, A.Greenwood, D.Rodgers, A.Jiang, H.Gutierrez, M.2020-08-05doi:10.1101/2020.08.05.237537Cold Spring Harbor Laboratory Press2020-08-05
<![CDATA[
Theory of genetic oscillations with external noisy regulation
]]>
https://biorxiv.org/cgi/content/short/2020.08.07.241042v1?rss=1"
Negrete, J.Lengyel, I. M.Rohde, L.Desai, R. A.Oates, A. C.Julicher, F.2020-08-07doi:10.1101/2020.08.07.241042Cold Spring Harbor Laboratory Press2020-08-07
<![CDATA[
Cellular barcoding of Toxoplasma reveals permissive host brain colonization
]]>
https://biorxiv.org/cgi/content/short/2020.08.06.239822v1?rss=1"
Wincott, C. J.Sritharan, G.Bunyan, M.Alves, E.Benns, H. J.Frickel, E. M.Ewald, S. E.Child, M. A.2020-08-07doi:10.1101/2020.08.06.239822Cold Spring Harbor Laboratory Press2020-08-07
<![CDATA[
Single amino acid-promoted reactions link a non-enzymatic chemical network to the early evolution of enzymatic pentose phosphate pathway
]]>
https://biorxiv.org/cgi/content/short/2020.08.11.245860v1?rss=1"
Piedrafita, G.Varma, S. J.Castro, C.Messner, C. B.Szyrwiel, L.Griffin, J. L.Ralser, M.2020-08-12doi:10.1101/2020.08.11.245860Cold Spring Harbor Laboratory Press2020-08-12
<![CDATA[
PairGP: Gaussian process modeling of longitudinal data from paired multi-condition studies
]]>
https://biorxiv.org/cgi/content/short/2020.08.11.245621v1?rss=1"
Vantini, M.Mannerström, H.Rautio, S.Ahlfors, H.Stockinger, B.Lähdesmäki, H.2020-08-12doi:10.1101/2020.08.11.245621Cold Spring Harbor Laboratory Press2020-08-12
<![CDATA[
Cisplatin is more mutagenic than carboplatin or oxaliplatin at equitoxic concentrations
]]>
https://biorxiv.org/cgi/content/short/2020.08.11.245969v1?rss=1"
Szikriszt, B.Poti, A.Nemeth, E.Kanu, N.Swanton, C.Szuts, D.2020-08-12doi:10.1101/2020.08.11.245969Cold Spring Harbor Laboratory Press2020-08-12
<![CDATA[
Automated and unbiased classification of motor neuron phenotypes with single cell resolution in ALS tissue.
]]>
https://biorxiv.org/cgi/content/short/2020.08.17.253773v1?rss=1"
Luisier, R.Serio, A.Patani, R.Newcombe, J.Greensmith, L.Devine, H.Taha, D. M.Tyzack, G. E.Hagemann, C.2020-08-17doi:10.1101/2020.08.17.253773Cold Spring Harbor Laboratory Press2020-08-17
<![CDATA[
Amino acids whose intracellular levels change most during aging alter chronological lifespan of fission yeast
]]>
https://biorxiv.org/cgi/content/short/2020.08.18.256164v1?rss=1"
Rallis, C.Mulleder, M.Smith, G.Au, Y. Z.Ralser, M.Bahler, J.2020-08-19doi:10.1101/2020.08.18.256164Cold Spring Harbor Laboratory Press2020-08-19
<![CDATA[
Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response
]]>
https://biorxiv.org/cgi/content/short/2020.08.15.250589v1?rss=1"
McGowan, E.Rosenthal, R.Fiore-Gartland, A.Macharia, G.Balinda, S.Kapaata, A.Muok, E.Umviligihozo, G.Dalel, J.Streatfield, C.Coutinho, H.Monaco, D.Morrison, D.Yue, L.Hunter, E.Nielsen, M.Gilmour, J.Hare, J.2020-08-15doi:10.1101/2020.08.15.250589Cold Spring Harbor Laboratory Press2020-08-15
<![CDATA[
Active Perception during Angiogenesis: Filopodia speed up Notch selection of tip cells in silico and in vivo
]]>
https://biorxiv.org/cgi/content/short/2020.08.22.261263v1?rss=1"
Zakirov, B.Charalambous, G.Aspalter, I. M.Van-Vuuren, K.Mead, T.Harrington, K.Thuret, R.Ravasz Regan, E.Herbert, S. P.Bentley, K.2020-08-23doi:10.1101/2020.08.22.261263Cold Spring Harbor Laboratory Press2020-08-23
<![CDATA[
MRE11 is crucial for malaria transmission and its absence affects expression of interconnected networks of key genes essential for life
]]>
https://biorxiv.org/cgi/content/short/2020.08.24.258657v1?rss=1"
Guttery, D.Ramaprasad, A.Ferguson, D.Zeeshan, M.Pandey, R.Brady, D.Holder, A. A.Pain, A.Tewari, R.2020-08-24doi:10.1101/2020.08.24.258657Cold Spring Harbor Laboratory Press2020-08-24
<![CDATA[
An essential amino acid synchronises malaria parasite development with daily host rhythms
]]>
https://biorxiv.org/cgi/content/short/2020.08.24.264689v1?rss=1"
Prior, K. F.Middleton, B.Owolabi, A. T.Westwood, M. L.Holland, J.O'Donnell, A. J.Blackman, M. J.Skene, D. J.Reece, S. E.2020-08-24doi:10.1101/2020.08.24.264689Cold Spring Harbor Laboratory Press2020-08-24
<![CDATA[
An Integrative Analysis of the Age-Associated Genomic, Transcriptomic and Epigenetic Landscape across Cancers
]]>
https://biorxiv.org/cgi/content/short/2020.08.25.266403v1?rss=1"
Chatsirisupachai, K.Lesluyes, T.Paraoan, L.Van Loo, P.de Magalhaes, J. P.2020-08-25doi:10.1101/2020.08.25.266403Cold Spring Harbor Laboratory Press2020-08-25
<![CDATA[
T-bet fate mapping identifies a novel ILC1-ILC2 subset in vivo
]]>
https://biorxiv.org/cgi/content/short/2020.08.21.261073v1?rss=1"
SCHROEDER, J.-H.Garrido-Mesa, N.Zabinski, T.Gallagher, A.Campbell, L.Roberts, L.Stolarczyk, E.Beattie, G.Lo, J.Iseppon, A.Moreira Heliodoro, C.Reis, R.Jenner, R.Lavender, P.Howard, J.Grencis, R.Helmby, H.Neves, J.Lord, G.2020-08-22doi:10.1101/2020.08.21.261073Cold Spring Harbor Laboratory Press2020-08-22
<![CDATA[
Plasmablast-derived antibody response to acute SARS-CoV-2 infection in humans
]]>
https://biorxiv.org/cgi/content/short/2020.08.28.267526v1?rss=1"
Huang, K.-Y. A.Tan, T.Chen, T.-H.Huang, C.-G.Harvey, R.Hussain, S.Chen, C.-P.Harding, A.Gilbert-Jaramillo, J.Liu, X.Knight, M.Schimanski, L.Shih, S.-R.Lin, Y.-C.Cheng, C.-Y.Cheng, S.-H.Huang, Y.-C.Lin, T.-Y.Rahikainen, R.Howarth, M.Jan, J.-T.Ma, C.James, W. S.Daniels, R.McCauley, J.Rijal, P.Townsend, A.2020-08-28doi:10.1101/2020.08.28.267526Cold Spring Harbor Laboratory Press2020-08-28
<![CDATA[
A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses
]]>
https://biorxiv.org/cgi/content/short/2020.08.31.275701v1?rss=1"
Tan, T. K.Rijal, P.Rahikainen, R.Keeble, A.Schimanski, L.Hussain, S.Harvey, R.Hayes, J.Edwards, J.McLean, R.Martini, V.Pedrera, M.Thakur, N.Conceicao, C.Dietrich, I.Shelton, H.Ludi, A. B.Wilsden, G.Browning, C.Zagrajek, A.Bialy, D.Bhat, S.Stevenson-Leggett, P.Hollinghurst, P.Tully, M.Moffat, K.Chiu, C.Waters, R.Gray, A.Azhar, M.Mioulet, V.Newman, J.Asfor, A. S.Burman, A.Crossley, S.Hammond, J.Tchilian, E.Charleston, B.Bailey, D.Tuthill, T. J.Graham, S.Malinauskas, T.Huo, J.Tree, J.Buttigieg, K.Owens, R.2020-08-31doi:10.1101/2020.08.31.275701Cold Spring Harbor Laboratory Press2020-08-31
<![CDATA[
Modulation of the cAMP levels with a conserved actinobacteria phosphodiesterase enzyme reduces antimicrobial tolerance in mycobacteria
]]>
https://biorxiv.org/cgi/content/short/2020.08.26.267864v1?rss=1"
Thomson, M.Nunta, K.Cheyne, A.Liu, Y.Garza-Garcia, A.Larrouy-Maumus, G.2020-08-26doi:10.1101/2020.08.26.267864Cold Spring Harbor Laboratory Press2020-08-26
<![CDATA[
Training a neural network to learn other dimensionality reduction removes data size restrictions in bioinformatics and provides a new route to exploring data representations
]]>
https://biorxiv.org/cgi/content/short/2020.09.03.269555v1?rss=1"
Dexter, A.Thomas, S. A.Steven, R. T.Robinson, K. N.Taylor, A. J.Elia, E.Nikula, C.Campbell, A. D.Panina, Y.Najumudeen, A. K.Murta, T.Yan, B.Grabowski, P.Hamm, G.Swales, J.Gilmore, I.Yuneva, M.Goodwin, R. J. A.Barry, S.Sansom, O. J.Takats, Z.Bunch, J.2020-09-03doi:10.1101/2020.09.03.269555Cold Spring Harbor Laboratory Press2020-09-03
<![CDATA[
Assessing the acoustic behaviour of Anopheles gambiae s.l. dsxF mutants: Implications for Vector Control
]]>
https://biorxiv.org/cgi/content/short/2020.09.06.284679v1?rss=1"
Su, M. P.Georgiades, M.Bagi, J.Kyrou, K.Crisanti, A.Albert, J.2020-09-06doi:10.1101/2020.09.06.284679Cold Spring Harbor Laboratory Press2020-09-06
<![CDATA[
Plasmodium falciparum guanylyl cyclase-alpha and the activity of its appended P4-ATPase domain are essential for cGMP synthesis and blood stage egress
]]>
https://biorxiv.org/cgi/content/short/2020.09.07.285734v1?rss=1"
Nofal, S. D.Patel, A.Blackman, M. J.Flueck, C.Baker, D. A.2020-09-07doi:10.1101/2020.09.07.285734Cold Spring Harbor Laboratory Press2020-09-07
<![CDATA[
Generating single-sex litters: development of CRISPR-Cas9 genetic tools to produce all-male offspring
]]>
https://biorxiv.org/cgi/content/short/2020.09.07.285536v1?rss=1"
Douglas, C.Maciulyte, V.Zohren, J.Snell, D. M.Ojarikre, O. A.Ellis, P. J.Turner, J. M. A.2020-09-07doi:10.1101/2020.09.07.285536Cold Spring Harbor Laboratory Press2020-09-07
<![CDATA[
Highly enriched hiPSC-derived midbrain dopaminergic neurons robustly models Parkinson's disease.
]]>
https://biorxiv.org/cgi/content/short/2020.09.08.287797v1?rss=1"
80%) of mDA neurons using only small molecules. We confirmed the identity of the mDA neurons using single-cell RNA-sequencing and detection of classical markers. Single-cell live imaging demonstrated neuronal calcium signalling and functional dopamine transport. Electrophysiology measures highlighted the ability to form synapses and networks in culture. Patient-specific hiPSC lines differentiated to produce functional mDA neurons that exhibit the hallmarks of synucleinopathy including: aggregate formation, oxidative stress as well as mitochondrial dysfunction and impaired lysosomal dynamics. In summary, we establish a robust differentiation paradigm to generate enriched mDA neurons from hiPSCs, which can be used to faithfully model key aspects of Parkinsons disease (PD), providing the potential to further elucidate molecular mechanisms contributing to disease development.
]]>Virdi, G. S.Choi, M. L.Yao, Z.Evans, J. R.Athauda, D.Melandri, D.Sylantyev, S.Abramov, A. Y.Patani, R.Gandhi, S.2020-09-08doi:10.1101/2020.09.08.287797Cold Spring Harbor Laboratory Press2020-09-08
<![CDATA[
The atypical Rho GTPase Rnd2 is critical for dentate granule neuron development and anxiety-like behavior during adult but not neonatal neurogenesis
]]>
https://biorxiv.org/cgi/content/short/2020.09.10.290866v1?rss=1"
Kerloch, T.Farrugia, F.Maitre, M.Terral, G.Koehl, M.Heng, J. I.-T.Blanchard, M.Doat, H.Leste-Lasserre, T.Goron, A.Gonzales, D.Guillemot, F.Abrous, N.Pacary, E.2020-09-10doi:10.1101/2020.09.10.290866Cold Spring Harbor Laboratory Press2020-09-10
<![CDATA[
ImmunoCluster: A computational framework for the non-specialist to immune profile cellular heterogeneity using liquid and imaging mass, and flow cytometry datasets
]]>
https://biorxiv.org/cgi/content/short/2020.09.09.289033v1?rss=1"
Opzoomer, J. W.Timms, J. A.Blighe, K.Mourikis, T. P.Chapuis, N.Bekoe, R.Kareemaghay, S.Nocerino, P.Apollonio, B.Ramsay, A. G.Tavassoli, M.Harrison, C.Ciccarelli, F.Parker, P.Fontenay, M.Barber, P.Arnold, J. N.Kordasti, S.2020-09-10doi:10.1101/2020.09.09.289033Cold Spring Harbor Laboratory Press2020-09-10
<![CDATA[
Acute depletion of METTL3 identifies a role for N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome
]]>
https://biorxiv.org/cgi/content/short/2020.09.10.291179v1?rss=1"
Wei, G.Almeida, M.Pintacuda, G.Coker, H.Bowness, J. S.Ule, J.Brockdorff, N.2020-09-11doi:10.1101/2020.09.10.291179Cold Spring Harbor Laboratory Press2020-09-11
<![CDATA[
Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing
]]>
https://biorxiv.org/cgi/content/short/2020.09.11.292656v1?rss=1"
Bliznina, A.Masunaga, A.Mansfield, M. J.Tan, Y.Liu, A. W.West, C.Rustagi, T.Chien, H.-C.Kumar, S.Pichon, J.Plessy, C.Luscombe, N. M.2020-09-12doi:10.1101/2020.09.11.292656Cold Spring Harbor Laboratory Press2020-09-12
<![CDATA[
A two-site flexible clamp mechanism for RET-GDNF-GFRα1 assembly reveals both conformational adaptation and strict geometric spacing
]]>
https://biorxiv.org/cgi/content/short/2020.09.13.286047v1?rss=1"
Adams, S.Purkiss, A. G.Knowles, P. P.Nans, A.Briggs, D. C.Borg, A.Earl, C. P.Goodman, K. M.Nawrotek, A.Borg, A. J.McIntosh, P. B.Houghton, F. M.Kjaer, S.McDonald, N. Q.2020-09-13doi:10.1101/2020.09.13.286047Cold Spring Harbor Laboratory Press2020-09-13
<![CDATA[
Single-molecule measurements reveal that PARP1 condenses DNA by loop formation
]]>
https://biorxiv.org/cgi/content/short/2020.09.15.297887v1?rss=1"
Bell, N. A. W.Haynes, P. J.Brunner, K.Maia de Oliveira, T.Flocco, M.Hoogenboom, B. W.Molloy, J. E.2020-09-15doi:10.1101/2020.09.15.297887Cold Spring Harbor Laboratory Press2020-09-15
<![CDATA[
The eukaryotic replisome requires an additional helicase to disarm dormant replication origins
]]>
https://biorxiv.org/cgi/content/short/2020.09.17.301366v1?rss=1"
Hill, J.Eickhoff, P.Drury, L.Costa, A.Diffley, J.2020-09-17doi:10.1101/2020.09.17.301366Cold Spring Harbor Laboratory Press2020-09-17
<![CDATA[
Primary sex determination in chickens depends on DMRT1 dosage, but gonadal sex does not determine secondary sexual characteristics in adult birds
]]>
https://biorxiv.org/cgi/content/short/2020.09.18.303040v1?rss=1"
Ioannidis, J.Taylor, G.Zhao, D.Liu, L.Idoko-Akoh, A.Gong, D.Lovell-Badge, R.Guioli, S.McGrew, M.Clinton, M.2020-09-19doi:10.1101/2020.09.18.303040Cold Spring Harbor Laboratory Press2020-09-19
<![CDATA[
MICAL2 acts through Arp3B isoform-specific Arp2/3 complexes to destabilize branched actin networks
]]>
https://biorxiv.org/cgi/content/short/2020.09.21.306522v1?rss=1"
Galloni, C.Carra, D.Abella, J. V. G.Kjaer, S.Singaravelu, P.Barry, D. J.Kogata, N.Guerin, C.Blanchoin, L.Way, M.2020-09-21doi:10.1101/2020.09.21.306522Cold Spring Harbor Laboratory Press2020-09-21
<![CDATA[
Dual-view oblique plane microscopy (dOPM)
]]>
https://biorxiv.org/cgi/content/short/2020.09.24.311613v1?rss=1"
Sparks, H.Dent, L.Bakal, C.Behrens, A.Salbreux, G.Dunsby, C.2020-09-25doi:10.1101/2020.09.24.311613Cold Spring Harbor Laboratory Press2020-09-25
<![CDATA[
Evaluating the fitness of PA/I38T-substituted influenza A viruses with reduced baloxavir susceptibility in a competitive mixtures ferret model
]]>
https://biorxiv.org/cgi/content/short/2020.09.28.316620v1?rss=1"
Lee, L. Y.Zhou, J.Koszalka, P.Frise, R.Farrukee, R.Baba, K.Miah, S.Shishido, T.Galiano, M.Hashimoto, T.Omoto, S.Uehara, T.Mifsud, E.Collinson, N.Kuhlbusch, K.Clinch, B.Wildum, S.Barclay, W. S.Hurt, A. C.2020-09-28doi:10.1101/2020.09.28.316620Cold Spring Harbor Laboratory Press2020-09-28
<![CDATA[
LRRK2-dependent Rab GTPase phosphorylation in response to endolysosomal damage depends on macrophage differentiation
]]>
https://biorxiv.org/cgi/content/short/2020.10.02.323873v1?rss=1"
Herbst, S.Gutierrez, M. G.2020-10-02doi:10.1101/2020.10.02.323873Cold Spring Harbor Laboratory Press2020-10-02
<![CDATA[
Differing total mRNA expression shapes the molecular and clinical phenotype of cancer
]]>
https://biorxiv.org/cgi/content/short/2020.09.30.306795v1?rss=1"
Cao, S.Wang, J. R.Ji, S.Yang, P.Chen, J.Montierth, M. D.Shen, J. P.Lee, J. J.Guerrero, P. A.Yu, K.Livingstone, J.Bhandari, V.Hubert, S. M.Daw, N. C.Futreal, A.Efstathiou, E.Lim, B.Viale, A.Zhang, J.Maitra, A.Kopetz, S.Campbell, P.Speed, T. P.Boutros, P. C.Urbanucci, A.Zhu, H.Demeulemeester, J.Van Loo, P.Wang, W.2020-10-02doi:10.1101/2020.09.30.306795Cold Spring Harbor Laboratory Press2020-10-02
<![CDATA[
Somatic chromosomal number alterations affecting driver genes inform in-vitro and clinical drug response in high-grade serous ovarian cancer
]]>
https://biorxiv.org/cgi/content/short/2020.10.04.325365v1?rss=1"
Correia Martins, F.Couturier, D.-L.Santiago, I.Sauer, C.Vias, M.Angelova, M.Sanders, D.Piskorz, A.Hall, J.Hosking, K.Amirthanayagam, A.Cosulich, S.Carnevalli, L.Davies, B.Watkins, T. B. K.Funingana, G.Bolton, H.Haldar, K.Latimer, J.Baldwin, P.Crawford, R.Eldridge, M.Basu, B.Jimenez-Linan, M.McGranahan, N.Litchfield, K.Shah, S.McNeish, I.Caldas, C.Evan, G.Swanton, C.Brenton, J. D.2020-10-04doi:10.1101/2020.10.04.325365Cold Spring Harbor Laboratory Press2020-10-04
<![CDATA[
Mutations in SKI in Shprintzen-Goldberg syndrome lead to attenuated TGF-β responses through SKI stabilization
]]>
https://biorxiv.org/cgi/content/short/2020.10.07.330407v1?rss=1"
Gori, I.George, R.Purkiss, A.Strohbuecker, S.Randall, R. A.Ogrodowicz, R.Carmignac, V.Faivre, L.Joshi, D.Kjaer, S.Hill, C. S.2020-10-09doi:10.1101/2020.10.07.330407Cold Spring Harbor Laboratory Press2020-10-09
<![CDATA[
ES-62 suppression of arthritis reflects epigenetic rewiring of synovial fibroblasts to a joint-protective phenotype
]]>
https://biorxiv.org/cgi/content/short/2020.10.08.331942v1?rss=1"
Corbet, M.Pineda, M. A.Yang, K.Tarafdar, A.McGrath, S.Nakagawa, R.Lumb, F. E.Harnett, W.Harnett, M. M.2020-10-08doi:10.1101/2020.10.08.331942Cold Spring Harbor Laboratory Press2020-10-08
<![CDATA[
GIANI: open-source software for automated analysis of 3D microscopy images
]]>
https://biorxiv.org/cgi/content/short/2020.10.15.340810v1?rss=1"
Barry, D. J.Gerri, C.Bell, D. M.D'Antuono, R.Niakan, K. K.2020-10-16doi:10.1101/2020.10.15.340810Cold Spring Harbor Laboratory Press2020-10-16
<![CDATA[
Computational and experimental analyses of mitotic chromosome formation pathways in fission yeast
]]>
https://biorxiv.org/cgi/content/short/2020.10.15.341305v1?rss=1"
Gerguri, T.Fu, X.Kakui, Y.Khatri, B. S.Barrington, C.Bates, P. A.Uhlmann, F.2020-10-16doi:10.1101/2020.10.15.341305Cold Spring Harbor Laboratory Press2020-10-16
<![CDATA[
Dual-view light-sheet imaging through tilted glass interface using a deformable mirror
]]>
https://biorxiv.org/cgi/content/short/2020.10.20.345306v1?rss=1"
Vladimirov, N.Preusser, F.Wisniewski, J.Yaniv, Z.Desai, R. A.Woehler, A.Preibisch, S.2020-10-21doi:10.1101/2020.10.20.345306Cold Spring Harbor Laboratory Press2020-10-21
<![CDATA[
Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes
]]>
https://biorxiv.org/cgi/content/short/2020.10.28.359240v1?rss=1"
Ansari-Pour, N.Zheng, Y.Pitt, J. J.Dentro, S.Yoshimatsu, T. F.Sanni, A.Ajani, M.Woodard, A.Rajagopal, P. S.Fitzgerald, D.Gruber, A. J.Odetunde, A.Popoola, A.Falusi, A. G.Babalola, C. P.Ogundiran, T.Obafunwa, J.Ojengbede, O.Ibrahim, N.Barretina, J.Van Loo, P.Chen, M.White, K. P.Huo, D.Wedge, D. C.Olopade, O. I.2020-10-28doi:10.1101/2020.10.28.359240Cold Spring Harbor Laboratory Press2020-10-28
<![CDATA[
GDV1 C-terminal truncation of 39 amino acids disrupts sexual commitment in Plasmodium falciparum
]]>
https://biorxiv.org/cgi/content/short/2020.10.28.360123v1?rss=1"
Tiburcio, M.Hitz, E.Niederwieser, I.Kelly, G.Davies, H.Doerig, C.Billker, O.Voss, T. S.Treeck, M.2020-10-30doi:10.1101/2020.10.28.360123Cold Spring Harbor Laboratory Press2020-10-30
<![CDATA[
Copy number-aware deconvolution of tumor-normal DNA methylation profiles
]]>
https://biorxiv.org/cgi/content/short/2020.11.03.366252v1?rss=1"
Larose Cadieux, E.Tanic, M.Wilson, G. A.Baker, T.Dietzen, M.Dhami, P.Vaikkinen, H.Watkins, T. B. K.Kanu, N.Veeriah, S.Jamal-Hanjani, M.McGranahan, N.Feber, A.Swanton, C.TRACERx Consortium,Beck, S.Demeulemeester, J.Van Loo, P.2020-11-04doi:10.1101/2020.11.03.366252Cold Spring Harbor Laboratory Press2020-11-04
<![CDATA[
9p21 Loss Defines the Evolutionary Patterns of Aggressive Renal Cell Carcinomas
]]>
https://biorxiv.org/cgi/content/short/2020.11.03.367433v1?rss=1"
Carbone, F.Huang, J. K.Perelli, L.Del Poggetto, E.Gutschner, T.Tomihara, H.Soeung, M.Lam, T. N. A.Xia, R.Zhu, C.Song, X.Zhang, J.Sircar, K.Malouf, G. G.Sgambato, A.Karam, J. A.Gao, J.Jonasch, E.Viale, A.Draetta, G. F.Futreal, A.Bakouny, Z.Van Allen, E. M.Choueiri, T.Msaouel, P.Litchfield, K.Turajlic, S.Heffernan, T. P.Chen, Y. B.DiNatale, R. G.Hakimi, A. A.Bristow, C. A.Tannir, N. M.Carugo, A.Genovese, G.2020-11-04doi:10.1101/2020.11.03.367433Cold Spring Harbor Laboratory Press2020-11-04
<![CDATA[
Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins
]]>
https://biorxiv.org/cgi/content/short/2020.11.05.369629v1?rss=1"
Belan, O.Barroso, C.Kaczmarczyk, A.Anand, R.Federico, S.O'Reilly, N.Newton, M. D.Maeots, E.Enchev, R. I.Martinez-Perez, E.Rueda, D. S.Boulton, S. J.2020-11-05doi:10.1101/2020.11.05.369629Cold Spring Harbor Laboratory Press2020-11-05
<![CDATA[
Temporal patterning of the central nervous system by a shared transcription factor code
]]>
https://biorxiv.org/cgi/content/short/2020.11.10.376491v1?rss=1"
Sagner, A.Zhang, I.Watson, T.Lazaro, J.Melchionda, M.Briscoe, J.2020-11-10doi:10.1101/2020.11.10.376491Cold Spring Harbor Laboratory Press2020-11-10
<![CDATA[
ECM remodeling and spatial cell cycle coordination determine tissue growth kinetics
]]>
https://biorxiv.org/cgi/content/short/2020.11.10.376129v1?rss=1"
Ainslie, A. P.Davis, J. R.Williamson, J. J.Ferreira, A.Torres-Sanchez, A.Hoppe, A.Mangione, F.Smith, M. B.Martin-Blanco, E.Salbreux, G.Tapon, N.2020-11-10doi:10.1101/2020.11.10.376129Cold Spring Harbor Laboratory Press2020-11-10
<![CDATA[
A FGF2-mediated incoherent feedforward loop inducesErk inhibition and promotes naive pluripotency
]]>
https://biorxiv.org/cgi/content/short/2020.11.11.378869v1?rss=1"
Gharibi, B.Goncalves, E.Nashun, B.Montoya, A.Mankalow, K.Strohbuecker, S.Malik Sheriff, R. S.Cicarrelli, A.Carvalho, J.Nye, E.Kramer, H.Rosewell, I.Hajkova, P.Beltrao, P.Santos, S.2020-11-11doi:10.1101/2020.11.11.378869Cold Spring Harbor Laboratory Press2020-11-11
<![CDATA[
Can a nick promote partial genome re-replication?
]]>
https://biorxiv.org/cgi/content/short/2020.11.14.381277v1?rss=1"
Johansson, E.Diffley, J. F. X.2020-11-15doi:10.1101/2020.11.14.381277Cold Spring Harbor Laboratory Press2020-11-15
<![CDATA[
EphB6 regulates TFEB-lysosomal pathway and survival of disseminated indolent breast cancer cells
]]>
https://biorxiv.org/cgi/content/short/2020.11.10.376186v1?rss=1"
MONTAGNER, M.Zangrossi, M.Chakravarty, P.Romani, P.Ratcliffe, C. D. H.Hooper, S.Dori, M.Forcato, M.Bicciato, S.Dupont, S.Sahai, E.2020-11-10doi:10.1101/2020.11.10.376186Cold Spring Harbor Laboratory Press2020-11-10
<![CDATA[
USP28 deletion and small molecule inhibition destabilises c-Myc and elicitsregression of squamous cell lung carcinoma
]]>
https://biorxiv.org/cgi/content/short/2020.11.17.377705v1?rss=1"
Ruiz, E. J.Pinto-Fernandez, A.Turnbull, A. P.Lan, L.Charlton, T. M.Scott, H. C.Damianou, A.Vere, G.Riising, E. M.Da Costa, C.Krajewski, W. W.Guerin, D.Kearns, J.Ioannidis, S.Katz, M.O'Connell, J. C.Moncaut, N.Rosewell, I.Nye, E.Jones, N.Heride, C.Gersch, M.Wu, M.Dinsmore, C. J.Hammonds, T. R.Kim, S.Komander, D.Urbe, S.Clague, M. J.Kessler, B. M.Behrens, A.2020-11-17doi:10.1101/2020.11.17.377705Cold Spring Harbor Laboratory Press2020-11-17
<![CDATA[
Subtractive CRISPR screen identifies factors involved in non-canonical LC3 lipidation.
]]>
https://biorxiv.org/cgi/content/short/2020.11.18.388306v1?rss=1"
Ulferts, R.Marcassa, E.Timimi, L.Lee, L. C.Daley, A.Montaner, B.Turner, S. D.Florey, O.Baillie, J. K.Beale, R.2020-11-18doi:10.1101/2020.11.18.388306Cold Spring Harbor Laboratory Press2020-11-18
<![CDATA[
Adipose Triglyceride Lipase protects the endocytosis of renal cells on a high fat diet in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2020.11.19.390146v1?rss=1"
Lubojemska, A.Stefana, M. I.Lampe, L.Yoshimura, A.Burrell, A.Collinson, L.Gould, A. P.2020-11-20doi:10.1101/2020.11.19.390146Cold Spring Harbor Laboratory Press2020-11-20
<![CDATA[
Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis
]]>
https://biorxiv.org/cgi/content/short/2020.11.20.391896v1?rss=1"
Lohoff, T.Ghazanfar, S.Missarova, A.Koulena, N.Pierson, N.Griffiths, J. A.Bardot, E. S.Eng, C.-H. L.Tyser, R. C. V.Argelaguet, R.Guibentif, C.Srinivas, S.Briscoe, J.Simons, B. D.Hadjantonakis, A.-K.Gottgens, B.Reik, W.Nichols, J.Cai, L.Marioni, J. C.2020-11-21doi:10.1101/2020.11.20.391896Cold Spring Harbor Laboratory Press2020-11-21
<![CDATA[
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study
]]>
https://biorxiv.org/cgi/content/short/2020.11.20.391300v1?rss=1"
Neely, B. A.Stemmer, P.Searle, B. C.Herring, L. E.Martin, L.Midha, M. K.Phinney, B. S.Shan, B.Palmblad, M.Wang, Y.Jagtap, P. D.Kirkpatrick, J. M.2020-11-20doi:10.1101/2020.11.20.391300Cold Spring Harbor Laboratory Press2020-11-20
<![CDATA[
Synergistic CDK control pathways maintain cell size homeostasis
]]>
https://biorxiv.org/cgi/content/short/2020.11.25.397943v1?rss=1"
Patterson, J. O.Basu, S.Rees, P.Nurse, P.2020-11-25doi:10.1101/2020.11.25.397943Cold Spring Harbor Laboratory Press2020-11-25
<![CDATA[
Intracellular localisation of Mycobacterium tuberculosis affects antibiotic efficacy
]]>
https://biorxiv.org/cgi/content/short/2020.11.25.398636v1?rss=1"
Santucci, P.Greenwood, D.Fearns, A.Chen, K.Jiang, H.Gutierrez, M. G.2020-11-25doi:10.1101/2020.11.25.398636Cold Spring Harbor Laboratory Press2020-11-25
<![CDATA[
Coupling of mouse olfactory bulb projection neurons to fluctuating odour pulses
]]>
https://biorxiv.org/cgi/content/short/2020.11.29.402610v1?rss=1"
Dasgupta, D.Warner, T. P. A.Erskine, A.Schaefer, A. T.2020-11-29doi:10.1101/2020.11.29.402610Cold Spring Harbor Laboratory Press2020-11-29
<![CDATA[
The metalloproteinase inhibitor Prinomastat reduces AML growth,prevents stem cell loss and improves chemotherapy effectiveness
]]>
https://biorxiv.org/cgi/content/short/2020.12.01.393157v1?rss=1"
Pirillo, C.Haltalli, M.Gonzalez Anton, S.Tini, V.Kong, I.Hawkins, E.Falini, B.Marra, A.Duarte, D.Lo Celso, C.2020-12-01doi:10.1101/2020.12.01.393157Cold Spring Harbor Laboratory Press2020-12-01
<![CDATA[
Molecular characterization of projection neuron subtypes in the mouse olfactory bulb
]]>
https://biorxiv.org/cgi/content/short/2020.11.30.405571v1?rss=1"
Zeppilli, S.Ackels, T.Attey, R.Klimpert, N.Boeing, S.Crombach, A.Schaefer, A.Fleischmann, A.2020-12-02doi:10.1101/2020.11.30.405571Cold Spring Harbor Laboratory Press2020-12-02
<![CDATA[
Recognition of Z-RNA by ADAR1 limits interferon responses
]]>
https://biorxiv.org/cgi/content/short/2020.12.04.411793v1?rss=1"
Tang, Q.Rigby, R. E.Young, G. R.Korning-Hvidt, A.Tang, T. K.Bridgeman, A.Townsend, A. R.Kassiotis, G.Rehwinkel, J.2020-12-04doi:10.1101/2020.12.04.411793Cold Spring Harbor Laboratory Press2020-12-04
<![CDATA[
Memory-like B cells emerging from germinal centres recycle through the subcapsular sinus
]]>
https://biorxiv.org/cgi/content/short/2020.12.08.415828v1?rss=1"
Zhang, Y.Garcia-Ibanez, L.Ulbricht, C.Lok, L. S. C.Dennison, T. W.Ferdinand, J. R.Mueller-Winkler, J.Burnett, C. J. M.Yam-Puc, J. C.Zhang, L.Brown, G.Tybulewicz, V.Rot, A.Hauser, A. E.Clatworthy, M. R.Toellner, K.-M.2020-12-09doi:10.1101/2020.12.08.415828Cold Spring Harbor Laboratory Press2020-12-09
<![CDATA[
Immunogenomic profile of colorectal cancer response to immune checkpoint blockade
]]>
https://biorxiv.org/cgi/content/short/2020.12.15.422831v1?rss=1"
Bortolomeazzi, M.Keddar, M. R.Montorsi, L.Acha-Sagredo, A.Benedetti, L.Temelkovski, D.Choi, S.Petrov, N.Todd, K.Wai, P.Kohl, J.Denner, T.Nye, E.Goldstone, R.Ward, S.Wilson, G. A.Al Bakir, M.Swanton, C.John, S.Miles, J.Larijani, B.Kunene, V.Fontana, E.Arkenau, H.-T.Parker, P. J.Rodriguez-Justo, M.Shiu, K.-K.Spencer, J.Ciccarelli, F. D.2020-12-15doi:10.1101/2020.12.15.422831Cold Spring Harbor Laboratory Press2020-12-15
<![CDATA[
Inhibition of protein N-myristoylation blocks Plasmodium falciparum intraerythrocytic development, egress, and invasion
]]>
https://biorxiv.org/cgi/content/short/2020.12.16.423054v1?rss=1"
Schlott, A. C.Knuepfer, E.Green, J. L.Hobson, P.Borg, A. J.Morales-Sanfrutos, J.Perrin, A. J.Snijders, A. P.Tate, E. W.Holder, A. A.2020-12-16doi:10.1101/2020.12.16.423054Cold Spring Harbor Laboratory Press2020-12-16
<![CDATA[
KLF17 promotes human naïve pluripotency but is not required for its establishment
]]>
https://biorxiv.org/cgi/content/short/2020.12.18.423466v1?rss=1"
Lea, R. A.McCarthy, A.Boeing, S.Niakan, K. K.2020-12-18doi:10.1101/2020.12.18.423466Cold Spring Harbor Laboratory Press2020-12-18
<![CDATA[
Molecular fluctuations as a ruler of force-induced protein conformations
]]>
https://biorxiv.org/cgi/content/short/2020.12.18.423481v1?rss=1"
Stannard, A.Mora, M.Beedle, A. E. M.Castro-Lopez, M.Board, S.Garcia-Manyes, S.2020-12-19doi:10.1101/2020.12.18.423481Cold Spring Harbor Laboratory Press2020-12-19
<![CDATA[
Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2
]]>
https://biorxiv.org/cgi/content/short/2020.12.18.423524v1?rss=1"
Nouailles, G.Wyler, E.Pennitz, P.Postmus, D.Vladimirova, D.Kazmierski, J.Pott, F.Dietert, K.Mülleder, M.Farztdinov, V.Obermayer, B.Wienhold, S.-M.Andreotti, S.Höfler, T.Sawitzki, B.Drosten, C.Sander, L. E.Suttorp, N.Ralser, M.Beule, D.Gruber, A. D.Goffinet, C.Landthaler, M.Trimpert, J.Witzenrath, M.2020-12-19doi:10.1101/2020.12.18.423524Cold Spring Harbor Laboratory Press2020-12-19
<![CDATA[
Targeted cancer therapy induces APOBEC fuelling the evolution of drug resistance
]]>
https://biorxiv.org/cgi/content/short/2020.12.18.423280v1?rss=1"
Mayekar, M. K.Caswell, D. R.Vokes, N. I.Law, E. K.Wu, W.Hill, W.Gronroos, E.Rowan, A.Al Bakir, M.McCoach, C. E.Blakely, C. M.Temiz, N. A.Nagano, A.Kerr, D. L.Rotow, J. K.Haderk, F.Dietzen, M.Ruiz, C. M.Almeida, B.Cech, L.Gini, B.Przewrocka, J.Moore, C.Murillo, M.Bakker, B.Rule, B.Durfee, C.Nanjo, S.Tan, L.Larson, L. K.Argyris, P. P.Brown, W. L.Yu, J.Gomez, C.Gui, P.Vogel, R. I.Yu, E. A.Thomas, N. J.Venkatesan, S.Hobor, S.Chew, S. K.Kanu, N.McGranahan, N.Van Allen, E. M.Downward, J.Harris, R. S.Bivona, T2020-12-18doi:10.1101/2020.12.18.423280Cold Spring Harbor Laboratory Press2020-12-18
<![CDATA[
A physical theory of larval Drosophila behaviour
]]>
https://biorxiv.org/cgi/content/short/2020.08.25.266163v1?rss=1"
Loveless, J.Garner, A.Issa, A. R.Webb, B.Ohyama, T.Alonso, C.2020-08-25doi:10.1101/2020.08.25.266163Cold Spring Harbor Laboratory Press2020-08-25
<![CDATA[
Dynamic regulation of hierarchical heterogeneity in Acute Myeloid Leukemia serves as a tumor immunoevasion mechanism
]]>
https://biorxiv.org/cgi/content/short/2020.12.21.414649v1?rss=1"
Pospori, C.Grey, W.Gonzalez-Anton, S.Gibson, S. V.Georgiou, C.Birch, F.Stevens, G.Williams, T.Khorshed, R.Haltalli, M. L. R.Skoufou-Papoutsaki, M.-N.Sloan, K.Encabo, H. H.Hopkins, J.Christodoulidou, C.Stampoulis, D.Hearn-Yates, F.Gribben, J.Stauss, H. J.Chakraverty, R.Bonnet, D.Lo Celso, C. L.2020-12-22doi:10.1101/2020.12.21.414649Cold Spring Harbor Laboratory Press2020-12-22
<![CDATA[
APOBEC3B expression generates an immunogenic model of Kras mutant lung cancer
]]>
https://biorxiv.org/cgi/content/short/2020.12.22.423126v1?rss=1"
de Carne Trecesson, S.Boumelha, J.Law, E.Romero-Clavijo, P.Mugarza, E.Coelho, M.Moore, C.Rana, S.Caswell, D.Murillo, M.Hancock, D.Argyris, P.Brown, W.Durfee, C.Larson, L.Vogel, R.Alejandro Suarez-Bonnet, A.Priestnall, S.East, P.Ross, S.Molina-Arcas, M.Swanton, C.Harris, R.Downward, J.2020-12-22doi:10.1101/2020.12.22.423126Cold Spring Harbor Laboratory Press2020-12-22
<![CDATA[
CKS1-dependent proteostatic regulation has dual roles combating acute myeloid leukemia whilst protecting normal hematopoiesis
]]>
https://biorxiv.org/cgi/content/short/2020.12.27.423419v1?rss=1"
Grey, W.Rio-Machin, A.Casado-Izquierdo, P.Miettinen, J.Copley, F.Parsons, A.Heckman, C.Cutillas, P.Gribben, J.Fitzgibbon, J.Bonnet, D.2020-12-28doi:10.1101/2020.12.27.423419Cold Spring Harbor Laboratory Press2020-12-28
<![CDATA[
Wnt/beta-catenin signalling is dispensable for adult neural stem cell homeostasis and activation.
]]>
https://biorxiv.org/cgi/content/short/2020.12.29.424694v1?rss=1"
Austin, S. H. L.Harris, L.Paun, O.Rigo, P.Guillemot, F.Urban Avellaneda, N.2020-12-29doi:10.1101/2020.12.29.424694Cold Spring Harbor Laboratory Press2020-12-29
<![CDATA[
Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation
]]>
https://biorxiv.org/cgi/content/short/2020.12.29.424684v1?rss=1"
Blassberg, R.Patel, H.Watson, T.Gouti, M.Metzis, V.Delas, J.Briscoe, J.2020-12-30doi:10.1101/2020.12.29.424684Cold Spring Harbor Laboratory Press2020-12-30
<![CDATA[
Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses
]]>
https://biorxiv.org/cgi/content/short/2020.12.31.424931v1?rss=1"
Banchenko, S.Krupp, F.Gotthold, C.Buerger, J.Graziadei, A.O' Reilly, F.Sinn, L.Ruda, O.Rappsilber, J.Spahn, C. M. T.Mielke, T.Taylor, I. A.Schwefel, D.2021-01-01doi:10.1101/2020.12.31.424931Cold Spring Harbor Laboratory Press2021-01-01
<![CDATA[
Single-molecule super-resolution imaging of T-cell plasma membrane CD4 redistribution upon HIV-1 binding
]]>
https://biorxiv.org/cgi/content/short/2021.01.05.425371v1?rss=1"
Yuan, Y.Jacobs, C.Llorente Garcia, I.Pereira, P. M.Lawrence, S.Laine, R. F.Marsh, M.Henriques, R.2021-01-05doi:10.1101/2021.01.05.425371Cold Spring Harbor Laboratory Press2021-01-05
<![CDATA[
Spontaneous selection of Cryptosporidium drug resistance in a calf model of infection
]]>
https://biorxiv.org/cgi/content/short/2021.01.04.425361v1?rss=1"
170-fold. Structural modeling of CpMetRS based on an inhibitor-bound Trypanosoma brucei MetRS crystal structure suggested that the resistance mutations reposition nearby hydrophobic residues, interfering with compound binding while minimally impacting substrate binding. This is the first report of naturally emerging Cryptosporidium drug resistance, highlighting the need to address the potential for anticryptosporidial resistance and establish strategies to limit its occurrence.
ImportanceCryptosporidium is a leading protozoan cause of diarrhea in young children with no reliable treatment. We report results of a dairy calf drug efficacy trial and the spontaneous emergence of drug resistance. Cryptosporidium parvum infected calves initially improved with drug treatment, but infection relapsed in two animals. Parasites shed by each recrudescent calf had mutations in the gene encoding the drug target that altered its amino acid sequence. Recapitulation of the drug target mutations by CRISPR/Cas9 genome editing resulted in highly drug-resistant parasites, and recombinant mutant enzymes were resistant to inhibition. This is the first report of naturally emerging Cryptosporidium drug resistance. There is a currently a great opportunity to impact public health with new drugs to treat cryptosporidiosis, and this report highlights the need to address the potential for anticryptosporidial resistance and establish strategies to limit its occurrence in order to realize their full potential.
One-sentence summaryDrug-target point mutations mediating anticryptosporidial resistance spontaneously arose in the dairy calf C. parvum infection model.
]]>Hasan, M. M.Stebbins, E. E.Choy, R. K. M.Gillespie, J. R.de Hostos, E.Miller, P. J.Mushtaq, A.Ranade, R. M.Teixeira, J. E.Verlinde, C. L. M. J.Sateriale, A.Zhang, Z.Osbourn, D. M.Griggs, D. W.Fan, E.Buckner, F. S.Huston, C. D.2021-01-05doi:10.1101/2021.01.04.425361Cold Spring Harbor Laboratory Press2021-01-05
<![CDATA[
Free recall scaling laws and short-term memory effects in a latching attractor network
]]>
https://biorxiv.org/cgi/content/short/2020.12.19.423464v1?rss=1"
Boboeva, V.Pezzotta, A.Clopath, C.2020-12-21doi:10.1101/2020.12.19.423464Cold Spring Harbor Laboratory Press2020-12-21
<![CDATA[
Neural stem cells alter nucleocytoplasmic partitioning and accumulate nuclear polyadenylated transcripts during quiescence
]]>
https://biorxiv.org/cgi/content/short/2021.01.06.425462v1?rss=1"
Rossi, A.Coum, A.Madelenat, M.Harris, L.Miedzik, A.Strohbuecker, S.Chai, A.Fiaz, H.Chaouni, R.Faull, P.Grey, W.Bonnet, D.Makeyev, E. V.Snijders, A. P.Kelly, G.Guillemot, F.Sousa-Nunes, R.2021-01-06doi:10.1101/2021.01.06.425462Cold Spring Harbor Laboratory Press2021-01-06
<![CDATA[
Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment
]]>
https://biorxiv.org/cgi/content/short/2021.01.08.425895v1?rss=1"
Gelabert, P.Sawyer, S.Bergstrom, A.Collin, T. C.Meshvelian, T.Belfer-Cohen, A.Lordkipanidze, D.Jakeli, N.Matskevich, Z.Bar-Oz, G.Fernandes, D. M.Cheronet, O.Ozdogan, K. T.Oberreiter, V.Feeney, R. N. M.Skoglund, P.Pinhasi, R.2021-01-08doi:10.1101/2021.01.08.425895Cold Spring Harbor Laboratory Press2021-01-08
<![CDATA[
Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron micro-tomography and volume electron microscopy
]]>
https://biorxiv.org/cgi/content/short/2021.01.13.426503v1?rss=1"
Bosch, C.Ackels, T.Pacureanu, A.Zhang, Y.Peddie, C. J.Berning, M.Rzepka, N.Zdora, M.-C.Whiteley, I.Storm, M.Bonnin, A.Rau, C.Margrie, T.Collinson, L.Schaefer, A. T.2021-01-14doi:10.1101/2021.01.13.426503Cold Spring Harbor Laboratory Press2021-01-14
<![CDATA[
Protein Phosphatase 1 regulates atypical chromosome segregation and cell polarity during mitotic and meiotic division in Plasmodium sexual stages
]]>
https://biorxiv.org/cgi/content/short/2021.01.15.426883v1?rss=1"
Zeeshan, M.Pandey, R.SUBUDHI, A. K.Ferguson, D. J. P.Kaur, G.Rashpa, R.Nugmanova, R.Brady, D.Bottrill, A.vaughan, s.Brochet, M.Bollen, M.Pain, A.Holder, A. A.Guttery, D. S.Tewari, R.2021-01-17doi:10.1101/2021.01.15.426883Cold Spring Harbor Laboratory Press2021-01-17
<![CDATA[
The impact of Spike mutations on SARS-CoV-2 neutralization
]]>
https://biorxiv.org/cgi/content/short/2021.01.15.426849v1?rss=1"
Rees-Spear, C.Muir, L.Griffith, S. A.Heaney, J.Aldon, Y.Snitselaar, J.Thomas, P.Graham, C.Seow, J.Lee, N.Rosa, A.Roustan, C.Houlihan, C. F.Sanders, R. W.Gupta, R. K.Cherepanov, P.Stauss, H.Nastouli, E.Doores, K. J.van Gils, M. J.McCoy, L. E.2021-01-19doi:10.1101/2021.01.15.426849Cold Spring Harbor Laboratory Press2021-01-19
<![CDATA[
Luminal nutrients activate distinct patterns in submucosal and myenteric neurons in the mouse small intestine
]]>
https://biorxiv.org/cgi/content/short/2021.01.19.427232v1?rss=1"
Fung, C.Hao, M. M.Obata, Y.Tack, J.Pachnis, V.Boesmans, W.Vanden Berghe, P.2021-01-20doi:10.1101/2021.01.19.427232Cold Spring Harbor Laboratory Press2021-01-20
<![CDATA[
Diminished miRNA activity is associated with aberrant cytoplasmic intron retention in ALS pathogenesis
]]>
https://biorxiv.org/cgi/content/short/2021.01.27.428555v1?rss=1"
Petric-Howe, M.Crerar, H.Neeves, J.Tyzack, G. E.Patani, R.Luisier, R.2021-01-28doi:10.1101/2021.01.27.428555Cold Spring Harbor Laboratory Press2021-01-28
<![CDATA[
The regulatory landscape of cells in the developing mouse cerebellum
]]>
https://biorxiv.org/cgi/content/short/2021.01.29.428632v1?rss=1"
Sarropoulos, I.Sepp, M.Frömel, R.Leiss, K.Trost, N.Leushkin, E.Okonechnikov, K.Joshi, P.Kutscher, L. M.Cardoso-Moreira, M.Pfister, S. M.Kaessmann, H.2021-01-29doi:10.1101/2021.01.29.428632Cold Spring Harbor Laboratory Press2021-01-29
<![CDATA[
Dendritic domain-specific sampling of long-range axons shapes feedforward and feedback connectivity of L5 neurons
]]>
https://biorxiv.org/cgi/content/short/2021.01.31.429033v1?rss=1"
Galloni, A. R.Ye, Z.Rancz, E.2021-02-01doi:10.1101/2021.01.31.429033Cold Spring Harbor Laboratory Press2021-02-01
<![CDATA[
Characterisation of tumour immune microenvironment remodelling following oncogene inhibition in preclinical studies using an optimised imaging mass cytometry workflow
]]>
https://biorxiv.org/cgi/content/short/2021.02.02.429358v1?rss=1"
van Maldegem, F.Valand, K.Cole, M.Patel, H.Angelova, M.Rana, S.Colliver, E.Enfield, K.Bah, N.Tsang, V.Mugarza, E.Moore, C.Hobson, P.Levi, D.Molina, M.Swanton, C.Downward, J.2021-02-02doi:10.1101/2021.02.02.429358Cold Spring Harbor Laboratory Press2021-02-02
<![CDATA[
Mixology: a tool for calculating required masses and volumes for laboratory solutions
]]>
https://biorxiv.org/cgi/content/short/2021.01.30.428948v1?rss=1"
Sanderson, T.2021-01-31doi:10.1101/2021.01.30.428948Cold Spring Harbor Laboratory Press2021-01-31
<![CDATA[
Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike
]]>
https://biorxiv.org/cgi/content/short/2021.02.03.429355v1?rss=1"
100 Spike-reactive monoclonal antibodies from SARS-CoV-2 infected individuals. ~45% showed neutralizing activity of which ~20% were NTD-specific. None of the S2-specific antibodies showed neutralizing activity. Competition ELISA revealed that NTD-specific mAbs formed two distinct groups: the first group was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Importantly, mutations present in B.1.1.7 Spike frequently conferred resistance to neutralization by the NTD-specific neutralizing antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes need to be considered when investigating antigenic drift in emerging variants.
]]>Graham, C.Seow, J.Huettner, I.Khan, H.Kouphou, N.Acors, S.Winstone, H.Pickering, S.Pedro Galao, R.Jose Lista, M.Jimenez-Guardeno, J. M.Laing, A. G.Wu, Y.Joseph, M.Muir, L.Ng, W. M.Duyvesteyn, H. M. E.Zhao, Y.Bowden, T. A.Shankar-Hari, M.Rosa, A.Cherepanov, P.McCoy, L. E.Hayday, A. C.Neil, S. J. D.Malim, M. H.Doores, K. J.2021-02-03doi:10.1101/2021.02.03.429355Cold Spring Harbor Laboratory Press2021-02-03
<![CDATA[
An extracellular redox signal triggers calcium release and impacts the asexual development of Toxoplasma gondii
]]>
https://biorxiv.org/cgi/content/short/2021.02.04.429728v1?rss=1"
Alves, E.Benns, H. J.Magnus, L.Dominicus, C.Dobai, T.Blight, J.Wincott, C. J.Child, M. A.2021-02-04doi:10.1101/2021.02.04.429728Cold Spring Harbor Laboratory Press2021-02-04
<![CDATA[
Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility
]]>
https://biorxiv.org/cgi/content/short/2021.02.05.429998v1?rss=1"
Zou, J.Gopalakrishnan, S.Parker, C. C.Nicod, J.Mott, R.Cai, N.Lionikas, A.Davies, R. W.Palmer, A. A.Flint, J.2021-02-07doi:10.1101/2021.02.05.429998Cold Spring Harbor Laboratory Press2021-02-07
<![CDATA[
Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2)
]]>
https://biorxiv.org/cgi/content/short/2021.02.06.428911v1?rss=1"
Karmakar, S.Ramirez, O.Paul, K. V.Gupta, A. K.Botti, V.Mozos, I. R. d. l.Neuenkirchen, N.Ross, R. J.Neugebauer, K. M.Pillai, M. M.2021-02-07doi:10.1101/2021.02.06.428911Cold Spring Harbor Laboratory Press2021-02-07
<![CDATA[
Comprehensive phenotypic analysis of the Dp1Tyb mouse strain reveals a broad range of Down Syndrome-related phenotypes
]]>
https://biorxiv.org/cgi/content/short/2021.02.11.430828v1?rss=1"
Lana-Elola, E.Cater, H.Watson-Scales, S.Greenaway, S.Mueller-Winkler, J.Gibbins, D.Nemes, M.Slender, A.Hough, T.Keskivali-Bond, P.Scudamore, C. L.Herbert, E.Banks, G. T.Mobbs, H.Canonica, T.Tosh, J.Noy, S.Llorian, M.Nolan, P. M.Griffin, J. L.Good, M.Simon, M.Mallon, A.-M.Wells, S.Fisher, E. M.Tybulewicz, V. L.2021-02-11doi:10.1101/2021.02.11.430828Cold Spring Harbor Laboratory Press2021-02-11
<![CDATA[
A Brownian ratchet model for DNA loop extrusion by the cohesin complex
]]>
https://biorxiv.org/cgi/content/short/2021.02.14.431132v1?rss=1"
Higashi, T. L.Tang, M.Pobegalov, G.Uhlmann, F.Molodtsov, M.2021-02-14doi:10.1101/2021.02.14.431132Cold Spring Harbor Laboratory Press2021-02-14
<![CDATA[
Favourable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases
]]>
https://biorxiv.org/cgi/content/short/2021.02.15.431291v1?rss=1"
Deakin, C.Cornish, G.Ng, K.Faulkner, N.Bolland, W.Panova, V.Hope, J.Rosa, A.Harvey, R.Hussain, S.Earl, C.Jebson, B.Wilkinson, M.Marshall, L.O'Brien, K.Rosser, L.Radziszewska, A.Peckham, H.Heaney, J.Rickman, H.Paraskevopoulou, S.Houlihan, C.Spyer, M.Gamblin, S.Mccauley, J.Nastouli, E.Cherepanov, P.Ciurtin, C.Wedderburn, L.Kassiotis, G.2021-02-16doi:10.1101/2021.02.15.431291Cold Spring Harbor Laboratory Press2021-02-16
<![CDATA[
Characterization of humoral and SARS-CoV-2 specific T cell responses in people living with HIV
]]>
https://biorxiv.org/cgi/content/short/2021.02.15.431215v1?rss=1"
Alrubayyi, A.Gea-Mallorqui, E.Touizer, E.Hameiri-Bowen, D.Kopycinski, J.Charlton, B.Fisher-Pearson, N.Muir, L.Rosa, A.Roustan, C.Earl, C.Cherepanov, P.Pellegrino, P.Waters, L.Burns, F.Kinloch, S.Dong, T.Dorrell, L.Rowland-Jones, S.McCoy, L. E.Peppa, D.2021-02-16doi:10.1101/2021.02.15.431215Cold Spring Harbor Laboratory Press2021-02-16
<![CDATA[
Inferring population histories for ancient genomes using genome-wide genealogies
]]>
https://biorxiv.org/cgi/content/short/2021.02.17.431573v1?rss=1"
0.5x mean coverage. Using Relate and Colate, we characterise dynamic population structure, such as repeated partial population replacements in Ireland, and gene-flow between early farmer and European hunter-gatherer groups. We further show that the previously reported increase in the TCC/TTC mutation rate, which is strongest in West Eurasians among present-day people, was already widespread across West Eurasia in the Late Glacial Period ~10k - 15k years ago, is strongest in Neolithic and Anatolian farmers, and is remarkably well predicted by the coalescence rates between other genomes and a 10,000-year-old Anatolian individual. This suggests that the driver of this signal originated in ancestors of ancient Anatolia >14k years ago, but was already absent by the Mesolithic and may indicate a genetic link between the Near East and European hunter-gatherer groups in the Late Paleolithic.
]]>Speidel, L.Cassidy, L.Davies, R. W.Hellenthal, G.Skoglund, P.Myers, S.2021-02-17doi:10.1101/2021.02.17.431573Cold Spring Harbor Laboratory Press2021-02-17
<![CDATA[
Rotavirus susceptibility of antibiotic-treated mice ascribed to diminished expression of interleukin-22
]]>
https://biorxiv.org/cgi/content/short/2021.02.18.431818v1?rss=1"
Schnepf, D.Hernandez, P.Mahlakoiv, T.Crotta, S.Sullender, M. E.Peterson, S. T.Ohnemus, A.Michiels, C.Gentle, I.Dumoutier, L.Reis, C. A.Diefenbach, A.Wack, A.Baldridge, M. T.Staeheli, P.2021-02-18doi:10.1101/2021.02.18.431818Cold Spring Harbor Laboratory Press2021-02-18
<![CDATA[
Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals
]]>
https://biorxiv.org/cgi/content/short/2021.02.24.432780v1?rss=1"
Torres-Mendez, A.Pop, S.Bonnal, S.Almudi, I.Roberts, R. J. V.Paolantoni, C.Alcaina, A.Avola, A.Martin Anduaga, A.Haussmann, I. H.Morin, V.Soller, M.Kadener, S.Roignant, J.-Y.Prieto-Godino, L.Irimia, M.2021-02-25doi:10.1101/2021.02.24.432780Cold Spring Harbor Laboratory Press2021-02-25
<![CDATA[
Whole-genome doubling-aware copy number phylogenies for cancer evolution with MEDICC2
]]>
https://biorxiv.org/cgi/content/short/2021.02.28.433227v1?rss=1"
Petkovic, M.Watkins, T. B.Colliver, E. C.Laskina, S.Swanton, C.Haase, K.Schwarz, R. F.2021-02-28doi:10.1101/2021.02.28.433227Cold Spring Harbor Laboratory Press2021-02-28
<![CDATA[
Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains
]]>
https://biorxiv.org/cgi/content/short/2021.03.01.433314v1?rss=1"
Faulkner, N.Ng, K.Wu, M.Harvey, R.Hussain, S.Greco, M.Bolland, W.Warchal, S.Margaritis, M.Paraskevopoulou, S.Heaney, J.Rickman, H.Houlihan, C.Spyer, M.Frampton, D.Byott, M.de Oliveira, T.Sigal, A.Kjaer, S.Swanton, C.Gandhi, S.Beale, R.Gamblin, S.Mccauley, J.Daniels, R.Howell, M.Bauer, D.Nastouli, E.Kassiotis, G.2021-03-01doi:10.1101/2021.03.01.433314Cold Spring Harbor Laboratory Press2021-03-01
<![CDATA[
Genome-wide screens identify calcium signaling as a key regulator of IgE+ plasma celldifferentiation and survival
]]>
https://biorxiv.org/cgi/content/short/2021.03.02.433398v1?rss=1"
Newman, R.Tolar, P.2021-03-02doi:10.1101/2021.03.02.433398Cold Spring Harbor Laboratory Press2021-03-02
<![CDATA[
Barcode Sequencing and a High-throughput Assay for Chronological Lifespan Uncover Ageing-associated Genes in Fission Yeast
]]>
https://biorxiv.org/cgi/content/short/2021.03.04.433786v1?rss=1"
Romila, C.Townsend, S.Malecki, M.Kamrad, S.Rodriguez-Lopez, M.Hillson, O.Cotobal, C.Ralser, M.Bahler, J.2021-03-04doi:10.1101/2021.03.04.433786Cold Spring Harbor Laboratory Press2021-03-04
<![CDATA[
Robust optical autofocus system utilizing neural networks trained for extended range and time-course and automated multiwell plate imaging including single molecule localization microscopy
]]>
https://biorxiv.org/cgi/content/short/2021.03.05.431171v1?rss=1"
Lightley, J.Görlitz, F.Kumar, S.Kalita, R.Kolbeinsson, A.Garcia, E.Alexandrov, Y.Bousgouni, V.Wysoczanski, R.Barnes, P.Donnelly, L.Bakal, C.Dunsby, C.Neil, M. A. A.Flaxman, S.French, P. M. W.2021-03-05doi:10.1101/2021.03.05.431171Cold Spring Harbor Laboratory Press2021-03-05
<![CDATA[
SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA
]]>
https://biorxiv.org/cgi/content/short/2021.03.05.434119v1?rss=1"
Kazachenka, A.Kassiotis, G.2021-03-05doi:10.1101/2021.03.05.434119Cold Spring Harbor Laboratory Press2021-03-05
<![CDATA[
High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe
]]>
https://biorxiv.org/cgi/content/short/2021.03.08.434385v1?rss=1"
Demichev, V.Yu, F.Teo, G. C.Szyrwiel, L.Rosenberger, G.Decker, J.Kaspar-Schoenefeld, S.Lilley, K. S.Muelleder, M.Nesvizhskii, A. I.Ralser, M.2021-03-09doi:10.1101/2021.03.08.434385Cold Spring Harbor Laboratory Press2021-03-09
<![CDATA[
Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation
]]>
https://biorxiv.org/cgi/content/short/2020.09.18.304139v1?rss=1"
Lulla, V.Wandel, M. P.Bandyra, K. J.Dendooven, T.Yang, X.Doyle, N.Oerum, S.O'Rourke, S.Randow, F.Maier, H. J.Scott, W.Ding, Y.Firth, A.Bloznelyte, K.Luisi, B.2020-09-19doi:10.1101/2020.09.18.304139Cold Spring Harbor Laboratory Press2020-09-19
<![CDATA[
A quantitative landscape of cell fate transitions identifies principles of cellular decision-making
]]>
https://biorxiv.org/cgi/content/short/2021.03.11.434982v1?rss=1"
Saez, M.Blassberg, R.Camacho-Aguilar, E.Siggia, E. D.Rand, D. A.Briscoe, J.2021-03-11doi:10.1101/2021.03.11.434982Cold Spring Harbor Laboratory Press2021-03-11
<![CDATA[
Crosstalk between enterocytes and innate lymphoid cells drives early IFN-g-mediated control of Cryptosporidium
]]>
https://biorxiv.org/cgi/content/short/2021.03.13.435244v1?rss=1"
Gullicksrud, J.Sateriale, A.Engiles, J. B.Gibson, A.Shaw, S.Hutchins, Z.Martin, L.Christian, D. A.Taylor, G. A.Yamamoto, M.Beiting, D. P.Striepen, B.Hunter, C.2021-03-14doi:10.1101/2021.03.13.435244Cold Spring Harbor Laboratory Press2021-03-14
<![CDATA[
High Content and High Throughout Phenotypic Assay for the Hourly Resolution of the Malaria Parasite Erythrocytic Cycle
]]>
https://biorxiv.org/cgi/content/short/2021.03.15.434938v1?rss=1"
Bell, D.Ridewood, S.Patel, A. P.Lee, S. H.Chang, Y.-T.Deu, E.2021-03-15doi:10.1101/2021.03.15.434938Cold Spring Harbor Laboratory Press2021-03-15
<![CDATA[
Development of novel MOG analogues with increased stability to explore MCT2 and α-ketoglutarate biology in vivo
]]>
https://biorxiv.org/cgi/content/short/2021.03.15.433711v1?rss=1"
Fets, L.Nunes, P. M.Campos, S.Silva dos Santos, M.Bevan, N.Sherriff, E. B.MacRae, J. I.House, D.Anastasiou, D.2021-03-15doi:10.1101/2021.03.15.433711Cold Spring Harbor Laboratory Press2021-03-15
<![CDATA[
Epiblast morphogenesis is controlled by selective mRNA decay triggered by LIN28A relocation
]]>
https://biorxiv.org/cgi/content/short/2021.03.15.433780v1?rss=1"
Modic, M.los Mozos, I. R. d.Steinhauser, S.van Genderen, E.Schirge, S.Bergant, V.Ryan, J.Mulholland, C. B.Lee, F. C. Y.Faraway, R.Klobucar, T.Merl-Pham, J.Hauck, S. M.Drukker, M.Bultmann, S.Leonhardt, H.Lickert, H.Luscombe, N. M.ten Berge, D.Ule, J.2021-03-16doi:10.1101/2021.03.15.433780Cold Spring Harbor Laboratory Press2021-03-16
<![CDATA[
HIV-1 requires capsid remodelling at the nuclear pore for nuclear entry and integration
]]>
https://biorxiv.org/cgi/content/short/2021.03.18.436028v1?rss=1"
Guedan, A.Donaldson, C. D.Cosnefroy, O.Taylor, I. A.Bishop, K. N.2021-03-18doi:10.1101/2021.03.18.436028Cold Spring Harbor Laboratory Press2021-03-18
<![CDATA[
N-myristoyltransferase inhibition is synthetic lethal in MYC-deregulated cancers
]]>
https://biorxiv.org/cgi/content/short/2021.03.20.436222v1?rss=1"
100 proteins. NMT is a promising target in cancer, but a mechanistic rationale for targeted therapy remains poorly defined. Here, large-scale cancer cell line screens against a panel of NMT inhibitors (NMTi) were combined with systems-level analyses to reveal that NMTi is synthetic lethal with deregulated MYC. Synthetic lethality is mediated by post-transcriptional failure in mitochondrial respiratory complex I protein synthesis concurrent with loss of myristoylation and degradation of complex I assembly factor NDUFAF4, followed by mitochondrial dysfunction specifically in MYC-deregulated cancer cells. NMTi eliminated MYC-deregulated tumors in vivo without overt toxicity, providing a new paradigm in which targeting a constitutive co-translational protein modification is synthetically lethal in MYC-deregulated cancers.
One-sentence summaryN-myristoyltransferase inhibition leads to post-transcriptional complex I failure and cell death in MYC-deregulated cancers
]]>Lueg, G. A.Faronato, M.Gorelik, A.Goya Grocin, A.Caamano-Gutierrez, E.Falciani, F.Solari, R.Carr, R.Bell, A. S.Bartlett, E.Hutton, J. A.Llorian-Sopena, M.Chakravarty, P.Brzezicha, B.Janz, M.Garnett, M. J.Calado, D. P.Tate, E. W.2021-03-20doi:10.1101/2021.03.20.436222Cold Spring Harbor Laboratory Press2021-03-20
<![CDATA[
ChromWave: Deciphering the DNA-encoded competition between transcription factors and nucleosomes with deep neural networks
]]>
https://biorxiv.org/cgi/content/short/2021.03.19.436198v1?rss=1"
Cakiroglu, S. A.Steinhauser, S.Smith, J.Xing, W.Luscombe, N. M.2021-03-20doi:10.1101/2021.03.19.436198Cold Spring Harbor Laboratory Press2021-03-20
<![CDATA[
TRIM28-dependent SUMOylation protects the adult ovary from the male pathway
]]>
https://biorxiv.org/cgi/content/short/2021.03.24.436749v1?rss=1"
Rossitto, M.Dejardin, S.Rands, C. M.Legras, S.Migale, R.Rafiee, M.-R.Neirijnck, Y.Pruvost, A.Nguyen, A. L.Bossis, G.Cammas, F. M.Le Gallic, L.Wilhelm, D.Boizet-Bonhoure, B.Lovell-Badge, R.Nef, S.Poulat, F.2021-03-24doi:10.1101/2021.03.24.436749Cold Spring Harbor Laboratory Press2021-03-24
<![CDATA[
In vitro teratogenicity testing using a 3D, embryo-like gastruloid system
]]>
https://biorxiv.org/cgi/content/short/2021.03.30.437698v1?rss=1"
Mantziou, V.Baillie-Benson, P.Jaklin, M.Kustermann, S.Martinez Arias, A.Moris, N.2021-03-30doi:10.1101/2021.03.30.437698Cold Spring Harbor Laboratory Press2021-03-30
<![CDATA[
Biallelic mutations in cancer genomes reveal local mutational determinants
]]>
https://biorxiv.org/cgi/content/short/2021.03.29.437407v1?rss=1"
Demeulemeester, J.Dentro, S. C.Gerstung, M.Van Loo, P.2021-03-30doi:10.1101/2021.03.29.437407Cold Spring Harbor Laboratory Press2021-03-30
<![CDATA[
Severity of SARS-CoV-2 infection as a function of the interferon landscape across the respiratory tract of COVID-19 patients.
]]>
https://biorxiv.org/cgi/content/short/2021.03.30.437173v1?rss=1"
Sposito, B.Broggi, A.Pandolfi, L.Crotta, S.Ferrarese, R.Sisti, S.Clementi, N.Ambrosi, A.Liu, E.Frangipane, V.Saracino, L.Marongiu, L.Facchini, F.Bottazzi, A.Fossali, T.Colombo, R.Clementi, M.Tagliabue, E.Pontiroli, A.Meloni, F.Wack, A.Mancini, N.Zanoni, I.2021-03-30doi:10.1101/2021.03.30.437173Cold Spring Harbor Laboratory Press2021-03-30
<![CDATA[
A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially resolved tissue phenotypingat single-cell resolution.
]]>
https://biorxiv.org/cgi/content/short/2021.04.01.437886v1?rss=1"
Bortolomeazzi, M.Montorsi, L.Temelkovski, D.Keddar, M. R.Acha-Sagredo, A.Pitcher, M. J.Basso, G.Laghi, L.Rodriguez-Justo, M.Spencer, J.Ciccarelli, F. D.2021-04-02doi:10.1101/2021.04.01.437886Cold Spring Harbor Laboratory Press2021-04-02
<![CDATA[
Oncogenic RAS activity predicts response to chemotherapy and outcome in lung adenocarcinoma
]]>
https://biorxiv.org/cgi/content/short/2021.04.02.437896v1?rss=1"
East, P.Kelly, G.Biswas, D.Marani, M.Hancock, D. C.Creasy, T.Sachsenmeier, K.Swanton, C.de Carne Trecesson, S.Downward, J.2021-04-04doi:10.1101/2021.04.02.437896Cold Spring Harbor Laboratory Press2021-04-04
<![CDATA[
Common ALS/FTD risk variants in UNC13A exacerbate its cryptic splicing and loss upon TDP-43 mislocalization
]]>
https://biorxiv.org/cgi/content/short/2021.04.02.438170v1?rss=1"
Brown, A.-L.Wilkins, O. G.Keuss, M. J.Hill, S. E.Zanovello, M.Lee, W. C.Lee, F. C. Y.Masino, L.Qi, Y. A.Bryce-Smith, S.Bampton, A.Gatt, A.Phatnani, H.NYGC ALS Consortium,Schiavo, G.Fisher, E. M. C.Raj, T.Secrier, M.Lashley, T.Ule, J.Buratti, E.Humphrey, J.Ward, M. E.Fratta, P.2021-04-04doi:10.1101/2021.04.02.438170Cold Spring Harbor Laboratory Press2021-04-04
<![CDATA[
Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp14/nsp10 Exoribonuclease
]]>
https://biorxiv.org/cgi/content/short/2021.04.07.438812v1?rss=1"
Basier, C.Basu, S.Beale, R.Bertolin, A. P.Canal, B.Curran, J. F.Deegan, T. D.Diffley, J. F.Drury, L. S.Fujisawa, R.Howell, M.Labib, K.McClure, A. W.Milligan, J.Roberts, E.Ulferts, R.Weissmann, F.Wu, M.Zeng, J.2021-04-08doi:10.1101/2021.04.07.438812Cold Spring Harbor Laboratory Press2021-04-08
<![CDATA[
Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp15 Endoribonuclease
]]>
https://biorxiv.org/cgi/content/short/2021.04.07.438811v1?rss=1"
Beale, R.Bertolin, A. P.Canal, B.Deegan, T. D.Diffley, J. F.Drury, L. S.Fujisawa, R.Howell, M.Labib, K.McClure, A. W.Ulferts, R.Weissmann, F.Wu, M.Zeng, J.2021-04-08doi:10.1101/2021.04.07.438811Cold Spring Harbor Laboratory Press2021-04-08
<![CDATA[
Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp3 Papain-like Protease
]]>
https://biorxiv.org/cgi/content/short/2021.04.07.438804v1?rss=1"
Armstrong, L. A.Beale, R.Bineva-Todd, G.Canal, B.Diffley, J. F.Drury, L. S.Howell, M.Kulathu, Y.Labib, K.Lim, C. T.Milligan, J.O'Reilly, N.Ozono, E.Tan, K. W.Ulferts, R.Weissmann, F.Wu, M.Zeisner, T. U.Zeng, J.2021-04-08doi:10.1101/2021.04.07.438804Cold Spring Harbor Laboratory Press2021-04-08
<![CDATA[
Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp13 Helicase
]]>
https://biorxiv.org/cgi/content/short/2021.04.07.438808v1?rss=1"
Beale, R.Bertolin, A. P.Borg, A.Canal, B.Diffley, J. F.Drury, L. S.Harvey, R.Howell, M.Hussain, S.Kjaer, S.McCauley, J.McCoy, L.Milligan, J.Posse, V.Roustan, C.Ulferts, R.Weissmann, F.Wu, M.Zeng, J.2021-04-08doi:10.1101/2021.04.07.438808Cold Spring Harbor Laboratory Press2021-04-08
<![CDATA[
Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp12/7/8 RNA-dependent RNA Polymerase
]]>
https://biorxiv.org/cgi/content/short/2021.04.07.438807v1?rss=1"
Beale, R.Bertolin, A. P.Canal, B.Diffley, J. F.Drury, L. S.Howell, M.Milligan, J.Posse, V.Ulferts, R.Weissmann, F.Wu, M.Zeng, J.2021-04-08doi:10.1101/2021.04.07.438807Cold Spring Harbor Laboratory Press2021-04-08
<![CDATA[
Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of nsp5 Main Protease
]]>
https://biorxiv.org/cgi/content/short/2021.04.07.438806v1?rss=1"
Basier, C.Beale, R.Bineva-Todd, G.Canal, B.Curran, J. F.Deegan, T. D.Diffley, J. F.Fujisawa, R.Howell, M.Joshi, D.Labib, K.Lim, C. T.Milligan, J.Nagaraj, H.O'Reilly, N.Papageorgiou, G.Soudy, C.Tan, K. W.Ulferts, R.Weissmann, F.Wu, M.Zeisner, T. U.2021-04-08doi:10.1101/2021.04.07.438806Cold Spring Harbor Laboratory Press2021-04-08
<![CDATA[
Identification of SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of the nsp14 RNA Cap Methyltransferase
]]>
https://biorxiv.org/cgi/content/short/2021.04.07.438810v1?rss=1"
Basier, C.Basu, S.Beale, R.Canal, B.Cowling, V. H.Curran, J. F.Deegan, T. D.Diffley, J. F.Drury, L. S.Fujisawa, R.Howell, M.Labib, K.Lim, C. T.Mak, T.McClure, A. W.Roberts, E.Tan, K. W.Ulferts, R.Weissmann, F.Wu, M.Zeisner, T. U.2021-04-08doi:10.1101/2021.04.07.438810Cold Spring Harbor Laboratory Press2021-04-08
<![CDATA[
Image-based deep learning reveals the responses of human motor neurons to stress and ALS
]]>
https://biorxiv.org/cgi/content/short/2021.04.08.439054v1?rss=1"
Verzat, C.Harley, J.Patani, R.Luisier, R.2021-04-09doi:10.1101/2021.04.08.439054Cold Spring Harbor Laboratory Press2021-04-09
<![CDATA[
Rad53 checkpoint kinase regulation of DNA replication fork rate via Mrc1 phosphorylation
]]>
https://biorxiv.org/cgi/content/short/2021.04.09.439171v1?rss=1"
McClure, A. W.Diffley, J.2021-04-10doi:10.1101/2021.04.09.439171Cold Spring Harbor Laboratory Press2021-04-10
<![CDATA[
Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis
]]>
https://biorxiv.org/cgi/content/short/2021.04.09.439198v1?rss=1"
Pereira, C.Arroyo-Martinez, G. A.Guo, M. Z.Kelly, E. R.Grive, K. J.Mahadevaiah, S. K.Sims, J.Faca, V. M.Tsai, C.Schiltz, C. J.Wit, N.Jacobs, H.Clark, N. L.Freire, R.Turner, J.Lyndaker, A. M.Brieno-Enriquez, M. A.Cohen, P. E.Smolka, M. B.Weiss, R. S.2021-04-10doi:10.1101/2021.04.09.439198Cold Spring Harbor Laboratory Press2021-04-10
<![CDATA[
Single cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human specific features
]]>
https://biorxiv.org/cgi/content/short/2021.04.12.439474v1?rss=1"
Rayon, T.Maizels, R. J.Barrington, C.Briscoe, J.2021-04-12doi:10.1101/2021.04.12.439474Cold Spring Harbor Laboratory Press2021-04-12
<![CDATA[
Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast
]]>
https://biorxiv.org/cgi/content/short/2021.04.14.437846v1?rss=1"
Kalita, R.Flanagan, W.Lightley, J.Kumar, S.Alexandrov, Y.Garcia, E.Hintze, M.Barkoulas, M.Dunsby, C.French, P. M. W.2021-04-14doi:10.1101/2021.04.14.437846Cold Spring Harbor Laboratory Press2021-04-14
<![CDATA[
A suite of activity-based probes to dissect the KLK activome in drug-resistant prostate cancer
]]>
https://biorxiv.org/cgi/content/short/2021.04.15.439906v1?rss=1"
Lovell, S.Zhang, L.Kryza, T.Neodo, A.Bock, N.Williams, E. D.Engelsberger, E.Xu, C.Bakker, A. T.De Vita, E.Maneiro, M.Tanaka, R. J.Bevan, C. L.Clements, J. A.Tate, E. W.2021-04-15doi:10.1101/2021.04.15.439906Cold Spring Harbor Laboratory Press2021-04-15
<![CDATA[
A gene regulatory network for neural induction
]]>
https://biorxiv.org/cgi/content/short/2021.04.16.440164v1?rss=1"
Trevers, K. E.Lu, H.-C.Yang, Y.Thiery, A.Strobl, A. C.Palinkasova, B.de Oliveira, N. M. M.de Almeida, I. M.Khan, M. A. F.Moncaut, N.Luscombe, N. M.Dale, L.Streit, A.Stern, C. D.2021-04-16doi:10.1101/2021.04.16.440164Cold Spring Harbor Laboratory Press2021-04-16
<![CDATA[
Developmental regulation of neuronal gene expression by Elongator complex protein 1 dosage.
]]>
https://biorxiv.org/cgi/content/short/2021.04.16.440179v1?rss=1"
Morini, E.Gao, D.Logan, E. M.Salani, M.Krauson, A. J.Chekuri, A.Chen, Y.-T.Ragavendran, A.Chakravarty, P.Erdin, S.Stortchevoi, A.Svejstrup, J. Q.Talkowski, M. E.Slaugenhaupt, S. A.2021-04-16doi:10.1101/2021.04.16.440179Cold Spring Harbor Laboratory Press2021-04-16
<![CDATA[
Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture
]]>
https://biorxiv.org/cgi/content/short/2021.04.19.440412v1?rss=1"
Alvarez, E. G.Demeulemeester, J.Jolly, C.Garcia-Souto, D.Otero, P.Pequeno, A.Zamora, J.Tojo, M.Temes, J.Baez-Ortega, A.Rodriguez-Martin, B.Li, Y.Oitaben, A.Bruzos, A. L.Martinez-Fernandez, M.Haase, K.Santamarina, M.Zumalave, S.Abal, R.Rodriguez-Castro, J.Rodriguez-Casanova, A.Diaz-Lagares, A.Raine, K.Butler, A. P.Ono, A.Aikata, H.Chayama, K.Ueno, M.Hayami, S.Yamaue, H.Blanco, M. G.Forns, X.Rivas, C.Perez-del-Pulgar, S.Torres-Ruiz, R.Rodriguez Perales, S.Garaigorta, U.Nakagawa, H.Campbell, P. J.Van Loo, P.Tubio, J.2021-04-19doi:10.1101/2021.04.19.440412Cold Spring Harbor Laboratory Press2021-04-19
<![CDATA[
Early immune pressure imposed by tissue resident memory T cells sculpts tumour evolution in non-small cell lung cancer
]]>
https://biorxiv.org/cgi/content/short/2021.04.20.440373v1?rss=1"
Weeden, C. E.Gayevskiy, V.Trussart, M.Marceaux, C.Tubau Ribera, N.Batey, D.Teh, C. E.Mitchell, A. J.Antippa, P.Leong, T.Steinfort, D.Irving, L.Gordon, C. L.Swanton, C.Speed, T. P.Gray, D. H.Asselin-Labat, M.-L.2021-04-21doi:10.1101/2021.04.20.440373Cold Spring Harbor Laboratory Press2021-04-21
<![CDATA[
A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines
]]>
https://biorxiv.org/cgi/content/short/2021.04.21.440736v1?rss=1"
Chen, Y.Davidson, N.Wan, Y. K.Patel, H.Yao, F.Low, H. M.Hendra, C.Watten, L.Sim, A.Sawyer, C.Iakovleva, V.Lee, P. L.Xin, L.Ng, H. E. V.Loo, J. M.Ong, X.Ng, H. Q. A.Wang, J.Koh, W. Q. C.Poon, S. Y. P.Stanojevic, D.Tran, H.-D.Lim, K. H. E.Toh, S. Y.Ewels, P.Ng, H.-H.Iyer, N. G.Thiery, A.Chng, W. J.Chen, L.DasGupta, R.Sikic, M.Chan, Y.-S.Tan, B. O. P.Wan, Y.Tam, W. L.Yu, Q.Khor, C. C.Wuestefeld, T.Pratanwanich, P. N.Love, M. I.Goh, W. S. S.Ng, S.Oshlack, A.Goeke, J.2021-04-22doi:10.1101/2021.04.21.440736Cold Spring Harbor Laboratory Press2021-04-22
<![CDATA[
Molecular reconstruction of recurrent evolutionary switching in olfactory receptor specificity
]]>
https://biorxiv.org/cgi/content/short/2021.04.23.440888v1?rss=1"
Prieto-Godino, L. L.Schmidt, H. R.Benton, R.2021-04-23doi:10.1101/2021.04.23.440888Cold Spring Harbor Laboratory Press2021-04-23
<![CDATA[
Sox8 is sufficient to reprogram ectoderm into ear vesicles and associated neurons
]]>
https://biorxiv.org/cgi/content/short/2021.04.20.440617v1?rss=1"
Buzzi, A. L.Chen, J.Thiery, A.Delile, J.Streit, A.2021-04-20doi:10.1101/2021.04.20.440617Cold Spring Harbor Laboratory Press2021-04-20
<![CDATA[
Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells
]]>
https://biorxiv.org/cgi/content/short/2021.04.30.442156v1?rss=1"
Karabag, C.Jones, M. L.Reyes-Aldasoro, C. C.2021-04-30doi:10.1101/2021.04.30.442156Cold Spring Harbor Laboratory Press2021-04-30
<![CDATA[
Signatures of copy number alterations in human cancer
]]>
https://biorxiv.org/cgi/content/short/2021.04.30.441940v1?rss=1"
Steele, C. D.Abbasi, A.Islam, A. S. M.Khandekar, A.Haase, K.Hames, S.Tarabichi, M.Lesluyes, T.Flanagan, A. M.Mertens, F.Van Loo, P.Alexandrov, L. B.Pillay, N.2021-04-30doi:10.1101/2021.04.30.441940Cold Spring Harbor Laboratory Press2021-04-30
<![CDATA[
Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria
]]>
https://biorxiv.org/cgi/content/short/2021.05.01.442251v1?rss=1"
Barr, D. A.Omollo, C. O.Mason, M.Koch, A.Wilkinson, R. J.Lalloo, D. G.Meintjes, G.Mizrahi, V.Warner, D. F.Davies, G. R.2021-05-01doi:10.1101/2021.05.01.442251Cold Spring Harbor Laboratory Press2021-05-01
<![CDATA[
Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2
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https://biorxiv.org/cgi/content/short/2021.05.07.443085v1?rss=1"
Kanagaraj, R.Mitter, R.Kantidakis, T.Edwards, M.Benitez, A.Chakravarty, P.Fu, B.Becherel, O.Yang, F.Lavin, M.Koren, A.Stewart, A.West, S.2021-05-08doi:10.1101/2021.05.07.443085Cold Spring Harbor Laboratory Press2021-05-08
<![CDATA[
Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability
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https://biorxiv.org/cgi/content/short/2021.05.11.443558v1?rss=1"
Geijer, M.Zhou, D.Selvam, K.Steurer, B.Evers, B.Mukherjee, C.Cugusi, S.van Toorn, M.van der Woude, M.Gong, W.Janssens, R.Raams, A.Lebbink, J.Geverts, B.Plummer, D.Bezstarosti, K.Theil, A.Mitter, R.Houtsmuller, A.Vermeulen, W.Demmers, J.Li, S.Lans, H.Bernards, R.Svejstrup, J.Ray Chaudhuri, A.Wyrick, J.Marteijn, J.2021-05-11doi:10.1101/2021.05.11.443558Cold Spring Harbor Laboratory Press2021-05-11
<![CDATA[
The Aspartyl Protease Ddi1 Is Essential for Erythrocyte Invasion by the Malaria Parasite
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https://biorxiv.org/cgi/content/short/2021.05.11.443575v1?rss=1"
Ridewood, S.Dirac-Svejstrup, B.Howell, S. A.Weston, A.Lehmann, C.Patel, A. P.Collinson, L.Bingham, R.Powell, D.Snijder, A.Svejstrup, J. Q.Deu, E.2021-05-11doi:10.1101/2021.05.11.443575Cold Spring Harbor Laboratory Press2021-05-11
<![CDATA[
SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease
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https://biorxiv.org/cgi/content/short/2021.05.12.443934v1?rss=1"
Tapia del Fierro, A.den Hamer, B.Jansz, N.Chen, K.Beck, T.Vanyai, H.Benetti, N.Gurzau, A. D.Daxinger, L.Xue, S.Nguyen Ly, T. T.Wanigasuriya, I.Breslin, K.Oey, H.Krom, Y.van der Hoorn, D.Bouwman, L. F.Ritchie, M. E.Reversade, B.Prin, F.Mohun, T.van der Maarel, S. M.McGlinn, E.Murphy, J. M.Keniry, A.de Greef, J. C.Blewitt, M. E.2021-05-13doi:10.1101/2021.05.12.443934Cold Spring Harbor Laboratory Press2021-05-13
<![CDATA[
Automatic instance segmentation of mitochondria in electron microscopy data
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https://biorxiv.org/cgi/content/short/2021.05.24.444785v1?rss=1"
Nightingale, L.de Folter, J.Spiers, H.Strange, A.Collinson, L. M.Jones, M. L.2021-05-24doi:10.1101/2021.05.24.444785Cold Spring Harbor Laboratory Press2021-05-24
<![CDATA[
Location and function of all Plasmodium kinesins: key roles in parasite proliferation, polarity, and transmission
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https://biorxiv.org/cgi/content/short/2021.05.26.445751v1?rss=1"
Zeeshan, M.Rashpa, R.Ferguson, D. J. P.Abel, S.Chahine, Z.Brady, D.Moores, C. A.Le Roch, K. G.Brochet, M.Holder, A. A.Tewari, R.2021-05-27doi:10.1101/2021.05.26.445751Cold Spring Harbor Laboratory Press2021-05-27
<![CDATA[
Notch controls the cell cycle to define leader versus follower identities during collective cell migration.
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https://biorxiv.org/cgi/content/short/2021.05.27.445572v1?rss=1"
Alhashem, Z.Feldner-Busztin, D.Revell, C.Alvarez-Garcillan Portillo, M.Richardson, J.Rocha, M.Gauert, A.Corbeaux, T.Prince, V. E.Bentley, K.Linker, C.2021-05-27doi:10.1101/2021.05.27.445572Cold Spring Harbor Laboratory Press2021-05-27
<![CDATA[
Cell-autonomous generation of the wave pattern within the vertebrate segmentation clock
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https://biorxiv.org/cgi/content/short/2021.05.29.446196v1?rss=1"
Rohde, L. A.Bercowsky-Rama, A.Negrete, J.Valentin, G.Naganathan, S. R.Desai, R. A.Strnad, P.Soroldoni, D.Julicher, F.Oates, A. C.2021-05-30doi:10.1101/2021.05.29.446196Cold Spring Harbor Laboratory Press2021-05-30
<![CDATA[
Eosinophils are an integral component of the pulmonary granulocyte response in Tuberculosis and promote host resistance in mice
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https://biorxiv.org/cgi/content/short/2021.05.29.446277v1?rss=1"
Bohrer, A. C.Castro, E.Hu, Z.Queiroz, A. T. L.Tocheny, C. E.Assmann, M.Sakai, S.Nelson, C.Baker, P. J.Ma, H.Wang, L.Zilu, W.du Bruyn, E.Riou, C.Kauffman, K. D.Tuberculosis Imaging Program,Moore, I. N.Del Nonno, F.Petrone, L.Goletti, D.Martineau, A. R. R.Lowe, D. M.Cronan, M. R.Wilkinson, R. J.Barry, C. E.Via, L. E.Barber, D. L.Klion, A. D.Andrade, B. B.Song, Y.Wong, K.-W.Mayer-Barber, K. D.2021-05-31doi:10.1101/2021.05.29.446277Cold Spring Harbor Laboratory Press2021-05-31
<![CDATA[
Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers
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https://biorxiv.org/cgi/content/short/2021.06.11.447968v1?rss=1"
Lange, J. T.Chen, C. Y.Pichugin, Y.Xie, F.Tang, J.Hung, K. L.Yost, K. E.Shi, Q.Erb, M. L.Rajkumar, U.Wu, S.Swanton, C.Liu, Z.Huang, W.Chang, H. Y.Bafna, V.Henssen, A. G.Werner, B.Mischel, P. S.2021-06-11doi:10.1101/2021.06.11.447968Cold Spring Harbor Laboratory Press2021-06-11
<![CDATA[
Early mismatch between cancer cells and their tumour microenvironment blocks long term growth
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https://biorxiv.org/cgi/content/short/2021.06.15.448466v1?rss=1"
Perdrix Rosell, A.Maiques, O.Chakravarty, P.Ombrato, L.Sanz-Moreno, V.Malanchi, I.2021-06-15doi:10.1101/2021.06.15.448466Cold Spring Harbor Laboratory Press2021-06-15
<![CDATA[
Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome
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https://biorxiv.org/cgi/content/short/2021.06.18.448936v1?rss=1"
Bacic, L.Gaullier, G.Sabantsev, A.Lehmann, L.Brackmann, K.Dimakou, D.Halic, M.Hewitt, G.Boulton, S. J.Deindl, S.2021-06-18doi:10.1101/2021.06.18.448936Cold Spring Harbor Laboratory Press2021-06-18
<![CDATA[
CDK1 controls CHMP7-dependent nuclear envelope reformation
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https://biorxiv.org/cgi/content/short/2020.04.20.050674v1?rss=1"
Gatta, A. T.Olmos, Y.Stoten, C. L.Carlton, J. G.2020-04-21doi:10.1101/2020.04.20.050674Cold Spring Harbor Laboratory Press2020-04-21
<![CDATA[
LAP1 regulates nuclear plasticity to enable constrained migration
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https://biorxiv.org/cgi/content/short/2021.06.23.449503v1?rss=1"
Jung Garcia, Y.Maiques, O.Rodriguez-Hernandez, I.Fanshawe, B.Domart, M.-C.Renshaw, M. J.Marti, R. M.Matias-Guiu, X.Collinson, L.Sanz-Moreno, V.Carlton, J. G.2021-06-23doi:10.1101/2021.06.23.449503Cold Spring Harbor Laboratory Press2021-06-23
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Sparse connectivity for MAP inference in linear models using sister mitral cells
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https://biorxiv.org/cgi/content/short/2021.06.28.450144v1?rss=1"
Tootoonian, S.Schaefer, A. T.Latham, P. E.2021-06-28doi:10.1101/2021.06.28.450144Cold Spring Harbor Laboratory Press2021-06-28
<![CDATA[
Global analysis of putative phospholipases in the malaria parasite Plasmodium falciparum reveals critical factors for parasite proliferation
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https://biorxiv.org/cgi/content/short/2021.06.28.450158v1?rss=1"
Burda, P.-C.Ramaprasad, A.Pietsch, E.Bielfeld, S.Söhnchen, C.Wilcke, L.Strauss, J.Schwudke, D.Sait, A.Collinson, L. M.Blackman, M. J.Gilberger, T.-W.2021-06-28doi:10.1101/2021.06.28.450158Cold Spring Harbor Laboratory Press2021-06-28
<![CDATA[
Exploitation of the Secretory Pathway by SARS-CoV-2 Envelope
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https://biorxiv.org/cgi/content/short/2021.06.30.450614v1?rss=1"
Pearson, G. J.Broncel, M.Snijders, A. P.Carlton, J. G.2021-06-30doi:10.1101/2021.06.30.450614Cold Spring Harbor Laboratory Press2021-06-30
<![CDATA[
Functional profiling of long intergenic non-coding RNAs in fission yeast
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https://biorxiv.org/cgi/content/short/2021.06.30.450572v1?rss=1"
Rodriguez-Lopez, M.Anver, S.Cotobal, C.Kamrad, S.Malecki, M.Correia-Melo, C.Hoti, M.Townsend, S.Marguerat, S. B.Pong, S.Wu, M.Montemayor, L.Howell, M.Ralser, M.Bahler, J.2021-07-01doi:10.1101/2021.06.30.450572Cold Spring Harbor Laboratory Press2021-07-01
<![CDATA[
Isoform resolved measurements of absolute translational efficiency define interplay of HIF and mTOR dysregulation in kidney cancer
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https://biorxiv.org/cgi/content/short/2021.07.06.451052v1?rss=1"
Sugimoto, Y.Ratcliffe, P. J.2021-07-06doi:10.1101/2021.07.06.451052Cold Spring Harbor Laboratory Press2021-07-06
<![CDATA[
TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells
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https://biorxiv.org/cgi/content/short/2021.07.10.451887v1?rss=1"
Osnato, A.Brown, S.Krueger, C.Andrews, S.Collier, A. J.Nakanoh, S.Quiroga Londono, M.Wesley, B. T.Muraro, D.Brumm, S.Niakan, K.Vallier, L.Ortmann, D.Rugg-Gunn, P. J.2021-07-11doi:10.1101/2021.07.10.451887Cold Spring Harbor Laboratory Press2021-07-11
<![CDATA[
Immunogenicity and pre-clinical efficacy of an OMV-based SARS-CoV-2 vaccine
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https://biorxiv.org/cgi/content/short/2021.07.12.452027v1?rss=1"
Grandi, A.Tomasi, M.Accordini, S.Bertelli, C.Vanzo, T.Gagliardi, A.Caproni, E.Tamburini, S.Fantappie, L.Di Lascio, G.Bisoffi, Z.Piubelli, C.Valenti, M. T.Dalle Carbonare, L.Zipeto, D.Rava, M.Fumagalli, V.Di Lucia, P.Marotta, D.Sala, E.Iannacone, M.Cherepanov, P.Bolognesi, M.Pizzato, M.Grandi, G.2021-07-13doi:10.1101/2021.07.12.452027Cold Spring Harbor Laboratory Press2021-07-13
<![CDATA[
Suppressed eusocial reproduction supports evolutionary convergence over co-option
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https://biorxiv.org/cgi/content/short/2021.07.11.451940v1?rss=1"
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org.highwire.dtl.DTLVardef@117ad33org.highwire.dtl.DTLVardef@16bf4f5org.highwire.dtl.DTLVardef@9f215aorg.highwire.dtl.DTLVardef@146c0f5_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO C_FIG
]]>Velasque, M.Yongkai, T.Liu, A. W.Luscombe, N. M.Denton, J. A.2021-07-12doi:10.1101/2021.07.11.451940Cold Spring Harbor Laboratory Press2021-07-12
<![CDATA[
Ribocutter: Cas9-mediated rRNA depletion from multiplexed riboseq libraries
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https://biorxiv.org/cgi/content/short/2021.07.14.451473v1?rss=1"
Wilkins, O. G.Ule, J.2021-07-14doi:10.1101/2021.07.14.451473Cold Spring Harbor Laboratory Press2021-07-14
<![CDATA[
Flight-tone mediated circadian control of audibility in mating swarms of Anopheles mosquitoes
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https://biorxiv.org/cgi/content/short/2021.07.12.452033v1?rss=1"
Somers, J.Georgiades, M.Su, M. P.Bagi, J.Andres, M.Mills, G.Ntabaliba, W.Moore, S. J.Spaccapelo, R.Albert, J. T.2021-07-12doi:10.1101/2021.07.12.452033Cold Spring Harbor Laboratory Press2021-07-12
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TAF4b transcription networks regulating early oocyte differentiation
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https://biorxiv.org/cgi/content/short/2021.07.18.452838v1?rss=1"
Gura, M. A.Relovska, S.Abt, K. M.Seymour, K. A.Wu, T.Kaya, H.Turner, J.Fazzio, T. G.Freiman, R. N.2021-07-18doi:10.1101/2021.07.18.452838Cold Spring Harbor Laboratory Press2021-07-18
<![CDATA[
Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling
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https://biorxiv.org/cgi/content/short/2021.07.20.453046v1?rss=1"
Gameiro, P. A.Encheva, V.Silva dos Santos, M.MacRae, J. I.Ule, J.2021-07-20doi:10.1101/2021.07.20.453046Cold Spring Harbor Laboratory Press2021-07-20
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Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy
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https://biorxiv.org/cgi/content/short/2021.07.25.453647v1?rss=1"
Peripolli, S.Singh, T.Patel, H.Meneguello, L.Kiso, K.Thorpe, P. H.Bertoli, C.de Bruin, R. A. M.2021-07-26doi:10.1101/2021.07.25.453647Cold Spring Harbor Laboratory Press2021-07-26
<![CDATA[
Cell-specific Bioorthogonal Tagging of Glycoproteins in Co-culture
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https://biorxiv.org/cgi/content/short/2021.07.28.454135v1?rss=1"
Cioce, A.Calle, B.Marchesi, A.Bineva-Todd, G.Flynn, H.Li, Z.Tastan, O. Y.Roustan, C.Keenan, T.Both, P.Huang, K.Parmeggiani, F.Snijders, A. P.Kjaer, S.Fascione, M. A.Flitsch, S. L.Schumann, B.2021-07-28doi:10.1101/2021.07.28.454135Cold Spring Harbor Laboratory Press2021-07-28
<![CDATA[
SIGNR1 promotes immune dysfunction in systemic candidiasis by modulating neutrophil lifespan via T cell-derived histones and G-CSF
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https://biorxiv.org/cgi/content/short/2021.08.09.455510v1?rss=1"
Ioannou, M.Hoving, D.Aramburu, I. V.De Vasconcelos, N. M.Temkin, M. I.Wang, Q.Vernardis, S.Demichev, V.Tsourouktsoglou, T.-D.Boeing, S.Goldstone, R.David, S.Klaus Stahl, K.Bode, C.Ralser, M.Papagiannopoulos, V.2021-08-09doi:10.1101/2021.08.09.455510Cold Spring Harbor Laboratory Press2021-08-09
<![CDATA[
Structural transitions in the GTP cap visualized by cryo-EM of catalytically inactive microtubules
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https://biorxiv.org/cgi/content/short/2021.08.13.456308v1?rss=1"
LaFrance, B. J.Roostalu, J.Henkin, G.Greber, B. J.Zhang, R.Normanno, D.McCollum, C.Surrey, T.Nogales, E.2021-08-13doi:10.1101/2021.08.13.456308Cold Spring Harbor Laboratory Press2021-08-13
<![CDATA[
Autophagy coordinates chondrocyte development and early joint formation in zebrafish
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https://biorxiv.org/cgi/content/short/2021.08.13.456237v1?rss=1"
Moss, J. J.Wirth, M.Tooze, S. A.Lane, J. D.Hammond, C. L.2021-08-13doi:10.1101/2021.08.13.456237Cold Spring Harbor Laboratory Press2021-08-13
<![CDATA[
RSC-mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription
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https://biorxiv.org/cgi/content/short/2021.08.16.456464v1?rss=1"
Wu, A.Vivori, C.Patel, H.Sideri, T.van Werven, F.2021-08-16doi:10.1101/2021.08.16.456464Cold Spring Harbor Laboratory Press2021-08-16
<![CDATA[
Direct reprogramming of human embryonic to trophoblast stem cells
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https://biorxiv.org/cgi/content/short/2021.08.18.456785v1?rss=1"
Fogarty, N. M.Abdelbaki, A.McCarthy, A.Devito, L.Chen, A. E.Munusamy, P.Blakeley, P.Elder, K.Snell, P.Christie, L.Serhal, P.Odia, R. A.Sangrithi, M.Niakan, K. K.2021-08-18doi:10.1101/2021.08.18.456785Cold Spring Harbor Laboratory Press2021-08-18
<![CDATA[
Toxoplasma-proximal and distal control by GBPs in human macrophages
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https://biorxiv.org/cgi/content/short/2021.08.24.457560v1?rss=1"
Fisch, D.Clough, B.Khan, R. T.Healy, L.Frickel, E.2021-08-24doi:10.1101/2021.08.24.457560Cold Spring Harbor Laboratory Press2021-08-24
<![CDATA[
An improved iCLIP protocol
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https://biorxiv.org/cgi/content/short/2021.08.27.457890v1?rss=1"
Lee, F. C. Y.Chakrabarti, A. M.Hänel, H.Monzon-Casanova, E.Hallegger, M.Militti, C.Capraro, F.Sadee, C.Toolan-Kerr, P.Wilkins, O.Turner, M.König, J.Sibley, C.Ule, J.2021-08-27doi:10.1101/2021.08.27.457890Cold Spring Harbor Laboratory Press2021-08-27
<![CDATA[
Comparative assessment of genes driving cancer and somatic evolution.
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https://biorxiv.org/cgi/content/short/2021.08.31.458177v1?rss=1"
Dressler, L.Bortolomeazzi, M.Keddar, M. R.Misetic, H.Sartini, G.Acha-Sagredo, A.Montorsi, L.Wijewardhane, N.Repana, D.Nulsen, J.Goldman, J.Pollit, M.Davis, P.Strange, A.Ambrose, K.Ciccarelli, F. D.2021-08-31doi:10.1101/2021.08.31.458177Cold Spring Harbor Laboratory Press2021-08-31
<![CDATA[
Axonal length determines distinct homeostatic phenotypes in human iPSC derived motor neurons on a bioengineered platform
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https://biorxiv.org/cgi/content/short/2021.08.30.458271v1?rss=1"
Hagemann, C.Moreno Gonzalez, C.Guetta, L.Tyzak, G.Chiappini, C.Legati, A.Patani, R.Serio, A.2021-09-01doi:10.1101/2021.08.30.458271Cold Spring Harbor Laboratory Press2021-09-01
<![CDATA[
Bringing TrackMate in the era of machine-learning and deep-learning.
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https://biorxiv.org/cgi/content/short/2021.09.03.458852v1?rss=1"
Ershov, D.Phan, M.-S.Pylvänäinen, J. W.Rigaud, S. U.Le Blanc, L.Charles-Orszag, A.Conway, J. R. W.Laine, R. F.Roy, N. H.Bonazzi, D.Dumenil, G.Jacquemet, G.Tinevez, J.-Y.2021-09-03doi:10.1101/2021.09.03.458852Cold Spring Harbor Laboratory Press2021-09-03
<![CDATA[
B cell-intrinsic requirement for WNK1 kinase in T cell-dependent antibody responses
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https://biorxiv.org/cgi/content/short/2021.09.09.459588v1?rss=1"
Hayward, D.Vanes, L.Wissmann, S.Sivapatham, S.Hartweger, H.Biggs O'May, J.De Boer, L.Mitter, R.Kochl, R.Stein, J. V.Tybulewicz, V. L.2021-09-09doi:10.1101/2021.09.09.459588Cold Spring Harbor Laboratory Press2021-09-09
<![CDATA[
Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology
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https://biorxiv.org/cgi/content/short/2021.09.07.459264v1?rss=1"
Harris, M. A.Rutherford, K. M.Hayles, J.Lock, A.Bähler, J.Oliver, S. G.Mata, J.Wood, V.2021-09-10doi:10.1101/2021.09.07.459264Cold Spring Harbor Laboratory Press2021-09-10
<![CDATA[
clipplotr - a comparative visualisation and analysis tool for CLIP data
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https://biorxiv.org/cgi/content/short/2021.09.10.459763v1?rss=1"
Chakrabarti, A. M.Capitanchik, C.Ule, J.Luscombe, N.2021-09-11doi:10.1101/2021.09.10.459763Cold Spring Harbor Laboratory Press2021-09-11
<![CDATA[
Chromodomain protein regulates the expression of a subset of RIFINs in P. falciparum
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https://biorxiv.org/cgi/content/short/2021.09.13.460021v1?rss=1"
Sethumadhavan, D. V.Tiburcio, M.Kanyal, A.Jabeena, C.Govindaraju, G.Karmodiya, K.Rajavelu, A.2021-09-13doi:10.1101/2021.09.13.460021Cold Spring Harbor Laboratory Press2021-09-13
<![CDATA[
BashTheBug: a crowd of volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates.
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https://biorxiv.org/cgi/content/short/2021.07.20.453060v1?rss=1"
Fowler, P. W.Wright, C.Spiers-Bowers, H.Zhu, T.Baeten, E. M.Hoosdally, S. W.Gibertoni Cruz, A. L.Roohi, A.Kouchaki, S.Walker, T. M.Peto, T. E.Miller, G.Lintott, C.Clifton, D.Crook, D. W.Walker, A. S.The CRyPTIC Consortium,2021-07-21doi:10.1101/2021.07.20.453060Cold Spring Harbor Laboratory Press2021-07-21
<![CDATA[
Comprehensive analysis of DNA replication timing in genetic diseases and gene knockouts identifies MCM10 as a novel regulator of the replication program
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https://biorxiv.org/cgi/content/short/2021.09.08.459433v1?rss=1"
Caballero, M.Ge, T.Rebelo, A. R.Seo, S.Kim, S.Brooks, K.Zuccaro, M. L.Kanagaraj, R.Vershkov, D.Kim, D.Smogorzewska, A.Smolka, M. B.Benvenisty, N.West, S. C.Egli, D. C.Mace, E. M.Koren, A.2021-09-09doi:10.1101/2021.09.08.459433Cold Spring Harbor Laboratory Press2021-09-09
<![CDATA[
Cdc6 is sequentially regulated by PP2A-Cdc55, Cdc14 and Sic1 for origin licensing in S. cerevisiae
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https://biorxiv.org/cgi/content/short/2021.09.14.460335v1?rss=1"
Philip, J.Ord, M.Silva, A.Singh, S.Diffley, J. F. X.Remus, D.Loog, M.Ikui, A. E.2021-09-15doi:10.1101/2021.09.14.460335Cold Spring Harbor Laboratory Press2021-09-15
<![CDATA[
Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes
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https://biorxiv.org/cgi/content/short/2021.09.14.460272v1?rss=1"
Earle, S. G.Wilson, D. J.The CRyPTIC Consortium,2021-09-16doi:10.1101/2021.09.14.460272Cold Spring Harbor Laboratory Press2021-09-16
<![CDATA[
A data compendium of Mycobacterium tuberculosis antibiotic resistance
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https://biorxiv.org/cgi/content/short/2021.09.14.460274v1?rss=1"
Brankin, A.Malone, K. M.The CRyPTIC Consortium,2021-09-15doi:10.1101/2021.09.14.460274Cold Spring Harbor Laboratory Press2021-09-15
<![CDATA[
A generalisable approach to drug susceptibility prediction for M. Tuberculosis using machine learning and whole-genome sequencing
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https://biorxiv.org/cgi/content/short/2021.09.14.458035v1?rss=1"
The CRyPTIC consortium,Lachapelle, A. S.2021-09-16doi:10.1101/2021.09.14.458035Cold Spring Harbor Laboratory Press2021-09-16
<![CDATA[
The master energy homeostasis regulator PGC-1alpha couples transcriptional co-activation and mRNA nuclear export
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https://biorxiv.org/cgi/content/short/2021.09.19.460961v1?rss=1"
Mihaylov, S. R.Castelli, L. M.Lin, Y.-H.Gul, A.Soni, N.Hastings, C.Flynn, H. R.Dickman, M. J.Snijders, A. P.Bandmann, O.Mortiboys, H.Ultanir, S. K.Hautbergue, G. M.2021-09-19doi:10.1101/2021.09.19.460961Cold Spring Harbor Laboratory Press2021-09-19
<![CDATA[
RNA polymerase II dynamics and mRNA stability feedback determine mRNA scaling with cell size
]]>
https://biorxiv.org/cgi/content/short/2021.09.20.461005v1?rss=1"
Swaffer, M. P.Marinov, G. K.Zheng, H.Jones, A. W.Kundaje, A.Snijders, A. P.Greenleaf, W. J.Reyes-Lamothe, R.Skotheim, J. M.2021-09-20doi:10.1101/2021.09.20.461005Cold Spring Harbor Laboratory Press2021-09-20
<![CDATA[
Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach
]]>
https://biorxiv.org/cgi/content/short/2021.09.14.460353v1?rss=1"
CRyPTIC Consortium,Carter, J. J.2021-09-16doi:10.1101/2021.09.14.460353Cold Spring Harbor Laboratory Press2021-09-16
<![CDATA[
JaponicusDB: Rapid deployment of a model organism database for an emerging model species
]]>
https://biorxiv.org/cgi/content/short/2021.09.23.461587v1?rss=1"
Rutherford, K. M.Harris, M. A.Oliferenko, S.Wood, V.2021-09-24doi:10.1101/2021.09.23.461587Cold Spring Harbor Laboratory Press2021-09-24
<![CDATA[
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
]]>
https://biorxiv.org/cgi/content/short/2021.09.15.460475v1?rss=1"
Hunt, M.Letcher, B.Malone, K. M.Nguyen, G.Hall, M. B.Colquhoun, R. M.Lima, L.Schatz, M.Ramakrishnan, S.The CRyPTIC Consortium,Iqbal, Z.2021-09-15doi:10.1101/2021.09.15.460475Cold Spring Harbor Laboratory Press2021-09-15
<![CDATA[
The Relative Binding Position of Nck and Grb2 Adaptors Dramatically Impacts Actin-Based Motility of Vaccinia Virus
]]>
https://biorxiv.org/cgi/content/short/2021.10.07.463509v1?rss=1"
Basant, A.Way, M.2021-10-08doi:10.1101/2021.10.07.463509Cold Spring Harbor Laboratory Press2021-10-08
<![CDATA[
Low dose pig anti-influenza virus monoclonal antibodies reduce lung pathology but do not prevent virus shedding
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https://biorxiv.org/cgi/content/short/2021.10.08.463636v1?rss=1"
Paudyal, B.McNee, A.Rijal, P.Carr, B. V.Nunez, A.McCauley, J. W.Daniels, R. S.Townsend, A. R.Hammond, J. A.Tchilian, E.2021-10-08doi:10.1101/2021.10.08.463636Cold Spring Harbor Laboratory Press2021-10-08
<![CDATA[
Single-Shot Optical Projection tomography for high-speed volumetric imaging
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https://biorxiv.org/cgi/content/short/2021.10.15.464407v1?rss=1"
Darling, C. J.Davis, S. P. X.Kumar, S.French, P. M. W.McGinty, J. A.2021-10-16doi:10.1101/2021.10.15.464407Cold Spring Harbor Laboratory Press2021-10-16
<![CDATA[
Therapeutic KRASG12C inhibition drives effective interferon-mediated anti-tumour immunity in immunogenic lung cancers
]]>
https://biorxiv.org/cgi/content/short/2021.10.18.464819v1?rss=1"
Mugarza, E.van Maldegem, F.Boumelha, J.Moore, C.Rana, S.Sopena, M. L.East, P.Ambler, R.Anastasiou, P.Clavijo, P. R.Valand, K.Cole, M.Molina-Arcas, M.Downward, J.2021-10-18doi:10.1101/2021.10.18.464819Cold Spring Harbor Laboratory Press2021-10-18
<![CDATA[
Combinatorial tumor suppressor inactivation efficiently initiates lung adenocarcinoma with therapeutic vulnerabilities
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https://biorxiv.org/cgi/content/short/2021.10.20.464849v1?rss=1"
Yousefi, M.Boross, G.Weiss, C.Murray, C. W.Hebert, J. D.Cai, H.Ashkin, E. L.Karmakar, S.Andrejka, L.Chen, L.Wang, M.Tsai, M. K.Lin, W.-Y.Li, C.Yakhchalian, P.Colon, C. I.Chew, S.-K.Chu, P.Swanton, C.Kunder, C. A.Petrov, D. A.Winslow, M. M.2021-10-21doi:10.1101/2021.10.20.464849Cold Spring Harbor Laboratory Press2021-10-21
<![CDATA[
In-vitro cellular reprogramming to model gonad development and its disorders
]]>
https://biorxiv.org/cgi/content/short/2021.10.22.465384v1?rss=1"
Gonen, N.Eozenou, C.Mitter, R.Bernardo, A.Chervova, A.Frachon, E.Commere, P.-H.Mazen, I.Gobaa, S.McElreavey, K.Lovell-Badge, R.Bashamboo, A.2021-10-24doi:10.1101/2021.10.22.465384Cold Spring Harbor Laboratory Press2021-10-24
<![CDATA[
ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari
]]>
https://biorxiv.org/cgi/content/short/2021.10.24.465596v1?rss=1"
D'Antuono, R.Pisignano, G.2021-10-24doi:10.1101/2021.10.24.465596Cold Spring Harbor Laboratory Press2021-10-24
<![CDATA[
The proteasome regulator PSME4 drives immune evasion and abrogates anti-tumor immunity in NSCLC
]]>
https://biorxiv.org/cgi/content/short/2021.10.24.464690v1?rss=1"
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org.highwire.dtl.DTLVardef@e87910org.highwire.dtl.DTLVardef@641843org.highwire.dtl.DTLVardef@175092corg.highwire.dtl.DTLVardef@ad34c2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMapping the degradation landscape in Non-Small Cell Lung Cancer (NSCLC) uncovers altered proteasome activity and composition
C_LIO_LIProteasome regulator PSME4 plays an anti-inflammatory role in NSCLC by attenuating immunoproteasome activity
C_LIO_LIPSME4 restricts tumor antigen presentation and cytokine secretion, defining a cold tumor environment
C_LIO_LIPSME4 drives tumor immune evasion and is associated with resistance to immunotherapy
C_LI
]]>Javitt, A.Shmueli, M. D.Kramer, M. P.Kolodziejczyk, A. A.Cohen, I. J.Kamer, I.Litchfield, K.Bab-Dinitz, E.Zadok, O.Neiens, V.Ulman, A.Radomir, L.Wolf-Levy, H.Eisenberg-Lerner, A.Kacen, A.Alon, M.Toste Rego, A.Stacher-Priehse, E.Linder, M.Koch, I.Bar, J.Swanton, C.Samuels, Y.Levin, Y.C. A. da Fonseca, P.Elinav, E.Friedman, N.Meiners, S.Merbl, Y.2021-10-24doi:10.1101/2021.10.24.464690Cold Spring Harbor Laboratory Press2021-10-24
<![CDATA[
RNA sensing via LGP2 is essential for the induction of a type I IFN response in ADAR1 deficiency
]]>
https://biorxiv.org/cgi/content/short/2021.10.27.465188v1?rss=1"
Stok, J. E.Oosenbrug, T.ter Haar, L. R.Gravekamp, D.Bromley, C. P.Zelenay, S.Reis e Sousa, C.van der Veen, A. G.2021-10-28doi:10.1101/2021.10.27.465188Cold Spring Harbor Laboratory Press2021-10-28
<![CDATA[
Chronumental: time tree estimation from very large phylogenies
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https://biorxiv.org/cgi/content/short/2021.10.27.465994v1?rss=1"
Sanderson, T.2021-10-28doi:10.1101/2021.10.27.465994Cold Spring Harbor Laboratory Press2021-10-28
<![CDATA[
N4BP1 is dimerization-dependent linear ubiquitin reader regulating TNFR1 signalling through linear ubiquitin binding and Caspase-8-mediated processing
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https://biorxiv.org/cgi/content/short/2021.11.02.466974v1?rss=1"
Kliza, K. W.Song, W.Pinzuti, I.Schaubeck, S.Kunzelmann, S.Kuntin, D.Fornili, A.Pandini, A.Hofmann, K.Garnett, J.Stieglitz, B.Husnjak, K.2021-11-02doi:10.1101/2021.11.02.466974Cold Spring Harbor Laboratory Press2021-11-02
<![CDATA[
DeepBacs: Bacterial image analysis using open-source deep learning approaches
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https://biorxiv.org/cgi/content/short/2021.11.03.467152v1?rss=1"
Spahn, C.Laine, R. F.Pereira, P. M.Gomez-de-Mariscal, E.von Chamier, L.Conduit, M.Pinho, M. G.Holden, S.Jacquemet, G.Heilemann, M.Henriques, R.2021-11-03doi:10.1101/2021.11.03.467152Cold Spring Harbor Laboratory Press2021-11-03
<![CDATA[
Increasing the throughput of sensitive proteomics by plexDIA
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https://biorxiv.org/cgi/content/short/2021.11.03.467007v1?rss=1"
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org.highwire.dtl.DTLVardef@144bba6org.highwire.dtl.DTLVardef@17bbf20org.highwire.dtl.DTLVardef@140f497org.highwire.dtl.DTLVardef@179faa9_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Derks, J.Leduc, A.Huffman, R. G.Specht, H.Ralser, M.Demichev, V.Slavov, N.2021-11-04doi:10.1101/2021.11.03.467007Cold Spring Harbor Laboratory Press2021-11-04
<![CDATA[
The molecular evolution of spermatogenesis across mammals
]]>
https://biorxiv.org/cgi/content/short/2021.11.08.467712v1?rss=1"
Murat, F.Mbengue, N.Winge, S. B.Trefzer, T.Leushkin, E.Sepp, M.Cardoso-Moreira, M.Schmidt, J.Schneider, C.Mössinger, K.Brüning, T.Lamanna, F.Belles, M. R.Conrad, C.Kondova, I.Bontrop, R.Behr, R.Khaitovich, P.Pääbo, S.Marques-Bonet, T.Grützner, F.Almstrup, K.Schierup, M. H.Kaessmann, H.2021-11-08doi:10.1101/2021.11.08.467712Cold Spring Harbor Laboratory Press2021-11-08
<![CDATA[
PHGDH is required for germinal center formation and is a therapeutic target in MYC-driven lymphoma
]]>
https://biorxiv.org/cgi/content/short/2021.11.11.468272v1?rss=1"
D'Avola, A.Legrave, N.Tajan, M.Chakravarty, P.Shearer, R.King, H.Cheung, E.Clear, A.Gunawan, A.Zhang, L.James, L.MacRae, J.Gribben, J.Calado, D.Vousden, K.Riches, J.2021-11-12doi:10.1101/2021.11.11.468272Cold Spring Harbor Laboratory Press2021-11-12
<![CDATA[
PPAR-delta acts as a metabolic master checkpoint for metastasis in pancreatic cancer
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https://biorxiv.org/cgi/content/short/2021.11.15.468579v1?rss=1"
Parejo-Alonso, B.Barneda, D.Trabulo, S. M.Courtois, S.Compte-Sancerni, S.Ruiz-Canas, L.Zheng, Q.Tang, J.Chen, M.Guo, Z.Schmitz, U.Irun, P.Penin-Peyta, L.Crusz, S. M.Cano-Galiano, A.Lopez-Escalona, S.Jagust, P.Espiau-Romera, P.Yuneva, M.Lin, M.-L.Lanas, A.Sainz, B.Heeschen, C.Sancho, P.2021-11-16doi:10.1101/2021.11.15.468579Cold Spring Harbor Laboratory Press2021-11-16
<![CDATA[
Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma
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https://biorxiv.org/cgi/content/short/2021.11.24.469674v1?rss=1"
Kato, T.Jenkins, R. P.Derzsi, S.Tozluoglu, M.Rullan, A.Hooper, S.Chaleil, R. A. G.Fu, X.Joyce, H.Thavaraj, S.Bates, P. A.Sahai, E.2021-11-24doi:10.1101/2021.11.24.469674Cold Spring Harbor Laboratory Press2021-11-24
<![CDATA[
A positive feedback loop mediates crosstalk between calcium, cyclic nucleotide and lipid signalling in Toxoplasma gondii
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https://biorxiv.org/cgi/content/short/2021.11.29.470317v1?rss=1"
Dominicus, C.Nofal, S. D.Broncel, M.Kastris, N. J.Flynn, H.Arrizabalaga, G.Botte, C. Y.Invergo, B. M.Treeck, M.2021-11-30doi:10.1101/2021.11.29.470317Cold Spring Harbor Laboratory Press2021-11-30
<![CDATA[
Broad human and animal coronavirus neutralisation by SARS-CoV-2 S2-targeted vaccination
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https://biorxiv.org/cgi/content/short/2021.11.30.470568v1?rss=1"
Ng, K.Faulkner, N.Finsterbusch, K.Wu, M.Harvey, R.Hussain, S.Greco, M.Liu, Y.Kjaer, S.Swanton, C.Gandhi, S.Beale, R.Gamblin, S.Cherepanov, P.Mccauley, J.Daniels, R.Howell, M.Arase, H.Wack, A.Bauer, D.Kassiotis, G.2021-12-01doi:10.1101/2021.11.30.470568Cold Spring Harbor Laboratory Press2021-12-01
<![CDATA[
Plasmodium SAS4/CPAP is a flagellum basal body component during male gametogenesis but is not essential for parasite transmission
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https://biorxiv.org/cgi/content/short/2021.12.03.471138v1?rss=1"
Zeeshan, M.Brady, D.Markus, R.Vaughan, S.Ferguson, D.Holder, A. A.Tewari, R.2021-12-03doi:10.1101/2021.12.03.471138Cold Spring Harbor Laboratory Press2021-12-03
<![CDATA[
Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP
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https://biorxiv.org/cgi/content/short/2021.12.07.471544v1?rss=1"
Kuret, K.Amalietti, A. G.Ule, J.2021-12-07doi:10.1101/2021.12.07.471544Cold Spring Harbor Laboratory Press2021-12-07
<![CDATA[
Fission of megamitochondria into multiple smaller well-defined mitochondria in the ageing zebrafish retina
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https://biorxiv.org/cgi/content/short/2021.12.09.471958v1?rss=1"
Burgoyne, T.Toms, M.Way, C.Tracey-White, D.Futter, C.Moosajee, M.2021-12-10doi:10.1101/2021.12.09.471958Cold Spring Harbor Laboratory Press2021-12-10
<![CDATA[
Visualizing pyrazinamide action by live single cell imaging of phagosome acidification and Mycobacterium tuberculosis pH homeostasis
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https://biorxiv.org/cgi/content/short/2021.12.20.473466v1?rss=1"
Santucci, P.Aylan, B.Botella, L.Bernard, E. M.Bussi, C.Pellegrino, E.Athanasiadi, N.Gutierrez, M. G.2021-12-20doi:10.1101/2021.12.20.473466Cold Spring Harbor Laboratory Press2021-12-20
<![CDATA[
Cellular development and evolution of the mammalian cerebellum
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https://biorxiv.org/cgi/content/short/2021.12.20.473443v1?rss=1"
Sepp, M.Leiss, K.Sarropoulos, I.Murat, F.Okonechnikov, K.Joshi, P.Leushkin, E.Mbengue, N.Schneider, C.Schmidt, J.Trost, N.Spaenig, L.Giere, P.Khaitovich, P.Lisgo, S.Palkovits, M.Kutscher, L. M.Anders, S.Cardoso-Moreira, M.Pfister, S. M.Kaessmann, H.2021-12-21doi:10.1101/2021.12.20.473443Cold Spring Harbor Laboratory Press2021-12-21
<![CDATA[
Study of an FBXO7 patient mutation reveals Fbxo7 and PI31 co-regulate proteasomes and mitochondria
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https://biorxiv.org/cgi/content/short/2021.12.22.473884v1?rss=1"
Al Rawi, S.Simpson, L.McDonald, N. Q.Chernuha, V.Elpeleg, O.Zeviani, M. Q.Barker, R. A.Spiegel, R.Laman, H.2021-12-23doi:10.1101/2021.12.22.473884Cold Spring Harbor Laboratory Press2021-12-23
<![CDATA[
Regulation of KHNYN antiviral activity by the extended di-KH domain and nucleo-cytoplasmic trafficking
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https://biorxiv.org/cgi/content/short/2021.12.22.473955v1?rss=1"
Lista, M. J.Galao, R. P.Ficarelli, M.Kmiec, D.Wilson, H.Winstone, H.Morris, E. R.Mischo, H. E.Wanford, J.Youle, R.Odendall, C.Taylor, I. A.Neil, S. J.Swanson, C.2021-12-24doi:10.1101/2021.12.22.473955Cold Spring Harbor Laboratory Press2021-12-24
<![CDATA[
Endosomal structure and APP biology are not altered in preclinical cellular models of Down syndrome
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https://biorxiv.org/cgi/content/short/2021.12.30.474570v1?rss=1"
Cannavo, C.Cleverley, K.Maduro, C.Mumford, P.Moulding, D.Fisher, E.Wiseman, F. K.2021-12-30doi:10.1101/2021.12.30.474570Cold Spring Harbor Laboratory Press2021-12-30
<![CDATA[
An RNA-binding switch drives ribosome biogenesis and tumorigenesis downstream of RAS oncogene
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https://biorxiv.org/cgi/content/short/2021.12.16.472890v1?rss=1"
Azman, M. S.Dodel, M.Capraro, F.Faraway, R.Dermit, M.Fan, W.Ule, J.Mardakheh, F. K.2021-12-16doi:10.1101/2021.12.16.472890Cold Spring Harbor Laboratory Press2021-12-16
<![CDATA[
Unraveling membrane properties at the organelle-level with LipidDyn
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https://biorxiv.org/cgi/content/short/2022.01.04.474788v1?rss=1"
Scrima, S.Tiberti, M.Campo, A.Corcelle-Termeau, E.Judith, D.Moller Foged, M.Bundgaard Clemmens, K. K.Tooze, S.Jäättelä, M.Maeda, K.Lambrughi, M.Papaleo, E.2022-01-05doi:10.1101/2022.01.04.474788Cold Spring Harbor Laboratory Press2022-01-05
<![CDATA[
Lactate regulation of activation in CD8+ T cells
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https://biorxiv.org/cgi/content/short/2021.12.14.472728v1?rss=1"
Barbieri, L.Velica, P.Gameiro, P. A.Cunha, P. P.Foskolou, I. P.Bargiela, D.Rundqvist, H.Johnson, R.2021-12-17doi:10.1101/2021.12.14.472728Cold Spring Harbor Laboratory Press2021-12-17
<![CDATA[
Interactions between influenza A virus nucleoprotein and gene segment UTRs facilitate selective modulation of viral gene expression
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https://biorxiv.org/cgi/content/short/2022.01.09.475567v1?rss=1"
Diefenbacher, M.Tan, T. J. C.Bauer, D. L. V.Stadtmueller, B.Wu, N. C.brooke, c.2022-01-09doi:10.1101/2022.01.09.475567Cold Spring Harbor Laboratory Press2022-01-09
<![CDATA[
Role of Yap1 in adult neural stem cell activation
]]>
https://biorxiv.org/cgi/content/short/2022.01.12.475985v1?rss=1"
Berninger, B.Fan, W.Jurado-Arjona, J.Alanis-Lobato, G.Peron, S.Berger, C.Andrade-Navarro, M. A.Falk, S.2022-01-13doi:10.1101/2022.01.12.475985Cold Spring Harbor Laboratory Press2022-01-13
<![CDATA[
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function
]]>
https://biorxiv.org/cgi/content/short/2022.01.14.476382v1?rss=1"
Martin, D. P.Lytras, S.Lucaci, A. G.Maier, W.Gruning, B.Shank, S. D.Weaver, S.MacLean, O. S.Orton, R. J.Lemey, P.Boni, M. F.Tegally, H.Harkins, G. W.Scheepers, C.Bhiman, J. N.Everatt, J.Amoako, D. G.San, J. E.Giandhari, J.Sigal, A.NGS-SA,Williamson, C.Hsiao, N.-y.von Gottberg, A.De Klerk, A.Shafer, R. W.Robertson, D. L.Wilkinson, R. J.Sewell, B. T.Lessells, R.Nekrutenko, A.Greaney, A. J.Starr, T. N.Bloom, J. D.Murrell, B.Wilkinson, E.Gupta, R. K.de Oliveira, T.Kosakovsky Pond, S. L.2022-01-18doi:10.1101/2022.01.14.476382Cold Spring Harbor Laboratory Press2022-01-18
<![CDATA[
CDC50 orthologues in Plasmodium falciparum have distinct roles in merozoite egress and trophozoite maturation
]]>
https://biorxiv.org/cgi/content/short/2022.01.18.476868v1?rss=1"
Patel, A.Nofal, S. D.Blackman, M.Baker, D. A.2022-01-20doi:10.1101/2022.01.18.476868Cold Spring Harbor Laboratory Press2022-01-20
<![CDATA[
Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring
]]>
https://biorxiv.org/cgi/content/short/2022.01.17.476508v1?rss=1"
Widman, A. J.Shah, M.Ogaard, N.Khamnei, C. C.Frydendahl, A.Deshpande, A.Arora, A.Zhang, M.Halmos, D.Bass, J.Langanay, T.Rajagopalan, S.Steinsnyder, Z.Liao, W.Rasmussen, M. H.Jensen, S. O.Nors, J.Therkildsen, C.Sotelo, J.Brand, R.Shah, R. H.Cheng, A. P.Maher, C.Spain, L.Krause, K.Frederick, D. T.Malbari, M. S.Marton, M.Manaa, D.Winterkorn, L.Callahan, M. K.Boland, G.Wolchok, J. D.Saxena, A.Turajlic, S.Imielinski, M.Berger, M. F.Altorki, N. K.Postow, M. A.Robine, N.Andersen, C. L.Landau, D. A.2022-01-20doi:10.1101/2022.01.17.476508Cold Spring Harbor Laboratory Press2022-01-20
<![CDATA[
SAIBR: A simple, platform-independent method for spectral autofluorescence correction
]]>
https://biorxiv.org/cgi/content/short/2022.01.19.476881v1?rss=1"
Rodrigues, N. T. L.Bland, T.Borrego-Pinto, J.Ng, K.Hirani, N.Gu, Y.Foo, S.Goehring, N. W.2022-01-20doi:10.1101/2022.01.19.476881Cold Spring Harbor Laboratory Press2022-01-20
<![CDATA[
m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast
]]>
https://biorxiv.org/cgi/content/short/2022.01.20.477035v1?rss=1"
Varier, R. A.Sideri, T.Capitanchik, C.Manova, Z.Calvani, E.Rossi, A.Edupuganti, R.Ensinck, I.Chan, V. W. C.Patel, H.Kirkpatrick, J.Faull, P.Snijders, A. P.Vermeulen, M.Ralser, M.Ule, J.Luscombe, N. M.van Werven, F.2022-01-21doi:10.1101/2022.01.20.477035Cold Spring Harbor Laboratory Press2022-01-21
<![CDATA[
Tissue-intrinsic γδ T cells critically regulate Tissue-Resident Memory CD8 T cells
]]>
https://biorxiv.org/cgi/content/short/2022.01.19.476598v1?rss=1"
Munoz-Ruiz, M.Llorian, M.D'Antuono, R.Pavlova, A.Mavrigiannaki, A. M.Mckenzie, D.Garcia-Cassani, B.Iannitto, M. L.Jandke, A.Ushakov, D.Adrian C. Hayday, A.2022-01-21doi:10.1101/2022.01.19.476598Cold Spring Harbor Laboratory Press2022-01-21
<![CDATA[
The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2
]]>
https://biorxiv.org/cgi/content/short/2022.01.25.477676v1?rss=1"
Domingo-Muelas, A.Morante-Redolat, J. M.Moncho-Amor, V.Jordan, A.Perez-Villalba, A.Carrillo-Barbera, P.Belenguer, G.Porlan, E.Kirstein, M.Bachs, O.Ferron, S. R.Lovell-Badge, R.Farinas, I.2022-01-25doi:10.1101/2022.01.25.477676Cold Spring Harbor Laboratory Press2022-01-25
<![CDATA[
ARPC5 Isoforms Drive Distinct Arp2/3-dependant Actin Remodeling Events in CD4 T Cells
]]>
https://biorxiv.org/cgi/content/short/2022.01.25.477674v1?rss=1"
Sadhu, L.Tsopoulidis, N.Laketa, V.Way, M.Fackler, O.2022-01-26doi:10.1101/2022.01.25.477674Cold Spring Harbor Laboratory Press2022-01-26
<![CDATA[
Transient RNA structures cause aberrant influenza virus replication and innate immune activation
]]>
https://biorxiv.org/cgi/content/short/2022.01.25.476955v1?rss=1"
French, H.Pitre, E.Oade, M. S.Elshina, E.Bisht, K.Jahun, A.King, A.Bauer, D. L. V.te Velthuis, A. J. W.2022-01-26doi:10.1101/2022.01.25.476955Cold Spring Harbor Laboratory Press2022-01-26
<![CDATA[
Yersinia pestis genomes reveal plague in Britain 4,000 years ago
]]>
https://biorxiv.org/cgi/content/short/2022.01.26.477195v1?rss=1"
Swali, P.Schutling, R.Gilardet, A.Kelly, M.Anastasiadou, K.Glocke, I.Audsley, T.Loe, L.Fernandez-Crespo, T.Ordono, J.Walker, D.Davy, T.Silva, M.Hajdinjak, M.Bergstrom, A.Booth, T.Skoglund, P.2022-01-26doi:10.1101/2022.01.26.477195Cold Spring Harbor Laboratory Press2022-01-26
<![CDATA[
Multivalent interactions essential for lentiviral integrase function
]]>
https://biorxiv.org/cgi/content/short/2022.01.26.477893v1?rss=1"
Ballandras-Colas, A.Chivukula, V.Gruszka, D. T.Shan, Z.Singh, P. K.Pye, V. E.McLean, R. K.Bedwell, G. J.Li, W.Nans, A.Cook, N. J.Fadel, H. J.Poeschla, E. M.Griffiths, D. J.Vargas, J.Taylor, I. A.Lyumkis, D.Yardimci, H.Engelman, A. N.Cherepanov, P.2022-01-27doi:10.1101/2022.01.26.477893Cold Spring Harbor Laboratory Press2022-01-27
<![CDATA[
SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export
]]>
https://biorxiv.org/cgi/content/short/2022.02.08.479664v1?rss=1"
Hall, R.Guedan, A.Yap, M. W.Young, G. R.Harvey, R.Stoye, J. P.Bishop, K. N.2022-02-09doi:10.1101/2022.02.08.479664Cold Spring Harbor Laboratory Press2022-02-09
<![CDATA[
Lem2 is essential for cardiac development by maintaining nuclear integrity
]]>
https://biorxiv.org/cgi/content/short/2022.02.10.477501v1?rss=1"
Ross, J.Arcos-Villacis, N.Battey, E.Boogerd, C.Marhuenda, E.Hodzic, D.Prin, F.Mohun, T.Catibog, N.Tapia, O.Gerace, L.Iskratsch, T.Shah, A.Stroud, M.2022-02-10doi:10.1101/2022.02.10.477501Cold Spring Harbor Laboratory Press2022-02-10
<![CDATA[
Spindle reorientation in response to mechanical stress is an emergent property of the spindle positioning mechanisms
]]>
https://biorxiv.org/cgi/content/short/2022.02.13.480269v1?rss=1"
Kelkar, M.Bohec, P.Smith, M.Sreenivasan, V.Lisica, A.Valon, L.Ferber, E.Baum, B.Salbreux, G.Charras, G.2022-02-14doi:10.1101/2022.02.13.480269Cold Spring Harbor Laboratory Press2022-02-14
<![CDATA[
A gradient border model for cell fate decisions at the neural plate border
]]>
https://biorxiv.org/cgi/content/short/2022.02.15.480567v1?rss=1"
Thiery, A.Buzzi, A. L.Hamrud, E.Cheshire, C.Luscombe, N.Briscoe, J.Streit, A.2022-02-16doi:10.1101/2022.02.15.480567Cold Spring Harbor Laboratory Press2022-02-16
<![CDATA[
Clonal behaviour of myogenic precursor cells throughout the vertebrate lifespan.
]]>
https://biorxiv.org/cgi/content/short/2022.02.17.480906v1?rss=1"
Hughes, S. M.Escaleira, R. C.Wanders, K.Koth, J.Wilkinson, D. G.Xu, Q.2022-02-18doi:10.1101/2022.02.17.480906Cold Spring Harbor Laboratory Press2022-02-18
<![CDATA[
Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using 2-photon, synchrotron X-ray and volume electron microscopy
]]>
https://biorxiv.org/cgi/content/short/2022.02.18.481045v1?rss=1"
Zhang, Y.Ackels, T.Pacureanu, A.Zdora, M.-C.Bonnin, A.Schaefer, A. T.Bosch, C.2022-02-20doi:10.1101/2022.02.18.481045Cold Spring Harbor Laboratory Press2022-02-20
<![CDATA[
Combining SLA 3D printing and soft lithography for fast, versatile, and accessible high-resolution fabrication of customised multiscale cell culture devices with complex designs
]]>
https://biorxiv.org/cgi/content/short/2022.02.22.481424v1?rss=1"
Hagemann, C.Bailey, M. C. D.Khokhar, N.Lionello, V. M.Suklai, P.Moreno-Gonzalez, C.O'Toole, K.Konstantinou, G.Giagnorio, E.Bergholt, M.Imbert, A.Tedesco, F. S.Serio, A.2022-02-23doi:10.1101/2022.02.22.481424Cold Spring Harbor Laboratory Press2022-02-23
<![CDATA[
Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan
]]>
https://biorxiv.org/cgi/content/short/2022.03.07.483228v1?rss=1"
Correia-Melo, C.Kamrad, S.Messner, C. B.Tengolics, R.Herrera-Dominguez, L.Townsend, S.Alam, M. T.Freiwald, A.Campbell, K.Aulakh, S.Szyrwiel, L.Yu, J. S. L.Zelezniak, A.Demichev, V.Muelleder, M.Papp, B.Ralser, M.2022-03-07doi:10.1101/2022.03.07.483228Cold Spring Harbor Laboratory Press2022-03-07
<![CDATA[
Diet suppresses tumour initiation by maintaining quiescence of mutation-bearing neural stem cells
]]>
https://biorxiv.org/cgi/content/short/2022.03.09.483611v1?rss=1"
Amodeo, V.Davies, T.Martinez-Segura, A.Clements, M.Simpson Ragdale, H.Bailey, A.Silva dos Santos, M.MacRae, J. I.Mokochinski, J.Kramer, H.Garcia-Diaz, C.Gould, A. P.Marguerat, S.Parrinello, S.2022-03-11doi:10.1101/2022.03.09.483611Cold Spring Harbor Laboratory Press2022-03-11
<![CDATA[
Hypoxia shapes the immune landscape in lung injury promoting inflammation persistence
]]>
https://biorxiv.org/cgi/content/short/2022.03.11.483935v1?rss=1"
Mirchandani, A. S.Jenkins, S. J.Bain, C. C.Lawson, H.Coelho, P.Murphy, F.Griffith, D.Zhang, A.Sanchez-Garcia, M. A.Reyes, L.Morrison, T.Arienti, S.Sadiku, P.Watts, E.Dickinson, R.Clark, S.Ly, T.Lewis, D.Kelly, V.Spanos, C.Musgrave, K.Delaney, L.Harper, I.Scott, J.Parkinson, N.Rostron, A.Baillie, J. K.Clohisey, S. M. R.Pridans, C.Campana, L.Starkey, P.Simpson, A. J.Dockrell, D.Schwarze, J.Hirani, N.Ratcliffe, P.Pugh, C.Kranc, K.Forbes, S.Whyte, M.Walmsley, S.2022-03-12doi:10.1101/2022.03.11.483935Cold Spring Harbor Laboratory Press2022-03-12
<![CDATA[
Genetic mapping of APP and amyloid-β biology modulation by trisomy 21
]]>
https://biorxiv.org/cgi/content/short/2022.03.10.483782v1?rss=1"
Mumford, P.Tosh, J.Anderle, S.Wikberg, E. G.Lau, G.Noy, S.Cleverley, K.Saito, T.Saido, T. C.Yu, E. Y.Brinkmalm, G.Portelius, E.Blennow, K.Zetterberg, H.Tybulewicz, V.Fisher, E.Wiseman, F. K.2022-03-12doi:10.1101/2022.03.10.483782Cold Spring Harbor Laboratory Press2022-03-12
<![CDATA[
Placental inflammation leads to abnormal embryonic heart development
]]>
https://biorxiv.org/cgi/content/short/2022.03.10.482611v1?rss=1"
Ward, E. J.Bert, S.Fanti, S.Dufton, N. P.Malone, K. M.Maughan, R. T.Prin, F.Volpato, L.-K.Piovesan, A. P.Perretti, M.Marelli-Berg, F. M.Nadkarni, S.2022-03-12doi:10.1101/2022.03.10.482611Cold Spring Harbor Laboratory Press2022-03-12
<![CDATA[
Deep learning in human neurons predicts mechanistic subtypes of Parkinson's
]]>
https://biorxiv.org/cgi/content/short/2022.03.10.482156v1?rss=1"
D'Sa, K.Evans, J. R.Virdi, G. S.Vecchi, G.Adam, A.Bertolli, O.Fleming, J.Chang, H.Athauda, D.Choi, M. L.Gandhi, S.2022-03-12doi:10.1101/2022.03.10.482156Cold Spring Harbor Laboratory Press2022-03-12
<![CDATA[
Systematic dissection of phosphorylation-dependent YAP1 complex formation elucidates a key role for PTPN14 in Hippo signal integration
]]>
https://biorxiv.org/cgi/content/short/2022.03.13.484137v1?rss=1"
Uliana, F.Ciuffa, R.Mishra, R.Fossati, A.Frommelt, F.Mehnert, M.Salmorin, E. B.Peter, M.Tapon, N.Aebersold, R.Gstaiger, M.2022-03-13doi:10.1101/2022.03.13.484137Cold Spring Harbor Laboratory Press2022-03-13
<![CDATA[
Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy
]]>
https://biorxiv.org/cgi/content/short/2022.03.14.484209v1?rss=1"
Yu, J. S.Heineike, B. M.Hartl, J.Correia-Melo, C.Aulakh, S. K.Lehmann, A.Lemke, O.Agostini, F.Lee, C. T.Demichev, V.Messner, C. B.Mülleder, M.Ralser, M.2022-03-14doi:10.1101/2022.03.14.484209Cold Spring Harbor Laboratory Press2022-03-14
<![CDATA[
T cell migration requires ion and water influx to regulate actin polymerization
]]>
https://biorxiv.org/cgi/content/short/2022.03.16.484584v1?rss=1"
de Boer, L.Melgrati, S.Vanes, L.Biggs O'May, J.Hayward, D.Koechl, R.Tybulewicz, V.2022-03-18doi:10.1101/2022.03.16.484584Cold Spring Harbor Laboratory Press2022-03-18
<![CDATA[
Water influx is required for CD4+ T cell activation and T cell-dependent antibody responses
]]>
https://biorxiv.org/cgi/content/short/2022.03.16.484637v1?rss=1"
Biggs O'May, J.Vanes, L.Hartweger, H.de Boer, L.Hayward, D.Koechl, R.Tybulewicz, V.2022-03-18doi:10.1101/2022.03.16.484637Cold Spring Harbor Laboratory Press2022-03-18
<![CDATA[
Molecular determinants of the Bacillus subtilis chromosome origin basal unwinding system
]]>
https://biorxiv.org/cgi/content/short/2022.03.18.484894v1?rss=1"
Pelliciari, S.Burnham, D. R.Merces, G.Yardimci, H.Murray, H.2022-03-19doi:10.1101/2022.03.18.484894Cold Spring Harbor Laboratory Press2022-03-19
<![CDATA[
Toxoplasma gondii ROP1 subverts murine and human innate immune restriction
]]>
https://biorxiv.org/cgi/content/short/2022.03.21.485090v1?rss=1"
Butterworth, S.Torelli, F.Lockyer, E. J.Wagener, J.Song, O.-R.Broncel, M.Russell, M.Young, J. C.Treeck, M.2022-03-21doi:10.1101/2022.03.21.485090Cold Spring Harbor Laboratory Press2022-03-21
<![CDATA[
Interacting active surfaces: a model for three-dimensional cell aggregates
]]>
https://biorxiv.org/cgi/content/short/2022.03.21.484343v1?rss=1"
Torres-Sanchez, A.Winter, M. K.Salbreux, G.2022-03-22doi:10.1101/2022.03.21.484343Cold Spring Harbor Laboratory Press2022-03-22
<![CDATA[
Occurrence and quantities of DNA modifications across the tree of life
]]>
https://biorxiv.org/cgi/content/short/2022.03.22.485282v1?rss=1"
Varma, S. J.Calvani, E.Gruening, N.-M.Messner, C. B.Grayson, N.Capuano, F.Muelleder, M.Ralser, M.2022-03-23doi:10.1101/2022.03.22.485282Cold Spring Harbor Laboratory Press2022-03-23
<![CDATA[
A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses
]]>
https://biorxiv.org/cgi/content/short/2022.03.26.485931v1?rss=1"
Harvey, W. T.Davies, V.Daniels, R. S.Whittaker, L.Gregory, V.Hay, A. J.Husmeier, D.McCauley, J. W.Reeve, R.2022-03-27doi:10.1101/2022.03.26.485931Cold Spring Harbor Laboratory Press2022-03-27
<![CDATA[
NDR1/2 kinases regulate membrane trafficking, enable efficient autophagy and prevent neurodegeneration
]]>
https://biorxiv.org/cgi/content/short/2022.03.28.486054v1?rss=1"
Ultanir, S. K.Rosianu, F.Mihaylov, S. R.Eder, N.Martiniuc, A.Claxton, S.Flynn, H.Jalal, S.Domart, M.-C.Collinson, L. M.Skehel, M.Snijders, A. P. P.Krause, M.Tooze, S. A.2022-03-29doi:10.1101/2022.03.28.486054Cold Spring Harbor Laboratory Press2022-03-29
<![CDATA[
The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids
]]>
https://biorxiv.org/cgi/content/short/2022.04.06.487392v1?rss=1"
Muenzner, J.Trebulle, P.Agostini, F.Messner, C. B.Steger, M.Lehmann, A.Caudal, E.Egger, A.-S.Amari, F.Barthel, N.De Chiara, M.Muelleder, M.Demichev, V.Liti, G.Schacherer, J.Gossmann, T.Berman, J.Ralser, M.2022-04-08doi:10.1101/2022.04.06.487392Cold Spring Harbor Laboratory Press2022-04-08
<![CDATA[
Phosphorylation of the novel mTOR substrate Unkempt regulates cellular morphogenesis
]]>
https://biorxiv.org/cgi/content/short/2022.04.08.487575v1?rss=1"
Baskaran, P.Mihaylov, S. R.Vinsland, E.Shah, K.Granat, L.Ultanir, S. K.Tee, A. R.Murn, J.Bateman, J. M.2022-04-10doi:10.1101/2022.04.08.487575Cold Spring Harbor Laboratory Press2022-04-10
<![CDATA[
High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation
]]>
https://biorxiv.org/cgi/content/short/2022.04.07.487490v1?rss=1"
Laine, R. F.Heil, H. S.Coelho, S.Nixon-Abell, J.Jimenez, A.Galgani, T.Stubb, A.Follain, G.Culley, S.Jacquemet, G.Hajj, B.Leterrier, C.Henriques, R.2022-04-08doi:10.1101/2022.04.07.487490Cold Spring Harbor Laboratory Press2022-04-08
<![CDATA[
A quantitative and spatial analysis of cell cycle regulators during the fission yeast cell cycle
]]>
https://biorxiv.org/cgi/content/short/2022.04.13.488127v1?rss=1"
Curran, S.Dey, G.Rees, P.Nurse, P.2022-04-13doi:10.1101/2022.04.13.488127Cold Spring Harbor Laboratory Press2022-04-13
<![CDATA[
Low-efficiency conversion of proliferative glia into induced neurons by Ascl1 in the postnatal mouse cerebral cortex in vivo
]]>
https://biorxiv.org/cgi/content/short/2022.04.13.488173v1?rss=1"
Galante, C.Marichal, N.Schuurmans, C.Berninger, B.Peron, S.2022-04-13doi:10.1101/2022.04.13.488173Cold Spring Harbor Laboratory Press2022-04-13
<![CDATA[
Multimodal single cell data integration challenge: results and lessons learned
]]>
https://biorxiv.org/cgi/content/short/2022.04.11.487796v1?rss=1"
Lance, C.Luecken, M. D.Burkhardt, D. B.Cannoodt, R.Rautenstrauch, P.Laddach, A. C.Ubingazhibov, A.Cao, Z.-J.Deng, K.Khan, S.Liu, Q.Russkikh, N.Ryazantsev, G.Ohler, U.NeurIPS 2021 Multimodal data integration competition participants,Pisco, A. O.Bloom, J. M.Krishnaswamy, S.Theis, F. J.2022-04-12doi:10.1101/2022.04.11.487796Cold Spring Harbor Laboratory Press2022-04-12
<![CDATA[
High-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA
]]>
https://biorxiv.org/cgi/content/short/2022.04.14.488299v1?rss=1"
6,000 proteins from a 62.5 ng load of human cell lysate with more than 5,000 proteins consistently quantified in triplicate injections with a median CV of 6%. Using 5-min analytical-flow-rate chromatography (800 {micro}l/min), Zeno SWATH identified 4,907 proteins from a triplicate injection of 2 {micro}g of a human cell lysate; or more than 3,000 proteins from 250 ng tryptic digest. Zeno SWATH hence facilitates precise proteomic experiments with small sample amounts using a fast and robust high flow-rate chromatographic method, broadening the application space that requires precise proteomic experiments on a large scale.
]]>Wang, Z.Muelleder, M.Batruch, I.Chelur, A.Textoris-Taube, K.Schwecke, T.Hartl, J.Causon, J.Castro-Perez, J.Demichev, V.Tate, S.Ralser, M.2022-04-14doi:10.1101/2022.04.14.488299Cold Spring Harbor Laboratory Press2022-04-14
<![CDATA[
Kinesin-1 transports morphologically distinct intracellular virions during vaccinia infection
]]>
https://biorxiv.org/cgi/content/short/2022.04.15.488437v1?rss=1"
Xu, A.Basant, A.Schleich, S.Newsome, T. P.Way, M.2022-04-15doi:10.1101/2022.04.15.488437Cold Spring Harbor Laboratory Press2022-04-15
<![CDATA[
Arousal neurons that anticipate deviations in blood glucose.
]]>
https://biorxiv.org/cgi/content/short/2022.04.14.488310v1?rss=1"
Viskaitis, P.Tesmer, A.Karnani, M. M.Arnold, M.Donegan, D.Bracey, E.Peleg-Raibstein, D.Burdakov, D.2022-04-15doi:10.1101/2022.04.14.488310Cold Spring Harbor Laboratory Press2022-04-15
<![CDATA[
The DNA replication initiation protein DnaD is recruited to a specific strand of the Bacillus subtilis chromosome origin
]]>
https://biorxiv.org/cgi/content/short/2022.04.18.488654v1?rss=1"
Winterhalter, C.Pelliciari, S.Stevens, D.Fenyk, S.Marchand, E.Cronin, N.Soultanas, P.Costa, T.Ilangovan, A.Murray, H.2022-04-18doi:10.1101/2022.04.18.488654Cold Spring Harbor Laboratory Press2022-04-18
<![CDATA[
Emergence of new subgenomic mRNAs in SARS-CoV-2
]]>
https://biorxiv.org/cgi/content/short/2022.04.20.488895v1?rss=1"
Mears, H. V.Young, G. R.Sanderson, T.Harvey, R.Crawford, M.Snell, D. M.Fowler, A. S.Hussain, S.Nicod, J.Peacock, T. P.Emmott, E.Finsterbusch, K.Luptak, J.Wall, E.Williams, B.Gandhi, S.Swanton, C.Bauer, D. L.2022-04-20doi:10.1101/2022.04.20.488895Cold Spring Harbor Laboratory Press2022-04-20
<![CDATA[
Crosslinker design determines microtubule network organization by opposing motors
]]>
https://biorxiv.org/cgi/content/short/2022.04.22.488007v1?rss=1"
Henkin, G.Chew, W.-X.Nedelec, F.Surrey, T.2022-04-22doi:10.1101/2022.04.22.488007Cold Spring Harbor Laboratory Press2022-04-22
<![CDATA[
Nodal signaling establishes a competency window for stochastic cell fate switching
]]>
https://biorxiv.org/cgi/content/short/2022.04.22.489156v1?rss=1"
Economou, A. D.Guglielmi, L.East, P.Hill, C. S.2022-04-22doi:10.1101/2022.04.22.489156Cold Spring Harbor Laboratory Press2022-04-22
<![CDATA[
Impaired immune response drives age-dependent severity of COVID-19
]]>
https://biorxiv.org/cgi/content/short/2022.04.21.489072v1?rss=1"
Beer, J.Crotta, S.Breithaupt, A.Ohnemus, A.Becker, J.Sachs, B.Kern, L.Llorian, M.Ebert, N.Labroussaa, F.Tran, T. T. N.Trueeb, B. S.Jores, J.Thiel, V.Beer, M.Fuchs, J.Kochs, G.Wack, A.Schwemmle, M.Schnepf, D.2022-04-22doi:10.1101/2022.04.21.489072Cold Spring Harbor Laboratory Press2022-04-22
<![CDATA[
Bimodal regulation of axonal transport by the GDNF-RET signalling axis in healthy and diseased motor neurons
]]>
https://biorxiv.org/cgi/content/short/2022.04.26.489550v1?rss=1"
Rhymes, E. R.Tosolini, A. P.Fellows, A. D.Mahy, W.McDonald, N. Q.Schiavo, G.2022-04-27doi:10.1101/2022.04.26.489550Cold Spring Harbor Laboratory Press2022-04-27
<![CDATA[
H4K16ac activates transcription of transposable elements and contribute to their cis regulatory function
]]>
https://biorxiv.org/cgi/content/short/2022.04.29.488986v1?rss=1"
Pal, D.Patel, M.Boulet, F.Sundarraj, J.Grant, O. A.Branco, M. R.Basu, S.Zabet, N. R.Scaffidi, P.Pradeepa, M. M.2022-04-30doi:10.1101/2022.04.29.488986Cold Spring Harbor Laboratory Press2022-04-30
<![CDATA[
PfHDAC1 is an essential regulator of parasite asexual growth with its altered genomic occupancy and activity associated with artemisinin drug resistance in Plasmodium falciparum
]]>
https://biorxiv.org/cgi/content/short/2022.05.01.490232v1?rss=1"
Kanyal, A.Davies, H.Deshmukh, B.Farheen, D.Treeck, M.Karmodiya, K.2022-05-02doi:10.1101/2022.05.01.490232Cold Spring Harbor Laboratory Press2022-05-02
<![CDATA[
Digital holography-based 3D particle localisation for single molecule tweezer techniques
]]>
https://biorxiv.org/cgi/content/short/2022.05.03.490423v1?rss=1"
Tolar, P.Flewellen, J.Minoughan, S.Llorente Garcia, I.2022-05-04doi:10.1101/2022.05.03.490423Cold Spring Harbor Laboratory Press2022-05-04
<![CDATA[
Nucleation and stability of branched versus linear Arp2/3-generated actin filaments
]]>
https://biorxiv.org/cgi/content/short/2022.05.06.490861v1?rss=1"
Cao, L.Ghasemi, F.Way, M.Jegou, A.Romet-Lemonne, G.2022-05-06doi:10.1101/2022.05.06.490861Cold Spring Harbor Laboratory Press2022-05-06
<![CDATA[
Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start.
]]>
https://biorxiv.org/cgi/content/short/2022.05.06.490863v1?rss=1"
Alva, A.Brito-Alarcon, E.Linares, A.Torres-Garcia, E.Hernandez, H. O.Pinto-Camara, R.Martinez, D.Hernandez-Herrera, P.D'Antuono, R.Wood, C.Guerrero, A.2022-05-06doi:10.1101/2022.05.06.490863Cold Spring Harbor Laboratory Press2022-05-06
<![CDATA[
Profile of Mycobacterium tuberculosis-specific CD4 T cells at the site of disease and blood in pericardial tuberculosis
]]>
https://biorxiv.org/cgi/content/short/2022.05.12.491749v1?rss=1"
Du Bruyn, E.Ruzive, S.Howlett, P. J.Jacobs, A. J.Lindestam Arlehamn, C. S.Sette, A.Sher, A.Mayer-Barber, K. D.Barber, D.Mayosi, B.Ntsekhe, M.Wilkinson, R. J.Riou, C.2022-05-13doi:10.1101/2022.05.12.491749Cold Spring Harbor Laboratory Press2022-05-13
<![CDATA[
From recency to the central tendency bias in working memory: a unifying attractor network model
]]>
https://biorxiv.org/cgi/content/short/2022.05.16.491352v1?rss=1"
Boboeva, V.Pezzotta, A.Akrami, A.Clopath, C.2022-05-16doi:10.1101/2022.05.16.491352Cold Spring Harbor Laboratory Press2022-05-16
<![CDATA[
Cachd1 is a novel Frizzled- and LRP6-interacting protein required for neurons to acquire left-right asymmetric character
]]>
https://biorxiv.org/cgi/content/short/2022.05.16.492129v1?rss=1"
Powell, G. T.Zhao, Y.Faro, A.Stickney, H. L.Novellasdemunt, L.Henriques, P.Gestri, G.Redhouse White, E.Ren, J.Lu, W.Young, R. M.Hawkins, T. A.Cavodeassi, F.Schwarz, Q.Dreosti, E.Raible, D. W.Li, V. S. W.Wright, G. J.Jones, E. Y.Wilson, S. W.2022-05-17doi:10.1101/2022.05.16.492129Cold Spring Harbor Laboratory Press2022-05-17
<![CDATA[
The Proteomic Landscape of Genome-Wide Genetic Perturbations
]]>
https://biorxiv.org/cgi/content/short/2022.05.17.492318v1?rss=1"
Messner, C. B.Demichev, V.Muenzner, J.Aulakh, S.Röhl, A.Herrera-DomInguez, L.Egger, A.-S.Kamrad, S.Lemke, O.Calvani, E.Mülleder, M.Lilley, K. S.Kustatscher, G.Ralser, M.2022-05-18doi:10.1101/2022.05.17.492318Cold Spring Harbor Laboratory Press2022-05-18
<![CDATA[
mNeonGreen-tagged fusion proteins and nanobodies reveal localization of tropomyosin to patches, cables, and contractile actomyosin rings in live yeast cells
]]>
https://biorxiv.org/cgi/content/short/2022.05.19.492673v1?rss=1"
Hatano, T.Lim, T. C.Billault-Chaumartin, I.Dhar, A.Gu, Y.Massam-Wu, T.Adhishesha, S.Springall, L.Scott, W.Sivashanmugam, L.Mishima, M.Martin, S. G.Oliferenko, S.Palani, S.BALASUBRAMANIAN, M. K.2022-05-20doi:10.1101/2022.05.19.492673Cold Spring Harbor Laboratory Press2022-05-20
<![CDATA[
PKN2 deficiency leads both to prenatal congenital cardiomyopathy and defective angiotensin II stress responses.
]]>
https://biorxiv.org/cgi/content/short/2022.05.24.493130v1?rss=1"
Marshall, J. J.Cull, J. J.Alharbi, H. O.Zaw Thin, M.Cooper, S. T.Barrington, C.Vanyai, H.Snoeks, T.Siow, B.Suaarez-Bonnet, A.Herbert, E.Stuckey, D. J.Cameron, A.Prin, F.Cook, A. C.Priestnall, S. L.Chotani, S.Rackham, O. J.Meijles, D. N.Mohun, T.Clerk, A.Parker, P.2022-05-24doi:10.1101/2022.05.24.493130Cold Spring Harbor Laboratory Press2022-05-24
<![CDATA[
Characterization of Plasmodium falciparum myosin B in complex with the calmodulin-like domain of its light chain MLC-B
]]>
https://biorxiv.org/cgi/content/short/2022.05.28.493848v1?rss=1"
Pires, I.Hung, Y.-F.Bergmann, U.Molloy, J. E.Kursula, I.2022-05-28doi:10.1101/2022.05.28.493848Cold Spring Harbor Laboratory Press2022-05-28
<![CDATA[
A nuclear export signal in KHNYN required for its antiviral activity evolved as ZAP emerged in tetrapods
]]>
https://biorxiv.org/cgi/content/short/2022.05.31.494266v1?rss=1"
Lista, M. J.Ficarelli, M.Wilson, H.Kmiec, D.Youle, R.Wanford, J.Winstone, H.Odendall, C.Taylor, I. A.Neil, S. J.Swanson, C. M.2022-06-01doi:10.1101/2022.05.31.494266Cold Spring Harbor Laboratory Press2022-06-01
<![CDATA[
Crosshair, semi-automated targeting for electron microscopy with a motorised ultramicrotome
]]>
https://biorxiv.org/cgi/content/short/2022.06.02.491151v1?rss=1"
Meechan, K.Guan, W.Riedinger, A.Stankova, V.Yoshimura, A.Pipitone, R.Milberger, A.Schaar, H.Romero-Brey, I.Templin, R.Peddie, C. J.Schieber, N. L.Jones, M. L.Collinson, L.Schwab, Y.2022-06-02doi:10.1101/2022.06.02.491151Cold Spring Harbor Laboratory Press2022-06-02
<![CDATA[
Diacylglycerol consumption at the inner nuclear membrane fuels nuclear envelope expansion required for closed mitosis
]]>
https://biorxiv.org/cgi/content/short/2022.06.01.494365v1?rss=1"
Foo, S.Cazenave-Gassiot, A.Wenk, M. R.Oliferenko, S.2022-06-02doi:10.1101/2022.06.01.494365Cold Spring Harbor Laboratory Press2022-06-02
<![CDATA[
OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale
]]>
https://biorxiv.org/cgi/content/short/2022.06.01.494393v1?rss=1"
White, M. E. H.Jones, D. M.de Folter, J.Aulakh, S. K.Flynn, H. R.Krüger, L.Demichev, V.Tober-Lau, P.Kurth, F.Mülleder, M.Blanchard, V.Messner, C. B.Ralser, M.2022-06-02doi:10.1101/2022.06.01.494393Cold Spring Harbor Laboratory Press2022-06-02
<![CDATA[
Reconstituting human somitogenesis in vitro
]]>
https://biorxiv.org/cgi/content/short/2022.06.03.494621v1?rss=1"
Yamanaka, Y.Yoshioka-Kobayashi, K.Hamidi, S.Munira, S.Sunadome, K.Zhang, Y.Kurokawa, Y.Mieda, A.Thompson, J. L.Kerwin, J.Lisgo, S.Yamamoto, T.Moris, N.Martinez-Arias, A.Tsujimura, T.Alev, C.2022-06-03doi:10.1101/2022.06.03.494621Cold Spring Harbor Laboratory Press2022-06-03
<![CDATA[
Taxonium: a web-based tool for exploring large phylogenetic trees
]]>
https://biorxiv.org/cgi/content/short/2022.06.03.494608v1?rss=1"
Sanderson, T.2022-06-03doi:10.1101/2022.06.03.494608Cold Spring Harbor Laboratory Press2022-06-03
<![CDATA[
Bumetanide increases microglia-interneuron contact following traumatic brain injury
]]>
https://biorxiv.org/cgi/content/short/2022.06.03.494659v1?rss=1"
Tessier, M.Garcia, M. S.Goubert, E.Tian, L.Molinari, F.Blasco, E.Laurin, J.Guillemot, F.Hubner, C.Pellegrino, c. A.Rivera, C.2022-06-05doi:10.1101/2022.06.03.494659Cold Spring Harbor Laboratory Press2022-06-05
<![CDATA[
Developmental cell fate choice employs two distinct cis regulatory strategies
]]>
https://biorxiv.org/cgi/content/short/2022.06.06.494792v1?rss=1"
Delas, M. J.Kalaitzis, C. M.Fawzi, T.Demuth, M.Zhang, I.Stuart, H. T.Costantini, E.Ivanovitch, K.Tanaka, E.Briscoe, J.2022-06-06doi:10.1101/2022.06.06.494792Cold Spring Harbor Laboratory Press2022-06-06
<![CDATA[
Structural conversion of α-synuclein at the mitochondria induces neuronal toxicity
]]>
https://biorxiv.org/cgi/content/short/2022.06.07.494932v1?rss=1"
Choi, M. L.Chappard, A.Singh, B. P.Maclachlan, C.Rodrigues, M.Fedotova, E.Berezhnov, A.De, S.Peddie, C.Athauda, D.Virdi, G. S.Zhang, W.Evans, J. R.Wernick, A.Zanjani, Z.Angelova, P. R.Esteras, N.Andrey, A.Morris, K.Jeacock, K.Tosatto, L.Little, D.Gissen, P.Collinson, L.Clarke, D. J.Kunath, T.Klenerman, D.Abramov, A. Y.Horrocks, M. H.Gandhi, S.2022-06-09doi:10.1101/2022.06.07.494932Cold Spring Harbor Laboratory Press2022-06-09
<![CDATA[
Cis-membrane association of human ATG8 proteins N-terminus mediates autophagy
]]>
https://biorxiv.org/cgi/content/short/2022.06.10.495627v1?rss=1"
Tooze, S.Zhang, W.Nishimura, T.Gahlot, D.Saito, C.Davis, C.Jefferies, H. B. J.Schreiber, A.Thukral, L.2022-06-10doi:10.1101/2022.06.10.495627Cold Spring Harbor Laboratory Press2022-06-10
<![CDATA[
Quantitative analysis of rabies virus-based synaptic connectivity tracing
]]>
https://biorxiv.org/cgi/content/short/2022.06.08.494952v1?rss=1"
Tran-Van-Minh, A.Ye, Z.Rancz, E.2022-06-10doi:10.1101/2022.06.08.494952Cold Spring Harbor Laboratory Press2022-06-10
<![CDATA[
Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis
]]>
https://biorxiv.org/cgi/content/short/2022.06.10.495597v1?rss=1"
Meier, S.Seddon, J. A.Maasdorp, E.Kleynhans, L.du Plessis, N.Loxton, A. G.Malherbe, S. T.Zak, D. E.Thompson, E.Duffy, F.Kaufmann, S. H. E.Ottenhoff, T. H. M.Scriba, T. J.Suliman, S.Sutherland, J. S.Winter, J.Kuivaniemi, H.Walzl, G.Tromp, G.GC6-74 Consortium,Catalysis TB Biomarkers Consortium,2022-06-11doi:10.1101/2022.06.10.495597Cold Spring Harbor Laboratory Press2022-06-11
<![CDATA[
A low-cost device for cryoanesthesia of neonate rodents
]]>
https://biorxiv.org/cgi/content/short/2022.06.09.495437v1?rss=1"
Jamieson, B. B.Konstantinou, G.Cano-Ferrer, X.de Launoit, E.Renier, N.Imbert, A.Kohl, J.2022-06-12doi:10.1101/2022.06.09.495437Cold Spring Harbor Laboratory Press2022-06-12
<![CDATA[
β-catenin obstructs γδ T cell immunosurveillance in colon cancer through loss of BTNL expression
]]>
https://biorxiv.org/cgi/content/short/2022.06.10.495115v1?rss=1"
Suzuki, T.Kilbey, A.Ridgway, R. A.Hayman, H.Byrne, R.Casa Rodriguez, N.Georgakopoulou, A.Chen, L.Verzi, M.Gay, D. M.Vzquez, E. G.Belnoue-Davis, H. L.Gilroy, K.Kostner, A. H.Kersten, C.Thuwajit, C.Andersen, D.Wiesheu, R.Jandke, A.Roberts, N.Blyth, K.Roseweir, A.Leedham, S. J.Dunne, P. D.Edwards, J.Hayday, A.Sansom, O. J.Coffelt, S. B.2022-06-12doi:10.1101/2022.06.10.495115Cold Spring Harbor Laboratory Press2022-06-12
<![CDATA[
Inhibition of vaccinia virus L1 N-myristoylation by the host N-myristoyltransferase inhibitor IMP-1088 generates non-infectious virions defective in cell entry
]]>
https://biorxiv.org/cgi/content/short/2022.06.13.495866v1?rss=1"
Priyamvada, L.Kallemeijn, W. W.Faronato, M.Wilkins, K.Goldsmith, C. S.Cotter, C. A.Ojeda, S.Solari, R.Moss, B.Tate, E. W.Satheshkumar, P. S.2022-06-13doi:10.1101/2022.06.13.495866Cold Spring Harbor Laboratory Press2022-06-13
<![CDATA[
Nanoscopic resolution within a single imaging frame
]]>
https://biorxiv.org/cgi/content/short/2021.10.17.464398v1?rss=1"
Torres, E.Pinto, R.Linares, A.Martinez, D.Abonza, V.Brito-Alarcon, E.Calcines-Cruz, C.Galindo, G.Torres, D.Jablonski, M.Torres-Martinez, H. H.Martinez, J. L.Hernandez, H. O.Ocelotl, J.Garces, Y.Barchi, M.Dubrovsky, J. G.Darszon, A.Buffone, M.Rodriguez, R.Rendon-Mancha, J. M.Wood, C.Hernandez, A.Krapf, D.Crevenna, A. H.Guerrero, A.2021-10-18doi:10.1101/2021.10.17.464398Cold Spring Harbor Laboratory Press2021-10-18
<![CDATA[
A choline-releasing glycerophosphodiesterase essential for phosphatidylcholine biosynthesis and blood stage development in the malaria parasite
]]>
https://biorxiv.org/cgi/content/short/2022.06.14.496138v1?rss=1"
Ramaprasad, A.Burda, P.-C.Calvani, E.Sait, A.Palma-Duran, S. A.Withers-Martinez, C.Hackett, F.MacRae, J. I.Collinson, L.Gilberger, T.Blackman, M.2022-06-14doi:10.1101/2022.06.14.496138Cold Spring Harbor Laboratory Press2022-06-14
<![CDATA[
Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction
]]>
https://biorxiv.org/cgi/content/short/2022.06.14.495937v1?rss=1"
Salcedo, A.Tarabichi, M.Buchanan, A.Espiritu, S. M. G.Zhang, H.Zhu, K.Yang, T.-H. O.Leshchiner, I.Anastassiou, D.Guan, Y.Jang, G. H.Haase, K.Deshwar, A. G.Zou, W.Umar, I.Dentro, S.Wintersinger, J. A.Chiotti, K.Demeulemeester, J.Jolly, C.Scyza, L.Ko, M.PCAWG-11 Working Group,SMC-Het Participants,Wedge, D. C.Morris, Q. D.Ellrot, K.Van Loo, P.Boutros, P. C.2022-06-15doi:10.1101/2022.06.14.495937Cold Spring Harbor Laboratory Press2022-06-15
<![CDATA[
A computationally-enhanced hiCLIP atlas reveals Staufen1 RNA binding features and links 3' UTR structure to RNA metabolism
]]>
https://biorxiv.org/cgi/content/short/2022.06.13.495933v1?rss=1"
Chakrabarti, A. M.Iosub, I. A.Lee, F. C. Y.Ule, J.Luscombe, N. M.2022-06-16doi:10.1101/2022.06.13.495933Cold Spring Harbor Laboratory Press2022-06-16
<![CDATA[
Comprehensive Analysis of CRISPR Base Editing Outcomes for Multimeric Protein
]]>
https://biorxiv.org/cgi/content/short/2022.06.20.496792v1?rss=1"
C, p.Leu144Pro) and explored the activity of two cytosine base editors mRNAs (CBEs, BE4max-WTCas9, and evoCDA-SpCas9-NG) as a proof-of-concept therapeutic option. We observed the KCNJ13-related retinopathy phenotype in patients harboring L144P mutation. Our in-silico prediction and in vitro validation demonstrated that L144P mutation affects the channel function. We observed high on-target efficiency in the CBEs treated L144P mutant gene expressing HEK-293 cells. Strikingly, our evaluation of base editing efficacy using electrophysiology showed negligible channel function. We found that the editing bystander Cs in the protospacer region led to a missense change (L143F) in evoCDA edited cells and only silent changes in BE4max edited cells. Upon investigation of the effect of the synonymous codon, our extended analysis revealed distortion of mRNA structure, altered half-life, and/or low abundance of the cognate tRNA. We propose that KCNJ13-L144P mutation or other genes that share similar genetic complexity may be challenging to correct with the current generation of CRISPR base editors, and a combinational therapy using CRISPR base editors with a tighter editing window and requisite cognate-tRNA supplementation could be an alternative therapeutic approach to restore Kir7.1 channel function in LCA16 patients. Other options for hard-to-rescue alleles could employ homology-directed repair using CRISPR/Cas9 nucleases, Prime editing, and AAV-mediated gene augmentation.
]]>Kabra, M.Moosajee, M.Newby, G.Molugu, K.Saha, K.Liu, D.Pattnaik, B. R.2022-06-20doi:10.1101/2022.06.20.496792Cold Spring Harbor Laboratory Press2022-06-20
<![CDATA[
Craniofacial dysmorphology in Down Syndrome is caused by increased dosage of Dyrk1a and at least three other genes
]]>
https://biorxiv.org/cgi/content/short/2022.06.27.497841v1?rss=1"
Redhead, Y.Gibbins, D.Lana-Elola, E.Watson-Scales, S.Dobson, L.Krause, M.Liu, K.Fisher, E.Green, J.Tybulewicz, V.2022-06-28doi:10.1101/2022.06.27.497841Cold Spring Harbor Laboratory Press2022-06-28
<![CDATA[
A conserved role of Hippo signaling in initiation of the first lineage specification event across mammals
]]>
https://biorxiv.org/cgi/content/short/2022.07.01.498418v1?rss=1"
Gerri, C.McCarthy, A.Scott, G. M.Regin, M.Brumm, S.Simon, C. S.Lee, J.Montesinos, C.Hassitt, C.Hockenhull, S.Hampshire, D.Elder, K.Snell, P.Christie, L.Fouladi-Nashta, A. A.Van de Velde, H.Niakan, K.2022-07-02doi:10.1101/2022.07.01.498418Cold Spring Harbor Laboratory Press2022-07-02
<![CDATA[
TRIM7 restricts Coxsackievirus and norovirus infection by detecting the C-terminalglutamine generated by 3C protease processing
]]>
https://biorxiv.org/cgi/content/short/2022.06.28.497919v1?rss=1"
Luptak, J.Mallery, D.Jahun, A. S.Albecka, A.Clift, D.Ather, O.Slodkowicz, G.Goodfellow, I.James, L.2022-07-05doi:10.1101/2022.06.28.497919Cold Spring Harbor Laboratory Press2022-07-05
<![CDATA[
Polymorphisms Predicting Phylogeny in Hepatitis B Virus (HBV)
]]>
https://biorxiv.org/cgi/content/short/2022.07.05.498824v1?rss=1"
Lourenco, J.McNaughton, A. L.Pley, C.Obolski, U. L.Gupta, S.Matthews, P. C.2022-07-05doi:10.1101/2022.07.05.498824Cold Spring Harbor Laboratory Press2022-07-05
<![CDATA[
Deep proteomic analysis of human microglia and model systems reveal fundamental biological differences of in vitro and ex vivo cells
]]>
https://biorxiv.org/cgi/content/short/2022.07.07.498804v1?rss=1"
Lloyd, A. F.Martinez-Muriana, A.Hou, P.Davis, E.Mancuso, R.Brenes-Murillo, A. J.Geric, I.Snellinx, A.Craessaerts, K.Theys, T.Fiers, M.De Strooper, B.Howden, A. J.2022-07-07doi:10.1101/2022.07.07.498804Cold Spring Harbor Laboratory Press2022-07-07
<![CDATA[
Enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants BA.4 and BA.5
]]>
https://biorxiv.org/cgi/content/short/2022.07.12.499603v1?rss=1"
Reuschl, A.-K.Thorne, L. G.Whelan, M. X. V.Mesner, D.Ragazzini, R.Dowgier, G.Bogoda, N.Turner, J. E.Furnon, W.Cowton, V. M.de Lorenzo, G.Bonfanti, P.Palmarini, M.Patel, A. H.Jolly, C.Towers, G. J.2022-07-12doi:10.1101/2022.07.12.499603Cold Spring Harbor Laboratory Press2022-07-12
<![CDATA[
A branching model of cell fate decisions in the enteric nervous system
]]>
https://biorxiv.org/cgi/content/short/2022.07.12.499640v1?rss=1"
Laddach, A. C.Chng, S. H.Lasrado, R.Progatzky, F.Shapiro, M.Artemov, A.Castaneda, M. S.Erickson, A.Bon-Frauches, A. C.Kleinjung, J.Boeing, S.Ultanir, S.Adameyko, I.Pachnis, V.2022-07-13doi:10.1101/2022.07.12.499640Cold Spring Harbor Laboratory Press2022-07-13
<![CDATA[
OptoPi: An open source flexible platform for the analysis of small animal behaviour
]]>
https://biorxiv.org/cgi/content/short/2022.07.12.499786v1?rss=1"
Cano-Ferrer, X.Roberts, R. J. V.French, A. S.de Folter, J.Gong, H.Nightingale, L.Strange, A.Imbert, A.Prieto-Godino, L. L.2022-07-13doi:10.1101/2022.07.12.499786Cold Spring Harbor Laboratory Press2022-07-13
<![CDATA[
Robust, single-shot, optical autofocus system utilizing cylindrical lenses to provide high precision and long range of operation
]]>
https://biorxiv.org/cgi/content/short/2022.07.14.498938v1?rss=1"
Lightley, J.Kumar, S.Garcia, E.Alexandrov, Y.Dunsby, C.Neil, M. A. A.French, P. M. W.2022-07-16doi:10.1101/2022.07.14.498938Cold Spring Harbor Laboratory Press2022-07-16
<![CDATA[
Phenotypic profile of Mycobacterium tuberculosis-specific CD4 T cell responses in HIV-positive patients who develop Tuberculosis-associated Immune Reconstitution Inflammatory Syndrome
]]>
https://biorxiv.org/cgi/content/short/2022.07.20.500909v1?rss=1"
Moseki, M. R.Barber, D.Du Bruyn, E.Shey, M.Van der Plas, H.Wilkinson, R. J.Meintjes, G.Riou, C.2022-07-22doi:10.1101/2022.07.20.500909Cold Spring Harbor Laboratory Press2022-07-22
<![CDATA[
The APE2 nuclease is essential for DNA double strand break repairby microhomology-mediated end-joining.
]]>
https://biorxiv.org/cgi/content/short/2022.07.21.500989v1?rss=1"
Fleury, H.MacEachern, M. K.Stiefel, C. M.Anand, R.Sempeck, C.Nebenfuehr, B.Dodd, B.Taylor, E.Dansoko, D.Ortega, R.Leung, J. W.Boulton, S. J.Arnoult, N.2022-07-22doi:10.1101/2022.07.21.500989Cold Spring Harbor Laboratory Press2022-07-22
<![CDATA[
Optimal control of gene regulatory networks for morphogen-driven tissue patterning
]]>
https://biorxiv.org/cgi/content/short/2022.07.26.501519v1?rss=1"
Pezzotta, A.Briscoe, J.2022-07-26doi:10.1101/2022.07.26.501519Cold Spring Harbor Laboratory Press2022-07-26
<![CDATA[
cloneMap: a R package to visualise clonal heterogeneity
]]>
https://biorxiv.org/cgi/content/short/2022.07.26.501523v1?rss=1"
Frankell, A.Colliver, E.McGranahan, N.Swanton, C.2022-07-27doi:10.1101/2022.07.26.501523Cold Spring Harbor Laboratory Press2022-07-27
<![CDATA[
How talin allosterically activates vinculin
]]>
https://biorxiv.org/cgi/content/short/2022.08.01.502287v1?rss=1"
Franz, F.Tapia-Rojo, R.Winograd-Katz, S. E.Boujemaa-Paterski, R.Li, W.Unger, T.Albeck, S.Aponte-Santamaria, C.Garcia-Manyes, S.Medalia, O.Geiger, B.Grater, F.2022-08-02doi:10.1101/2022.08.01.502287Cold Spring Harbor Laboratory Press2022-08-02
<![CDATA[
Improved memory CD8 T cell response to delayed vaccine boost is associated with a distinct molecular signature.
]]>
https://biorxiv.org/cgi/content/short/2022.08.04.502772v1?rss=1"
Natalini, A.Simonetti, S.Favaretto, G.Lucantonio, L.Peruzzi, G.Munoz-Ruiz, M.Kelly, G.Contino, A. M.Sbrocchi, R.Battella, S.Capone, S.Folgori, A.Nicosia, A.Santoni, A.Hayday, A. C.Di Rosa, F.2022-08-05doi:10.1101/2022.08.04.502772Cold Spring Harbor Laboratory Press2022-08-05
<![CDATA[
Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism
]]>
https://biorxiv.org/cgi/content/short/2022.08.09.503288v1?rss=1"
Bussi, C.Heunis, T.Pellegrino, E.Bernard, E. M.Bah, N.Silva Dos Santos, M.Santucci, P.Aylan, B.Rodgers, A.Fearns, A.Mitschke, J.Moore, C.MacRae, J. I.Greco, M.Reinheckel, T.Trost, M.Gutierrez, M. G.2022-08-09doi:10.1101/2022.08.09.503288Cold Spring Harbor Laboratory Press2022-08-09
<![CDATA[
Neural plate progenitors give rise to both anterior and posterior pituitary cells
]]>
https://biorxiv.org/cgi/content/short/2022.06.12.495791v1?rss=1"
Chen, Q.Leshkowitz, D.Li, H.van Impel, A.Schulte-Merker, S.Amit, I.Levkowitz, G.2022-06-12doi:10.1101/2022.06.12.495791Cold Spring Harbor Laboratory Press2022-06-12
<![CDATA[
Sequential roles for red blood cell binding proteins enable phased commitment to invasion for malaria parasites
]]>
https://biorxiv.org/cgi/content/short/2022.08.09.503398v1?rss=1"
Hart, M. N.Mohring, F.Donvito, S. M.Thomas, J. A.Muller-Sienerth, N.Wright, G. J.Knuepfer, E.Saibil, H. R.Moon, R. W.2022-08-11doi:10.1101/2022.08.09.503398Cold Spring Harbor Laboratory Press2022-08-11
<![CDATA[
Cryo-ET of infected cells reveals that a succession of two lattices drives vaccinia virus assembly
]]>
https://biorxiv.org/cgi/content/short/2022.08.11.503617v1?rss=1"
Hernandez-Gonzalez, M.Calcraft, T.Nans, A.Rosenthal, P. B.Way, M.2022-08-12doi:10.1101/2022.08.11.503617Cold Spring Harbor Laboratory Press2022-08-12
<![CDATA[
The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe
]]>
https://biorxiv.org/cgi/content/short/2022.08.09.503427v1?rss=1"
Masunaga, A.Mansfield, M. J.Tan, Y.Liu, A. W.Bliznina, A.Barzaghi, P.Hodgetts, T. L.Ferrandez-Roldan, A.Canestro, C.Onuma, T.Plessy, C.Luscombe, N. M.2022-08-11doi:10.1101/2022.08.09.503427Cold Spring Harbor Laboratory Press2022-08-11
<![CDATA[
RTEL-1 and DNA polymerase theta promote subtelomeric DNA synthesis and telomere fusion in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2022.09.04.506531v1?rss=1"
Ahmed, S.Lister-Shimauchi, E.Brady, M.Frenk, S.Harris, B.Ortiz, A.-M. L.Memili, A.Nguyen, M.Boulton, S.2022-09-04doi:10.1101/2022.09.04.506531Cold Spring Harbor Laboratory Press2022-09-04
<![CDATA[
Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers
]]>
https://biorxiv.org/cgi/content/short/2022.09.05.506481v1?rss=1"
4) which also shows allele frequency deviations indicative of a selective sweep following admixture (p =1x10-29). This could reflect negative frequency dependent selection on MHC alleles common in Neolithic populations, or that Mesolithic alleles were positively selected for and facilitated adaptation by Neolithic populations to pathogens, new diets, or other environmental factors. Our results extend previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age, and demonstrate that admixture facilitated selection by contributing new genetic variation.
]]>Davy, T.Ju, D.Mathieson, I.Skoglund, P.2022-09-06doi:10.1101/2022.09.05.506481Cold Spring Harbor Laboratory Press2022-09-06
<![CDATA[
Design principles for selective polarization of PAR proteins by cortical flows
]]>
https://biorxiv.org/cgi/content/short/2022.09.05.506621v1?rss=1"
Illukkumbura, R.Hirani, N.Borrego-Pinto, J.Bland, T.Ng, K.Hubatsch, L.McQuade, J.Endres, R.Goehring, N.2022-09-06doi:10.1101/2022.09.05.506621Cold Spring Harbor Laboratory Press2022-09-06
<![CDATA[
Long-term retention of antigens in germinal centres is controlled by the spatial organisation of the follicular dendritic cell network
]]>
https://biorxiv.org/cgi/content/short/2022.09.06.506650v1?rss=1"
Martinez-Riano, A.Wang, S.Boeing, S.Minoughan, S.Casal, A.Spillane, K. M.Ludewig, B.Tolar, P.2022-09-07doi:10.1101/2022.09.06.506650Cold Spring Harbor Laboratory Press2022-09-07
<![CDATA[
Dual role of brain endothelial Gpr126 in blood-brain barrier development and ischemic stroke
]]>
https://biorxiv.org/cgi/content/short/2022.09.09.507316v1?rss=1"
Kakogiannos, N.Scalise, A. A.Martini, E.Maderna, C.Magni, S.Gullotta, G. S.Lampugnani, M. G.Iannelli, F.Beznusenko, G.Mironov, A.Cerutti, C.Bentley, K.Philippides, A.Zanardi, F.Bacigaluppi, M.Martino, G.Dejana, E.Giannotta, M.2022-09-10doi:10.1101/2022.09.09.507316Cold Spring Harbor Laboratory Press2022-09-10
<![CDATA[
Sister chromatid cohesion establishment during DNA replication termination
]]>
https://biorxiv.org/cgi/content/short/2022.09.15.508094v1?rss=1"
Cameron, G.Gruszka, D.Xie, S.Nasmyth, K. A.Srinivasan, M.Yardimci, H.2022-09-16doi:10.1101/2022.09.15.508094Cold Spring Harbor Laboratory Press2022-09-16
<![CDATA[
O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Contribute to the Mutational Trajectory in Variants of Concern
]]>
https://biorxiv.org/cgi/content/short/2022.09.15.508093v1?rss=1"
View larger version (26K):
org.highwire.dtl.DTLVardef@71b54eorg.highwire.dtl.DTLVardef@1361b4aorg.highwire.dtl.DTLVardef@139bdd9org.highwire.dtl.DTLVardef@1df192b_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Gonzalez-Rodriguez, E.Zol-Hanlon, M.Bineva-Todd, G.Marchesi, A.Skehel, M.Mahoney, K.Roustan, C.Borg, A.Di Vagno, L.Kjaer, S.Wrobel, A. G.Benton, D. J.Nawrath, P.Flitsch, S. L.Joshi, D.Gonzalez-Ramirez, A. M.Wilkinson, K. A.Wilkinson, R. J.Hurtado-Guerrero, R.Malaker, S. A.Schumann, B.2022-09-15doi:10.1101/2022.09.15.508093Cold Spring Harbor Laboratory Press2022-09-15
<![CDATA[
Towards In-Silico CLIP-seq: Predicting Protein-RNA Interaction via Sequence-to-Signal Learning
]]>
https://biorxiv.org/cgi/content/short/2022.09.16.508290v1?rss=1"
Horlacher, M.Wagner, N.Moyon, L.Kuret, K.Goedert, N.Salvatore, M.Ule, J.Gagneur, J.Winther, O.Marsico, A.2022-09-19doi:10.1101/2022.09.16.508290Cold Spring Harbor Laboratory Press2022-09-19
<![CDATA[
USP7 inactivation suppresses APC-mutant intestinal hyperproliferation and tumor development
]]>
https://biorxiv.org/cgi/content/short/2022.09.22.508986v1?rss=1"
Novellasdemunt, L.Kucharska, A.Baulies, A.Vlachogiannis, G.Repana, D.Rowan, A.Suarez-Bonnet, A.Ciccarelli, F.Valeri, N.Li, V. S. W.2022-09-23doi:10.1101/2022.09.22.508986Cold Spring Harbor Laboratory Press2022-09-23
<![CDATA[
Plzf mediates a switch between Fgf signalling regimes in the developing hindbrain
]]>
https://biorxiv.org/cgi/content/short/2022.09.23.509139v1?rss=1"
Leino, S.Constable, S. C. J.Streit, A.Wilkinson, D. G.2022-09-23doi:10.1101/2022.09.23.509139Cold Spring Harbor Laboratory Press2022-09-23
<![CDATA[
Resolving chaperone-assisted protein folding on the ribosome at the peptide level
]]>
https://biorxiv.org/cgi/content/short/2022.09.23.509153v1?rss=1"
Wales, T. E.Pajak, A.Roeselova, A.Shivakumaraswamy, S.Howell, S.Hartl, F.-U.Engen, J. R.Balchin, D.2022-09-23doi:10.1101/2022.09.23.509153Cold Spring Harbor Laboratory Press2022-09-23
<![CDATA[
Small-molecule Polθ inhibitors provide safe and effective tumor radiosensitization in preclinical models
]]>
https://biorxiv.org/cgi/content/short/2022.09.27.509658v1?rss=1"
Rodriguez-Berriguete, G.Ranzani, M.Prevo, R.Puliyadi, R.Machado, N.Bolland, H. R.Millar, V.Ebner, D.Boursier, M.Cerutti, A.Cicconi, A.Galbiati, A.Grande, D.Grinkevich, V.Majithiya, J.Piscitello, D.Rajendra, E.Stockley, M.Boulton, S. J.Hammond, E. M.Heald, R.Smith, G. C. M.Robinson, H.Higgins, G. S.2022-09-28doi:10.1101/2022.09.27.509658Cold Spring Harbor Laboratory Press2022-09-28
<![CDATA[
m6A-ELISA, a simple method for quantifying N6-methyladenosine from mRNA populations
]]>
https://biorxiv.org/cgi/content/short/2022.09.27.509679v1?rss=1"
Ensinck, I.Sideri, T.Modic, M.Capitanchik, C.Toolan-Kerr, P.van Werven, F.2022-09-28doi:10.1101/2022.09.27.509679Cold Spring Harbor Laboratory Press2022-09-28
<![CDATA[
Treenome Browser: co-visualization of enormous phylogenies and millions of genomes
]]>
https://biorxiv.org/cgi/content/short/2022.09.28.509985v1?rss=1"
Kramer, A. M.Sanderson, T.Corbett-Detig, R.2022-09-30doi:10.1101/2022.09.28.509985Cold Spring Harbor Laboratory Press2022-09-30
<![CDATA[
Lineage segregation in human pre-implantation embryos is specified by YAP1 and TEAD1
]]>
https://biorxiv.org/cgi/content/short/2022.09.29.509946v1?rss=1"
Regin, M.Essahib, W.Demtschenko, A.Dewandre, D.David, L.Gerri, C.Niakan, K.Verheyen, G.Tournaye, H.Sterckx, J.Sermon, K.Van de Velde, H.2022-09-30doi:10.1101/2022.09.29.509946Cold Spring Harbor Laboratory Press2022-09-30
<![CDATA[
ASCL1 interacts with the mSWI/SNF at distal regulatory elements to regulate neural differentiation
]]>
https://biorxiv.org/cgi/content/short/2022.10.09.510609v1?rss=1"
Paun, O.Tan, Y. X.Patel, H.Strohbuecker, S.Ghanate, A.Cobolli Gigli, C.Sopena, M. L.Gerontogianni, L.Goldstone, R.Ang, S.-L.Guillemot, F.Dias, C.2022-10-09doi:10.1101/2022.10.09.510609Cold Spring Harbor Laboratory Press2022-10-09
<![CDATA[
Genome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides
]]>
https://biorxiv.org/cgi/content/short/2022.10.10.511318v1?rss=1"
Balendra, R.Ruiz de los Mozos, I.Glaria, I.Milioto, C.Odeh, H. M.Wilson, K. M.Ule, A. M.Hallegger, M.Masino, L.Martin, S.Patani, R.Shorter, J.Ule, J.Isaacs, A.2022-10-11doi:10.1101/2022.10.10.511318Cold Spring Harbor Laboratory Press2022-10-11
<![CDATA[
Restoration of functional PAX6 in aniridia patient iPSC-derived ocular tissue models using repurposed nonsense suppression drugs
]]>
https://biorxiv.org/cgi/content/short/2022.10.12.511600v1?rss=1"
Lima Cunha, D.Eintracht, J.Harding, P.Zhou, J. H.Moosajee, M.2022-10-12doi:10.1101/2022.10.12.511600Cold Spring Harbor Laboratory Press2022-10-12
<![CDATA[
Rates of global cellular translation and transcription during cell growth and the cell cycle in fission yeast.
]]>
https://biorxiv.org/cgi/content/short/2022.10.17.512486v1?rss=1"
Basier, C.Nurse, P.2022-10-17doi:10.1101/2022.10.17.512486Cold Spring Harbor Laboratory Press2022-10-17
<![CDATA[
Refphase: Multi-sample reference phasing reveals haplotype-specific copy number heterogeneity
]]>
https://biorxiv.org/cgi/content/short/2022.10.13.511885v1?rss=1"
Watkins, T. B.Colliver, E. C.Huska, M. R.Kaufmann, T. L.Lim, E. L.Haase, K.Van Loo, P.Swanton, C.McGranahan, N.Schwarz, R. F.2022-10-17doi:10.1101/2022.10.13.511885Cold Spring Harbor Laboratory Press2022-10-17
<![CDATA[
Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories
]]>
https://biorxiv.org/cgi/content/short/2022.10.19.512927v1?rss=1"
Bouhaddou, M.Reuschl, A.-K.Polacco, B. J.Thorne, L. G.Ummadi, M. R.Ye, C.Ramirez, R. R.Pelin, A.Batra, J.Jang, G. M.Xu, J.Moen, J. M.Richards, A. L.Zhou, Y.Harjai, B.Stevenson, E.Rojc, A.Ragazzini, R.Whelan, M. V. X.Furnon, W.De Lorenzo, G.Cowton, V.Syed, A. M.Ciling, A.Deutsch, N.Pirak, D.Dowgier, G.Mesner, D.Turner, J. L.McGovern, B. L.Rodriguez, M. L.Leiva-Rebollo, R.Dunham, A. S.Zhong, X.Eckhardt, M.Fossati, A.Liotta, N.Kehrer, T.Cupic, A.Rutkowska, M.Mena, N.Aslam, S.Hoffert, A.Foussard, H.Pham, J.Ly2022-10-21doi:10.1101/2022.10.19.512927Cold Spring Harbor Laboratory Press2022-10-21
<![CDATA[
Pseudogenes limit the identification of novel common transcripts generated by their parent genes
]]>
https://biorxiv.org/cgi/content/short/2022.10.21.513169v1?rss=1"
Gustavsson, E. K.Sethi, S.Gao, Y.Brenton, J.Garcia Ruiz, S.Zhang, D.Garza, R.Reynolds, R. H.Evans, J. R.Chen, Z.Grant-Peters, M.MacPherson, H.Montgomery, K.Dore, R.Wernick, A. I.Arber, C.Wray, S.Gandhi, S.Esselborn, J.Blauwendraat, C.Douse, C. H.Adami, A.Atacho, D. A. M.Kouli, A.Quaegebeur, A.Barker, R. A.Englund, E.Platt, F. M.Jakobsson, J.Wood, N. W.Houlden, H.Saini, H.Bento, C. F.Hardy, J.Ryten, M.2022-10-21doi:10.1101/2022.10.21.513169Cold Spring Harbor Laboratory Press2022-10-21
<![CDATA[
Blood and site of disease inflammatory profiles differ in HIV-1-infected pericardial tuberculosis patients
]]>
https://biorxiv.org/cgi/content/short/2022.10.21.513232v1?rss=1"
Mutavhatsindi, H.Du Bruyn, E.Ruzive, S.Howlett, P.Sher, A.Mayer-Barber, K. D.Barber, D. L.Ntsekhe, M.Wilkinson, R. J.Riou, C.2022-10-24doi:10.1101/2022.10.21.513232Cold Spring Harbor Laboratory Press2022-10-24
<![CDATA[
A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.513556v1?rss=1"
Altea-Manzano, P.Doglioni, G.Cuadros, A. M.Nolan, E.Fernandez-Garcia, J.Wu, Q.Cidre-Aranaz, F.Montagne, A.Planque, M.Marin-Bejar, O.Van Elsen, J.Vermeire, I.Broekaert, D.Riera-Domingo, C.Richard, F.Geukens, T.De Schepper, M.Leduc, S.Hatse, S.Lambrechts, Y.Kay, E.Lilla, S.Demeyer, S.Geldhof, V.Boeckx, B.Alekseenko, A.de la Calle Arregui, C.Floris, G.Marine, J.-C.Lambrechts, D.Pelechano, V.Mazzone, M.Zanivan, S.Cools, J.Wildiers, H.Baud, V.Gruenewald, T. G. P.Desmedt, C.Malanchi, I.Fendt, S.-M.2022-10-24doi:10.1101/2022.10.24.513556Cold Spring Harbor Laboratory Press2022-10-24
<![CDATA[
The identification of a gene expression signature of primordial follicle activation in mouse pregranulosa cells
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.513438v1?rss=1"
Frost, E. R.Taylor, G.Boeing, S.Galichet, C.Baker, M. A.Sutherland, J. M.Lovell-Badge, R.2022-10-24doi:10.1101/2022.10.24.513438Cold Spring Harbor Laboratory Press2022-10-24
<![CDATA[
Intracellular calcium elevations drive the nucleation of FIP200- and ATG13-containing pre-autophagosomal structures that become omegasomes
]]>
https://biorxiv.org/cgi/content/short/2022.11.02.514842v1?rss=1"
Smith, M.Schoenfelder, P.Manifava, M.Polson, H.Tooze, S.Roderick, L.Ktistakis, N.2022-11-02doi:10.1101/2022.11.02.514842Cold Spring Harbor Laboratory Press2022-11-02
<![CDATA[
HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion
]]>
https://biorxiv.org/cgi/content/short/2022.10.27.514062v1?rss=1"
View larger version (52K):
org.highwire.dtl.DTLVardef@ef0a5org.highwire.dtl.DTLVardef@d907a5org.highwire.dtl.DTLVardef@85176aorg.highwire.dtl.DTLVardef@1c4306a_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Lin, J. Q.Khuperkar, D.Pavlou, S.Makarchuk, S.Patikas, N.Lee, F. C. Y.Kang, J.Field, S. F.Zbiegly, J. M.Freeman, J. L.Ule, J.Metzakopian, E.Ruepp, M.-D.Mallucci, G. R.2022-10-27doi:10.1101/2022.10.27.514062Cold Spring Harbor Laboratory Press2022-10-27
<![CDATA[
Protein aggregation and calcium dysregulation are the earliest hallmarks of synucleinopathy in human midbrain dopaminergic neurons
]]>
https://biorxiv.org/cgi/content/short/2022.10.28.514238v1?rss=1"
80%). We characterised their molecular identity using single-cell RNA sequencing and their functional identity through the synthesis and secretion of dopamine, the ability to generate action potentials, and form functional synapses and networks. RNA velocity analyses confirmed the developmental transcriptomic trajectory of midbrain neural precursors into mDA neurons using our approach, and identified key driver genes in mDA neuronal development. To characterise the synucleinopathy, we adopted super-resolution methods to determine the number, size and structure of aggregates in SNCA-mutant mDA neurons. At one week of differentiation, prior to maturation to mDA neurons of molecular and functional identity, we demonstrate the formation of small aggregates; specifically, {beta}-sheet rich oligomeric aggregates, in SNCA-mutant midbrain immature neurons. The aggregation progresses over time to accumulate phosphorylated aggregates, and later fibrillar aggregates. When the midbrain neurons were functional, we observed evidence of impaired physiological calcium signalling, with raised basal calcium, and impairments in cytosolic and mitochondrial calcium efflux. Once midbrain identity fully developed, SNCA-mutant neurons exhibited bioenergetic impairments, mitochondrial dysfunction and oxidative stress. During the maturation of mDA neurons, upregulation of mitophagy and autophagy occured, and ultimately these multiple cellular stresses lead to an increase in cell death by six weeks post-differentiation. Our differentiation paradigm generates an efficient model for studying disease mechanisms in PD, and highlights that protein misfolding to generate intraneuronal oligomers is one of the earliest critical events driving disease in human neurons, rather than a late-stage hallmark of the disease.
]]>Virdi, G. S.Choi, M. L.Evans, J. R.Yao, Z.Athauda, D.Strohbuecker, S.Wernick, A. I.Alrashidi, H.Melandri, D.Perez-lloret, J.Stroh, P. R.Sylantyev, S.Eaton, S.Heales, S.Kunath, T.Horrocks, M. H.Abramov, A. Y.Patani, R.Gandhi, S.2022-10-28doi:10.1101/2022.10.28.514238Cold Spring Harbor Laboratory Press2022-10-28
<![CDATA[
An improved Erk biosensor reveals oscillatory Erk dynamics driven by mitotic erasure during early development
]]>
https://biorxiv.org/cgi/content/short/2022.11.03.515001v1?rss=1"
Wilcockson, S. G.Guglielmi, L.Araguas Rodriguez, P.Amoyel, M.Hill, C. S.2022-11-04doi:10.1101/2022.11.03.515001Cold Spring Harbor Laboratory Press2022-11-04
<![CDATA[
Subcytoplasmic location of translation controls protein output
]]>
https://biorxiv.org/cgi/content/short/2022.11.04.515216v1?rss=1"
Horste, E. L.Zhen, G.Fansler, M. M.Chen, X.Lee, F. C. Y.Ule, J.Mayr, C.2022-11-04doi:10.1101/2022.11.04.515216Cold Spring Harbor Laboratory Press2022-11-04
<![CDATA[
Pituitary stem cells differ according to their position in the gland and maintenance of their progeny depends on physiological context
]]>
https://biorxiv.org/cgi/content/short/2022.11.07.515440v1?rss=1"
Rizzoti, K.Chakravarty, P.Sheridan, D.Lovell-Badge, R.2022-11-07doi:10.1101/2022.11.07.515440Cold Spring Harbor Laboratory Press2022-11-07
<![CDATA[
Aryl hydrocarbon receptor utilises cellular zinc signals to maintain the gut epithelial barrier
]]>
https://biorxiv.org/cgi/content/short/2022.11.03.515052v1?rss=1"
Hu, X.Xiao, W.Lei, Y.Green, A. J.Li, X.Maradana, M. R.Gao, Y.Xie, X.Wang, R.Chennell, G.Basson, M. A.Kille, P.Maret, W.Bewick, G.Zhou, Y.Hogstrand, C.2022-11-04doi:10.1101/2022.11.03.515052Cold Spring Harbor Laboratory Press2022-11-04
<![CDATA[
Structural basis for ubiquitylation by HOIL-1
]]>
https://biorxiv.org/cgi/content/short/2022.11.13.516300v1?rss=1"
Wu, Q.Koliopoulos, M. G.Rittinger, K.Stieglitz, B.2022-11-13doi:10.1101/2022.11.13.516300Cold Spring Harbor Laboratory Press2022-11-13
<![CDATA[
Cell response to extracellular matrix energy dissipation outweighs rigidity sensing
]]>
https://biorxiv.org/cgi/content/short/2022.11.16.516826v1?rss=1"
Huerta-Lopez, C.Clemente-Manteca, A.Velazquez-Carreras, D.Espinosa, F. M.Sanchez, J. G.Saez, P.Martinez-del-Pozo, A.Garcia-Garcia, M.Martin-Colomo, S.Rodriguez-Blanco, A.Esteban-Gonzalez, R.Martin-Zamora, F. M.Gutierrez-Rus, L.Garcia, R.Roca-Cusachs, P.Elosegui-Artola, A.del Pozo, M. A.Herrero-Galan, E.Plaza, G. R.Alegre-Cebollada, J.2022-11-17doi:10.1101/2022.11.16.516826Cold Spring Harbor Laboratory Press2022-11-17
<![CDATA[
Whole genome error-corrected sequencing for sensitive circulating tumor DNA cancer monitoring
]]>
https://biorxiv.org/cgi/content/short/2022.11.17.516904v1?rss=1"
Cheng, A. P.Widman, A. J.Arora, A.Rusinek, I.Hooper, W. F.Murray, R.Halmos, D.Langanay, T.Inghirami, G.Germer, S.Marton, M.Manaa, D.Helland, A.Furatero, R.McClintock, J.Winterkorn, L.Steinsnyder, Z.Wang, Y.Rajagopalan, S.Alimohamed, A. I.Malbari, M. S.Saxena, A.Callahan, M. K.Frederick, D. T.Spain, L.Jaimovich, A.Lipson, D.Turajlic, S.Zody, M. C.Altorki, N. K.Wolchok, J. D.Postow, M. A.Robine, N.Boland, G.Landau, D. A.2022-11-17doi:10.1101/2022.11.17.516904Cold Spring Harbor Laboratory Press2022-11-17
<![CDATA[
Structural basis for Fc receptor recognition of immunoglobulin M
]]>
https://biorxiv.org/cgi/content/short/2022.11.18.517032v1?rss=1"
Chen, Q.Menon, R.Tolar, P.Rosenthal, P. B.2022-11-18doi:10.1101/2022.11.18.517032Cold Spring Harbor Laboratory Press2022-11-18
<![CDATA[
Multi-site assessment of reproducibility in high-content live cell imaging data
]]>
https://biorxiv.org/cgi/content/short/2022.11.18.516878v1?rss=1"
Hu, J.Serra-Picamal, X.Bakker, G.-J.Troys, M. V.Winograd-katz, S.Ege, N.Gong, X.Didan, Y.Grosheva, I.Polansky, O.Bakkali, K.Hamme, E. V.Erp, M. v.Vullings, M.Weiss, F.Clucas, J.Dowbaj, A. M.Sahai, E.Ampe, C.Geiger, B.Friedl, P.Bottai, M.Stromblad, S.2022-11-20doi:10.1101/2022.11.18.516878Cold Spring Harbor Laboratory Press2022-11-20
<![CDATA[
The Response of the Eukaryotic Replisome to G-quadruplex- and i-motif-forming Sequences
]]>
https://biorxiv.org/cgi/content/short/2022.11.18.517070v1?rss=1"
Williams, S. L.Casas-Delucchi, C. S.Raguseo, F.Guneri, D.Minamino, M.Fletcher, E. E.Yeeles, J. T.Waller, Z. A.Di Antonio, M.Coster, G.2022-11-18doi:10.1101/2022.11.18.517070Cold Spring Harbor Laboratory Press2022-11-18
<![CDATA[
Structure and function of Plasmodium actin II in the parasite mosquito stages
]]>
https://biorxiv.org/cgi/content/short/2022.11.22.517348v1?rss=1"
Lopez, A. J.Andreadaki, M.Vahokoski, J.Deligianni, E.Calder, L. J.Camerini, S.Freitag, A.Bergmann, U.Rosenthal, P. B.Siden-Kiamos, I.Kursula, I.2022-11-24doi:10.1101/2022.11.22.517348Cold Spring Harbor Laboratory Press2022-11-24
<![CDATA[
Epilepsy-linked kinase CDKL5 phosphorylates voltage-gated calcium channel Cav2.3, altering inactivation kinetics and neuronal excitability
]]>
https://biorxiv.org/cgi/content/short/2022.11.24.517538v1?rss=1"
Sampedro-Castaneda, M.Baltussen, L. L.Lopes, A. T.Qiu, Y.Sirvio, L.Mihaylov, S. R.Claxton, S.Richardson, J. C.Lignani, G.Ultanir, S. K.2022-11-24doi:10.1101/2022.11.24.517538Cold Spring Harbor Laboratory Press2022-11-24
<![CDATA[
Rarity: Discovering rare cell populations from single-cell imaging data
]]>
https://biorxiv.org/cgi/content/short/2022.07.15.500256v1?rss=1"
Marten, K.Bortolomeazzi, M.Montorsi, L.Spencer, J.Ciccarelli, F. D.Yau, C.2022-07-18doi:10.1101/2022.07.15.500256Cold Spring Harbor Laboratory Press2022-07-18
<![CDATA[
Tsetse flies choose birthing sites guided by environmental but not pheromonal cues
]]>
https://biorxiv.org/cgi/content/short/2022.11.30.518495v1?rss=1"
Adden, A. K.Haines, L. R.Acosta-Serrano, A.Prieto-Godino, L. L.2022-12-01doi:10.1101/2022.11.30.518495Cold Spring Harbor Laboratory Press2022-12-01
<![CDATA[
A role for MCH neuron firing in hippocampal plasticity and learning
]]>
https://biorxiv.org/cgi/content/short/2022.12.01.518339v1?rss=1"
Harris, J. J.Concetti, C.Peleg-Raibstein, D.Burdakov, D.2022-12-01doi:10.1101/2022.12.01.518339Cold Spring Harbor Laboratory Press2022-12-01
<![CDATA[
Investigating the genetic diversity of H5 avian influenza in the UK 2020-2022
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https://biorxiv.org/cgi/content/short/2022.12.03.518823v1?rss=1"
Byrne, A. M.James, J.Mollett, B. C.Meyer, S. M.Lewis, T.Czepiel, M.Seekings, A. H.Mahmood, S.Thomas, S. S.Ross, C. S.Byrne, D. J.McMenamy, M. J.Bailie, V.Lemon, K.Hansen, R. D.Falchieri, M.Lewis, N. S.Reid, S. M.Brown, I. H.Banyard, A. C.2022-12-03doi:10.1101/2022.12.03.518823Cold Spring Harbor Laboratory Press2022-12-03
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A heterotrimeric complex of Toxoplasma proteins promotes parasite survival in interferon gamma stimulated human cells
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https://biorxiv.org/cgi/content/short/2022.12.08.519568v1?rss=1"
Lockyer, E.Torelli, F.Butterworth, S.Song, O.-R.Howell, S.Weston, A.East, P.Treeck, M.2022-12-08doi:10.1101/2022.12.08.519568Cold Spring Harbor Laboratory Press2022-12-08
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p38γ and p38δ modulate innate immune response by regulating MEF2D activation
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https://biorxiv.org/cgi/content/short/2022.12.09.519777v1?rss=1"
Cuenda, A.Escos, A.Diaz-Mora, E.Fajardo, P.Gonzalez-Romero, D.Risco, A.Martin-Gomez, J.Bonneil, E.Sonenberg, N.Jafarnejad, S. M.Pattison, M.Sanz-Ezquerro, J. J.Ley, S. C.2022-12-09doi:10.1101/2022.12.09.519777Cold Spring Harbor Laboratory Press2022-12-09
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Structure of Toxoplasma gondii glideosome-associated connector suggests a role as an elastic element in actomyosin force generation for gliding motility
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https://biorxiv.org/cgi/content/short/2022.12.09.519741v1?rss=1"
Hung, Y.-F.Chen, Q.Pires, I.Rosenthal, P. B.Kursula, I.2022-12-10doi:10.1101/2022.12.09.519741Cold Spring Harbor Laboratory Press2022-12-10
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The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes
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https://biorxiv.org/cgi/content/short/2022.12.20.521107v1?rss=1"
Barreiro, R. A. S.Guardia, G. D. A.Meliso, F. M.Lei, X.Savio, A.Fellermeyer, M.Conceicao, H. B.Mercuri, R. L. V.Landry, T.Qiao, M.Blazquez, L.Ule, J.Penalva, L. O.Galante, P. A. F.2022-12-20doi:10.1101/2022.12.20.521107Cold Spring Harbor Laboratory Press2022-12-20
<![CDATA[
Back to the Future: Unleashing your cytometers spectral potential
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https://biorxiv.org/cgi/content/short/2022.12.21.521417v1?rss=1"
Walker, R. V.Hall, C.Ibrahim, H.Thompson, S.Hobson, P.Crofts, J.-A.Nobes, P.Lim, S.Burpee, T.2022-12-22doi:10.1101/2022.12.21.521417Cold Spring Harbor Laboratory Press2022-12-22
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Identification of novel coloboma candidate genes through conserved gene expression analyses across four vertebrate species
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https://biorxiv.org/cgi/content/short/2022.12.22.521600v1?rss=1"
Trejo-Reveles, V.Owen, N.Chan, B. H. C.Toms, M.Schoenebeck, J. J.Moosajee, M.Rainger, J.2022-12-22doi:10.1101/2022.12.22.521600Cold Spring Harbor Laboratory Press2022-12-22
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Cleavage furrow-directed cortical flows bias mechanochemical pathways for PAR polarization in the C. elegans germ lineage
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https://biorxiv.org/cgi/content/short/2022.12.22.521633v1?rss=1"
Ng, K.Hirani, N.Bland, T.Pinto, J. B.Goehring, N. W.2022-12-23doi:10.1101/2022.12.22.521633Cold Spring Harbor Laboratory Press2022-12-23
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Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation
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https://biorxiv.org/cgi/content/short/2022.12.23.521684v1?rss=1"
Ramirez Montero, D.Sanchez, H.van Veen, E.van Laar, T.Solano, B.Diffley, J. F. X.Dekker, N. H.2022-12-23doi:10.1101/2022.12.23.521684Cold Spring Harbor Laboratory Press2022-12-23
<![CDATA[
Discovery and characterization of cyclic peptides selective for the C-terminal bromodomains of BET family proteins
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https://biorxiv.org/cgi/content/short/2022.12.25.521885v1?rss=1"
Franck, C.Patel, K.Walport, L. J.Christie, M. T.Norman, A.Passioura, T.Payne, R. J.Suga, H.Mackay, J. P.2022-12-26doi:10.1101/2022.12.25.521885Cold Spring Harbor Laboratory Press2022-12-26
<![CDATA[
A practical extraction and spatial statistical pipeline for large 3D bioimages
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https://biorxiv.org/cgi/content/short/2022.12.29.521787v1?rss=1"
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]]>Adams, G.Tissot, F.Liu, C.Brunsdon, C.Duffy, K.Lo Celso, C.2022-12-29doi:10.1101/2022.12.29.521787Cold Spring Harbor Laboratory Press2022-12-29
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Optimization of energy production and central carbon metabolism in a non-respiring eukaryote
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https://biorxiv.org/cgi/content/short/2022.12.29.522219v1?rss=1"
Alam, S.Gu, Y.Reichert, P.Bahler, J.Oliferenko, S.2022-12-29doi:10.1101/2022.12.29.522219Cold Spring Harbor Laboratory Press2022-12-29
<![CDATA[
Control of atypical PKC{iota} membrane dissociation by tyrosine phosphorylation within a PB1-C1 interdomain interface
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https://biorxiv.org/cgi/content/short/2023.01.03.522491v1?rss=1"
Cobbaut, M.McDonald, N. Q.Parker, P. J.2023-01-03doi:10.1101/2023.01.03.522491Cold Spring Harbor Laboratory Press2023-01-03
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Genomic evolution of non-small cell lung cancer patient-derived xenograft models
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https://biorxiv.org/cgi/content/short/2023.01.06.521078v1?rss=1"
Hynds, R. E.Huebner, A.Pearce, D. R.Akarca, A. U.Moore, D. A.Ward, S.Gowers, K. H. C.Karasaki, T.Hill, M. S.Al Bakir, M.Wilson, G. A.Pich, O.Sivakumar, M.Ben Aissa, A.Gronroos, E.Chandrasekharan, D.Kolluri, K. K.Towns, R.Wang, K.Cook, D. E.Bosshard-Carter, L.Naceur-Lombardelli, C.Rowan, A. J.Veeriah, S.Litchfield, K.Quezada, S. A.Janes, S. M.Jamal-Hanjani, M.Marafioti, T.TRACERx Consortium,McGranahan, N.Swanton, C.2023-01-06doi:10.1101/2023.01.06.521078Cold Spring Harbor Laboratory Press2023-01-06
<![CDATA[
Analysis of CDPK1 targets identifies a trafficking adaptor complex that regulates microneme exocytosis in Toxoplasma
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https://biorxiv.org/cgi/content/short/2023.01.11.523553v1?rss=1"
Chan, A. W.Broncel, M.Haseley, N. R.Chakladar, S.Andree, E.Herneisen, A. L.Shortt, E.Treeck, M.Lourido, S.2023-01-11doi:10.1101/2023.01.11.523553Cold Spring Harbor Laboratory Press2023-01-11
<![CDATA[
Femtosecond laser preparation of resin embedded samples for correlative microscopy workflows in life sciences
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https://biorxiv.org/cgi/content/short/2023.01.10.523473v1?rss=1"
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C_FIG
]]>Bosch, C.Lindenau, J.Pacureanu, A.Peddie, C. J.Majkut, M.Douglas, A. C.Carzaniga, R.Rack, A.Collinson, L.Schaefer, A.Stegmann, H.2023-01-12doi:10.1101/2023.01.10.523473Cold Spring Harbor Laboratory Press2023-01-12
<![CDATA[
spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content
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https://biorxiv.org/cgi/content/short/2023.01.12.523500v1?rss=1"
de Jonghe, J.Kaminski, T. S.Morse, D.Tabaka, M.Ellermann, A. L.Kohler, T. N.Amadei, G.Handford, C.Findlay, G.Zernicka-Goetz, M.Teichmann, S.Hollfelder, F.2023-01-13doi:10.1101/2023.01.12.523500Cold Spring Harbor Laboratory Press2023-01-13
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Automated staging of zebrafish embryos with KimmelNet
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https://biorxiv.org/cgi/content/short/2023.01.13.523922v1?rss=1"
Barry, D. J.Jones, R. A.Renshaw, M. J.2023-01-14doi:10.1101/2023.01.13.523922Cold Spring Harbor Laboratory Press2023-01-14
<![CDATA[
Biomimetic actin cortices shape cell-sized lipid vesicles
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https://biorxiv.org/cgi/content/short/2023.01.15.524117v1?rss=1"
Baldauf, L.Frey, F.Perez, M. A.Mladenov, M.Way, M.Idema, T.Koenderink, G.2023-01-18doi:10.1101/2023.01.15.524117Cold Spring Harbor Laboratory Press2023-01-18
<![CDATA[
ARPC5 deficiency leads to severe early onset systemic inflammation and early mortality
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https://biorxiv.org/cgi/content/short/2023.01.19.524688v1?rss=1"
Sindram, E.Caballero-Oteyza, A.Cogata, N.Huang, S. C. M.Alizadeh, Z.Gamez-Diaz, L.Fazlollahi, M. R.Peng, X.Grimbacher, B.Way, M.Proietti, M.2023-01-21doi:10.1101/2023.01.19.524688Cold Spring Harbor Laboratory Press2023-01-21
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Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD
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https://biorxiv.org/cgi/content/short/2023.01.23.525149v1?rss=1"
Seddighi, S.Qi, Y. A.Brown, A.-L.Wilkins, O. G.Bereda, C.Belair, C.Zhang, Y.Prudencio, M.Keuss, M.Khandeshi, A.Pickles, S.Hill, S.Hawrot, J.Ramos, D.Yuan, H.Roberts, J.Kelmer Sacramento, E.Shah, S.Nalls, M. A.Colon-Mercado, J.Reyes, J.Ryan, V.Nelson, M.Cook, C.Li, Z.Screven, L.Kwan, J.Shantaraman, A.Ping, L.Koike, Y.Oskarsson, B.Staff, N.Duong, D.Ahmed, A.Secrier, M.Ule, J.Jacobson, S.Rohrer, J.Malaspina, A.Glass, J.Ori, A.Seyfried, N.Maragkakis, M.Petrucelli, L.Fratta, P.Ward, M. E.2023-01-23doi:10.1101/2023.01.23.525149Cold Spring Harbor Laboratory Press2023-01-23
<![CDATA[
Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment
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https://biorxiv.org/cgi/content/short/2023.01.24.525325v1?rss=1"
Misetic, H.Keddar, M. R.Jeannon, J.-P.Ciccarelli, F. D.2023-01-24doi:10.1101/2023.01.24.525325Cold Spring Harbor Laboratory Press2023-01-24
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Phenotyping of lymphoproliferative tumours generated in xenografts of non-small cell lung cancer
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https://biorxiv.org/cgi/content/short/2023.01.24.520089v1?rss=1"
Pearce, D. R.Akarca, A. U.De Maeyer, R. P. H.Kostina, E.Huebner, A.Sivakumar, M.Karasaki, T.Shah, K.Janes, S. M.McGranahan, N. E.Reddy, V.Akbar, A.Moore, D. A.Marafioti, T.Swanton, C.Hynds, R. E.2023-01-24doi:10.1101/2023.01.24.520089Cold Spring Harbor Laboratory Press2023-01-24
<![CDATA[
Extracellular vesicles and co-isolated endogenous retroviruses differently affect dendritic cells
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https://biorxiv.org/cgi/content/short/2023.01.27.525863v1?rss=1"
Cocozza, F.martin jaular, l.lippens, l.di cicco, a.arribas, y. a.dingli, f.richard, m.merle, l.Poullet, P.loew, d.Hendrix, A.Kassiotis, G.joliot, a.tkach, m.Thery, C.2023-01-28doi:10.1101/2023.01.27.525863Cold Spring Harbor Laboratory Press2023-01-28
<![CDATA[
Plasmodium ARK2-EB1 axis drives the unconventional spindle dynamics, scaffold formation, and chromosome segregation of sexual transmission stages
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https://biorxiv.org/cgi/content/short/2023.01.29.526106v1?rss=1"
Zeeshan, M.Rea, E.Abel, S.Vukusic, K.Markus, R.Brady, D.Eze, A. A.Rashpa, R.Balestra, A.Bottrill, A.Brochet, M.Guttery, D.Tolic, I. M.Holder, A. A.Le Roch, K. G.Tromer, E.Tewari, R.2023-01-31doi:10.1101/2023.01.29.526106Cold Spring Harbor Laboratory Press2023-01-31
<![CDATA[
The C9Orf72 hexanucleotide repeat expansion transcript forms insoluble aggregates facilitated by multimolecular G-quadruplex structures
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https://biorxiv.org/cgi/content/short/2023.01.31.526399v1?rss=1"
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]]>Raguseo, F.Tanase, D.Malouf, L.Rubio Sanchez, R.Elani, Y.Di Michele, L.Di Antonio, M.2023-01-31doi:10.1101/2023.01.31.526399Cold Spring Harbor Laboratory Press2023-01-31
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Imprinted anti-hemagglutinin and anti-neuraminidase antibody responses after childhood infections of A(H1N1) and A(H1N1)pdm09 influenza viruses
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https://biorxiv.org/cgi/content/short/2023.02.01.526741v1?rss=1"
Daulagala, P.Mann, B.Leung, K.Lau, E.Yung, L.Lei, R.Nizami, S. I. N.Wu, J. T.Chiu, S. S.Daniels, R. S.Wu, N. C.Wentworth, D. E.Peiris, J. S. M.Yen, H.-L.2023-02-02doi:10.1101/2023.02.01.526741Cold Spring Harbor Laboratory Press2023-02-02
<![CDATA[
PerTurboID: A targeted in situ method to measure changes in a local protein environment reveals the impact of kinase deletion on cytoadhesion in malaria causing parasites
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https://biorxiv.org/cgi/content/short/2023.02.02.526785v1?rss=1"
Davies, H.Belda, H.Broncel, M.Dalimot, J.Treeck, M.2023-02-03doi:10.1101/2023.02.02.526785Cold Spring Harbor Laboratory Press2023-02-03
<![CDATA[
A chemoproteomic platform for reactive fragment profiling against the deubiquitinases
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https://biorxiv.org/cgi/content/short/2023.02.01.526632v1?rss=1"
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]]>Cookson, R.Vuorinen, A.Pettinger, J.Kennedy, C. R.Kirkpatrick, J. M.Peltier-Heap, R. E.Powell, A.Snijders, A. P.Skehel, M.House, D.Rittinger, K.Bush, J. T.2023-02-03doi:10.1101/2023.02.01.526632Cold Spring Harbor Laboratory Press2023-02-03
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MICA: A multi-omics method to predict gene regulatory networks in early human embryos
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https://biorxiv.org/cgi/content/short/2023.02.03.527081v1?rss=1"
Alanis-Lobato, G.Bartlett, T. E.Huang, Q.Simon, C.McCarthy, A.Elder, K.Snell, P.Christie, L.Niakan, K.2023-02-03doi:10.1101/2023.02.03.527081Cold Spring Harbor Laboratory Press2023-02-03
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A Potent and Selective CDKL5/GSK3 Chemical Probe is Neuroprotective
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https://biorxiv.org/cgi/content/short/2023.02.09.527935v1?rss=1"
Ong, H. W.Liang, Y.Richardson, W.Lowry, E. R.Wells, C. I.Chen, X.Silvestre, M.Dempster, K.Silvaroli, J. A.Smith, J. L.Wichterle, H.Pabla, N. S.Ultanir, S. K.Bullock, A. N.Drewry, D.Axtman, A. D.2023-02-10doi:10.1101/2023.02.09.527935Cold Spring Harbor Laboratory Press2023-02-10
<![CDATA[
Palmitoyl transferase ZDHHC20 promotes pancreatic cancer metastasis
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https://biorxiv.org/cgi/content/short/2023.02.08.527637v1?rss=1"
Tomic, G.Sheridan, C.Refermat, A.Baggelaar, M.Sipthorp, J.Sudarshan, B.Ocasio, C. A.Suarez-Bonnet, A.Priestnall, S.Herbert, E.Tate, E.Downward, J.2023-02-08doi:10.1101/2023.02.08.527637Cold Spring Harbor Laboratory Press2023-02-08
<![CDATA[
Enzyme-less nanopore detection of post-translational modifications within long polypeptides
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https://biorxiv.org/cgi/content/short/2023.02.09.527483v1?rss=1"
Martin-Baniandres, P.Lan, W.-H.Board, S.Romero-ruiz, M.Garcia-Manyes, S.Qing, Y.Bayley, H.2023-02-09doi:10.1101/2023.02.09.527483Cold Spring Harbor Laboratory Press2023-02-09
<![CDATA[
The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles
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https://biorxiv.org/cgi/content/short/2023.02.10.528004v1?rss=1"
Ensinck, I.Maman, A.Albihlal, W.Lassandro, M.Salzano, G.Sideri, T.Howell, S.Calvani, E.Patel, H.Bushkin, G. G.Snijders, A. P.Ralser, M.Skehel, M.Casanal, A.Schwartz, S.van Werven, F.2023-02-10doi:10.1101/2023.02.10.528004Cold Spring Harbor Laboratory Press2023-02-10
<![CDATA[
The ecdysone receptor promotes or suppresses proliferation according toligand level
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https://biorxiv.org/cgi/content/short/2023.02.10.527985v1?rss=1"
Perez-Mockus, G.Cocconi, L.Alexandre, C.Aerne, B. L.Salbreux, G.Vincent, J.-P.2023-02-11doi:10.1101/2023.02.10.527985Cold Spring Harbor Laboratory Press2023-02-11
<![CDATA[
Unique Amphipathic α-helix Drives Membrane Insertion and Enzymatic Activity of ATG3
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https://biorxiv.org/cgi/content/short/2023.02.11.528101v1?rss=1"
Nishimura, T.Lazzeri, G.Mizushima, N.Covino, R.Tooze, S.2023-02-12doi:10.1101/2023.02.11.528101Cold Spring Harbor Laboratory Press2023-02-12
<![CDATA[
Stabilisation of β-Catenin-WNT signalling by USP10 in APC-truncated colorectal cancer drives cancer stemness and enables super-competitor signalling
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https://biorxiv.org/cgi/content/short/2023.02.10.527983v1?rss=1"
Reissland, M.Hartmann, O.Tauch, S.Prieto-Garcia, C.Schulte, C.Solvei, D.Loebbert, S.Jacomin, A. C.Pesic, M.Bugter, J. M.Schuelein-Voelk, C.Fuss, C.Pahor, N.Ade, C.Buck, V.Potente, M.Li, V.Beliu, G.Wiegering, A.Bitman-Lotan, E.Grossmann, T.Rosenfeldt, M.Eilers, M.Maric, H.Maurice, M.Greten, F.Dikic, I.Orian, A.Gallant, P.Diefenbacher, M. E.2023-02-11doi:10.1101/2023.02.10.527983Cold Spring Harbor Laboratory Press2023-02-11
<![CDATA[
Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity
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https://biorxiv.org/cgi/content/short/2023.02.17.528960v1?rss=1"
Rohban, S.Rafiee, M.-R.Ule, J.Luscombe, N.2023-02-17doi:10.1101/2023.02.17.528960Cold Spring Harbor Laboratory Press2023-02-17
<![CDATA[
Discovery of multi-state gene cluster switches determining the adaptive mitochondrial and metabolic landscape of breast cancer
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https://biorxiv.org/cgi/content/short/2023.02.17.528922v1?rss=1"
Menegollo, M.Bentham, R. B.Henriques, T.Ng, S. Q.Ren, Z.Esculier, C.Agarwal, S.Tong, E.Ilangovan, S.Szabadkai, Z.Suman, M.Patani, N.Ghanate, A.Bryson, K.Stein, R. C.Yuneva, M.Szabadkai, G.2023-02-18doi:10.1101/2023.02.17.528922Cold Spring Harbor Laboratory Press2023-02-18
<![CDATA[
Active mesh and neural network pipeline for cell aggregate segmentation
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https://biorxiv.org/cgi/content/short/2023.02.17.528925v1?rss=1"
Smith, M. B.Salbreux, G.Dunsby, C.Sparks, H.Almagro, J.Behrens, A.Chaigne, A.2023-02-21doi:10.1101/2023.02.17.528925Cold Spring Harbor Laboratory Press2023-02-21
<![CDATA[
Pan-genotypic probe-based enrichment to improve efficiency of Hepatitis B virus sequencing
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https://biorxiv.org/cgi/content/short/2023.02.20.529276v1?rss=1"
Lumley, S. F.Jennings, D.Waddilove, E.Trebes, A.Delphin, M.Downs, L. O.Macintyre-Crockett, G.Wu, Y.Chaudron, S.de Lara, C.Chai, H.Maponga, T.Martin, J.Collier, J.Ip, C.Barnes, E.Bonsall, D.Piazza, P.Ansari, M. A.Matthews, P. C.2023-02-21doi:10.1101/2023.02.20.529276Cold Spring Harbor Laboratory Press2023-02-21
<![CDATA[
Signalling-dependent refinement of cell fate choice during tissue remodelling
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https://biorxiv.org/cgi/content/short/2023.02.21.529250v1?rss=1"
Herszterg, S.de Gennes, M.Cicolini, S.Huang, A.Alexandre, C.Smith, M. B.Araujo, H.Vincent, J.-P.Salbreux, G.2023-02-22doi:10.1101/2023.02.21.529250Cold Spring Harbor Laboratory Press2023-02-22
<![CDATA[
The level of Nck rather than N-WASP determines the rate of actin-based motility of Vaccinia
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https://biorxiv.org/cgi/content/short/2023.02.24.529907v1?rss=1"
Basant, A.Way, M.2023-02-24doi:10.1101/2023.02.24.529907Cold Spring Harbor Laboratory Press2023-02-24
<![CDATA[
Notochord and axial progenitor generation by timely BMP and NODAL inhibition during vertebrate trunk formation
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https://biorxiv.org/cgi/content/short/2023.02.27.530267v1?rss=1"
Rito, T.Libby, A. R.Demuth, M.Briscoe, J.2023-02-28doi:10.1101/2023.02.27.530267Cold Spring Harbor Laboratory Press2023-02-28
<![CDATA[
Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size
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https://biorxiv.org/cgi/content/short/2023.03.06.531353v1?rss=1"
Gu, Y.Alam, S.Oliferenko, S.2023-03-07doi:10.1101/2023.03.06.531353Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins
]]>
https://biorxiv.org/cgi/content/short/2023.03.07.531515v1?rss=1"
Mas, A. M.Goni, E.Ruiz de los Mozos, I.Arcas, A.Statello, L.Gonzalez, J.Blazquez, L.Lee, W. T. C.Gupta, D.Sejas, A.Hoshina, S.Armaos, A.Tartaglia, G. G.Waga, S.Ule, J.Rothenberg, E.Gomez, M.Huarte, M.2023-03-07doi:10.1101/2023.03.07.531515Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
Dissecting the subcellular forces sculpting early C. elegans embryos
]]>
https://biorxiv.org/cgi/content/short/2023.03.07.531437v1?rss=1"
Yamamoto, K.Ichbiah, S.Pinto, J.Delbary, F.Goehring, N.Turlier, H.Charras, G.2023-03-09doi:10.1101/2023.03.07.531437Cold Spring Harbor Laboratory Press2023-03-09
<![CDATA[
Nondestructive Spatial Lipidomics for Glioma Classification
]]>
https://biorxiv.org/cgi/content/short/2023.03.09.531882v1?rss=1"
Martella, D. A.Rose, L. A.Rouatbi, N.Gu, C.Caprettini, V.Jensen, M.Hagemann, C.Serio, A.Al-Jamal, K.Parsons, M.Bergholt, M.Brennan, P.Zaritski, A.Chiappini, C.2023-03-12doi:10.1101/2023.03.09.531882Cold Spring Harbor Laboratory Press2023-03-12
<![CDATA[
RNA allelic frequencies of somatic mutations encode substantial functional information in cancers
]]>
https://biorxiv.org/cgi/content/short/2023.03.09.531725v1?rss=1"
Black, J. R. M.Jones, T. P.Martinez-Ruiz, C.Litovchenko, M.Puttick, C.McGranahan, N.2023-03-11doi:10.1101/2023.03.09.531725Cold Spring Harbor Laboratory Press2023-03-11
<![CDATA[
Metabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic target
]]>
https://biorxiv.org/cgi/content/short/2023.03.12.531945v1?rss=1"
Vande Voorde, J.Najumudeen, A. K.Steven, R. T.Nikula, C. J.Dexter, A.Zeiger, L. B.Elia, E. A.Nassif, A.Gonzalez-Fernandez, A.Murta, T.Gillespie, M.Ford, C. A.Lannagan, T. R. M.Vlahov, N.Ridgway, R. A.Nixon, C.Gilroy, K.Gay, D. M.Burton, A.Yan, B.Sellers, K.Wu, V.Xiang, Y.Shokry, E.Clark, W.Li, V. S. W.Barry, S. T.Goodwin, R. J. A.Takats, Z.Maddocks, O. D. K.Sumpton, D.Yuneva, M. O.Campbell, A. D.Bunch, J.Sansom, O. J.2023-03-12doi:10.1101/2023.03.12.531945Cold Spring Harbor Laboratory Press2023-03-12
<![CDATA[
A malaria parasite phospholipase facilitates efficient asexual blood stage egress
]]>
https://biorxiv.org/cgi/content/short/2023.03.13.532312v1?rss=1"
Ramaprasad, A.Burda, P.-C.Koussis, K.Thomas, J. A.Pietsch, E.Calvani, E.Howell, S. A.MacRae, J. I.Snijders, A. P.Gilberger, T. W.Blackman, M. J.2023-03-13doi:10.1101/2023.03.13.532312Cold Spring Harbor Laboratory Press2023-03-13
<![CDATA[
Insufficient evidence for natural selection associated with the Black Death
]]>
https://biorxiv.org/cgi/content/short/2023.03.14.532615v1?rss=1"
Barton, A. R.Santander, C. G.Skoglund, P.Moltke, I.Reich, D.Mathieson, I.2023-03-15doi:10.1101/2023.03.14.532615Cold Spring Harbor Laboratory Press2023-03-15
<![CDATA[
Dietary environmental factors shape the defence against infection with Cryptosporidium
]]>
https://biorxiv.org/cgi/content/short/2023.03.30.534739v1?rss=1"
Sateriale, A.Maradana, M. R.Marzook, N. B.Diaz Perez, O.Mkandawire, T.Diny, N. L.Li, Y.Liebert, A.Shah, K.Tolaini, M.Kvac, M.Stockinger, B.2023-04-01doi:10.1101/2023.03.30.534739Cold Spring Harbor Laboratory Press2023-04-01
<![CDATA[
The minus end depolymerase KIF2A drives flux-like treadmilling of γTuRC-uncapped microtubules
]]>
https://biorxiv.org/cgi/content/short/2023.04.06.535808v1?rss=1"
Henkin, G.Brito, C.Thomas, C.Surrey, T.2023-04-06doi:10.1101/2023.04.06.535808Cold Spring Harbor Laboratory Press2023-04-06
<![CDATA[
Spatiotemporal Genomic Profiling of Intestinal Metaplasia Reveals Clonal Dynamics of Gastric Cancer Progression
]]>
https://biorxiv.org/cgi/content/short/2023.04.10.536195v1?rss=1"
Huang, K. K.Ma, H.Uchihara, T.Sheng, T.Chong, R. H. H.Zhu, F.Srivastava, S.Tay, S. T.Sundar, R.Tan, A. L. K.Ong, X.Lee, M.Ho, S. W. T.Lesluyes, T.Van Loo, P.Chua, J. S.Ramnarayanan, K.Ang, T. L.Khor, C.Lee, J. W. J.Tsao, S. K. K.Teh, M.Chung, H.So, J. B. Y.Yeoh, K. G.Tan, P.2023-04-11doi:10.1101/2023.04.10.536195Cold Spring Harbor Laboratory Press2023-04-11
<![CDATA[
FOXL2 interaction with different binding partners regulates the dynamics of granulosa cell differentiation across ovarian development
]]>
https://biorxiv.org/cgi/content/short/2023.04.14.536403v1?rss=1"
Migale, R.Neumann, M.Mitter, R.Rafiee, M.-R.Wood, S.Olsen, J.Lovell-Badge, R.2023-04-14doi:10.1101/2023.04.14.536403Cold Spring Harbor Laboratory Press2023-04-14
<![CDATA[
In vivo CRISPR screen identifies KRAS-induced COX-2 as a driver of immune evasion and immunotherapy resistance in lung cancer
]]>
https://biorxiv.org/cgi/content/short/2023.04.13.536740v1?rss=1"
Boumelha, J.de Castro, A.Bah, N.Cha, H.de Carne Trecesson, S.Rana, S.Anastasiou, P.Mugarza, E.Moore, C.Goldstone, R.East, P.Litchfield, K.Lee, S.-H.Molina-Arcas, M.Downward, J.2023-04-14doi:10.1101/2023.04.13.536740Cold Spring Harbor Laboratory Press2023-04-14
<![CDATA[
A palmitoyl transferase chemical genetic system to map ZDHHC-specific S-acylation
]]>
https://biorxiv.org/cgi/content/short/2023.04.18.537386v1?rss=1"
300 unique and shared substrates across multiple cell lines and S-acylation sites for novel functionally diverse substrates. We expect that this powerful and versatile platform will open a new window on S-acylation biology for a wide range of models and organisms.
]]>Ocasio, C. A.Baggelaar, M. P.Sipthorp, J.Losada de la Lastra, A.Volaric, J.Soudy, C.Storck, E. M.Palma-Duran, S. A.MacRae, J. I.Tomic, G.Carr, L.Downward, J.Eggert, U.Tate, E. W.2023-04-18doi:10.1101/2023.04.18.537386Cold Spring Harbor Laboratory Press2023-04-18
<![CDATA[
ER-dependent membrane repair of mycobacteria-induced vacuole damage
]]>
https://biorxiv.org/cgi/content/short/2023.04.17.537276v1?rss=1"
Anand, A.Mazur, A.-C.Rosell-Arevalo, P.Franzkoch, R.Breitsprecher, L.Listian, S. A.Hüttel, S. V.Müller, D.Schäfer, D. G.Vormittag, S.Hilbi, H.Maniak, M.Gutierrez, M.Barisch, C.2023-04-19doi:10.1101/2023.04.17.537276Cold Spring Harbor Laboratory Press2023-04-19
<![CDATA[
CRISPR-Cas9 mediated endogenous utrophin upregulation improves Duchenne Muscular Dystrophy
]]>
https://biorxiv.org/cgi/content/short/2023.04.18.536394v1?rss=1"
Guiraud, S.Dastidar, S.Mazed, F.Amor, F.Ralu, M.de Cian, A.Richard, I.Ronzitti, G.Tedesco, F. S.Amendola, M.2023-04-19doi:10.1101/2023.04.18.536394Cold Spring Harbor Laboratory Press2023-04-19
<![CDATA[
Altered neutrophil extracellular traps in response to Mycobacterium tuberculosis in persons living with HIV with no previous TB and negative TST and IGRA
]]>
https://biorxiv.org/cgi/content/short/2023.04.19.537498v1?rss=1"
Kroon, E. E.Correa de Macedo, W.Evans, R.Seeger, A.Engelbrecht, L.Kriel, J.Loos, B.Okugbeni, N.Orlova, M. O.Cassart, P.Kinnear, C.Tromp, G.Moller, M.Wilkinson, R. J.Coussens, A. K.2023-04-21doi:10.1101/2023.04.19.537498Cold Spring Harbor Laboratory Press2023-04-21
<![CDATA[
Circulating neutrophils from patients with early breast cancer have distinct subtype-dependent phenotypes
]]>
https://biorxiv.org/cgi/content/short/2023.04.19.537022v1?rss=1"
Ramessur, A.Ambasager, B.Aramburu, I. V.Peakman, F.Gleason, K.Lehmann, C.Papayannopoulos, V.Coombes, C.Malanchi, I.2023-04-21doi:10.1101/2023.04.19.537022Cold Spring Harbor Laboratory Press2023-04-21
<![CDATA[
Mapping host-microbe transcriptional interactions by dual perturb-seq
]]>
https://biorxiv.org/cgi/content/short/2023.04.21.537779v1?rss=1"
Butterworth, S.Kordova, K.Chandrasekaran, S.Thomas, K. K.Torelli, F.Lockyer, E. J.Edwards, A.Goldstone, R.Koshy, A. A.Treeck, M.2023-04-21doi:10.1101/2023.04.21.537779Cold Spring Harbor Laboratory Press2023-04-21
<![CDATA[
Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology
]]>
https://biorxiv.org/cgi/content/short/2023.04.24.538049v1?rss=1"
Castano, A.Silvestre, M.Wells, C. I.Sanderson, J. L.Ferrer, C. A.Ong, H. W.Lang, Y.Richardson, W.Silvaroli, J. A.Bashore, F. M.Smith, J. L.Genereux, I. M.Dempster, K.Drewry, D. H.Pabla, N. S.Bullock, A. N.Benke, T. A.Ultanir, S.Axtman, A. D.2023-04-24doi:10.1101/2023.04.24.538049Cold Spring Harbor Laboratory Press2023-04-24
<![CDATA[
Abundant capped RNAs are derived from mRNA cleavage at 3'UTR G-Quadruplexes
]]>
https://biorxiv.org/cgi/content/short/2023.04.27.538568v1?rss=1"
View larger version (15K):
org.highwire.dtl.DTLVardef@3f2ca7org.highwire.dtl.DTLVardef@18ca1b6org.highwire.dtl.DTLVardef@1ccdd8dorg.highwire.dtl.DTLVardef@e58938_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Haberman, N.Digby, H.Faraway, R.Cheung, R.Jobbins, A. M.Parr, C.Yasuzawa, K.Kasukawa, T.Yip, C. W.Kato, M.Takahashi, H.Carninci, P.Ule, J.Sibley, C. R.Martinez-sanchez, A.Lenhard, B.Vernia, S.2023-04-27doi:10.1101/2023.04.27.538568Cold Spring Harbor Laboratory Press2023-04-27
<![CDATA[
Rare SH2B3 coding variants identified in lupus patients impair B cell tolerance and predispose to autoimmunity
]]>
https://biorxiv.org/cgi/content/short/2023.04.27.538529v1?rss=1"
Zhang, Y.Morris, R.Lorenzo, A. M. D.Meng, X.Kershaw, N. J.Kiridena, P.Brown, G. J.Burgio, G.Cappello, J. Y.Shen, Q.Wang, H.Turnbull, C. M.Lea-Henry, T.Stanley, M.Yu, Z.Ballard, F.Chuah, A.Lee, J. C.Hatch, A.-M.Headley, A. P.Trnka, P.Mallon, D.Fletcher, J. T.Walters, G. D.Sestan, M.Jelusic, M.Cook, M. C.Athanasopoulos, V.Fulcher, D. A.Babon, J. J.Vinuesa, C. G.Ellyard, J. I.2023-04-29doi:10.1101/2023.04.27.538529Cold Spring Harbor Laboratory Press2023-04-29
<![CDATA[
An image segmentation method based on the spatial correlation coefficient of Local Moran's I
]]>
https://biorxiv.org/cgi/content/short/2023.05.02.539063v1?rss=1"
David, C.Giber, K.Kerti-Szigeti, K.Kollo, M.Nusser, Z.Acsady, L.2023-05-02doi:10.1101/2023.05.02.539063Cold Spring Harbor Laboratory Press2023-05-02
<![CDATA[
A disease-associated gene desert orchestrates macrophage inflammatory responses via ETS2
]]>
https://biorxiv.org/cgi/content/short/2023.05.05.539522v1?rss=1"
Stankey, C. T.Bourges, C.Turner-Stokes, T.Piedade, A. P.Palmer-Jones, C.Papa, I.Silva dos Santos, M.Randzavola, L. O.Speidel, L.Parkes, E. C.Edwards, W.Rochford, A. P.Murray, C.MacRae, J. I.Skoglund, P.Wallace, C.Cader, M. Z.Thomas, D. C.Lee, J. C.2023-05-07doi:10.1101/2023.05.05.539522Cold Spring Harbor Laboratory Press2023-05-07
<![CDATA[
CLEM-Reg: An automated point cloud based registration algorithm for correlative light and volume electron microscopy
]]>
https://biorxiv.org/cgi/content/short/2023.05.11.540445v1?rss=1"
Krentzel, D.Elphick, M.Domart, M.-C.Peddie, C. J.Laine, R. F.Henriques, R.Collinson, L. M.Jones, M. L.2023-05-12doi:10.1101/2023.05.11.540445Cold Spring Harbor Laboratory Press2023-05-12
<![CDATA[
mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome
]]>
https://biorxiv.org/cgi/content/short/2023.05.17.541126v1?rss=1"
Low, J. K.Patel, K.Solomon, P.Norman, A.Pachl, P.Jones, N.Payne, R. J.Passioura, T.Suga, H.Walport, L. J.Mackay, J.2023-05-17doi:10.1101/2023.05.17.541126Cold Spring Harbor Laboratory Press2023-05-17
<![CDATA[
Antigenic mapping of the hemagglutinin of the H9 subtype influenza A viruses using sera from Japanese quail (Coturnix c. japonica).
]]>
https://biorxiv.org/cgi/content/short/2023.05.18.541344v1?rss=1"
Carnaccini, S.Caceres, C. J.Gay, L. C.Ferreri, L.Skepner, E.Burke, D. F.Brown, I. H.Geiger, G.Obadan, A.Rajao, D. S.Lewis, N. S.Perez, D. R.2023-05-19doi:10.1101/2023.05.18.541344Cold Spring Harbor Laboratory Press2023-05-19
<![CDATA[
Drosophila AHR limits tumor growth and stem cell proliferation in the intestine
]]>
https://biorxiv.org/cgi/content/short/2023.05.17.538815v1?rss=1"
Tsai, M.Sun, J.Alexandre, C.Shapiro, M.Franchet, A.Li, Y.Gould, A. P.Vincent, J.-P.Stockinger, B.Diny, N. L.2023-05-19doi:10.1101/2023.05.17.538815Cold Spring Harbor Laboratory Press2023-05-19
<![CDATA[
RPM: an open-source rotation platform for open- and closed-loop vestibular stimulation in head-fixed mice
]]>
https://biorxiv.org/cgi/content/short/2023.05.19.541416v1?rss=1"
Cano-Ferrer, X.Tran-Van-Minh, A.Rancz, E.2023-05-22doi:10.1101/2023.05.19.541416Cold Spring Harbor Laboratory Press2023-05-22
<![CDATA[
A chromatinized origin reduces ORC mobility and spatially constrains MCM
]]>
https://biorxiv.org/cgi/content/short/2023.05.18.541303v1?rss=1"
Sanchez, H.Liu, Z.van Veen, E.van Laar, T.Solano, B.Diffley, J. F. X.Dekker, N. H.2023-05-22doi:10.1101/2023.05.18.541303Cold Spring Harbor Laboratory Press2023-05-22
<![CDATA[
PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages
]]>
https://biorxiv.org/cgi/content/short/2023.05.23.541898v1?rss=1"
Pain, A.Subudhi, A. K.Green, J.Satyam, R.Lenz, T.Salunke, R. P.Shuaib, M.Isaioglou, I.Abel, S.Gupta, M.Esau, L.Mourier, T.Mfarrej, S.Sivapurkar, R.Stead, Z.Ben-Rached, F.Otswal, Y.Sougrat, R.Dada, A.Kadamany, A. F.Fishle, W.Merzaban, J.Knuepfer, E.Ferguson, D. J. P.Gupta, I.Le Roch, K. G.Holder, A. A.2023-05-24doi:10.1101/2023.05.23.541898Cold Spring Harbor Laboratory Press2023-05-24
<![CDATA[
Dichotomy of neutralizing antibody, B cell and T cell responses to SARS-CoV-2 vaccination and protection in healthy adults
]]>
https://biorxiv.org/cgi/content/short/2023.05.24.541920v1?rss=1"
Carr, E. J.Townsley, H.Wu, M. Y.Wilkinson, K. A.Hobson, P. S.Levi, D.Namjou, S.Mears, H. V.Hobbs, A.Ragno, M.Herman, L. S.Harvey, R.Bailey, C.Fowler, A. S.Hatipoglu, E.Ngai, Y.Clayton, B.Miah, M.Bawumia, P.Miranda, M.Smith, C.Sawyer, C.Kelly, G.Mahalingasivam, V.Zheng, B.Evans, S. J.Libri, V.Riddell, A.Nicod, J.O'Reilly, N.Howell, M.Williams, B.Wilkinson, R. J.Kassiotis, G.Swanton, C.Gandhi, S.Beale, R. C.Bauer, D. L.Wall, E. C.2023-05-25doi:10.1101/2023.05.24.541920Cold Spring Harbor Laboratory Press2023-05-25
<![CDATA[
Divergent evolution of sleep functions
]]>
https://biorxiv.org/cgi/content/short/2023.05.27.541573v1?rss=1"
Joyce, M.Falconio, F. A.Blackhurst, L.Prieto-Godino, L. L.French, A. S.Gilestro, G. F.2023-05-28doi:10.1101/2023.05.27.541573Cold Spring Harbor Laboratory Press2023-05-28
<![CDATA[
Delay of human early development via in vitro diapause
]]>
https://biorxiv.org/cgi/content/short/2023.05.29.541316v1?rss=1"
Bulut-Karslioglu, A.Iyer, D.van der Weijden, V.Heidari Khoei, H.McCarthy, A.Rayon, T.Simon, C.Dunkel, I.Wamaitha, S.Schulz, E.Niakan, K.Rivron, N. C.2023-05-29doi:10.1101/2023.05.29.541316Cold Spring Harbor Laboratory Press2023-05-29
<![CDATA[
Single cell-guided prenatal derivation of primary epithelial organoids from the human amniotic and tracheal fluids.
]]>
https://biorxiv.org/cgi/content/short/2023.05.31.539801v1?rss=1"
Gerli, M. F. M.Cala, G.Beesley, M. A.Sina, B.Tullie, L.Panariello, F.Michielin, F.Sun, K. Y.Davidson, J. R.Russo, F. M.Jones, B. C.Lee, D.Savvidis, S.Xenakis, T.Simcock, I. C.Straatman-Iwanowska, A. A.Hirst, R. A.David, A. L.O'Callaghan, C.Olivo, A.Eaton, S.Loukogeorgakis, S. P.Cacchiarelli, D.Deprest, J.Li, V. S.Giobbe, G. G.De Coppi, P.2023-06-01doi:10.1101/2023.05.31.539801Cold Spring Harbor Laboratory Press2023-06-01
<![CDATA[
Frictiotaxis underlies adhesion-independent durotaxis
]]>
https://biorxiv.org/cgi/content/short/2023.06.01.543217v1?rss=1"
Shellard, A.Hampshire, P.Stillman, N.Dix, C.Thorogate, R.Imbert, A.Charras, G.Alert, R.Mayor, R.2023-06-01doi:10.1101/2023.06.01.543217Cold Spring Harbor Laboratory Press2023-06-01
<![CDATA[
Bridging Imaging Users to Imaging Analysis - A community survey
]]>
https://biorxiv.org/cgi/content/short/2023.06.05.543701v1?rss=1"
Sivagurunathan, S.Marcotti, S.Nelson, C. J.Jones, M. L.Barry, D. J.Slater, T. J. A.Eliceiri, K. W.Cimini, B. A.2023-06-05doi:10.1101/2023.06.05.543701Cold Spring Harbor Laboratory Press2023-06-05
<![CDATA[
Saturation Genome Editing Resolves the Functional Spectrum of Pathogenic VHL Alleles
]]>
https://biorxiv.org/cgi/content/short/2023.06.10.542698v1?rss=1"
Buckley, M.Kajba, C. M.Forrester, N. M.Terwagne, C.Sawyer, C.Shepherd, S. T. C.De Jonghe, J.Dace, P.Turajlic, S.Findlay, G. M.2023-06-10doi:10.1101/2023.06.10.542698Cold Spring Harbor Laboratory Press2023-06-10
<![CDATA[
Evolution of chromosome arm aberrations in breast cancer through genetic network rewiring
]]>
https://biorxiv.org/cgi/content/short/2023.06.10.544434v1?rss=1"
Kuzmin, E.Baker, T.Lesluyes, T.Monlong, J.Abe, K. T.Coelho, P. P.Schwartz, M.Zou, D.Morin, G.Pacis, A.Yang, Y.Martinez, C.Barber, J.Kuasne, H.Li, R.Bourgey, M.Fortier, A.-M.Davison, P. G.Omeroglu, A.Guiot, M. C.Morris, Q.Kleinman, C. L.Huang, S.Gingras, A.-C.Bourque, G.Van Loo, P.Park, M. M.2023-06-12doi:10.1101/2023.06.10.544434Cold Spring Harbor Laboratory Press2023-06-12
<![CDATA[
Beclin1 is essential for intestinal homeostasis.
]]>
https://biorxiv.org/cgi/content/short/2023.06.14.545007v1?rss=1"
Tran, S.Juliani, J.Harris, T. J.Evangelista, M.Ratcliffe, J.Ellis, S. L.Baloyan, D.Reehorst, C. M.Nightingale, R.Luk, I. Y.Jenkins, L. J.Ghilas, S.Yakou, M. H.Inguanti, C.Johnson, C.Buchert, M.Lee, J. C.De Cruz, P.Duszyc, K.Gleeson, P. A.Kile, B. T.Mielke, L. A.Yap, A. S.Mariadason, J.Fairlie, W. D.Lee, E. F.2023-06-15doi:10.1101/2023.06.14.545007Cold Spring Harbor Laboratory Press2023-06-15
<![CDATA[
Gastruloid-derived Primordial Germ Cell-like Cells (Gld-PGCLCs) develop dynamically within integrated tissues
]]>
https://biorxiv.org/cgi/content/short/2023.06.15.545059v1?rss=1"
Cooke, C. B.Barrington, C.Baillie-Benson, P.Nichols, J.Moris, N.2023-06-15doi:10.1101/2023.06.15.545059Cold Spring Harbor Laboratory Press2023-06-15
<![CDATA[
Impact of Streptococcus pneumoniae biosynthesis gene mutations on epithelial microinvasion and cellular responses
]]>
https://biorxiv.org/cgi/content/short/2023.06.15.545009v1?rss=1"
View larger version (24K):
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]]>Weight, C. M.Pollara, G. M.Betts, M.Ragazzini, R.Connor, M.Ramos-Sevillano, E.Reine, J.Whelan, M.Guerra-Assuncao, J. A.Bonfanti, P.Jolly, C.Noursadeghi, M. C.Ferreira, D.Brown, J.Heyderman, R. S.2023-06-15doi:10.1101/2023.06.15.545009Cold Spring Harbor Laboratory Press2023-06-15
<![CDATA[
The T766M-EGFR lung cancer mutation promotes tumor growth by exploiting newfound assembly mechanisms in ligand-free EGFR oligomers
]]>
https://biorxiv.org/cgi/content/short/2023.06.16.545259v1?rss=1"
Martin-Fernandez, M. L.Iyer, S.Needham, S. R.Galgadas, I.Davis, B. M.Roberts, S. K.Man, R. C.Zanetti-Domingues, L. C.Clarke, D. T.Fruhwirth, G. O.Parker, P. J.Rolfe, D. J.Gervasio, F. L.2023-06-19doi:10.1101/2023.06.16.545259Cold Spring Harbor Laboratory Press2023-06-19
<![CDATA[
Structure-guided design and optimization of covalent VHL-targeted sulfonyl fluoride PROTACs
]]>
https://biorxiv.org/cgi/content/short/2023.06.20.545773v1?rss=1"
View larger version (17K):
org.highwire.dtl.DTLVardef@da22e5org.highwire.dtl.DTLVardef@1290278org.highwire.dtl.DTLVardef@1611c0eorg.highwire.dtl.DTLVardef@7902d2_HPS_FORMAT_FIGEXP M_FIG C_FIG Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that have emerged as a therapeutic modality to induce targeted protein degradation (TPD) by harnessing cellular proteolytic degradation machinery. PROTACs which ligand the E3 ligase in a covalent manner have attracted intense interest, however, covalent PROTACs with a broad protein of interest (POI) scope have proven challenging to discover by design. Here, we report structure-guided design and optimization of Von Hippel-Lindau (VHL) protein-targeted sulfonyl fluorides which covalently bind Ser110 in the HIF1 binding site. We demonstrate that their incorporation in bifunctional degraders induces targeted protein degradation of BRD4 or androgen receptor (AR) without further linker optimization. Our study discloses the first covalent VHL ligands which can be implemented directly in bifunctional degrader design expanding the substrate scope of covalent E3 ligase PROTACs.
]]>Shah, R. R.De Vita, E.Conole, D.Sathyamurthi, P. S.Zhang, X.Fellows, E.Fleites, C. M.Queisser, M. A.Harling, J. D.Tate, E. W.2023-06-20doi:10.1101/2023.06.20.545773Cold Spring Harbor Laboratory Press2023-06-20
<![CDATA[
Wireless monitoring of respiration with EEG reveals relationships between respiration, behaviour and brain activity in freely moving mice
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https://biorxiv.org/cgi/content/short/2023.06.19.544346v1?rss=1"
Dasgupta, D.Schneider-Luftman, D.Schaefer, A.Harris, J. J.2023-06-21doi:10.1101/2023.06.19.544346Cold Spring Harbor Laboratory Press2023-06-21
<![CDATA[
Dynamic X-chromosomal reactivation enhances female brain resilience
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https://biorxiv.org/cgi/content/short/2023.06.17.545424v1?rss=1"
Kaeseberg, S.Bertin, M.Menon, R.Gabassi, E.Todorov, H.Frank, S.Brennenstuhl, H.Lohrer, B.Winter, J.Krummeich, J.Winkler, J.Winner, B.Weis, E.Hartwich, D.Diederich, S.Luck, K.Gerber, S.Lunt, P.Berninger, B.Falk, S.Schweiger, S.Karow, M.2023-06-21doi:10.1101/2023.06.17.545424Cold Spring Harbor Laboratory Press2023-06-21
<![CDATA[
p97/VCP targets Toxoplasma gondii vacuoles for parasite restriction in interferon-stimulated human cells
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https://biorxiv.org/cgi/content/short/2023.06.20.545566v1?rss=1"
Clough, B.Fisch, D.Mize, T. H.Encheva, V.Snijders, A.Frickel, E.2023-06-23doi:10.1101/2023.06.20.545566Cold Spring Harbor Laboratory Press2023-06-23
<![CDATA[
Comparative analysis of N-terminal cysteine dioxygenation and prolyl-hydroxylation as oxygen sensing pathways in mammalian cells
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https://biorxiv.org/cgi/content/short/2023.06.25.545688v1?rss=1"
Tian, Y.-M.Holdship, P.To, T. Q.Ratcliffe, P. J.Keeley, T. P.2023-06-26doi:10.1101/2023.06.25.545688Cold Spring Harbor Laboratory Press2023-06-26
<![CDATA[
Clonal neural tube organoids self-organise floorplate through BMP-mediated cluster competition
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https://biorxiv.org/cgi/content/short/2023.06.25.546258v1?rss=1"
Krammer, T.Stuart, H. T.Gromberg, E.Ishihara, K.Melchionda, M.Wang, J.Costantini, E.Lehr, S.Cislo, D.Arbanas, L.Hoermann, A.Neumueller, R. A.Elvassore, N.Siggia, E.Briscoe, J.Kicheva, A.Tanaka, E. M.2023-06-26doi:10.1101/2023.06.25.546258Cold Spring Harbor Laboratory Press2023-06-26
<![CDATA[
Two-color coincidence single-molecule pull-down for the specific detection of disease-associated protein aggregates
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https://biorxiv.org/cgi/content/short/2023.06.27.546642v1?rss=1"
Saleeb, R. S.Leighton, C.Lee, J.-E.O'Shaughnessy, J.Jeacock, K.Chappard, A.Cumberland, R.Ball, S. R.Sunde, M.Clarke, D. J.Piche, K.McPhail, J. A.Louwrier, A.Angers, R.Gandhi, S.Downey, P.Kunath, T.Horrocks, M. H.2023-06-29doi:10.1101/2023.06.27.546642Cold Spring Harbor Laboratory Press2023-06-29
<![CDATA[
Neuronal wiring diagram of an adult brain
]]>
https://biorxiv.org/cgi/content/short/2023.06.27.546656v1?rss=1"
Dorkenwald, S.Matsliah, A.Sterling, A. R.Schlegel, P.Yu, S.-c.McKellar, C. E.Lin, A.Costa, M.Eichler, K.Yin, Y.Silversmith, W.Schneider-Mizell, C.Jordan, C. S.Brittain, D.Halageri, A.Kuehner, K.Ogedengbe, O.Morey, R.Gager, J.Kruk, K.Perlman, E.Yang, R.Deutsch, D.Bland, D.Sorek, M.Lu, R.Macrina, T.Lee, K.Bae, J. A.Mu, S.Nehoran, B.Mitchell, E.Popovych, S.Wu, J.Jia, Z.Castro, M.Kemnitz, N.Ih, D.Bates, A. S.Eckstein, N.Funke, J.Collman, F.Bock, D. D.Jefferis, G. S. X. E.Seung, H. S.Murthy, M.the FlyWire Co2023-06-30doi:10.1101/2023.06.27.546656Cold Spring Harbor Laboratory Press2023-06-30
<![CDATA[
Applying high-resolution spatial transcriptomics to characterise the amyloid plaque cell niche in Alzheimer's Disease
]]>
https://biorxiv.org/cgi/content/short/2023.06.29.546675v1?rss=1"
Mallach, A.Zielonka, M.van Lieshout, V.An, Y.Khoo, J. H.Vanheusden, M.Chen, W.-T.Moechars, D.Arancibia-Carcamo, I. L.Fiers, M.De Strooper, B.2023-07-01doi:10.1101/2023.06.29.546675Cold Spring Harbor Laboratory Press2023-07-01
<![CDATA[
The substrate quality of CK2 target sites has a determinant role on their function and evolution
]]>
https://biorxiv.org/cgi/content/short/2023.07.03.547533v1?rss=1"
Bradley, D.Garand, C.Belda, H.Gagnon-Arsenault, I.Treeck, M.Elowe, S.Landry, C.2023-07-03doi:10.1101/2023.07.03.547533Cold Spring Harbor Laboratory Press2023-07-03
<![CDATA[
Interrogation of RNA-protein interaction dynamics in bacterial growth
]]>
https://biorxiv.org/cgi/content/short/2023.07.03.547468v1?rss=1"
Monti, M.Herman, R.Davey, K.Dawson, C. S.Ule, J.Thomas, G. H.Willis, A. E.Lilley, K. S.Villanueva, E.2023-07-03doi:10.1101/2023.07.03.547468Cold Spring Harbor Laboratory Press2023-07-03
<![CDATA[
Deep dynamical modelling of developmental trajectories with temporal transcriptomics
]]>
https://biorxiv.org/cgi/content/short/2023.07.06.547989v1?rss=1"
Maizels, R. J.Snell, D. M.Briscoe, J.2023-07-07doi:10.1101/2023.07.06.547989Cold Spring Harbor Laboratory Press2023-07-07
<![CDATA[
Cancer cell - fibroblast crosstalk signature promotes macrophage recruitment via HB-EGF and stromal EGFR/MEK signalling
]]>
https://biorxiv.org/cgi/content/short/2023.07.13.548733v1?rss=1"
Giangreco, G.Rullan, A.Naito, Y.Biwas, D.Liu, Y.-H.Hooper, S.Nenclares, P.Bhide, S.Cheang, M.Chakravarty, P.Hirata, E.Swanton, C.Melcher, A.Harrington, K.Sahai, E.2023-07-14doi:10.1101/2023.07.13.548733Cold Spring Harbor Laboratory Press2023-07-14
<![CDATA[
Hif-2α programmes oxygen chemosensitivity in chromaffin cells
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https://biorxiv.org/cgi/content/short/2023.07.14.548982v1?rss=1"
Prange-Barczynska, M.Jones, H.Sugimoto, Y.Cheng, X.Lima, J.Ratnayaka, I.Douglas, G.Buckler, K.Ratcliffe, P.Keeley, T.Bishop, T.2023-07-14doi:10.1101/2023.07.14.548982Cold Spring Harbor Laboratory Press2023-07-14
<![CDATA[
Regulation of BCR-mediated Ca2+ mobilization by MIZ1-TIMBIM4 safeguards IgG1+ GC B cell positive selection
]]>
https://biorxiv.org/cgi/content/short/2023.07.18.549490v1?rss=1"
Zhang, L.Toboso-Navasa, A.Gunawan, A.Camara, A.Nakagawa, R.Finsterbusch, K.Chakravarty, P.Newman, R.Zhang, Y.Eilers, M.Wack, A.Tolar, P.Toellner, K.-M.Calado, D. P.2023-07-19doi:10.1101/2023.07.18.549490Cold Spring Harbor Laboratory Press2023-07-19
<![CDATA[
Loss of REP1 impacts choroidal melanogenesis in choroideremia
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https://biorxiv.org/cgi/content/short/2023.07.20.549875v1?rss=1"
Sarkar, H.Tracey-White, D.Hagag, A. M.Burgoyne, T.Jensen, L. D.Edwards, M.Moosajee, M.2023-07-20doi:10.1101/2023.07.20.549875Cold Spring Harbor Laboratory Press2023-07-20
<![CDATA[
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data
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https://biorxiv.org/cgi/content/short/2023.07.20.549584v1?rss=1"
60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health.
]]>Zuffa, S.Schmid, R.Bauermeister, A.P. Gomes, P. W.Caraballo-Rodriguez, A. M.El Abiead, Y.Aron, A. T.Gentry, E. C.Zemlin, J.Meehan, M. J.Avalon, N. E.Cichewicz, R. H.Buzun, E.Carrillo Terrazas, M.Hsu, C.-Y.Oles, R.Vasquez Ayala, A.Zhao, J.Chu, H.Kuijpers, M. C. M.Jackrel, S. L.Tugizimana, F.Nephali, L. P.Dubery, I. A.Madala, N. E.Moreira, E. A.Costa-Lotufo, L. V.Lopes, N. P.Rezende-Teixeira, P.Jimenez, P. C.Rimal, B.Patterson, A. D.Traxler, M. F.Pessotti, R. d. C.Alvarado-Villalobos, D.Tamayo-Castillo, G.Chaverri, P.Escud2023-07-20doi:10.1101/2023.07.20.549584Cold Spring Harbor Laboratory Press2023-07-20
<![CDATA[
Investigating Brain Alterations in the Dp1Tyb Mouse Model of Down Syndrome
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https://biorxiv.org/cgi/content/short/2023.07.26.550698v1?rss=1"
Navacerrada, M. E. S.Kim, E.Siow, B.Ma, D.Gonzalez, L. R.Simmons, C.Hayward, D.Gibbins, D.Singh, N.Strydom, A.Fisher, E. M. C.Tybulewicz, V. L. J.Cash, D.2023-07-28doi:10.1101/2023.07.26.550698Cold Spring Harbor Laboratory Press2023-07-28
<![CDATA[
Sox3-null hypopituitarism depends on median eminence NG2-glia and is influenced by aspirin and gut microbiota
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https://biorxiv.org/cgi/content/short/2023.07.26.550616v1?rss=1"
Galichet, C.Rizzoti, K.Lovell-Badge, R.2023-07-28doi:10.1101/2023.07.26.550616Cold Spring Harbor Laboratory Press2023-07-28
<![CDATA[
Proneural genes form a combinatorial code to diversify neocortical neural progenitor cells
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https://biorxiv.org/cgi/content/short/2023.07.29.551096v1?rss=1"
Moffat, A.Oproescu, A.-M.Okawa, S.Han, S.Vasan, L.Ghazale, H.Dennis, D. J.Zinyk, D.Guillemot, F.del Sol, A.Schuurmans, C.2023-07-31doi:10.1101/2023.07.29.551096Cold Spring Harbor Laboratory Press2023-07-31
<![CDATA[
MiR-155 epigenetically counteracts hypoxia for mitochondrial fitness during germinal center positive selection
]]>
https://biorxiv.org/cgi/content/short/2023.07.31.551250v1?rss=1"
Nakagawa, R.Llorian-Sopena, M.Varsani-brown, S.Chakravarty, P.Camarillo, J. M.Barry, D.George, R.Blackledge, N. P.Duddy, G.Klose, R.Turner, M.Calado, D. P.2023-08-02doi:10.1101/2023.07.31.551250Cold Spring Harbor Laboratory Press2023-08-02
<![CDATA[
SCD inhibition eradicates AML displaying high de novo fatty acid desaturation and synergizes with chemotherapy
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https://biorxiv.org/cgi/content/short/2023.08.02.551656v1?rss=1"
Dembitz, V.Lawson, H.Burt, R.Philippe, C.James, S. C.Atkinson, S.Durko, J.Wang, L. M.Campos, J.Magee, A. M.Woodley, K.Austin, M. J.Rio-Machin, A.Casado-Izquierdo, P.Bewicke-Copley, F.Rodriguez, G.Pereira, D.Oudejans, L.Boet, E.von Kriegsheim, A.Schwaller, J.Finch, A. J.Pate, B.Sarry, J.-E.Tamburini, J.Schuringa, J. J.Hazlehurst, L.Copland, J. A.Yuneva, M.Peck, B.Cutillas, P.Fitzgibbon, J.Rouault-Pierre, K.Kranc, K.Gallipoli, P.2023-08-05doi:10.1101/2023.08.02.551656Cold Spring Harbor Laboratory Press2023-08-05
<![CDATA[
Optimized dimerization of the PAR-2 RING domain drives cooperative and selective membrane recruitment for robust feedback-driven cell polarization
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https://biorxiv.org/cgi/content/short/2023.08.10.552581v1?rss=1"
Bland, T.Hirani, N.Briggs, D.Rossetto, R.Ng, K.McDonald, N. Q.Zwicker, D.Goehring, N. W.2023-08-10doi:10.1101/2023.08.10.552581Cold Spring Harbor Laboratory Press2023-08-10
<![CDATA[
Cortactin stabilizes actin branches by bridging activated Arp2/3 to its nucleated actin filament
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https://biorxiv.org/cgi/content/short/2023.08.16.553490v1?rss=1"
Liu, T.Cao, L.Mladenov, M.JEGOU, A.Way, M.Moores, C.2023-08-16doi:10.1101/2023.08.16.553490Cold Spring Harbor Laboratory Press2023-08-16
<![CDATA[
Therapeutic inhibition of monocyte recruitment prevents checkpoint inhibitor-induced hepatitis
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https://biorxiv.org/cgi/content/short/2023.08.14.553197v1?rss=1"
Gudd, C. L. C.Atkinson, S. R.Mitchell, E.Mawhin, M.-A.Turajlic, S.Larkin, J.Thursz, M. R.Goldin, R. D.Powell, N.Antoniades, C. G.Woollard, K. J.Possamai, L. A.Triantafyllou, E.2023-08-16doi:10.1101/2023.08.14.553197Cold Spring Harbor Laboratory Press2023-08-16
<![CDATA[
CDK activity at the centrosome regulates the cell cycle
]]>
https://biorxiv.org/cgi/content/short/2023.08.16.553560v1?rss=1"
Roberts, E. L.Kapadia, N.Auchynnikava, T.Basu, S.Nurse, P.2023-08-16doi:10.1101/2023.08.16.553560Cold Spring Harbor Laboratory Press2023-08-16
<![CDATA[
Mutual homeostasis of charged proteins
]]>
https://biorxiv.org/cgi/content/short/2023.08.21.554177v1?rss=1"
Faraway, R.Heaven, N. C.Digby, H.Wilkins, O. G.Chakrabarti, A. M.Iosub, I. A.Knez, L.Ameres, S. L.Plaschka, C.Ule, J.2023-08-21doi:10.1101/2023.08.21.554177Cold Spring Harbor Laboratory Press2023-08-21
<![CDATA[
Hypoxia inducible factors regulate infectious SARS-CoV-2, epithelial damage and respiratory symptoms in a hamster COVID-19 model.
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https://biorxiv.org/cgi/content/short/2022.03.15.484379v1?rss=1"
Wing, P. A.Prange-Barczynska, M.Cross, A.Crotta, S.Orbegozo Rubio, C.Cheng, X.Harris, J. M.Zhuang, X.Johnson, R. L.Ryan, K. A.Hall, Y.Carroll, M. W.Issa, F.Balfe, P.Wack, A.Bishop, T.Salguero, F. J.McKeating, J. A.2022-03-15doi:10.1101/2022.03.15.484379Cold Spring Harbor Laboratory Press2022-03-15
<![CDATA[
Defective cytoskeletal dynamics underlies the essential role of MRTF-SRF in IL-2 delivery to CD8+ T cells during infectious challenge
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https://biorxiv.org/cgi/content/short/2023.08.26.554941v1?rss=1"
Maurice, D.Costello, P.Gualdrini, F.Frederico, B.Treisman, R.2023-08-27doi:10.1101/2023.08.26.554941Cold Spring Harbor Laboratory Press2023-08-27
<![CDATA[
Flow: a web platform and open database to analyse, store, curate and share bioinformatics data at scale
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https://biorxiv.org/cgi/content/short/2023.08.22.544179v1?rss=1"
Capitanchik, C.Ireland, S.Harston, A.Cheshire, C.Jones, D. M.Lee, F. C. Y.Ruiz de los Mozos, I.Iosub, I. A.Kuret, K.Faraway, R.Wilkins, O. G.Arora, R.Hallegger, M.Modic, M.Chakrabarti, A. M.Luscombe, N. M.Ule, J.2023-08-29doi:10.1101/2023.08.22.544179Cold Spring Harbor Laboratory Press2023-08-29
<![CDATA[
Unanticipated interacting features of human gut-associated lymphoid tissues link microbiota, intestinal immunity and autoimmunity
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https://biorxiv.org/cgi/content/short/2023.08.29.555265v1?rss=1"
Montorsi, L.Pitcher, M. J.Zhao, Y.Demonti, A.Tull, T. J.Dionisi, C.Dhami, P.Ellis, R. J.Bishop, C.Sanderson, J.Jain, S.D'Cruz, D.Gibbons, D.Winkler, T. H.Bemark, M.Ciccarelli, F. D.Spencer, J.2023-08-31doi:10.1101/2023.08.29.555265Cold Spring Harbor Laboratory Press2023-08-31
<![CDATA[
DLL4 and PDGF-BB regulate migration of human iPSC-derived skeletal myogenic progenitors
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https://biorxiv.org/cgi/content/short/2021.02.28.431778v1?rss=1"
Ferrari, G.Choi, S.Moyle, L. A.Mackinlay, K.Naouar, N.Wells, C.Muntoni, F.Tedesco, F. S.2021-02-28doi:10.1101/2021.02.28.431778Cold Spring Harbor Laboratory Press2021-02-28
<![CDATA[
GOT1 primes the cellular response to hypoxia by supporting glycolysis and HIF1α stabilisation
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https://biorxiv.org/cgi/content/short/2023.09.06.556522v1?rss=1"
Anastasiou, D.Grimm, F.Asuaje, A.Jain, A.Silva dos Santos, M.Kleinjung, J.Nunes, P. M.Gehrig, S.Fets, L.MacRae, J.2023-09-07doi:10.1101/2023.09.06.556522Cold Spring Harbor Laboratory Press2023-09-07
<![CDATA[
Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features
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https://biorxiv.org/cgi/content/short/2023.09.04.556195v1?rss=1"
Etherington, G. J.Nieduszynski, C.Oliferenko, S.Wu, P.-S.Uhlmann, F.2023-09-06doi:10.1101/2023.09.04.556195Cold Spring Harbor Laboratory Press2023-09-06
<![CDATA[
Schizosaccharomyces versatilis represents a distinct evolutionary lineage.
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https://biorxiv.org/cgi/content/short/2023.09.04.556188v1?rss=1"
Etherington, G. J.Nieduszynski, C.Oliferenko, S.Gomez Gil, E.Haerty, W.2023-09-06doi:10.1101/2023.09.04.556188Cold Spring Harbor Laboratory Press2023-09-06
<![CDATA[
Molecular model of a bacterial flagellar motor in situ reveals a "parts-list" of protein adaptations to increase torque
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https://biorxiv.org/cgi/content/short/2023.09.08.556779v1?rss=1"
Drobnic, T.Cohen, E. J.Alzheimer, M.Froschauer, K.Svensson, S.Singh, N.Garg, S. G.Henderson, L.Umrekar, T.Nans, A.Ribardo, D.Hochberg, G.Hendrixson, D. R.Sharma, C. M.Rosenthal, P.Beeby, M.2023-09-08doi:10.1101/2023.09.08.556779Cold Spring Harbor Laboratory Press2023-09-08
<![CDATA[
m6a methylation orchestrates IMP1 regulation of microtubules during human neuronal differentiation
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https://biorxiv.org/cgi/content/short/2023.09.12.557394v1?rss=1"
Klein, P.Harley, J.Crook, H.Serna, S. E.Roumeliotis, T. I.Choudhary, J. S.Chakrabarti, A. M.Luisier, R.Patani, R.Ramos, A.2023-09-12doi:10.1101/2023.09.12.557394Cold Spring Harbor Laboratory Press2023-09-12
<![CDATA[
Sensory neuron population expansion enhances odour tracking through relaxed projection neuron adaptation
]]>
https://biorxiv.org/cgi/content/short/2023.09.15.556782v1?rss=1"
Takagi, S.Abuin, L.Stupski, S. D.Arguello, J. R.Prieto-Godino, L. L.Stern, D. L.Cruchet, S.Alvarez-Ocana, R.Wienecke, C. F. R.van Breugel, F.Auer, T. O.Benton, R.2023-09-15doi:10.1101/2023.09.15.556782Cold Spring Harbor Laboratory Press2023-09-15
<![CDATA[
Blimp-1 and c-Maf regulate common and unique gene networks to protect against distinct pathways of pathobiont-induced colitis
]]>
https://biorxiv.org/cgi/content/short/2023.09.14.557705v1?rss=1"
Alvarez-Martinez, M.Cox, L. S.Pearson, C. F.Branchett, W. J.Chakravarty, P.Wu, X.Slawinski, H.Al Dibouni, A.Samelis, V.Gabrysova, L.Priestnall, S. L.Suarez-Bonnet, A.Mikolajczak, A.Briscoe, J.Powrie, F.O'Garra, A.2023-09-16doi:10.1101/2023.09.14.557705Cold Spring Harbor Laboratory Press2023-09-16
<![CDATA[
Congenital heart defects in Down syndrome are caused by increased dosage of DYRK1A
]]>
https://biorxiv.org/cgi/content/short/2023.09.18.558244v1?rss=1"
Lana-Elola, E.Aoidi, R.Llorian, M.Gibbins, D.Buechsenschuetz, C.Bussi, C.Flynn, H.Gilmore, T.Watson-Scales, S.Haugsten Hansen, M.Hayward, D.Song, O.-R.Brault, V.Herault, Y.Deau, E.Meijer, L.Snijders, A.Gutierrez, M.Fisher, E.Tybulewicz, V.2023-09-19doi:10.1101/2023.09.18.558244Cold Spring Harbor Laboratory Press2023-09-19
<![CDATA[
Multi-signal regulation of the GSK-3β homolog Rim11 governs meiosis entry in yeast
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https://biorxiv.org/cgi/content/short/2023.09.21.558844v1?rss=1"
Kociemba, J.Joergensen, A. C. S.Tadic, N.Harris, A.Sideri, T.Chan, W. Y.Ibrahim, F.Unal, E.Skehel, M.Shahrezaei, V.Arguello-Miranda, O.van Werven, F. J.2023-09-22doi:10.1101/2023.09.21.558844Cold Spring Harbor Laboratory Press2023-09-22
<![CDATA[
Regeneration of actin filament branches from the same Arp2/3 complex
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https://biorxiv.org/cgi/content/short/2023.09.22.558980v1?rss=1"
Ghasemi, F.Cao, L.Mladenov, M.Guichard, B.Way, M.Jegou, A.Romet-Lemonne, G.2023-09-22doi:10.1101/2023.09.22.558980Cold Spring Harbor Laboratory Press2023-09-22
<![CDATA[
ARID3A coordinates the proliferation-differentiation switch of transit-amplifying cells in the intestine
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https://biorxiv.org/cgi/content/short/2023.09.25.559311v1?rss=1"
Angelis, N.Baulies, A.Kucharska, A.Kelly, G.Sopena, M.Boeing, S.Li, V. S. W.2023-09-25doi:10.1101/2023.09.25.559311Cold Spring Harbor Laboratory Press2023-09-25
<![CDATA[
Bmp9 regulates Notch signaling and the temporal dynamics of angiogenesis via Lunatic Fringe
]]>
https://biorxiv.org/cgi/content/short/2023.09.25.557123v1?rss=1"
Ristori, T.Thuret, R.Hooker, E.Quicke, P.Lanthier, K.Ntumba, K.Aspalter, I. M.Uroz, M.Herbert, S. P.Chen, C. S.Larrivee, B.Bentley, K.2023-09-25doi:10.1101/2023.09.25.557123Cold Spring Harbor Laboratory Press2023-09-25
<![CDATA[
LRRK2 kinase dependent and independent function on endolysosomal repair promotes macrophage cell death
]]>
https://biorxiv.org/cgi/content/short/2023.09.27.559807v1?rss=1"
Morrison, R.Mihaylov, S. R. G.Luk, C. H.Rodgers, A.Athanasiadi, N.Morris, H.Pellegrino, E.Ultanir, S. K.Gutierrez, M. G.2023-09-27doi:10.1101/2023.09.27.559807Cold Spring Harbor Laboratory Press2023-09-27
<![CDATA[
Divergent downstream biosynthetic pathways are supported by L-cysteine synthases of Mycobacterium tuberculosis
]]>
https://biorxiv.org/cgi/content/short/2023.10.03.560673v1?rss=1"
Khan, M.Hunt, D. M.Singha, B.Kapoor, Y.Singh, N.Prasad, D. V. S.Dharmarajan, S.Sowpati, D. T.de Carvalho, L.Nandicoori, V. K.2023-10-05doi:10.1101/2023.10.03.560673Cold Spring Harbor Laboratory Press2023-10-05
<![CDATA[
Aminoglycoside heteroresistance in Enterobacter cloacae is driven by the cell envelope stress response.
]]>
https://biorxiv.org/cgi/content/short/2023.10.11.561937v1?rss=1"
Choi, A. J.Bennison, D. J.Kulkarni, E.Sun, H.Li, H.Bradshaw, J.Yeap, H. W.Mishra, V.Crespo-Puig, A.Davies, F.Sriskandan, S.Shenoy, A. R.2023-10-11doi:10.1101/2023.10.11.561937Cold Spring Harbor Laboratory Press2023-10-11
<![CDATA[
Pan-cancer evolution signatures link clonal expansion to dynamic changes in the tumour immune microenvironment
]]>
https://biorxiv.org/cgi/content/short/2023.10.12.560630v1?rss=1"
Yang, X.Liu, W.Mackintyre, G.Loo, P. V.Markowetz, F.Bailey, P.Yuan, K.2023-10-13doi:10.1101/2023.10.12.560630Cold Spring Harbor Laboratory Press2023-10-13
<![CDATA[
Cross-species imputation and comparison of single-cell transcriptomic profiles
]]>
https://biorxiv.org/cgi/content/short/2023.10.19.563173v1?rss=1"
Zhang, R.Yang, M.Schreiber, J.ODay, D. R.Turner, J.Shendure, J.Disteche, C. M.Deng, X.Noble, W. S.2023-10-20doi:10.1101/2023.10.19.563173Cold Spring Harbor Laboratory Press2023-10-20
<![CDATA[
Genome-wide CRISPR/Cas9 screen identifies MAT2A as a critical host factor for BK Polyomavirus
]]>
https://biorxiv.org/cgi/content/short/2023.10.20.563362v1?rss=1"
Caller, L.Ho, S.Brown, K.Dupont, L.Zaletel, T.Beale, R.Lehner, P. J.Crump, C. M.2023-10-21doi:10.1101/2023.10.20.563362Cold Spring Harbor Laboratory Press2023-10-21
<![CDATA[
The history of chromosomal instability in genome doubled tumors
]]>
https://biorxiv.org/cgi/content/short/2023.10.22.563273v1?rss=1"
Baker, T. M.Lai, S.Lesluyes, T.Yan, H.Verfaillie, A.Dentro, S.Lynch, A. R.Bowes, A. L.Pillay, N.Flanagan, A. M.Swanton, C.Tarabichi, M.Van Loo, P.2023-10-25doi:10.1101/2023.10.22.563273Cold Spring Harbor Laboratory Press2023-10-25
<![CDATA[
Telomere protein arrays stall DNA loop extrusion by condensin
]]>
https://biorxiv.org/cgi/content/short/2023.10.29.564563v1?rss=1"
Analikwu, B. T.Deshayes, A.van der Torre, J.Guerin, T.Katan, A. J.Beneut, C.Barth, R.Phipps, J.Scolari, V.Veaute, X.Barrington, C.Busso, D.Uhlmann, F.Dubrana, K.Mattarocci, S.Dekker, C.Marcand, S.2023-10-29doi:10.1101/2023.10.29.564563Cold Spring Harbor Laboratory Press2023-10-29
<![CDATA[
Atypical Protein Kinase C Promotes its own Asymmetric Localisation by Phosphorylating Cdc42 in Polarising Cells
]]>
https://biorxiv.org/cgi/content/short/2023.10.27.563985v1?rss=1"
View larger version (43K):
org.highwire.dtl.DTLVardef@e0ec65org.highwire.dtl.DTLVardef@c00b8dorg.highwire.dtl.DTLVardef@36565dorg.highwire.dtl.DTLVardef@160149a_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Packer, J.Gubieda, A. G.Brooks, A.Deutz, L. N.Squires, I.Ellison, S.Naganathan, S. R.Wollman, A. J. M.Dickinson, D. J.Rodriguez, J.2023-10-28doi:10.1101/2023.10.27.563985Cold Spring Harbor Laboratory Press2023-10-28
<![CDATA[
BDNF controls phosphorylation and transcriptional networks governing cytoskeleton organization and axonal regeneration
]]>
https://biorxiv.org/cgi/content/short/2023.11.06.565775v1?rss=1"
Vargas, J. N. S.Brown, A.-L.Sun, K.Hagemann, C.Geary, B.Villarroel-Campos, D.Bryce-Smith, S.Zanovello, M.Lombardo, M.Ryandov, E.Stepic, A.Meysman, L.Majewski, S.Tosolini, A.Secrier, M.Keuss, M. J.Serio, A.Sleigh, J. N.Fratta, P.Schiavo, G.2023-11-06doi:10.1101/2023.11.06.565775Cold Spring Harbor Laboratory Press2023-11-06
<![CDATA[
Single cell RNA-seq reveals protracted germ line X chromosome reactivation dynamics directed by a PRC2 dependent mechanism
]]>
https://biorxiv.org/cgi/content/short/2023.11.06.565813v1?rss=1"
Liu, Y.Lau, X.Munusamy, P.Sanchez, C. A. S.Snell, D.Sangrithi, M.2023-11-06doi:10.1101/2023.11.06.565813Cold Spring Harbor Laboratory Press2023-11-06
<![CDATA[
Creation of de novo cryptic splicing for ALS/FTD precision medicine
]]>
https://biorxiv.org/cgi/content/short/2023.11.15.565967v1?rss=1"
Wilkins, O. G.Chien, M. Z. Y. J.Wlaschin, J. J.Pisliakova, M.Thompson, D.Digby, H.Simkin, R. L.Diaz, J. A.Mehta, P. R.Keuss, M. J.Zanovello, M.Brown, A.-L.Harley, P.Darbey, A.Karda, R.Fisher, E. M. C.Cunningham, T. J.Le Pichon, C. E.Ule, J.Fratta, P.2023-11-15doi:10.1101/2023.11.15.565967Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
3D-Imaging of synapses in neuronal tissues with synchrotron X-ray ptychography
]]>
https://biorxiv.org/cgi/content/short/2023.11.16.567403v1?rss=1"
Bosch, C.Diaz, A.Holler, M.Guizar-Sicairos, M.Aidukas, T.Pacureanu, A.Mueller, E.Peddie, C. J.Collinson, L.Zhang, Y.Menzel, A.Wanner, A.Schaefer, A.2023-11-17doi:10.1101/2023.11.16.567403Cold Spring Harbor Laboratory Press2023-11-17
<![CDATA[
Nonlinear readout of spatial cues underlies robustness of asymmetric cell division
]]>
https://biorxiv.org/cgi/content/short/2023.11.21.568006v1?rss=1"
Rodrigues, N. T. L.Bland, T.Ng, K.Hirani, N.Goehring, N.2023-11-21doi:10.1101/2023.11.21.568006Cold Spring Harbor Laboratory Press2023-11-21
<![CDATA[
CK-666 and CK-869 differentially inhibit Arp2/3 iso-complexes
]]>
https://biorxiv.org/cgi/content/short/2023.11.26.568719v1?rss=1"
Cao, L.Huang, S.Basant, A.Mladenov, M.Way, M.2023-11-26doi:10.1101/2023.11.26.568719Cold Spring Harbor Laboratory Press2023-11-26
<![CDATA[
Cohesin chromatin loop formation by an extrinsic motor
]]>
https://biorxiv.org/cgi/content/short/2023.11.30.569410v1?rss=1"
Guerin, T. M.Barrington, C.Pobegalov, G.Molodtsov, M. I.Uhlmann, F.2023-11-30doi:10.1101/2023.11.30.569410Cold Spring Harbor Laboratory Press2023-11-30
<![CDATA[
Reconstructing oral cavity tumor evolution through brush biopsy
]]>
https://biorxiv.org/cgi/content/short/2023.11.29.569216v1?rss=1"
John, E.Lesluyes, T.Baker, T.Tarabichi, M.Gillenwater, A.Wang, J. R.Van Loo, P.Zhao, X.2023-12-01doi:10.1101/2023.11.29.569216Cold Spring Harbor Laboratory Press2023-12-01
<![CDATA[
Antigenic and genetic diversity of H1 and H3 influenza A viruses in swine in Brazil
]]>
https://biorxiv.org/cgi/content/short/2023.12.01.569635v1?rss=1"
Lopes, S.Anderson, T. K.Schaefer, R.Tochetto, C.Gava, D.Cantao, M. E.Ciacci-Zanella, J. R.Vincent Baker, A. L.Lewis, N. S.2023-12-02doi:10.1101/2023.12.01.569635Cold Spring Harbor Laboratory Press2023-12-02
<![CDATA[
Four-Core Genotypes mice harbour a 3.2MB X-Y translocation that perturbs Tlr7 dosage
]]>
https://biorxiv.org/cgi/content/short/2023.12.04.569933v1?rss=1"
Panten, J.Del Prete, S.Cleland, J. P.Saunders, L. M.van Riet, J.Schneider, A.Ginno, P. A.Schneider, N.Koch, M.-L.Gerstung, M.Stegle, O.Turner, J. M. A.Heard, E.Odom, D. T.2023-12-05doi:10.1101/2023.12.04.569933Cold Spring Harbor Laboratory Press2023-12-05
<![CDATA[
The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans
]]>
https://biorxiv.org/cgi/content/short/2023.12.10.570962v1?rss=1"
Rehman, S.Antonovic, A.McIntire, I.Zheng, H.Cleaver, L.Adams, C.Portlock, T.Richardson, K.Shaw, R.Oregioni, A.Mastroianni, G.Whittaker, S.Kelly, G.Fornili, A.Cianciotto, N.Garnett, J.2023-12-10doi:10.1101/2023.12.10.570962Cold Spring Harbor Laboratory Press2023-12-10
<![CDATA[
Brain-wide activity-identity mapping of neural networks associated with prosocial motivation in rats
]]>
https://biorxiv.org/cgi/content/short/2023.12.10.570980v1?rss=1"
Ruzal, K.Trachtenberg, E.Kantor, B.Flumin, H.Roemer, A.Crespo, A.Kohl, J.Ben-Ami Bartal, I.2023-12-11doi:10.1101/2023.12.10.570980Cold Spring Harbor Laboratory Press2023-12-11
<![CDATA[
A cyclic peptide toolkit reveals mechanistic principles of peptidylarginine deiminase IV (PADI4) regulation
]]>
https://biorxiv.org/cgi/content/short/2023.12.12.571217v1?rss=1"
1012 cyclic peptides for high-affinity, conformation-selective binders. We report PADI4_3, an inhibitor specific for the active conformation of PADI4; PADI4_7, an inert binder, which we functionalised for the isolation and study of cellular PADI4; and PADI4_11, a first-in-class activator. Using a newly developed method for the quantification of cellular PADI4 activity, we show that PADI4_3 and PADI4_11 are effective in cells. Structural studies with PADI4_11 reveal an allosteric binding mode that may reflect the mechanism that promotes cellular PADI4 activation. This work offers new understanding of PADI4 regulation and a toolkit for the study and modulation of PADI4 across physiological and pathophysiological contexts.
]]>Bertran, M. T.Walmsley, R.Cummings, T. F. M.Aramburu, I.Benton, D. J.Assalaarachchi, J.Chasampalioti, M.Swanton, T.Joshi, D.Federico, S.Okkenhaug, H.Yu, L.Oxley, D.Walker, S.Papayannopoulos, V.Suga, H.Christophorou, M. A.Walport, L. J.2023-12-12doi:10.1101/2023.12.12.571217Cold Spring Harbor Laboratory Press2023-12-12
<![CDATA[
Live-imaging reveals Coordinated Cell Migration and Cardiac Fate Determination during Mammalian Gastrulation.
]]>
https://biorxiv.org/cgi/content/short/2023.12.19.572445v1?rss=1"
Abukar, S.Embacher, P.Cicarrelli, A.Varsani-Brown, S.Dean, J. A.Briscoe, J.Ivanovitch, k.2023-12-19doi:10.1101/2023.12.19.572445Cold Spring Harbor Laboratory Press2023-12-19
<![CDATA[
Xylosyltransferase Bump-and-hole Engineering to Chemically Manipulate Proteoglycans in Mammalian Cells
]]>
https://biorxiv.org/cgi/content/short/2023.12.20.572522v1?rss=1"
Li, Z.Di Vagno, L.Ni Cheallaigh, A.Sammon, D.Briggs, D. C.Chung, N.Chang, V.Mahoney, K. E.Cioce, A.Murphy, L. D.Chen, Y.-H.Narimatsu, Y.Miller, R. L.Willems, L. I.Malaker, S. A.Miller, G. J.Hohenester, E.Schumann, B.2023-12-20doi:10.1101/2023.12.20.572522Cold Spring Harbor Laboratory Press2023-12-20
<![CDATA[
The V-ATPase/ATG16L1 axis is controlled by the V1H subunit
]]>
https://biorxiv.org/cgi/content/short/2023.12.19.572309v1?rss=1"
Timimi, L.Wrobel, A. G.Chiduza, G. N.Maslen, S. L.Torres-Mendez, A.Montaner, B.Davis, C.Skehel, M.Rubinstein, J. L.Schreiber, A. L.Beale, R.2023-12-19doi:10.1101/2023.12.19.572309Cold Spring Harbor Laboratory Press2023-12-19
<![CDATA[
Imaging the master regulator of the antioxidant response in non-small cell lung cancer with positron emission tomography
]]>
https://biorxiv.org/cgi/content/short/2023.12.16.572007v1?rss=1"
200 cytoprotective proteins controlled by NRF2, which can be non-invasively imaged by (S)-4-(3-18F-fluoropropyl)--glutamate ([18F]FSPG) positron emission tomography (PET). Through genetic and pharmacologic manipulation, we show that [18F]FSPG provides a sensitive and specific marker of NRF2 activation in advanced preclinical models of NSCLC. We validate imaging readouts with metabolomic measurements of system xc- activity and their coupling to intracellular glutathione concentration. A redox gene signature was measured in patients from the TRACERx 421 cohort, suggesting an opportunity for patient stratification prior to imaging. Furthermore, we reveal that system xc- is a metabolic vulnerability that can be therapeutically targeted for sustained tumour growth suppression in aggressive NSCLC. Our results establish [18F]FSPG as predictive marker of therapy resistance in NSCLC and provide the basis for the clinical evaluation of both imaging and therapeutic agents that target this important antioxidant pathway.
]]>Greenwood, H. E.Edwards, R. S.Tyrrell, W. E.Barber, A. R.Baark, F.Tanc, M.Khalil, E.Falzone, A.Ward, N. P.DeBlasi, J. M.Torrente, L.Pearce, D. R.Firth, G.Smith, L. M.Vilhelmsson Timmermand, O.Huebner, A.George, M. E.Swanton, C.Hynds, R. E.DeNicola, G. M.Witney, T. H.2023-12-17doi:10.1101/2023.12.16.572007Cold Spring Harbor Laboratory Press2023-12-17
<![CDATA[
RASP: Optimal single fluorescent puncta detection in complex cellular backgrounds
]]>
https://biorxiv.org/cgi/content/short/2023.12.18.572148v1?rss=1"
Fu, B.Brock, E. E.Breiter, J. C.Tian, R.Andrews, R.Toomey, C. E.Lachica, J.Lashley, T.Ryten, M.Wood, N. W.Vendruscolo, M.Gandhi, S.Weiss, L. E.Beckwith, J. S.Lee, S. F.2023-12-18doi:10.1101/2023.12.18.572148Cold Spring Harbor Laboratory Press2023-12-18
<![CDATA[
Shieldin and CST co-orchestrate DNA polymerase-dependent tailed-end joining reactions independently of 53BP1-governed repair pathway choice
]]>
https://biorxiv.org/cgi/content/short/2023.12.20.572534v1?rss=1"
King, A.Reichl, P.Metson, J. S.Parker, R.Munro, D.Oliveira, C.Becker, J. R.Biggs, D.Preece, C.Davies, B.Chapman, J. R.2023-12-21doi:10.1101/2023.12.20.572534Cold Spring Harbor Laboratory Press2023-12-21
<![CDATA[
Oncogenic PIK3CA corrupts growth factor signaling specificity
]]>
https://biorxiv.org/cgi/content/short/2023.12.23.573207v1?rss=1"
Madsen, R. R.Le Marois, A.Voliotis, M.Yin, S.Sufi, J.Qin, X.Zhao, S. J.Gorczynska, J.Morelli, D.Davidson, L.Sahai, E.Korolchuk, V. I.Tape, C. J.Vanhaesebroeck, B.2023-12-23doi:10.1101/2023.12.23.573207Cold Spring Harbor Laboratory Press2023-12-23
<![CDATA[
Glutaminase as a metabolic target of choice to counter acquired resistance to Palbociclib by colorectal cancer cells
]]>
https://biorxiv.org/cgi/content/short/2024.01.04.574237v1?rss=1"
Tarrado-Castellarnau, M.Foguet, C.Tarrago-Celada, J.Palobart, M.Hernandez-Carro, C.Perarnau, J.Zodda, E.Polat, I. H.Marin, S.Suarez-Bonnet, A.Lozano, J. J.Yuneva, M.Thomson, T. M.Cascante, M.2024-01-05doi:10.1101/2024.01.04.574237Cold Spring Harbor Laboratory Press2024-01-05
<![CDATA[
Deciphering the diversity and sequence of extracellular matrix and cellular spatial patterns in lung adenocarcinoma using topological data analysis
]]>
https://biorxiv.org/cgi/content/short/2024.01.05.574362v1?rss=1"
Yoon, I. H. R.Jenkins, R.Colliver, E.Zhang, H.Novo, D.Moore, D.Ramsden, Z.Rullan, A.Fu, X.Yuan, Y.Harrington, H. A.Swanton, C.Byrne, H. M.Sahai, E.2024-01-07doi:10.1101/2024.01.05.574362Cold Spring Harbor Laboratory Press2024-01-07
<![CDATA[
Single-cell transcriptional dynamics in a living vertebrate
]]>
https://biorxiv.org/cgi/content/short/2024.01.03.574108v1?rss=1"
Eck, E.Moretti, B.Schlomann, B. H.Bragantini, J.Lange, M.Zhao, X.VijayKumar, S.Valentin, G.Loureiro, C.Soroldoni, D.Royer, L. A.Oates, A. C.Garcia, H. H.2024-01-05doi:10.1101/2024.01.03.574108Cold Spring Harbor Laboratory Press2024-01-05
<![CDATA[
Cell Cycle Regulation has Shaped Budding Yeast Replication Origin Structure and Function
]]>
https://biorxiv.org/cgi/content/short/2024.01.10.575016v1?rss=1"
Diffley, J.Lim, C. T.Miller, T. C.Tan, K. W.Talele, s.Early, A.East, P.Sanchez, H.Dekker, N. H.Costa, A.2024-01-10doi:10.1101/2024.01.10.575016Cold Spring Harbor Laboratory Press2024-01-10
<![CDATA[
Mixed Alkyl/Aryl Phosphonates Identify Metabolic Serine Hydrolases as Antimalarial Targets
]]>
https://biorxiv.org/cgi/content/short/2024.01.11.575224v1?rss=1"
Bennett, J. M.Narwal, S. K.Kabeche, S.Abegg, D.Hackett, F.Yeo, T.Li, V.Muir, R. K.Faucher, F. F.Lovell, S.Blackman, M.Adibekian, A.Yeh, E.Fidock, D. A.Bogyo, M.2024-01-11doi:10.1101/2024.01.11.575224Cold Spring Harbor Laboratory Press2024-01-11
<![CDATA[
Targeting the Plasmodium falciparum UCHL3 ubiquitin hydrolase using chemically constrained peptides
]]>
https://biorxiv.org/cgi/content/short/2024.01.11.575158v1?rss=1"
King, H. R.Bycroft, M.Nguyen, T.-B.Kelly, G.Vinogradov, A. A.Rowling, P. J.Stott, K.Ascher, D. B.Suga, H.Itzhaki, L. S.Artavanis-Tsakonas, K.2024-01-13doi:10.1101/2024.01.11.575158Cold Spring Harbor Laboratory Press2024-01-13
<![CDATA[
A scaleable inducible knockout systemfor studying essential gene function inthe malaria parasite
]]>
https://biorxiv.org/cgi/content/short/2024.01.14.575607v1?rss=1"
Ramaprasad, A.Blackman, M.2024-01-15doi:10.1101/2024.01.14.575607Cold Spring Harbor Laboratory Press2024-01-15
<![CDATA[
Quantifying spectral information about source separation in multisource odour plumes
]]>
https://biorxiv.org/cgi/content/short/2024.01.14.575605v1?rss=1"
Tootoonian, S.True, A. C.Crimaldi, J. P.Schaefer, A. T.2024-01-15doi:10.1101/2024.01.14.575605Cold Spring Harbor Laboratory Press2024-01-15
<![CDATA[
Combining RASG12C(ON) inhibitor with SHP2 inhibition sensitises immune excluded lung tumours to immune checkpoint blockade: a strategy for turning cold tumours hot
]]>
https://biorxiv.org/cgi/content/short/2024.01.15.575765v1?rss=1"
Anastasiou, P.Moore, C.Rana, S.de Castro, A.Tomaschko, M.Boumelha, J.Mugarza, E.Blaj, C.de Carne Trecesson, S.Goldstone, R.Smith, J.Quintana, E.Molina-Arcas, M.Downward, J.2024-01-16doi:10.1101/2024.01.15.575765Cold Spring Harbor Laboratory Press2024-01-16
<![CDATA[
Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes
]]>
https://biorxiv.org/cgi/content/short/2024.01.17.576008v1?rss=1"
Pyle, E.Zanetti, G.2024-01-17doi:10.1101/2024.01.17.576008Cold Spring Harbor Laboratory Press2024-01-17
<![CDATA[
ImmCellTyper: an integrated computational pipeline for systematic mining of Mass Cytometry data to assist deep immune profiling
]]>
https://biorxiv.org/cgi/content/short/2024.01.15.575790v1?rss=1"
Sun, J.Choy, D.Sompairac, N.Jamshidi, S.Mishto, M.Kordasti, S.2024-01-17doi:10.1101/2024.01.15.575790Cold Spring Harbor Laboratory Press2024-01-17
<![CDATA[
Mechanism of chaperone coordination during cotranslational protein folding in bacteria
]]>
https://biorxiv.org/cgi/content/short/2024.01.22.576655v1?rss=1"
Roeselova, A.Maslen, S. L.Shivakumaraswamy, S.Pellowe, G. A.Howell, S.Joshi, D.Redmond, J.Kjaer, S.Skehel, M.Balchin, D.2024-01-23doi:10.1101/2024.01.22.576655Cold Spring Harbor Laboratory Press2024-01-23
<![CDATA[
Smad4 is essential for epiblast scaling and morphogenesis after implantation, but nonessential prior to implantation in the mouse
]]>
https://biorxiv.org/cgi/content/short/2024.01.23.576717v1?rss=1"
Kruger, R.Frum, T.Brumm, A. S.Hickey, S. L.Niakan, K.Aziz, F.Shammami, M.Roberts, J.Ralston, A.2024-01-24doi:10.1101/2024.01.23.576717Cold Spring Harbor Laboratory Press2024-01-24
<![CDATA[
Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of oesophageal cancer
]]>
https://biorxiv.org/cgi/content/short/2024.01.24.576991v1?rss=1"
Ganguli, P.Colomina-Basanta, C.Mendez, A.Armero-Pineiro, M.Zahra, A.Acha-Sagrado, A.Misetic, H.Devonshire, G.Kelly, G.Freeman, A.Green, M.Nye, E.Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium,Rodriguez-Justo, M.Spencer, J.Fitzgerald, R. C.Ciccarelli, F. D.2024-01-26doi:10.1101/2024.01.24.576991Cold Spring Harbor Laboratory Press2024-01-26
<![CDATA[
The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir
]]>
https://biorxiv.org/cgi/content/short/2024.01.26.577387v1?rss=1"
150- fold resistance to the inhibitor compared to the WT virus. By rationally modifying PIR we have developed its analog EKC110, which readily induced hyper-multimerization of INY99H/A128T in vitro and was [~]14-fold more potent against HIV-1(Y99H/A128T IN) than the parent inhibitor. These findings suggest a path for developing improved PIR chemotypes with a higher barrier to resistance for their potential clinical use.
IMPORTANCEAntiretroviral therapies save the lives of millions of people living with HIV (PLWH). However, evolution of multi-drug-resistant viral phenotypes is a major clinical problem, and there are limited or no treatment options for heavily treatment-experienced PLWH. Allosteric HIV-1 integrase inhibitors (ALLINIs) are a novel class of antiretroviral compounds which work by a unique mechanism of binding to the non-catalytic site on the viral protein and inducing aberrant integrase multimerization. Accordingly, ALLINIs potently inhibit both wild type HIV-1 and all drug-resistant viral phenotypes that have so far emerged against currently used therapies. Pirmitegravir, a highly potent and safe investigational ALLINI, is currently advancing through clinical trials. Here we have elucidated structural and mechanistic bases behind the emergence of HIV-1 integrase mutations in infected cell that confer resistance to pirmitegravir. In turn, our findings allowed us to rationally develop an improved ALLINI with substantially enhanced potency against the pirmitegravir resistant virus.
]]>Dinh, T.Tber, Z.Rey, J. S.Mengshetti, S.Annamalai, A. S.Haney, R.Briganti, L.Amblard, F.Fuchs, J. R.Cherepanov, P.Kim, K.Schinazi, R. F.Perilla, J. R.Kim, B.Kvaratskhelia, M.2024-01-26doi:10.1101/2024.01.26.577387Cold Spring Harbor Laboratory Press2024-01-26
<![CDATA[
Force-transducing molecular ensembles at growing microtubule tips control mitotic spindle size
]]>
https://biorxiv.org/cgi/content/short/2024.02.01.578443v1?rss=1"
Chu, L.-Y.Stedman, D.Gannon, J.Cox, S.Pobegalov, G.Molodtsov, M.2024-02-02doi:10.1101/2024.02.01.578443Cold Spring Harbor Laboratory Press2024-02-02
<![CDATA[
Activation loop phosphorylation and cGMP saturation of PKG regulate egress of malaria parasites.
]]>
https://biorxiv.org/cgi/content/short/2024.02.04.578801v1?rss=1"
Koussis, K.Haase, S.Withers-Martinez, C.Flynn, H. R.Kunzelmann, S.Christodoulou, E.Ibrahim, F.Skehel, M.Baker, D. A.Blackman, M. J.2024-02-04doi:10.1101/2024.02.04.578801Cold Spring Harbor Laboratory Press2024-02-04
<![CDATA[
Plasmodium NEK1 coordinates MTOC organisation and kinetochore attachment during rapid mitosis in male gamete formation
]]>
https://biorxiv.org/cgi/content/short/2024.02.05.578160v1?rss=1"
Zeeshan, M.Rashpa, R.Ferguson, D. J.Mckeown, G.Nugmanova, R.Subodhi, A. K.Beyeler, R.Pashley, S. L.Markus, R.Brady, D.Roques, M.Bottrill, A. R.Fry, A. M.Pain, A.vaughan, s.Holder, A. A.Tromer, E. C.Brochet, M.Tewari, R.2024-02-05doi:10.1101/2024.02.05.578160Cold Spring Harbor Laboratory Press2024-02-05
<![CDATA[
Preservation of memory B cell homeostasis in an individual producing broadly neutralising antibodies against HIV-1
]]>
https://biorxiv.org/cgi/content/short/2024.02.05.578789v1?rss=1"
Griffith, S.Muir, L.Suchanek, O.Hope, J.Pade, C.Gibbons, J. M.Tuong, Z. K.Fung, A.Touizer, E.Rees-Spear, C.Nans, A.Roustan, C.Alguel, Y.Fink, D.Orkin, C.Deayton, J.Anderson, J.Gupta, R. K.Doores, K. J.Cherepanov, P.McKnight, A.Clatworthy, M.McCoy, L. E.2024-02-06doi:10.1101/2024.02.05.578789Cold Spring Harbor Laboratory Press2024-02-06
<![CDATA[
Focal Deletions of a Promoter Tether Activate the IRX3 Oncogene in T Cell Acute Lymphoblastic Leukemia
]]>
https://biorxiv.org/cgi/content/short/2024.02.06.579027v1?rss=1"
Rahman, S.Bloye, G.Farah, N.Demeulemeester, J.Costa, J. R.O'Connor, D.Pocock, R.Turna, A.Wang, L.Lee, S.Fielding, A. K.Roels, J.Jaksik, R.Dawidowska, M.Vlierberghe, P. V.Hadjur, S.Hughes, J. R.Davies, J. O. J.Gutierrez, A.Kelliher, M. A.Loo, P. V.Dawson, M. A.Mansour, M. R.2024-02-08doi:10.1101/2024.02.06.579027Cold Spring Harbor Laboratory Press2024-02-08
<![CDATA[
Zebrafish reveal new roles for Fam83f in hatching and the DNA damage-mediated autophagic response
]]>
https://biorxiv.org/cgi/content/short/2024.02.10.579757v1?rss=1"
Jones, R. A.Cooper, F.Kelly, G.Barry, D.Renshaw, M. J.Sapkota, G.Smith, J. C.2024-02-12doi:10.1101/2024.02.10.579757Cold Spring Harbor Laboratory Press2024-02-12
<![CDATA[
Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst
]]>
https://biorxiv.org/cgi/content/short/2024.02.01.578414v1?rss=1"
Simon, C. S.McCarthy, A.Woods, L.Staneva, D.Huang, Q.Linneberg-Agerholm, M.Faulkner, A.Papathanasiou, A.Elder, K.Snell, P.Christie, L.Garcia, P.Shaikly, V.Taranissi, M.Choudhary, M.Herbert, M.Brickman, J. M.Niakan, K. K.2024-02-04doi:10.1101/2024.02.01.578414Cold Spring Harbor Laboratory Press2024-02-04
<![CDATA[
Micromolar fluoride contamination arising from glass NMR tubes and a simple solution for biomolecular applications
]]>
https://biorxiv.org/cgi/content/short/2024.02.12.579991v1?rss=1"
Matwani, K.Cornish, J.DeBenedictis, E. A.Heller, G. T.2024-02-12doi:10.1101/2024.02.12.579991Cold Spring Harbor Laboratory Press2024-02-12
<![CDATA[
Optical tweezers reveal that PfEBA and PfRH ligands, not PfMSP1, play a central role in Plasmodium-falciparum merozoite-erythrocyte attachment
]]>
https://biorxiv.org/cgi/content/short/2024.02.13.580055v1?rss=1"
Kals, E.Kals, M.Lees, R. A.Introini, V.Kemp, A.Silvester, E.Collins, C. R.Umrekar, T.Kotar, J.Cicuta, P.Rayner, J. C.2024-02-13doi:10.1101/2024.02.13.580055Cold Spring Harbor Laboratory Press2024-02-13
<![CDATA[
Large-scale visualisation of α-synuclein oligomers in Parkinson's disease brain tissue
]]>
https://biorxiv.org/cgi/content/short/2024.02.17.580698v1?rss=1"
Andrews, R.Fu, B.Toomey, C. E.Breiter, J. C.Lachica, J.Tian, R.Beckwith, J. S.Needham, L.-M.Chant, G. J.Loiseau, C.Deconfin, A.Baspin, K.Magill, P. J.Jaunmuktane, Z.Freeman, O. J.Taylor, B. J. M.Hardy, J.Lashley, T.Ryten, M.Vendruscolo, M.Wood, N. W.Weiss, L. E.Gandhi, S.Lee, S. F.2024-02-19doi:10.1101/2024.02.17.580698Cold Spring Harbor Laboratory Press2024-02-19
<![CDATA[
A single amino acid in the Salmonella effector SarA/SteE triggers supraphysiological activation of STAT3 for anti-inflammatory target gene expression
]]>
https://biorxiv.org/cgi/content/short/2024.02.14.580367v1?rss=1"
Gaggioli, M. R.Jones, A. G.Panagi, I.Washington, E. J.Loney, R. E.Muench, J. H.Brennan, R. G.Thurston, T. L. M.Ko, D. C.2024-02-14doi:10.1101/2024.02.14.580367Cold Spring Harbor Laboratory Press2024-02-14
<![CDATA[
Evolution and inhibition of the FIKK effector kinase family in P. falciparum
]]>
https://biorxiv.org/cgi/content/short/2024.02.22.581535v1?rss=1"
95% of all [~]500,000 annual fatalities. Phylogenetically, P. falciparum belongs to the Laverania subgenus, a group of Plasmodium species that infect great apes. Common to Laverania species is the family of FIKK kinases. One million years ago, a single FIKK kinase conserved in all Plasmodium species gained an export element in the Laverania subgenus and expanded into the family of [~]20 atypical FIKK kinases, most of which are exported into the host cell. The fikk genes are conserved in syntenic loci across the Laverania, arguing for a rapid expansion controlling important functions in host cell remodelling and pathogenesis. We provide evidence that the FIKK paralogues evolved specific and mutually exclusive phosphorylation motif preferences, conserved across their Laverania orthologues, in a short evolutionary timeframe. Surprisingly, we find that FIKK13 has evolved exclusive tyrosine-phosphorylation preference, which was thought to be absent in Plasmodium species. Combining a crystal structure with AlphaFold2 predictions, we identify residues that determine kinase-specificity within the FIKK family in a fast-evolving flexible loop. Finally, we show that all expressed members of the FIKK kinase family can be chemically inhibited in vitro using a single compound. Such a pan-specific inhibitor of this kinase family important for virulence could reduce the ability of the parasite to gain escape-mutations and resistance.
]]>Belda, H.Bradley, D.Christodoulou, E.Nofal, S. D.Broncel, M.Jones, D. A.Davies, H.Bertran, M. T.Purkiss, A. G.Ogrodowicz, R. W.Joshi, D.O'Reilly, N.Walport, L.Claessens, A.Powell, A.House, D.Kjaer, S.Landry, C. R.Treeck, M.2024-02-23doi:10.1101/2024.02.22.581535Cold Spring Harbor Laboratory Press2024-02-23
<![CDATA[
A targetable PREX2/RAC1/PI3Kβ signalling axis confers resistance to clinically relevant therapeutic approaches in melanoma
]]>
https://biorxiv.org/cgi/content/short/2024.02.26.580534v1?rss=1"
Ford, C. A.Koludrovic, D.Centeno, P. P.Foth, M.Tsonou, E.Vlahov, N.Sphyris, N.Gilroy, K.Bull, C.Nixon, C.Serrels, B.Munro, A. F.Dawson, J. C.Carragher, N. O.Pavet, V.Hornigold, D. C.Dunne, P. D.Downward, J.Welch, H. C. E.Barry, S. T.Sansom, O. J.Campbell, A. D.2024-02-28doi:10.1101/2024.02.26.580534Cold Spring Harbor Laboratory Press2024-02-28
<![CDATA[
Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
]]>
https://biorxiv.org/cgi/content/short/2024.02.26.582055v1?rss=1"
D'Sa, K.Choi, M. L.Wagen, A. Z.Seto-Salvia, N.Kopach, O.Evans, J. R.Rodrigues, M.Lopez-Garcia, P.Ghareeb, A.Bayne, J.Grant-Peters, M.Garcia-Ruiz, S.Chen, Z.Rodriques, S.Athauda, D.Gustavsson, E.Gagliano Taliun, S. A.Reynolds, R. H.Young, G.Strohbuecker, S.Warner, T.Rusakov, D. A.Patani, R.Bryant, C.Klenerman, D. A.Gandhi, S.Ryten, M.2024-02-28doi:10.1101/2024.02.26.582055Cold Spring Harbor Laboratory Press2024-02-28
<![CDATA[
GLP-1 receptor agonism ameliorates Parkinsons disease through modulation of neuronal insulin signalling and glial suppression
]]>
https://biorxiv.org/cgi/content/short/2024.02.28.582460v1?rss=1"
Athauda, D.Evans, J. R.Sanchez, L.Virdi, G.Lopez Garcia, P.Wernick, A.Wagen, A.D'Sa, K.Lachica, J.Strohbuecker, S.Vecchi, G.Leighton, C.Saleeb, R. S.OShaughnessy, J.Toomey, C.Vijiaratnam, N.Girges, C.Li, Y.Mustapic, M.Ismail, K.Davies, M.Kapogiannis, D.Choi, M. L.Ryten, M.Horrocks, M. H.Greig, N. H.Foltynie, T.Gandhi, S.2024-02-28doi:10.1101/2024.02.28.582460Cold Spring Harbor Laboratory Press2024-02-28
<![CDATA[
TrajectoryGeometry suggests cell fate decisions involve branches rather than bifurcations
]]>
https://biorxiv.org/cgi/content/short/2024.02.26.582231v1?rss=1"
Laddach, A. C.Shapiro, M.2024-02-28doi:10.1101/2024.02.26.582231Cold Spring Harbor Laboratory Press2024-02-28
<![CDATA[
The Molecular Landscape of Cellular Metal Ion Biology
]]>
https://biorxiv.org/cgi/content/short/2024.02.29.582718v1?rss=1"
Aulakh, S. K.Lemke, O.Szyrwiel, L.Kamrad, S.Chen, Y.Hartl, J.Muelleder, M.Nielsen, J.Ralser, M.2024-03-03doi:10.1101/2024.02.29.582718Cold Spring Harbor Laboratory Press2024-03-03
<![CDATA[
A male-essential microRNA is key for avian sex chromosome dosage compensation
]]>
https://biorxiv.org/cgi/content/short/2024.03.06.581755v1?rss=1"
Fallahshahroudi, A.Rodriguez-Montes, L.Yousefi Taemeh, S.Trost, N.Tellez, M.Ballantyne, M.Idoko-Akoh, A.Taylor, L.Sherman, A.Sorato, E.Johnsson, M.Cardoso Moreira, M.McGrew, M.Kaessmann, H.2024-03-07doi:10.1101/2024.03.06.581755Cold Spring Harbor Laboratory Press2024-03-07
<![CDATA[
Solvent Precipitation SP3 (SP4) enhances recovery for proteomics sample preparation without magnetic beads
]]>
https://biorxiv.org/cgi/content/short/2021.09.24.461247v1?rss=1"
View larger version (49K):
org.highwire.dtl.DTLVardef@1ba615corg.highwire.dtl.DTLVardef@14df25dorg.highwire.dtl.DTLVardef@62f0c1org.highwire.dtl.DTLVardef@1ac436a_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Johnston, H. E.Yadav, K.Kirkpatrick, J. M.Biggs, G. S.Oxley, D.Kramer, H. B.Samant, R. S.2021-09-24doi:10.1101/2021.09.24.461247Cold Spring Harbor Laboratory Press2021-09-24
<![CDATA[
Physiologic media renders human iPSC-derived macrophages permissive for M. tuberculosis by rewiring organelle function and metabolism
]]>
https://biorxiv.org/cgi/content/short/2024.03.15.585248v1?rss=1"
Bussi, C.Lai, R.Athanasiadi, N.Gutierrez, M. G.2024-03-17doi:10.1101/2024.03.15.585248Cold Spring Harbor Laboratory Press2024-03-17
<![CDATA[
High-resolution genomic ancestry reveals mobility in early medieval Europe
]]>
https://biorxiv.org/cgi/content/short/2024.03.15.585102v1?rss=1"
Speidel, L.Silva, M.Booth, T.Raffield, B.Anastasiadou, K.Barrington, C.Gotherstrom, A.Heather, P.Skoglund, P.2024-03-19doi:10.1101/2024.03.15.585102Cold Spring Harbor Laboratory Press2024-03-19
<![CDATA[
mRNA display in cell lysates enables identification of cyclic peptides targeting the BRD3 extraterminal domain
]]>
https://biorxiv.org/cgi/content/short/2024.03.20.585962v1?rss=1"
1012 cyclic peptides against a protein target, enabling the rapid discovery of high affinity ligands. These cyclic peptides are particularly well suited to challenging protein targets that have been difficult to drug with small molecules. However, target choice can still be limited as screens are typically performed against purified proteins which often demands the use of isolated domains and precludes the use of aggregation-prone targets. Here, we report a method to perform mRNA display selections in mammalian cell lysates without the need for prior target purification, vastly expanding the potential target scope of mRNA display. We have applied the methodology to identify low to sub-nanomolar peptide binders for two targets; a NanoLuc subunit (LgBiT) and full-length bromodomain-containing protein 3 (BRD3). Our cyclic peptides for BRD3 were found to bind to the extraterminal (ET) domain of BRD3 and the closely related BRD proteins, BRD2 and BRD4. While many chemical probes exist for the bromodomains of BRD proteins, the ET domain is relatively underexplored, making these peptides valuable additions to the BRD toolbox.
]]>Hurd, C. A.Bush, J.Powell, A. J.Walport, L. J.2024-03-20doi:10.1101/2024.03.20.585962Cold Spring Harbor Laboratory Press2024-03-20
<![CDATA[
Caspase cleavage of Influenza A virus M2 disrupts M2-LC3 interaction and regulates virion production
]]>
https://biorxiv.org/cgi/content/short/2024.04.04.588074v1?rss=1"
Beale, R.Figueras-Novoa, C.Akutsu, M.Murata, D.Jiang, M.Montaner, B.Dubois, C.Shenoy, A. R.2024-04-04doi:10.1101/2024.04.04.588074Cold Spring Harbor Laboratory Press2024-04-04
<![CDATA[
HIV-1 Capsid Rapidly Induces Long Lived CPSF6 Puncta in Non-dividing Cells but Similar Puncta Already Exist in Uninfected T-cells
]]>
https://biorxiv.org/cgi/content/short/2024.03.29.587340v1?rss=1"
Guedan, A.Burley, M.Caroe, E.Bishop, K. N.2024-03-29doi:10.1101/2024.03.29.587340Cold Spring Harbor Laboratory Press2024-03-29
<![CDATA[
High-throughput screening of human genetic variants by pooled prime editing
]]>
https://biorxiv.org/cgi/content/short/2024.04.01.587366v1?rss=1"
Herger, M.Kajba, C. M.Buckley, M.Cunha, A.Strom, M.Findlay, G. M.2024-04-01doi:10.1101/2024.04.01.587366Cold Spring Harbor Laboratory Press2024-04-01
<![CDATA[
HIV-1 Vpr causes separate cell cycle arrests in G2 and M that activate alternative DNA damage pathways
]]>
https://biorxiv.org/cgi/content/short/2024.04.02.587683v1?rss=1"
Hall, R.Ahern, L. M.Yap, M. W.Tsai, M.-H. C.Boucherit, V. C.Takaki, T.Boulton, S. J.Bishop, K. N.2024-04-02doi:10.1101/2024.04.02.587683Cold Spring Harbor Laboratory Press2024-04-02
<![CDATA[
Robust encoding of sub-sniff temporal information in the mouse olfactory bulb
]]>
https://biorxiv.org/cgi/content/short/2024.03.26.586830v1?rss=1"
Warner, T. P. A.Tootoonian, S.Schaefer, A. T.2024-03-29doi:10.1101/2024.03.26.586830Cold Spring Harbor Laboratory Press2024-03-29
<![CDATA[
Plasmodium falciparum protein phosphatase PP7 is required for early ring-stage development
]]>
https://biorxiv.org/cgi/content/short/2024.04.08.588616v1?rss=1"
Patel, A.Rey, J. A.Flynn, H. R.Kousis, K.Skehel, M. J.Blackman, M.Baker, D. A.2024-04-09doi:10.1101/2024.04.08.588616Cold Spring Harbor Laboratory Press2024-04-09
<![CDATA[
Monolayer force generation and transmission is dictated by focal adhesion distribution
]]>
https://biorxiv.org/cgi/content/short/2024.04.10.588783v1?rss=1"
Davis, J. R.Solowiej-Wedderburn, J.Vega, S. L.Burdick, J. A.Dunlop, C.Tapon, N.2024-04-10doi:10.1101/2024.04.10.588783Cold Spring Harbor Laboratory Press2024-04-10
<![CDATA[
MCM Double Hexamer Loading Visualised with Human Proteins
]]>
https://biorxiv.org/cgi/content/short/2024.04.10.588848v1?rss=1"
Weissmann, F.Greiwe, J. F.Pühringer, T.Miller, T. C. R.Diffley, J. F. X.Costa, A.2024-04-10doi:10.1101/2024.04.10.588848Cold Spring Harbor Laboratory Press2024-04-10
<![CDATA[
Spatial proteomic analysis of a lung cancer model reveals regulatory T cells attenuate KRAS-G12C inhibitor-induced immune responses
]]>
https://biorxiv.org/cgi/content/short/2024.04.11.588725v1?rss=1"
Cole, M.Anastasiou, P.Lee, C.Moore, C.Mugarza, E.Jones, M.Valand, K.Rana, S.Colliver, E.Angelova, M.Enfield, K.Magness, A.Mullokandov, A.Kelly, G.de Gruijl, T.Molina-Arcas, M.Swanton, C.Downward, J.van Maldegem, F.2024-04-13doi:10.1101/2024.04.11.588725Cold Spring Harbor Laboratory Press2024-04-13
<![CDATA[
Mutations in the IgG B cell receptor associated with class-switched B cell lymphomas
]]>
https://biorxiv.org/cgi/content/short/2024.04.12.585865v1?rss=1"
Wasim, L.Chu, S. W. T.Sale, B.Pickard, L.Leonard, S.Zhang, L.Tolarova, H.Tean, Z. S.Engels, N.Calado, D. P.Tarte, K.Okosun, J.Forconi, F.Tolar, P.2024-04-13doi:10.1101/2024.04.12.585865Cold Spring Harbor Laboratory Press2024-04-13
<![CDATA[
Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region
]]>
https://biorxiv.org/cgi/content/short/2023.11.23.568045v1?rss=1"
Bennison, A.Byrne, A. M.Reid, S. M.Lynton-Jenkins, J. G.Mollett, B.De Sliva, D.Peers-Dent, J.Finlayson, K. E.Hall, R.Blockley, F.Blyth, M.Falchieri, M.Fowler, Z.Fitzcharles, E.Brown, I. H.James, J.Banyard, A. C.2023-11-24doi:10.1101/2023.11.23.568045Cold Spring Harbor Laboratory Press2023-11-24
<![CDATA[
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
]]>
https://biorxiv.org/cgi/content/short/2024.04.17.589864v1?rss=1"
Zhang, I.Boezio, G. L.Cornwall-Scoones, J.Frith, T.Jiang, M.Howell, M.Lovell-Badge, R.Sagner, A.Briscoe, J.Delas, M. J.2024-04-17doi:10.1101/2024.04.17.589864Cold Spring Harbor Laboratory Press2024-04-17
<![CDATA[
Accurate evaluation of live-virus microneutralisation for SARS-CoV-2 variant JN.1
]]>
https://biorxiv.org/cgi/content/short/2024.04.17.589886v1?rss=1"
Dowgier, G.Hobbs, A.Greenwood, D.Shawe-Taylor, M.Stevenson-Leggett, P.Bazire, J.Penn, R.Harvey, R.Libri, V.Kassiotis, G.Gamblin, S.Lewis, N. S.Williams, B.Swanton, C.Gandhi, S.Bauer, D. L.Carr, E. J.Wall, E. C.Wu, M. Y.2024-04-18doi:10.1101/2024.04.17.589886Cold Spring Harbor Laboratory Press2024-04-18
<![CDATA[
Rapid mortality in captive bush dogs (Speothos venaticus) caused by influenza A of avian origin (H5N1) at a wildlife collection in the United Kingdom
]]>
https://biorxiv.org/cgi/content/short/2024.04.18.590032v1?rss=1"
Falchieri, M.Reid, S.Dastderji, A.Cracknell, J.Warren, C. J.Mollett, B.Peers-Dent, J.Schlachter, A.-L.Mcginn, N.Hepple, R.Thomas, S.Ridout, S.Quayle, J.Pizzi, R.Nunez, A.Byrne, A. M. P.James, J.Banyard, A. C.2024-04-18doi:10.1101/2024.04.18.590032Cold Spring Harbor Laboratory Press2024-04-18
<![CDATA[
Spherical Phenotype Clustering
]]>
https://biorxiv.org/cgi/content/short/2024.04.19.590313v1?rss=1"
Nightingale, L.Tuersley, J.Cairoli, A.Howes, J.Powell, A.Green, D.Strange, A.Warchal, S.Howell, M.2024-04-25doi:10.1101/2024.04.19.590313Cold Spring Harbor Laboratory Press2024-04-25
<![CDATA[
Spatiotemporal Orchestration of Mitosis by Cyclin-Dependent Kinase
]]>
https://biorxiv.org/cgi/content/short/2024.04.29.591629v1?rss=1"
Kapadia, N.Nurse, P.2024-04-30doi:10.1101/2024.04.29.591629Cold Spring Harbor Laboratory Press2024-04-30
<![CDATA[
The Streptococcus pneumoniae transcriptome in patient cerebrospinal fluid identifies novel virulence factors required for meningitis
]]>
https://biorxiv.org/cgi/content/short/2024.04.30.591261v1?rss=1"
Wall, E. C.Guerra-Assuncao, J.-A.Yang, M.Konig, R.Audshasai, T.Proust, A.Aprianto, R.Ramos-Sevillano, E.Ercoli, G.Bordin, N.Agostinho-Terra, V. S.Veening, J.-W.Lalloo, D. G.Wren, B. W.Wilkinson, R. J.Brouwer, M. C.van de Beek, D.Kadiloglu, A.Heyderman, R. S.Brown, J. S.2024-04-30doi:10.1101/2024.04.30.591261Cold Spring Harbor Laboratory Press2024-04-30
<![CDATA[
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
]]>
https://biorxiv.org/cgi/content/short/2024.04.29.591666v1?rss=1"
Hunt, M.Hinrichs, A. S.Anderson, D.Karim, L.Dearlove, B. L.Knaggs, J.Constantinides, B.Fowler, P. W.Rodger, G.Street, T. L.Lumley, S. F.Webster, H.Sanderson, T.Ruis, C.De Maio, N.Amenga-Etego, L. N.Amuzu, D. S.Avaro, M.Awandare, G. A.Ayivor-Djanie, R.Bashton, M.Batty, E. M.Bediako, Y.De Belder, D.Benedetti, E.Bergthaler, A.Boers, S. A.Campos, J.Carr, R. A. A.Cuba, F.Dattero, M. E.Dejnirattisai, W.Dilthey, A. T.Duedu, K. O.Endler, L.Engelmann, I.Francisco, N. M.Fuchs, J.Gnimpieba Z., E.Groc, S.Gyamfi, J.Heemskerk,2024-04-30doi:10.1101/2024.04.29.591666Cold Spring Harbor Laboratory Press2024-04-30
<![CDATA[
An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast
]]>
https://biorxiv.org/cgi/content/short/2024.05.16.594506v1?rss=1"
Libby, A. R.Rito, T.Radley, A.Briscoe, J.2024-05-16doi:10.1101/2024.05.16.594506Cold Spring Harbor Laboratory Press2024-05-16
<![CDATA[
Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2
]]>
https://biorxiv.org/cgi/content/short/2024.05.12.593776v1?rss=1"
Bashore, F. M.Min, S. M.Chen, X.Howell, S.Rinderle, C. H.Morel, G.Silvaroli, J. A.Wells, C. I.Bunnell, B. A.Drewry, D.Pabla, N. S.Ultanir, S. K.Bullock, A. N.Axtman, A. D.2024-05-14doi:10.1101/2024.05.12.593776Cold Spring Harbor Laboratory Press2024-05-14
<![CDATA[
Imaging of MAP kinase dynamics reveals endocytic regulation of pulsatile signalling and network re-wiring in response to targeted therapy in EGFR-mutant non-small cell lung cancer
]]>
https://biorxiv.org/cgi/content/short/2024.05.14.594112v1?rss=1"
Le Marois, A. M. I.Bailey, S.Hooper, S.Kumar, S.Sparks, H.Alexandrov, Y.Caswell, D. R.Fröhlich, F.Schlegelmilch, K.Valand, K.Martin, M. J.Narvaez, A. J.Swanton, C.Downward, J.Dunsby, C.French, P. M.Sahai, E.2024-05-17doi:10.1101/2024.05.14.594112Cold Spring Harbor Laboratory Press2024-05-17
<![CDATA[
p53 and TIGAR promote redox control to protect against metabolic dysfunction-associated steatohepatitis
]]>
https://biorxiv.org/cgi/content/short/2024.05.20.594983v1?rss=1"
Wittke, C. I.Cheung, E. C.Athineos, D.Clements, N.Butler, L.Hughes, M.Morrison, V.Watt, D.Blyth, K.Vousden, K.Humpton, T. J.2024-05-21doi:10.1101/2024.05.20.594983Cold Spring Harbor Laboratory Press2024-05-21
<![CDATA[
Sympathetic neuron-derived NPY protects from obesity by sustaining the mural progenitors of thermogenic adipocytes.
]]>
https://biorxiv.org/cgi/content/short/2024.05.18.594804v1?rss=1"
Zhu, Y.Yao, L.Gallo-Ferraz, A. L.Bombassaro, B.Simoes, M. R.Abe, I.Chen, J.Sarker, G.Ciccarelli, A.Zhou, L.Lee, C.Martinez-Sanchez, N.Dustin, M.Anderson, K.Zhan, C.Horvath, T.Velloso, L.Kajimura, S.Domingos, A. I.2024-05-21doi:10.1101/2024.05.18.594804Cold Spring Harbor Laboratory Press2024-05-21
<![CDATA[
Marsupial single-cell transcriptomics provides an atlas of developmental heterochrony
]]>
https://biorxiv.org/cgi/content/short/2024.05.26.595746v1?rss=1"
Menchero, S.Barrington, C.Alanis-Lobato, G.Varsally, W.Niakan, K. K.Turner, J. M. A.2024-05-26doi:10.1101/2024.05.26.595746Cold Spring Harbor Laboratory Press2024-05-26
<![CDATA[
Genesis: A Modular Protein Language Modelling Approach to Immunogenicity Prediction
]]>
https://biorxiv.org/cgi/content/short/2024.05.22.595296v1?rss=1"
O'Brien, H.Salm, M.Morton, L. T.Szukszto, M.O'Farrell, F.Boulton, C.King, L.Bola, S. K.Becker, P.Craig, A.Nielsen, M.Samuels, Y.Swanton, C.Mansour, M. R.Hadrup, S. R.Quezada, S.2024-05-26doi:10.1101/2024.05.22.595296Cold Spring Harbor Laboratory Press2024-05-26
<![CDATA[
The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution
]]>
https://biorxiv.org/cgi/content/short/2024.05.27.596037v1?rss=1"
Lemke, O.Heineike, B. M.Viknander, S.Cohen, N.Steenwyk, J. L.Spranger, L.Li, F.Agostini, F.Lee, C. T.Aulakh, S. K.Nielsen, J.Rokas, A.Berman, J.Zelezniak, A.Gossmann, T. I.Ralser, M.2024-05-27doi:10.1101/2024.05.27.596037Cold Spring Harbor Laboratory Press2024-05-27
<![CDATA[
The CSF transcriptome in pneumococcal meningitis reveals compartmentalised host inflammatory responses associated with mortality.
]]>
https://biorxiv.org/cgi/content/short/2024.05.24.592913v1?rss=1"
Guerra-Assuncao, J.-A.Chakroborty, P.Pollara, G.Venturini, C.Mlozowa, V. S.Denis, B.Nyirenda, M.Lalloo, D. G.Noursadeghi, M.Heyderman, R. S.Brown, J. S.Wall, E. C.2024-05-28doi:10.1101/2024.05.24.592913Cold Spring Harbor Laboratory Press2024-05-28
<![CDATA[
North Pontic crossroads: Mobility in Ukraine from the Bronze Age to the early modern period
]]>
https://biorxiv.org/cgi/content/short/2024.05.24.595769v1?rss=1"
Saag, L.Utevska, O.Zadnikov, S.Shramko, I.Gorbenko, K.Bandrivskyi, M.Pavliv, D.Bruyako, I.Grechko, D.Okatenko, V.Toshev, G.Andrukh, S.Radziyevska, V.Buynov, Y.Kotenko, V.Smyrnov, O.Petrauskas, O.Magomedov, B.Didenko, S.Heiko, A.Reida, R.Sapiehin, S.Aksonov, V.Laptiev, O.Terskyi, S.Skorokhod, V.Zhyhola, V.Sytyi, Y.Jarve, M.Scheib, C. L.Anastasiadou, K.Kelly, M.Williams, M.Silva, M.Barrington, C.Gilardet, A.Macleod, R.Skoglund, P.Thomas, M. G.2024-05-28doi:10.1101/2024.05.24.595769Cold Spring Harbor Laboratory Press2024-05-28
<![CDATA[
The diversity of SNCA transcripts in neurons, and its impact on antisense oligonucleotide therapeutics
]]>
https://biorxiv.org/cgi/content/short/2024.05.30.596437v1?rss=1"
Evans, J. R.Gustavsson, E. K.Doykov, I.Murphy, D.Virdi, G.Lachica, J.Rontgen, A.Murtada, M. H.Pang, C. W.Macpherson, H.Wernick, A. I.Toomey, C. E.Athauda, D.Choi, M.Hardy, J.Wood, N. W.Vendruscolo, M.Mills, K.Heywood, W.Ryten, M.Gandhi, S.2024-05-31doi:10.1101/2024.05.30.596437Cold Spring Harbor Laboratory Press2024-05-31
<![CDATA[
Growth-induced physiological hypoxia correlates with growth deceleration during normal development
]]>
https://biorxiv.org/cgi/content/short/2024.06.04.597345v1?rss=1"
Zhao, Y.Alexandre, C.Kelly, G.Perez-Mockus, G.Vincent, J.-P.2024-06-05doi:10.1101/2024.06.04.597345Cold Spring Harbor Laboratory Press2024-06-05
<![CDATA[
Illuminating morphogen and patterning dynamics with optogenetic control of morphogen production
]]>
https://biorxiv.org/cgi/content/short/2024.06.11.598403v1?rss=1"
Benzinger, D.Briscoe, J.2024-06-11doi:10.1101/2024.06.11.598403Cold Spring Harbor Laboratory Press2024-06-11
<![CDATA[
Structural Insight into the Function of Human Peptidyl Arginine Deiminase 6
]]>
https://biorxiv.org/cgi/content/short/2024.06.10.598250v1?rss=1"
Williams, J. P.Mouilleron, S.Hernandez Trapero, R.Bertran, M. T.Marsh, J. A.Walport, L. J.2024-06-10doi:10.1101/2024.06.10.598250Cold Spring Harbor Laboratory Press2024-06-10
<![CDATA[
Mycobacterium tuberculosis ESX-T7SS impacts the 3D architecture of tuberculous lesion in susceptible mice
]]>
https://biorxiv.org/cgi/content/short/2024.06.14.599018v1?rss=1"
Beltran, C. G. G.Kriel, J.Nolan, M. B.Botha, S. M.Ciccarelli, A.Loos, B.Gutierrez, M.Walzl, G.2024-06-14doi:10.1101/2024.06.14.599018Cold Spring Harbor Laboratory Press2024-06-14
<![CDATA[
Metabolic remodelling in hiPSC-derived myofibres carrying the m.3243A>G mutation
]]>
https://biorxiv.org/cgi/content/short/2024.06.11.598565v1?rss=1"
G mutation is the major cause of Mitochondrial Encephalomyopathy Lactic Acidosis and Stroke Like episodes (MELAS). Experimental models that recapitulate the disease phenotype in vitro for disease modelling or drug screening are very limited. We have therefore generated hiPSC-derived muscle fibres with variable heteroplasmic mtDNA mutation load without significantly affecting muscle differentiation potential. The cells are excitable and show physiological characteristics of muscle fibres and show well organised myofibrillar structure. In cells carrying the m.3243A>G, the mitochondrial membrane potential and oxygen consumption were reduced in relation to the mutant load. We have shown through proteomic, phosphoproteomic, and metabolomic analyses that the m.3243A>G mutation variably affects the cell phenotype in relation to the mutant load. This variation is reflected by an increase in the NADH/NAD+ ratio, which in turns influences key nutrient-sensing pathways in the myofibres. This model enables detailed study of the impact of the mutation on cellular bioenergetics and on muscle physiology with the potential to provide a platform for drug screening.
]]>Valdebenito, G. E.Chacko, A. R.Chung, C.-Y.Sheshadri, P.Chi, H.O'Callaghan, B.Houlden, H.Rouse, H.Morales, V.Bianchi, K.Tedesco, F. S.Pitceathly, R. D.Duchen, M. R.2024-06-13doi:10.1101/2024.06.11.598565G mutation]]>Cold Spring Harbor Laboratory Press2024-06-13
<![CDATA[
Network nature of ligand-receptor interactions underlies disease comorbidity in the brain
]]>
https://biorxiv.org/cgi/content/short/2024.06.15.599140v1?rss=1"
Grant-Peters, M.Fairbrother-Browne, A.Hicks, A.Guo, B.Reynolds, R. H.Huuki-Myers, L. A.Eagles, N.Brenton, J.Garcia-Ruiz, S.Wood, N.Gandhi, S.Martinowich, K.Maynard, K.Collado-Torres, L.Ryten, M.2024-06-16doi:10.1101/2024.06.15.599140Cold Spring Harbor Laboratory Press2024-06-16
<![CDATA[
Inferring gene regulatory networks using DNA methylation data
]]>
https://biorxiv.org/cgi/content/short/2024.04.23.590858v1?rss=1"
Bartlett, T. E.2024-04-25doi:10.1101/2024.04.23.590858Cold Spring Harbor Laboratory Press2024-04-25
<![CDATA[
SubtiToolKit - a bioengineering kit for Bacillus subtilis and Gram-positive bacteria.
]]>
https://biorxiv.org/cgi/content/short/2024.06.24.600474v1?rss=1"
Caro Astorga, J.Malci, K.Ellis, T.James, P.Debenedictis, E.Ming, H.Rogan, M.2024-06-25doi:10.1101/2024.06.24.600474Cold Spring Harbor Laboratory Press2024-06-25
<![CDATA[
Dynamics of positional information in the vertebrate neural tube
]]>
https://biorxiv.org/cgi/content/short/2024.07.01.601514v1?rss=1"
Markovic, A.Briscoe, J.Page, K. M.2024-07-01doi:10.1101/2024.07.01.601514Cold Spring Harbor Laboratory Press2024-07-01
<![CDATA[
Pan-cancer subclonal mutation analysis of 7,827 tumors predicts clinical outcome
]]>
https://biorxiv.org/cgi/content/short/2024.07.03.601939v1?rss=1"
Jiang, Y.Montierth, M. D.Yu, K.Ji, S.Guo, S.Tran, Q.Liu, X.Shin, S. J.Cao, S.Li, R.Tang, Y.Lesluyes, T.Kopetz, S.Ajani, J.Msaouel, P.Subudhi, S. K.Aparicio, A.Sharma, P.Shen, J. P.Sood, A. K.Tarabichi, M.Wang, J. R.Kimmel, M.Loo, P. V.Zhu, H.Wang, W.2024-07-06doi:10.1101/2024.07.03.601939Cold Spring Harbor Laboratory Press2024-07-06
<![CDATA[
Human Gastric Multi-Regional Assembloids Favour Functional Parietal Maturation and Allow Modelling of Antral Foveolar Hyperplasia
]]>
https://biorxiv.org/cgi/content/short/2024.07.08.602480v1?rss=1"
Jones, B. C.Benedetti, G.Cala, G.Tullie, L.Simcock, I.Lutman, R.Balys, M.Amiri, R.Sufi, J.Arthurs, O.Eaton, S.Anderson, G.Elvassore, N.Li, V. S.Jones, K. D.Tape, C. J.Luni, C.Giobbe, G. G.De Coppi, P.2024-07-11doi:10.1101/2024.07.08.602480Cold Spring Harbor Laboratory Press2024-07-11
<![CDATA[
The bat Influenza A virus subtype H18N11 induces nanoscale MHCII clustering upon host cell attachment
]]>
https://biorxiv.org/cgi/content/short/2024.07.12.603249v1?rss=1"
Osman, M. K.Robert, J.Broich, L.Frank, D.Grosse, R.Schwemmle, M.Wrobel, A.Ciminski, K.Sieben, C.Reuther, P.2024-07-12doi:10.1101/2024.07.12.603249Cold Spring Harbor Laboratory Press2024-07-12
<![CDATA[
PP1 PNUTS binds the restrictor and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination
]]>
https://biorxiv.org/cgi/content/short/2024.07.12.603302v1?rss=1"
Bentley, D.Treisman, R.Erickson, B.Fong, N.Hansen, K.Sheridan, R. M.Larson, K.Saviola, A.Fedoryshchak, R.Mouilleron, S.2024-07-13doi:10.1101/2024.07.12.603302Cold Spring Harbor Laboratory Press2024-07-13
<![CDATA[
Molecular basis of FIGNL1 in dissociating RAD51 from DNA and chromatin
]]>
https://biorxiv.org/cgi/content/short/2024.07.16.603765v1?rss=1"
Carver, A.Yu, T.-Y.Yates, L.White, T.Wang, R.Lister, K.Jasin, M.Zhang, X.2024-07-16doi:10.1101/2024.07.16.603765Cold Spring Harbor Laboratory Press2024-07-16
<![CDATA[
Branched actin networks in innate immune cells mediate host microbiota homeostasis.
]]>
https://biorxiv.org/cgi/content/short/2024.07.18.604111v1?rss=1"
Vasconcellos, L. R.Huang, S. C. M.Suarez-Bonnet, A.Priestnall, S.Varsani-Brown, S.Winder, M. L.Shah, K.Kogata, N.Stockinger, B.Way, M.2024-07-18doi:10.1101/2024.07.18.604111Cold Spring Harbor Laboratory Press2024-07-18
<![CDATA[
Ancient Borrelia genomes document the evolutionary history of louse-borne relapsing fever
]]>
https://biorxiv.org/cgi/content/short/2024.07.18.603748v1?rss=1"
Swali, P.Booth, T.Tan, C. C. S.McCabe, J.Anastasiadou, K.Barrington, C.Borrini, M.Bricking, A.Buckberry, J.Buster, L.Carlin, R.Gilardet, A.Glocke, I.Irish, J.Kelly, M.King, M.Petchey, F.Peto, J.Silva, M.Speidel, L.Tait, F.Teoaca, A.Valoriani, S.Williams, M.Madgwick, R.Mullan, G.Wilson, L.Cootes, K.Armit, I.Gutierrez, M. G.van Dorp, L.Skoglund, P.2024-07-19doi:10.1101/2024.07.18.603748Cold Spring Harbor Laboratory Press2024-07-19
<![CDATA[
Systematic identification of Y-chromosome gene functions in mouse spermatogenesis
]]>
https://biorxiv.org/cgi/content/short/2024.07.18.604063v1?rss=1"
Subrini, J.Varsally, W.Balaguer Balsells, I.Bensberg, M.Sioutas, G.Ojarikre, O.Maciulyte, V.Gylemo, B.Crawley, K.Courtis, K.de Rooij, D. G.Turner, J. M.2024-07-19doi:10.1101/2024.07.18.604063Cold Spring Harbor Laboratory Press2024-07-19
<![CDATA[
Structures of TGF-beta with betaglycan and the signaling receptors reveal the mechanism whereby betaglycan potentiates receptor complex assembly and signaling
]]>
https://biorxiv.org/cgi/content/short/2024.07.19.604101v1?rss=1"
Wieteska, L.Taylor, A. B.Punch, E.Coleman, J. A.Conway, I. O.Lin, Y.-F.Byeon, C.-H.Hinck, C. S.Krzysiak, T.Ishima, R.Lopez-Casillas, F.Cherepanov, P.Bernard, D. J.Hill, C. S.Hinck, A. P.2024-07-22doi:10.1101/2024.07.19.604101Cold Spring Harbor Laboratory Press2024-07-22
<![CDATA[
Multi-Omic Analysis Reveals Lipid Dysregulation Associated with Mitochondrial Dysfunction in Parkinson's Disease Brain
]]>
https://biorxiv.org/cgi/content/short/2024.07.18.604051v1?rss=1"
View larger version (48K):
org.highwire.dtl.DTLVardef@d4851eorg.highwire.dtl.DTLVardef@6f9d00org.highwire.dtl.DTLVardef@1ac9d7dorg.highwire.dtl.DTLVardef@197808e_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Hallqvist, J.Toomey, C. E.Pinto, R.Wernick, A.Shahrani, M.Heales, S.Eaton, S.Mills, K.Gandhi, S.Heywood, W. E.2024-07-22doi:10.1101/2024.07.18.604051Cold Spring Harbor Laboratory Press2024-07-22
<![CDATA[
STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair
]]>
https://biorxiv.org/cgi/content/short/2024.07.22.604575v1?rss=1"
van den Heuvel, D.Rodriguez-Martinez, M.van der Meer, P. J.Nieto Moreno, N.Park, J.Kim, H.-S.van Schie, J. J.Wondergem, A. P.D'Souza, A.Yakoub, G.Herlihy, A.Kashyap, K.Boissiere, T.Walker, J.Mitter, R.Apelt, K.de Lint, K.Kirdok, I.Ljungman, M.Wolthuis, R. M.Cramer, P.Scharer, O. D.Kokic, G.Svejstrup, J. Q.Luijsterburg, M. S.2024-07-22doi:10.1101/2024.07.22.604575Cold Spring Harbor Laboratory Press2024-07-22
<![CDATA[
Super-resolution imaging of proteins inside live mammalian cells with mLIVE-PAINT
]]>
https://biorxiv.org/cgi/content/short/2024.07.22.604574v1?rss=1"
Bhaskar, H.Gidden, Z.Virdi, G.Kleinjan, D.-J.Rosser, S. J.Gandhi, S.Regan, L.Horrocks, M. H.2024-07-22doi:10.1101/2024.07.22.604574Cold Spring Harbor Laboratory Press2024-07-22
<![CDATA[
ATG9A and ARFIP2 cooperate to regulate PI4P levels for lysosomal repair
]]>
https://biorxiv.org/cgi/content/short/2024.07.23.604321v1?rss=1"
De Tito, S.Almacellas, E.Yu, D. D.Zhang, W.Millard, E.Hervas, J. H.Pellegrino, E.Panagi, I.Fodge, D.Thurston, T. L. M.Gutierrez, M.Tooze, S.2024-07-24doi:10.1101/2024.07.23.604321Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
Multiscale mechanics drive functional maturation of the vertebrate heart
]]>
https://biorxiv.org/cgi/content/short/2024.07.24.604962v1?rss=1"
Andrews, T. G.Cornwall Scoones, J.Ramel, M.-C.Gupta, K.Briscoe, J.Priya, R.2024-07-24doi:10.1101/2024.07.24.604962Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
ETV4 and ETV5 Orchestrate FGF-Mediated Lineage Specification and Epiblast Maturation during Early Mouse Development
]]>
https://biorxiv.org/cgi/content/short/2024.07.24.604964v1?rss=1"
Simon, C. S.Garg, V.Kuo, Y.-Y.Niakan, K. K.Hadjantonakis, A.-K.2024-07-24doi:10.1101/2024.07.24.604964Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
2'-O-Methyl-guanosine 3-base RNA fragments mediate essential natural TLR7/8 antagonism
]]>
https://biorxiv.org/cgi/content/short/2024.07.25.605091v1?rss=1"
Alharbi, A.Sapkota, S.Zhang, Z.Jin, R.Jayasekara, W. S.Rupasinghe, E.Speir, M.Wilkinson-White, L.Gamsjaeger, R.Cubeddu, L.Ellyard, J. I.Wenholz, D.McAllan, A.Rezwan, R.Ying, L.Hosseini Far, H.Bones, J.He, S.Yu, D.Lennox, K.Hertzog, P. J.Vinuesa, C.Behlke, M. A.Ohto, U.Laczka, O.Corry, B.Shimizu, T.Gantier, M. P.2024-07-25doi:10.1101/2024.07.25.605091Cold Spring Harbor Laboratory Press2024-07-25
<![CDATA[
Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics
]]>
https://biorxiv.org/cgi/content/short/2024.07.25.605137v1?rss=1"
400 ligand-protein interactions. Hits were validated through concentration-response experiments and the platform was utilised for hit expansion and live cell experiments. This label-free platform represents a significant step forward in high-throughput proteomics to evaluate ligandability of cysteines across the human proteome.
]]>Biggs, G. S.Cawood, E. E.Vuorinen, A.McCarthy, W. J.Wilders, H.Riziotis, I. G.van der Zouwen, A. J.Pettinger, J.Nightingale, L.Chen, P.Powell, A. J.House, D.Boulton, S. J.Skehel, J. M.Rittinger, K.Bush, J. T.2024-07-25doi:10.1101/2024.07.25.605137Cold Spring Harbor Laboratory Press2024-07-25
<![CDATA[
Human-like APOBEC3 gene expression and anti-viral responses following replacement of mouse Apobec3 with the 7-gene human APOBEC3 locus
]]>
https://biorxiv.org/cgi/content/short/2024.07.30.605801v1?rss=1"
Kirkwood, N. K.Prosser, H.Yap, M. W.Gibson, J.Cook, R.Reddin, I.Stranger, A.Howes, E.Zainal, N.Periyasamy, M.Thomas, G. J.Scott, J.Bishop, K. N.Ali, S.Bradley, A.Fenton, T. R.2024-07-30doi:10.1101/2024.07.30.605801Cold Spring Harbor Laboratory Press2024-07-30
<![CDATA[
Protein degradation shapes developmental tempo in mouse and human neural progenitors
]]>
https://biorxiv.org/cgi/content/short/2024.08.01.604391v1?rss=1"
Nakanoh, S.Stamataki, D.Garcia-Perez, L.Azzi, C.Carr, H. L.Pokhilko, A.Howell, S.Yu, L.Skehel, M.Oxley, D.Andrews, S.Briscoe, J.Rayon, T.2024-08-01doi:10.1101/2024.08.01.604391Cold Spring Harbor Laboratory Press2024-08-01
<![CDATA[
Biallelic Loss of Molecular Chaperone Molecule AIP Results in a Novel Severe Multisystem Disease Defined by Defective Proteostasis
]]>
https://biorxiv.org/cgi/content/short/2024.08.08.604602v1?rss=1"
Korbonits, M.Wang, X.Barry, S.Lim, C.Suleyman, O.De-Tito, S.Begum, N.Vignola, M. L.Hall, C.Perna, L.Chapple, P.Henson, S.Morales, V.Bianchi, K.Edvardsson, V. O.Ragnarsson, K. A.Kristinsdottir, V. E.Debeer, A.Sleyp, Y.Zinchenko, R.Anderson, G.Duchen, M.Singh, K.Chung, C.-Y.Yuan, Y.Patel, S.Aksoy, E.Borovikov, A. O.Bjornsson, H. T.Van Esch, H.Czibik, G.Tooze, S.Brennan, C. H.Haworth, O.2024-08-08doi:10.1101/2024.08.08.604602Cold Spring Harbor Laboratory Press2024-08-08
<![CDATA[
The eduWOSM: an advanced optical microscope for education
]]>
https://biorxiv.org/cgi/content/short/2024.08.10.607181v1?rss=1"
Carter, N. J.Martin, D. S.Molloy, J. E.Cross, R. A.2024-08-10doi:10.1101/2024.08.10.607181Cold Spring Harbor Laboratory Press2024-08-10
<![CDATA[
Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design
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https://biorxiv.org/cgi/content/short/2024.08.12.606135v1?rss=1"
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]]>Armer, C.Kane, H.Cortade, D. L.Redestig, H.Estell, D. A.Yusuf, A.Rollins, N. J.Spinner, H.Marks, D.Brunette, T.Kelly, P. J.DeBenedictis, E.2024-08-12doi:10.1101/2024.08.12.606135Cold Spring Harbor Laboratory Press2024-08-12
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Arp2/3 iso-complexes limit t-tubule overgrowth to ensure myofiber formation and synchronous contraction
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https://biorxiv.org/cgi/content/short/2024.08.13.607563v1?rss=1"
Pereira, A. R.Soares, A. d. R.Liu, T.Ferreira, J. L.Leal, G.Faleiro, I.Kogata, N.Way, M.Moores, C.Gomes, E. R.2024-08-13doi:10.1101/2024.08.13.607563Cold Spring Harbor Laboratory Press2024-08-13
<![CDATA[
A Biologically Inspired Attention Model for Neural Signal Analysis
]]>
https://biorxiv.org/cgi/content/short/2024.08.13.607787v1?rss=1"
Skatchkovsky, N.Glazman, N.Sadeh, S.Iacaruso, F.2024-08-16doi:10.1101/2024.08.13.607787Cold Spring Harbor Laboratory Press2024-08-16
<![CDATA[
Early atrial remodelling drives arrhythmia in Fabry Disease
]]>
https://biorxiv.org/cgi/content/short/2024.08.13.607853v1?rss=1"
Roy, A.O'Shea, C.Dasi, A.Patel, L.CUMBERLAND, M.NIEVES, D.Canagarajah, H. S.THOMPSON, S.AZAD, A.Price, A. M.HALL, C.Alvior, A. M. B.RATH, P.DAVIES, B.Rodriguez, B.Holmes, A. P.Pavlovic, D.Townend, J. N.Geberhiwot, T.GEHMLICH, K.Steeds, R. P.2024-08-17doi:10.1101/2024.08.13.607853Cold Spring Harbor Laboratory Press2024-08-17
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Horizontal gene transfer-initiated reorganization of lipid metabolism drives lifestyle innovation in a eukaryote
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https://biorxiv.org/cgi/content/short/2024.08.21.608818v1?rss=1"
Rao, B. D.Gomez Gil, E.Peter, M.Balogh, G.Nunes, V.MacRae, J. I.Chen, Q.Rosenthal, P. B.Oliferenko, S.2024-08-21doi:10.1101/2024.08.21.608818Cold Spring Harbor Laboratory Press2024-08-21
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Paracrine rescue of MYR1-deficient Toxoplasma gondii mutants reveals limitations of pooled in vivo CRISPR screens
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https://biorxiv.org/cgi/content/short/2024.08.23.609334v1?rss=1"
Torelli, F.Matos da Fonseca, D.Butterworth, S.Young, J. C.Treeck, M.2024-08-23doi:10.1101/2024.08.23.609334Cold Spring Harbor Laboratory Press2024-08-23
<![CDATA[
Synchronous L1 retrotransposition events promote chromosomal crossover early in human tumorigenesis
]]>
https://biorxiv.org/cgi/content/short/2024.08.27.596794v1?rss=1"
Zumalave, S.Santamarina, M.Espasandin, N. P.Garcia-Souto, D.Temes, J.Baker, T. M.Valtierra, A. P.Otero, I.Rodriguez-Castro, J.Oitaben, A.Alvarez, E. G.Otero, P.Diaz-Arias, I.Martinez-Fernandez, M.Van Loo, P.Cristofari, G.Rodriguez-Martin, B.Tubio, J. M.2024-08-27doi:10.1101/2024.08.27.596794Cold Spring Harbor Laboratory Press2024-08-27
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CDKL5's role in microtubule-based transport and cognitive function
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https://biorxiv.org/cgi/content/short/2024.08.28.610038v1?rss=1"
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org.highwire.dtl.DTLVardef@12e50a2org.highwire.dtl.DTLVardef@1aff4b4org.highwire.dtl.DTLVardef@ea7b37org.highwire.dtl.DTLVardef@3f7826_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Lopes, A. T.Janiv, O.Claxton, S.Ultanir, S. K.2024-08-29doi:10.1101/2024.08.28.610038Cold Spring Harbor Laboratory Press2024-08-29
<![CDATA[
M. tuberculosis invades and disrupts the blood-brain barrier directly to initiate meningitis
]]>
https://biorxiv.org/cgi/content/short/2024.08.30.610462v1?rss=1"
Proust, A.Wilkinson, K. A.Wilkinson, R. J.2024-08-30doi:10.1101/2024.08.30.610462Cold Spring Harbor Laboratory Press2024-08-30
<![CDATA[
Malaria parasites undergo a rapid and extensive metamorphosis after invasion of the host erythrocyte
]]>
https://biorxiv.org/cgi/content/short/2024.09.03.610831v1?rss=1"
Freville, A.Moreira-Leite, F.Roussel, C.Russell, M. R. G.Fricot, A.Carret, V.Sissoko, A.Hayes, M. J.Dialo, A. B.Kerkhoven, N.Ressurreicao, M.Dokmak, S.Blackman, M.Collinson, L.Buffet, P. A.Vaughan, S.Ndour, A.van Ooij, C.2024-09-03doi:10.1101/2024.09.03.610831Cold Spring Harbor Laboratory Press2024-09-03
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Subtype-specific Patterns of Evolution and Clinically Relevant Genomic Instability in Wilms Tumour
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https://biorxiv.org/cgi/content/short/2024.09.04.610994v1?rss=1"
Cresswell, G. D.Chagtai, T.Al-Saadi, R.Treger, T. D.Madhan, G.Mifsud, B.Vujanic, G.Williams, R. D.Luscombe, N. M.Pritchard-Jones, K.Mifsud, W.2024-09-07doi:10.1101/2024.09.04.610994Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
Human DNA replication initiation sites are specified epigenetically by oxidation of 5-methyl-deoxycytidine
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https://biorxiv.org/cgi/content/short/2024.09.06.611651v1?rss=1"
Krude, T.Bi, J.Doran, R.Jones, R. A.Smith, J. C.2024-09-07doi:10.1101/2024.09.06.611651Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
Gonadotrophs have a dual origin, with most derived from pituitary stem cells during minipuberty.
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https://biorxiv.org/cgi/content/short/2024.09.09.610834v1?rss=1"
Sheridan, D.Chakravarty, P.Golan, G.Shiakola, Y.Galichet, C.Mollard, P.Melamed, P.Lovell-Badge, R.Rizzoti, K.2024-09-09doi:10.1101/2024.09.09.610834Cold Spring Harbor Laboratory Press2024-09-09
<![CDATA[
In vivo CRISPR screens identify GRA12 as a transcendent secreted virulence factor across Toxoplasma gondii strains and mouse subspecies
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https://biorxiv.org/cgi/content/short/2024.09.10.611481v1?rss=1"
Torelli, F.Butterworth, S. W.Lockyer, E. J.Song, O.-R.Pearson-Farr, J.Treeck, M.2024-09-10doi:10.1101/2024.09.10.611481Cold Spring Harbor Laboratory Press2024-09-10
<![CDATA[
An integrated stress response-independent role of GCN2 prevents excessive ribosome biogenesis and mRNA translation
]]>
https://biorxiv.org/cgi/content/short/2024.09.10.611650v1?rss=1"
Roman-Trufero, M.Kleijn, I. T.Blighe, K.Zhou, J.Saavedra-Garcia, P.Gaffar, A.Christoforou, M.Bellotti, A.Abrahams, J.Atrih, A.Lamont, D. J.Gierlinski, M.Jayaprakash, P.Michel, A. M.Aboagye, E.Yuneva, M.Masson, G. R.Shahrezaei, V.Auner, H. W.2024-09-13doi:10.1101/2024.09.10.611650Cold Spring Harbor Laboratory Press2024-09-13
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Mutations in PSEN1 predispose inflammation in an astrocyte model of familial Alzheimer's disease through disrupted regulated intramembrane proteolysis
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https://biorxiv.org/cgi/content/short/2024.09.09.611621v1?rss=1"
Ziff, O. J.Jolly, S.Casey, J. M.Granat, L.Samra, S.Seto-Salvia, N.Alatza, A.Phadke, L.Galet, B.Ravassard, P.Potier, M.-C.Fox, N. C.Hardy, J.Salih, D.Whiting, P.Ducotterd, F.Patani, R.Wray, S.Arber, C.2024-09-13doi:10.1101/2024.09.09.611621Cold Spring Harbor Laboratory Press2024-09-13
<![CDATA[
SOX2 drives fetal reprogramming and reversible dormancy in colorectal cancer
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https://biorxiv.org/cgi/content/short/2024.09.11.612412v1?rss=1"
Baulies, A.Moncho-Amor, V.Drago-Garcia, D.Kucharska, A.Chakravarty, P.Moreno-Valladares, M.Cruces-Salguero, S.Hubl, F.Hutton, C.Kim, H.Matheu, A.Lovell-Badge, R.Li, V. S. W.2024-09-16doi:10.1101/2024.09.11.612412Cold Spring Harbor Laboratory Press2024-09-16
<![CDATA[
Asparagine availability controls germinal centre B cell homeostasis
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https://biorxiv.org/cgi/content/short/2023.04.03.535433v1?rss=1"
Marin, E.Bentkowska, K.Yazicioglu, Y. F.Clarke, A.2023-04-05doi:10.1101/2023.04.03.535433Cold Spring Harbor Laboratory Press2023-04-05
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SIRPalpha+ PD-L1+ bone marrow macrophages aid AML growth by modulating T cell function
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https://biorxiv.org/cgi/content/short/2024.09.15.613123v1?rss=1"
Birch, F.Gonzalez-Anton, S.Haltalli, M. L. R.Chakravarty, P.Bruno, F.Georgiou, C.Mai, C.Todd, Y.Payne, E.Blum, S.Pospori, C.Arber, C.Burt, R.Tissot, F. S.Celso, C. L.2024-09-19doi:10.1101/2024.09.15.613123Cold Spring Harbor Laboratory Press2024-09-19
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The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking
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https://biorxiv.org/cgi/content/short/2024.09.19.613857v1?rss=1"
Pellowe, G. A.Voisin, T. B.Karpauskaite, L.Maslen, S. L.Roeselova, A.Skehel, M.Roustan, C.George, R.Nans, A.Kjaer, S.Taylor, I. A.Balchin, D.2024-09-19doi:10.1101/2024.09.19.613857Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
An intrinsically disordered RNA-binding region provides local target selectivity and is essential for LARP6 function.
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https://biorxiv.org/cgi/content/short/2024.09.20.614075v1?rss=1"
Capraro, F.Abis, G.Karimzadeh, M.Masino, L.Barley, A.Bui, T. T. T.Goodarzi, H.Conte, M. R.Mardakheh, F. K.2024-09-20doi:10.1101/2024.09.20.614075Cold Spring Harbor Laboratory Press2024-09-20
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Divergent Plasmodium protein kinases drive MTOC, kinetochore and axoneme organisation in male gametogenesis
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https://biorxiv.org/cgi/content/short/2024.09.22.613647v1?rss=1"
Yanase, R.Zeeshan, M.Ferguson, D. J.Markus, R.Brady, D.Bottrill, A. R.Holder, A. A.Guttery, D. S.Tewari, R.2024-09-22doi:10.1101/2024.09.22.613647Cold Spring Harbor Laboratory Press2024-09-22
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PDZ-directed substrate recruitment is the primary determinant of specific 4E-BP1dephosphorylation by PP1-Neurabin
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https://biorxiv.org/cgi/content/short/2024.09.23.614477v1?rss=1"
Fedoryshchak, R. O.El-Bouri, K.Joshi, D.Mouilleron, S.Treisman, R.2024-09-23doi:10.1101/2024.09.23.614477Cold Spring Harbor Laboratory Press2024-09-23
<![CDATA[
A Drosophila holidic diet optimised for growthand development
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https://biorxiv.org/cgi/content/short/2024.09.24.614722v1?rss=1"
Sorge, S.Girard, V.Lampe, L.Tixier, V.Weaver, A.Higgins, T.Gould, A. P.2024-09-24doi:10.1101/2024.09.24.614722Cold Spring Harbor Laboratory Press2024-09-24
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Capture, mutual inhibition and release mechanism for aPKC-Par6 and its multi-site polarity substrate Lgl
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https://biorxiv.org/cgi/content/short/2024.09.26.615224v1?rss=1"
Earl, C. P.Cobbaut, M.Carvalho, A. B.Ivanova, M. E.Briggs, D. C.Morais-de-Sa, E.Parker, P. J.McDonald, N. Q.2024-09-26doi:10.1101/2024.09.26.615224Cold Spring Harbor Laboratory Press2024-09-26
<![CDATA[
Live imaging human embryos reveals mitotic errors and lineage specification prior to implantation
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https://biorxiv.org/cgi/content/short/2024.09.26.614906v1?rss=1"
Abdelaal, A. A.Mccarthy, A.Karsa, A.Muresan, L.Elder, K.Papathanasiou, A.Snell, P.Christie, L.Wilding, M.Steventon, B.Niakan, K.2024-09-26doi:10.1101/2024.09.26.614906Cold Spring Harbor Laboratory Press2024-09-26
<![CDATA[
Differential responses and recovery dynamics of HSPC populations following Plasmodium chabaudi infection.
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https://biorxiv.org/cgi/content/short/2024.09.25.614952v1?rss=1"
Bruno, F.Georgiou, C.Cunningham, D.Atkinson, S.Bett, L.Secchi, M.Birch, F.Gonzalez Anton, S.langhorne, j.Lo Celso, C. L.2024-09-27doi:10.1101/2024.09.25.614952Cold Spring Harbor Laboratory Press2024-09-27
<![CDATA[
Mycobacterium tuberculosis overcomes phosphate starvation by extensively remodelling its lipidome with phosphorus-free lipids
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https://biorxiv.org/cgi/content/short/2024.09.27.615480v1?rss=1"
Gray, R. M.Hunt, D. M.Silva dos Santos, M.Liu, J.Agapova, A.Rodgers, A.Garza-Garcia, A.MacRae, J. I.Gutierrez, M. G.Lee, R.Carvalho, L. P.2024-09-27doi:10.1101/2024.09.27.615480Cold Spring Harbor Laboratory Press2024-09-27
<![CDATA[
A depth map of visual space in the primary visual cortex
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https://biorxiv.org/cgi/content/short/2024.09.27.615442v1?rss=1"
He, Y.Colas Nieto, A.Blot, A.Znamenskiy, P.2024-09-30doi:10.1101/2024.09.27.615442Cold Spring Harbor Laboratory Press2024-09-30
<![CDATA[
A stable Netrin-1 fluorescent reporter chicken reveals cell-specific molecular signaturesduring optic fissure closure.
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https://biorxiv.org/cgi/content/short/2024.10.01.616014v1?rss=1"
Chan, B. H. C.Hardy, H.Requena, T.Findlay, A.Ioannidis, J.Meunier, D.Toms, M.Moosajee, M.Raper, A.McGrew, M.Rainger, J.2024-10-02doi:10.1101/2024.10.01.616014Cold Spring Harbor Laboratory Press2024-10-02
<![CDATA[
Meru co-ordinates spindle orientation with cell polarity and cell cycle progression
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https://biorxiv.org/cgi/content/short/2024.10.01.616065v1?rss=1"
McLellan, M. M.Aerne, B. L.Dhoul, J. J. B.Tapon, N.2024-10-02doi:10.1101/2024.10.01.616065Cold Spring Harbor Laboratory Press2024-10-02
<![CDATA[
Growth compensation upon changes in tissue size in the Drosophila abdomen
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https://biorxiv.org/cgi/content/short/2024.10.02.616326v1?rss=1"
Ferreira, A.Cairoli, A.Mangione, F.Holder, M. V.Ainslie, A.Aerne, B. L.Salbreux, G.Tapon, N.2024-10-03doi:10.1101/2024.10.02.616326Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
DYRK1A kinase triplication is the major cause of Otitis Media in Down Syndrome
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https://biorxiv.org/cgi/content/short/2024.10.03.616443v1?rss=1"
Tateossian, H.Southern, A.Vikhe, P.Lana-Elola, E.Watson-Scales, S.Gibbins, D.Williams, D.Purnell, T.Mburu, P.Parker, A.Norris, D. P.Santos-Cortez, R. L. P.Herrmann, B. W.Wells, S.Lad, H. V.Fisher, E.Tybulewicz, V. L.Brown, S. D. M.2024-10-03doi:10.1101/2024.10.03.616443Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
Presynaptic filopodia form kinapses and modulate membrane mechanics for synchronous neurotransmission and seizure generation.
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https://biorxiv.org/cgi/content/short/2024.10.07.616970v1?rss=1"
Jain, A.Kroll, J.Webster, J. F.Moss, J.Ultanir, S. K.Gonzalez-Sulser, A.Rosenmund, C.Cousin, M. A.Ivanova, D.2024-10-07doi:10.1101/2024.10.07.616970Cold Spring Harbor Laboratory Press2024-10-07
<![CDATA[
Mapping the niche of breast cancer metastases in lung and liver
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https://biorxiv.org/cgi/content/short/2024.10.04.616491v1?rss=1"
Sznurkowska, M. K.Castro-Giner, F.Zhang, Y.Ring, A.Schwab, F. D.Albrecht, F.Mertz, K. D.Strittmatter, K.Ozimski, L. L.Budinjas, S.Auray, G.Giachino, C.Taylor, V.Gvozdenovic, A.Malanchi, I.Frauchiger-Heuer, H.Wicki, A.Vetter, M.Aceto, N.2024-10-07doi:10.1101/2024.10.04.616491Cold Spring Harbor Laboratory Press2024-10-07
<![CDATA[
The PHD3-FOXO3 axis modulates the interferon type I response in microglia aggravating Alzheimer's disease progression
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https://biorxiv.org/cgi/content/short/2024.10.01.616066v1?rss=1"
Sanchez-Garcia, M. A.Lara-Urena, N.March-Diaz, R.Ortega-de San Luis, C.Quinones-Canete, S.Barba-Reyes, J. M.Cabello-Rivera, D.Munoz-Cabello, A. M.Mora-Romero, B.Romero-Molina, C.Heras-Garvin, A.Navarro, V.Lopez-Barneo, J.Vizuete, M.Vitorica, J.Munoz-Machado, A. B.Cockman, M.Rosales-Nieves, A. E.Pascual, A.2024-10-03doi:10.1101/2024.10.01.616066Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
Identification of RING E3 pseudoligases in the TRIM protein family
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https://biorxiv.org/cgi/content/short/2024.10.15.614675v1?rss=1"
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]]>Dudley-Fraser, J.Esposito, D.McPhie, K.Morley-Williams, C.Auchynnikava, T.Rittinger, K.2024-10-17doi:10.1101/2024.10.15.614675Cold Spring Harbor Laboratory Press2024-10-17
<![CDATA[
Identification of a specialized lipid barrier for Drosophila metamorphosis
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https://biorxiv.org/cgi/content/short/2024.10.11.617838v1?rss=1"
Lampe, L.Newell, C. L.Wang, B.-J.Makki, R.Alexandre, C.Gilmore, I. S.Zhao, L.Gould, A. P.2024-10-12doi:10.1101/2024.10.11.617838Cold Spring Harbor Laboratory Press2024-10-12
<![CDATA[
Integrative analysis of higher-order transcriptome organisation and RNA condensation principles
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https://biorxiv.org/cgi/content/short/2024.10.14.618182v1?rss=1"
Klobucar, T.Novljan, J.Iosub, I. A.Kokot, B.Urbancic, I.Jones, D. M.Chakrabarti, A. M.Luscombe, N.Ule, J.Modic, M.2024-10-16doi:10.1101/2024.10.14.618182Cold Spring Harbor Laboratory Press2024-10-16
<![CDATA[
Deletions Rate-Limit Breast and Ovarian Cancer Initiation
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https://biorxiv.org/cgi/content/short/2024.10.17.618945v1?rss=1"
Houlahan, K.Bihie, M.Contreras, J. G.Fulop, D.Lopez, G.Huang, H.-H.Van Loo, P.Curtis, C.Boutros, P.Huang, K.-l.2024-10-21doi:10.1101/2024.10.17.618945Cold Spring Harbor Laboratory Press2024-10-21
<![CDATA[
A distinctive PI(4,5)P2 compartment forms during entosis and related engulfment processes
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https://biorxiv.org/cgi/content/short/2024.10.22.619613v1?rss=1"
Durgan, J.Sloan, K.Domart, M.-C.Collinson, L.Florey, O.2024-10-22doi:10.1101/2024.10.22.619613Cold Spring Harbor Laboratory Press2024-10-22
<![CDATA[
Imaging of live bacterial whole-cell biosensors illuminates spatial sialic acid availability within the inflamed mammalian gut
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https://biorxiv.org/cgi/content/short/2024.10.23.619804v1?rss=1"
Carreno, D.Robinson, C. M.Jackson, R.Li, P.Nunes, V.Palma-Duran, S. A.Nye, E.MacRae, J. I.Riglar, D. T.2024-10-23doi:10.1101/2024.10.23.619804Cold Spring Harbor Laboratory Press2024-10-23
<![CDATA[
Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma
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https://biorxiv.org/cgi/content/short/2024.10.22.619657v1?rss=1"
2) and do not co-amplify other oncogenes on the same ecDNA particles. In contrast, PDGFRA ecDNAs have lower mean copy number (mean of 15 copies per cell), are under weaker positive selection and frequently co-amplify other oncogenes on the same ecDNA. Evolutionary modeling suggests that EGFR ecDNAs often accumulate prior to clonal expansion. EGFR structural variants, including vIII and c-terminal deletions are under strong positive selection, are found exclusively on ecDNA, and are intermixed with wild-type EGFR ecDNAs. Simulations show EGFRvIII ecDNA likely arises after ecDNA formation in a cell with high wild-type EGFR copy number (> 10) before the onset of the most recent clonal expansion. This remains true even in cases of co-selection and co-amplification of multiple oncogenic ecDNA species in a subset of patients. Overall, our results suggest a potential time window in which early ecDNA detection may provide an opportunity for more effective intervention.
HighlightsO_LIecDNA is the most common mechanism of focal oncogene amplification in IDHwt glioblastoma.
C_LIO_LIEGFR and its variants on ecDNA are particularly potent, likely arising early in tumor development, providing a strong oncogenic stimulus to drive tumorigenesis.
C_LIO_LIWild-type and variant EGFR ecDNA heteroplasmy (co-occurrence) is common with EGFRvIII or c-terminal deletions being derived from EGFR wild-type ecDNA prior to the most recent clonal expansion.
C_LIO_LITumors with ecDNA amplified EGFR versus PDGFRA exhibit different evolutionary trajectories.
C_LIO_LISPECIES model can infer spatial evolutionary dynamics of ecDNA in cancer.
C_LIO_LIA delay between ecDNA accumulation and subsequent oncogenic mutation may give a therapeutic window for early intervention.
C_LI
]]>Noorani, I.Haughey, M.Luebeck, J.Rowan, A.Grönroos, E.Terenzi, F.Wong, I. T.-L.Kittel, J.Bailey, C.Weeden, C.Bell, D.Joo, E.Barbe, V.Jones, M. G.Nye, E.Green, M.Meader, L.Norton, E. J.Fabian, M.Kanu, N.Jamal-Hanjani, M.Santarius, T.Nicoll, J.Boche, D.Chang, H. Y.Bafna, V.Huang, W.Mischel, P. S.Swanton, C.Werner, B.2024-10-25doi:10.1101/2024.10.22.619657Cold Spring Harbor Laboratory Press2024-10-25
<![CDATA[
Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells.
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https://biorxiv.org/cgi/content/short/2024.10.29.620545v1?rss=1"
Rigo, P.Ahmed-de-Prado, S.Johnston, R. L.Choudhury, C.Guillemot, F.Harris, L.2024-10-31doi:10.1101/2024.10.29.620545Cold Spring Harbor Laboratory Press2024-10-31
<![CDATA[
Replisome passage through the cohesin ring
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https://biorxiv.org/cgi/content/short/2024.10.30.621121v1?rss=1"
Glaser, S.Molodtsov, M. I.Diffley, J. F.Uhlmann, F.2024-11-01doi:10.1101/2024.10.30.621121Cold Spring Harbor Laboratory Press2024-11-01
<![CDATA[
DNA replication fork stabilization and restart mechanisms revealed by biochemical reconstitution
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https://biorxiv.org/cgi/content/short/2024.11.01.621508v1?rss=1"
Canal, B.Bertolin, A. P.Lee, G. C.Minamino, M.Diffley, J. F. X.2024-11-03doi:10.1101/2024.11.01.621508Cold Spring Harbor Laboratory Press2024-11-03
<![CDATA[
The mechanism of checkpoint-dependent DNA replication fork stabilization in human cells
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https://biorxiv.org/cgi/content/short/2024.11.01.621514v1?rss=1"
Bertolin, A. P.Canal, B.Yekezare, M.Zeng, J.Instrell, R.Howell, M.Diffley, J. F. X.2024-11-03doi:10.1101/2024.11.01.621514Cold Spring Harbor Laboratory Press2024-11-03
<![CDATA[
Functionally important binding site for a volatile anesthetic in a voltage-gated sodium channel identified by X-ray crystallography
]]>
https://biorxiv.org/cgi/content/short/2024.11.04.621342v1?rss=1"
Hollingworth, D.Herold, K. F.Kelly, G.Mykhaylyk, V. B.Xiang, J.Wallace, B. A.Hemmings, H. C.2024-11-04doi:10.1101/2024.11.04.621342Cold Spring Harbor Laboratory Press2024-11-04
<![CDATA[
Metabolic and neuroactivity imbalances in plasma from aniridia patients with PAX6 haploinsufficiency
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https://biorxiv.org/cgi/content/short/2024.11.07.622475v1?rss=1"
Cunha, D. L.Kit, V.Skinner, J.Welch, A. A.Moosajee, M.2024-11-08doi:10.1101/2024.11.07.622475Cold Spring Harbor Laboratory Press2024-11-08
<![CDATA[
Generation of morphologically distinct astrocyte subtypes from human iPSCs reveals a link between glial shape, function and reactivity
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https://biorxiv.org/cgi/content/short/2024.11.11.622998v1?rss=1"
O'Toole, K.Guetta, L.Urbanaviciute, P.Suklai, P.Wright, C.Fisher, T.Liddelow, S.Luisier, R.Marzi, S. J.Serio, A.2024-11-11doi:10.1101/2024.11.11.622998Cold Spring Harbor Laboratory Press2024-11-11
<![CDATA[
From naïve pluripotency to human neural organoids through a three-dimensional morphogenetic continuum
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https://biorxiv.org/cgi/content/short/2024.11.14.623407v1?rss=1"
Laterza, C.Cesare, E.Stuart, H. T.D'Ercole, M.Gesualdo, A.La Barbera, M. G.Brignani, S.Ribecco, C.Polli, R.Frison, R.Angiolillo, S.Maseta, A.Gagliano, O.Cacchiarelli, D.Briscoe, J.Tanaka, E. M.Murgia, A.Elvassore, N.2024-11-15doi:10.1101/2024.11.14.623407Cold Spring Harbor Laboratory Press2024-11-15
<![CDATA[
The AMPK-TORC1 signalling axis regulates caffeine-mediated DNA damage checkpoint override and cell cycle effects in fission yeast
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https://biorxiv.org/cgi/content/short/2022.11.08.515652v1?rss=1"
Alao, J.-P.Rallis, C.2022-11-08doi:10.1101/2022.11.08.515652Cold Spring Harbor Laboratory Press2022-11-08
<![CDATA[
RNA editing is a molecular clock in unmodified human cells
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https://biorxiv.org/cgi/content/short/2024.11.18.624170v1?rss=1"
Ghareeb, A. E.Bayne, J.Wagen, A. Z.Abdelhafid, A. M.Miller, D.Cubitt, L.Meran, L.Hill, C.Cribbs, A. P.Ryten, M.Gandhi, S.Gaffney, E.Coles, M.Young, G.Rodriques, S. G.2024-11-19doi:10.1101/2024.11.18.624170Cold Spring Harbor Laboratory Press2024-11-19
<![CDATA[
Progressive chromosome shape changes during cell divisions, recapitulated by loop capture simulations
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https://biorxiv.org/cgi/content/short/2024.11.19.623756v1?rss=1"
Kakui, Y.Kusano, Y.Clarence, T.Lopez, M.Hirota, T.Khatri, B. S.Uhlmann, F.2024-11-20doi:10.1101/2024.11.19.623756Cold Spring Harbor Laboratory Press2024-11-20
<![CDATA[
Ancestry-specific gene expression in peripheral monocytes mediates risk of neurodegenerative disease
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https://biorxiv.org/cgi/content/short/2024.11.20.624489v1?rss=1"
Wagen, A. Z.Reynolds, R. H.Nee Foo, J.Fairbrother-Browne, A.Gustavsson, E. K.Gagliano-Turin, S. A.Wood, N. W.Blauwendraat, C. K.Gandhi, S.Ryten, M.2024-11-22doi:10.1101/2024.11.20.624489Cold Spring Harbor Laboratory Press2024-11-22
<![CDATA[
Targeted CRISPR Screens Reveal Genes Essential for Cryptosporidium Survival in the Host Intestine
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https://biorxiv.org/cgi/content/short/2024.11.22.624643v1?rss=1"
Watson, L. C.Sala, K. A.Bernitz, N.Baumgartel, L.Pallett, M. A.Marzook, N. B.Straker, L. C.Peng, D.Collinson, L.Sateriale, A.2024-11-22doi:10.1101/2024.11.22.624643Cold Spring Harbor Laboratory Press2024-11-22
<![CDATA[
The ALS- and FTD-associated proteins Annexin A11 and CHMP2B act sequentially in membrane repair
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https://biorxiv.org/cgi/content/short/2024.11.19.624330v1?rss=1"
Heffner, C. M.Starling, G. P.Isaacs, A.Carlton, J. G.2024-11-21doi:10.1101/2024.11.19.624330Cold Spring Harbor Laboratory Press2024-11-21
<![CDATA[
Integration of hunger and hormonal state gates infant-directed aggression
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https://biorxiv.org/cgi/content/short/2024.11.25.625278v1?rss=1"
Cao, M.Ammari, R.Chen, M. X.Wai, P.Sahni, A.Liang, S.Legrave, N.MacRae, J. I.Strom, M.Kohl, J.2024-11-25doi:10.1101/2024.11.25.625278Cold Spring Harbor Laboratory Press2024-11-25
<![CDATA[
Sex chromosomes shape the transcriptional landscape of the preimplantation mouseembryo
]]>
https://biorxiv.org/cgi/content/short/2024.11.26.625424v1?rss=1"
Snell, D. M.Varsally, W.Courtois, A.Menchero, S.Munusamy, P.Rietdijk, R.Ojarikre, O. A.Strohbuecker, S.Kaya, H.Sangrithi, M. N.Turner, J. M.2024-11-26doi:10.1101/2024.11.26.625424Cold Spring Harbor Laboratory Press2024-11-26
<![CDATA[
Sensing of extracellular L-Proline availability by the integrated stress response determines the outcome of cell competition.
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https://biorxiv.org/cgi/content/short/2024.11.28.625863v1?rss=1"
Krishnan, S.Lima, A.Low, Y. T.Montero, S. P.Tan, S.Gregorio, A. D.Barreto, A. P.Bowling, S.Vousden, K.Rodriguez, T. A.2024-11-28doi:10.1101/2024.11.28.625863Cold Spring Harbor Laboratory Press2024-11-28
<![CDATA[
Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanism
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https://biorxiv.org/cgi/content/short/2024.11.28.625692v1?rss=1"
Sidorov, S.Pal, K.Lenhard, B.Luscombe, N. M.2024-11-29doi:10.1101/2024.11.28.625692Cold Spring Harbor Laboratory Press2024-11-29
<![CDATA[
The essential host genome for Cryptosporidium intracellular survival exposes metabolic dependencies that can be leveraged for treatment
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https://biorxiv.org/cgi/content/short/2024.12.04.626561v1?rss=1"
Marzook, N. B.Song, O.-R.Baumgärtel, L.Bernitz, N.Mkandawire, T. T.Watson, L. C.Nunes, V.Warchal, S.MacRae, J. I.Howell, M.Sateriale, A.2024-12-05doi:10.1101/2024.12.04.626561Cold Spring Harbor Laboratory Press2024-12-05
<![CDATA[
HIFalpha isoform specific activities drive cell-type specificity of VHL-associated oncogenesis
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https://biorxiv.org/cgi/content/short/2024.11.28.625663v1?rss=1"
Lima, J. D. C. C.Hooker, M.Li, R.Barros, A. B.Masson, N.Pugh, C. W.Mole, D. R.Adam, J.Ratcliffe, P. J.Kurlekar, S.2024-12-03doi:10.1101/2024.11.28.625663Cold Spring Harbor Laboratory Press2024-12-03
<![CDATA[
Non canonical Sun1-Allan complex orchestrates nuclear envelope remodelling and Basal Body/MTOC Segregation during rapid mitosis in Plasmodium
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https://biorxiv.org/cgi/content/short/2024.12.04.625416v1?rss=1"
Zeeshan, M.Blatov, I.Yanase, R.Ferguson, D. J. P.Pashley, S. L.Chahine, Z.Botte, Y. Y.Mishra, A.Marche, B.Bhanvadia, S.Hair, M.Batra, S.Markus, R.Brady, D.Bottrill, A.vaughan, s.Botte, C. Y.Le Roch, K. G.Holder, A. A.Tromer, E. C.Tewari, R.2024-12-05doi:10.1101/2024.12.04.625416Cold Spring Harbor Laboratory Press2024-12-05
<![CDATA[
Epigenetic investigation of multifocal small intestinal neuroendocrine tumours reveals accelerated ageing of tumours and epigenetic alteration of metabolic genes
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https://biorxiv.org/cgi/content/short/2024.12.02.626017v1?rss=1"
Webster, A. P.Makinen, N.Mensah, N.Castignani, C.Larose Cadieux, E.Shivdasani, R.Singh, P.Vaikkinen, H.Dhami, P.Ecker, S.Brown, M.Rimmer, B.Henderson, S.Herrero, J.Suderman, M.Yousefi, P. D.Beck, S.Van Loo, P.Nakakura, E.Thirlwell, C.2024-12-05doi:10.1101/2024.12.02.626017Cold Spring Harbor Laboratory Press2024-12-05
<![CDATA[
Divergent regulatory element programs steer sex-specific supporting cell differentiation along mouse gonadal development
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https://biorxiv.org/cgi/content/short/2024.12.09.627451v1?rss=1"
Stevant, I.Abberbock, E.Ridnik, M.Weiss, R.Swisa, L.Futtner, C.Maatouk, D.Lovell-Badge, R.Malysheva, V.Gonen, N.2024-12-12doi:10.1101/2024.12.09.627451Cold Spring Harbor Laboratory Press2024-12-12
<![CDATA[
Modelling co-development between somites and neural tube with human Trunk-like Structures (hTLS)
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https://biorxiv.org/cgi/content/short/2024.12.16.628661v1?rss=1"
Makwana, K.Tilley, L.Chakravarty, P.Thompson, J.Baillie-Benson, P.Rodriguez-Polo, I.Moris, N.2024-12-17doi:10.1101/2024.12.16.628661Cold Spring Harbor Laboratory Press2024-12-17
<![CDATA[
Mechanistic studies of autophagic cargo recruitment and membrane expansion through in vitro reconstitution
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https://biorxiv.org/cgi/content/short/2024.12.24.630225v1?rss=1"
Zhang, W.Litschel, T.D'Antuono, R.Davis, C.Schreiber, A.Tooze, S.2024-12-24doi:10.1101/2024.12.24.630225Cold Spring Harbor Laboratory Press2024-12-24
<![CDATA[
Structural and functional characterization of the KHNYN extended-diKH domain for mediating ZAP antiviral activity
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https://biorxiv.org/cgi/content/short/2024.12.23.630104v1?rss=1"
Youle, R. L.Lista, M. J.Bouton, C.Kunzelmann, S.Wilson, H.Cottee, M. A.Purkiss, A. G.Morris, E. R.Neil, S. J.Taylor, I. A.Swanson, C. M.2024-12-23doi:10.1101/2024.12.23.630104Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
Dominant RDH12-retinitis pigmentosa impairs photoreceptor development and cone function in retinal organoids
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https://biorxiv.org/cgi/content/short/2024.12.11.627489v1?rss=1"
Mejecase, C.Zhou, Y.Owen, N.Soro-Barrio, P.Cheloni, R.Nair, N.Sarkar, H.Toualbi, L.Moosajee, M.2024-12-15doi:10.1101/2024.12.11.627489Cold Spring Harbor Laboratory Press2024-12-15
<![CDATA[
Bounded optimality of time investments in rats, mice, and humans
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https://biorxiv.org/cgi/content/short/2024.12.09.627552v1?rss=1"
Ott, T.Bosc, M.Sanders, J. I.Masset, P.Kepecs, A.2024-12-15doi:10.1101/2024.12.09.627552Cold Spring Harbor Laboratory Press2024-12-15
<![CDATA[
Cell volume regulates terminal differentiation of cultured human epidermal keratinocytes
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https://biorxiv.org/cgi/content/short/2024.12.09.627463v1?rss=1"
Watt, F. M.Zijl, S.Hiratsuka, T.Mobasseri, A.Ebrahimkutty, M.Boermel, M.Garcia-Manyes, S.2024-12-09doi:10.1101/2024.12.09.627463Cold Spring Harbor Laboratory Press2024-12-09
<![CDATA[
Gene network architecture, mutation and selection collectively drive developmental pattern evolvability and predictability
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https://biorxiv.org/cgi/content/short/2024.12.23.630099v1?rss=1"
Booth, H.Hadjivasiliou, Z.2024-12-23doi:10.1101/2024.12.23.630099Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
Type I interferons induced upon respiratory viral infection impair lung metastatic initiation
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https://biorxiv.org/cgi/content/short/2024.12.23.630113v1?rss=1"
Farias, A.Bridgeman, V.Rodrigues, F.Owen, A.Ruhland, S.Ferreira, R.Mack, M.Malanchi, I.Johansson, C.2024-12-23doi:10.1101/2024.12.23.630113Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
Covalent inhibitors of the RAS binding domain of PI3Ka impair tumor growth driven by RAS and HER2
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https://biorxiv.org/cgi/content/short/2024.12.17.629001v1?rss=1"
Klebba, J. E.Roy, N.Bernard, S. M.Grabow, S.Hoffman, M. A.Miao, H.Tamiya, J.Wang, J.Berry, C.Esparza-Oros, A.Lin, R.Liu, Y.Pariollaud, M.Parker, H.Mochalkin, I.Rana, S.Snead, A. N.Walton, E. J.Wyrick, T. E.Aitichson, E.Bedke, K.Brannon, J. C.Chick, J. M.Hee, K.Horning, B. D.Ismail, M.Lamb, K. N.Lin, W.Metzger, J.Pastuszka, M. K.Pollock, J.Sigler, J. J.Tomaschko, M.Tran, E.Kinsella, T. M.Molina-Arcas, M.Simon, G. M.Weinstein, D. S.Downward, J.Patricelli, M. P.2024-12-20doi:10.1101/2024.12.17.629001Cold Spring Harbor Laboratory Press2024-12-20
<![CDATA[
Transcriptomic analysis of repeat expansion-ataxias uncovers distinct non-neuronal cell type-specific signatures of disease across the human brain
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https://biorxiv.org/cgi/content/short/2025.01.03.631007v1?rss=1"
Chen, Z.Hicks, A.Brenton, J.Grant-Peters, M.Reynolds, R. H.Gustavsson, E. K.Rocca, C.Rocamora-Perez, G.Garza, R.Garcia-Ruiz, S.Dominik, N.Anderson, C.Curless, T.Montgomery, K.Macpherson, H.Nethisinghe, S.Gavriouchkina, D.Blunskyte-Hendley, M.Fairbrother-Browne, A.Lee, J.Luo, H.Efthymiou, S.Murphy, D.Hinton, F.Botia, J. A.Cortese, A.Wood, N.Giunti, P.Hardy, J.Jakobsson, J.Gandhi, S.Tucci, A.McLean, C.Jaunmuktane, Z.Houlden, H.Ryten, M.2025-01-03doi:10.1101/2025.01.03.631007Cold Spring Harbor Laboratory Press2025-01-03
<![CDATA[
Timed chromatin invasion during mitosis governs prototype foamy virus integration site selection and infectivity
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https://biorxiv.org/cgi/content/short/2025.01.10.632130v1?rss=1"
Lagadec, F.Singh, P. K.Calmels, C.Lapaillerie, D.Lindemann, D.Parissi, V.Cherepanov, P.Engelman, A. N.Lesbats, P.2025-01-11doi:10.1101/2025.01.10.632130Cold Spring Harbor Laboratory Press2025-01-11
<![CDATA[
Endogenous gene tagging with FnCas9 to track and sort neural lineages from 3D cortical organoids
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https://biorxiv.org/cgi/content/short/2025.01.09.631995v1?rss=1"
Kumar, M.Torras, B. T.Guillemot, F.Chakraborty, D.2025-01-13doi:10.1101/2025.01.09.631995Cold Spring Harbor Laboratory Press2025-01-13
<![CDATA[
Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration
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https://biorxiv.org/cgi/content/short/2025.01.14.632683v1?rss=1"
Schwayer, C.Barbiero, S.Brückner, D. B.Baader, C.Repina, N. A.Diaz, O. E.Meylan, L. C.Kalck, V.Suppinger, S.Yang, Q.Schnabl, J.Kilik, U.Camp, J. G.Stockinger, B.Bühler, M.Stadler, M. B.Hannezo, E.Liberali, P.2025-01-15doi:10.1101/2025.01.14.632683Cold Spring Harbor Laboratory Press2025-01-15
<![CDATA[
Unlocking the Secrets of NSP3: AlphaFold2-assisted Domain Determination in SARS-CoV-2 Protein
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https://biorxiv.org/cgi/content/short/2025.01.14.632924v1?rss=1"
Edich, M.Briggs, D.Gao, Y.Thorn, A.2025-01-15doi:10.1101/2025.01.14.632924Cold Spring Harbor Laboratory Press2025-01-15
<![CDATA[
Evolutionary trajectories of immune escape across cancers
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https://biorxiv.org/cgi/content/short/2025.01.17.632799v1?rss=1"
Chen, W.Baker, T.Zhang, Z.Ogilvie, H. A.Van Loo, P.Gu, S.2025-01-18doi:10.1101/2025.01.17.632799Cold Spring Harbor Laboratory Press2025-01-18
<![CDATA[
RAS-PI3K Pathway in CAFs Shapes Physicochemical Properties of Tumor ECM and restrains Tumor progression
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https://biorxiv.org/cgi/content/short/2025.01.20.633776v1?rss=1"
Cuesta, C.Alcon-Perez, M.Zheng, J.Procel, N.Cota, R. R.Fennema, D.Rosell, A.Meson, D. L.Martinez-Castedo, B.Arafat, Y.Sanz-Fraile, H.Rajeeve, V.Alonso, D.Hynds, R. E.Swanton, C.Alcaraz, J.Cutillas, P.Reyes-Aldasoro, C. C.Wang, H.Castellano, E.2025-01-22doi:10.1101/2025.01.20.633776Cold Spring Harbor Laboratory Press2025-01-22
<![CDATA[
Capturing Nematic Order on Tissue Surfaces of Arbitrary Geometry
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https://biorxiv.org/cgi/content/short/2025.01.28.635015v1?rss=1"
Eckert, J.Andrews, T. G.Pollard, J.Priya, R.Yap, A. S.Morris, R. G.2025-01-29doi:10.1101/2025.01.28.635015Cold Spring Harbor Laboratory Press2025-01-29
<![CDATA[
Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers in metazoans
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https://biorxiv.org/cgi/content/short/2025.01.31.635869v1?rss=1"
Liu, T.Cao, L.Mladenov, M.Romet-Lemonne, G.Way, M.Moores, C.2025-01-31doi:10.1101/2025.01.31.635869Cold Spring Harbor Laboratory Press2025-01-31
<![CDATA[
Non-Redundant Roles of Topoisomerase 2α and 2β in the Cytosolic Replication of Vaccinia Virus
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https://biorxiv.org/cgi/content/short/2025.02.05.636656v1?rss=1"
Dalla Rosa, I.Way, M.2025-02-06doi:10.1101/2025.02.05.636656Cold Spring Harbor Laboratory Press2025-02-06
<![CDATA[
Insect wings arose with a genetic circuit that extends the useful range of a BMP morphogen
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https://biorxiv.org/cgi/content/short/2025.02.07.637038v1?rss=1"
Huang, A.Cocconi, L.Nicholls-Mindlin, B.Alexandre, C.Salbreux, G.Vincent, J.-P.2025-02-08doi:10.1101/2025.02.07.637038Cold Spring Harbor Laboratory Press2025-02-08
<![CDATA[
Self-supervised image restoration in coherent X-rayneuronal microscopy
]]>
https://biorxiv.org/cgi/content/short/2025.02.10.633538v1?rss=1"
Laugros, A.Cloetens, P.Bosch, C.Schoonhoven, R.Pavlovic, L.Kuan, A. T.Livingstone, J.Zhang, Y.Hendriksen, A.Holler, M.Wanner, A. A.Azevedo, A.Batenburg, K. J.Tuthill, J. C.Lee, W.-C. A.Schaefer, A. T.Vigano, N.Pacureanu, A.2025-02-10doi:10.1101/2025.02.10.633538Cold Spring Harbor Laboratory Press2025-02-10
<![CDATA[
Enhancing Reproducibility Through Bioimage Analysis: The Significance of Effect Sizes and Controls
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https://biorxiv.org/cgi/content/short/2025.02.10.637409v1?rss=1"
Barry, D. J.Marcotti, S.Gerontogianni, L.Kelly, G.2025-02-11doi:10.1101/2025.02.10.637409Cold Spring Harbor Laboratory Press2025-02-11
<![CDATA[
Generation of C9orf72h370 mice, an intron 1 humanised C9orf72 repeat-expansion knock-in model
]]>
https://biorxiv.org/cgi/content/short/2025.02.06.636691v1?rss=1"
Nair, R. R.Carcole, M.Thompson, D.Tibbit, C.McLeod, R.Cammack, A.Jakubcova, T.Biggs, D.Wyles, M.Parker, M.Caulder, A.Teboul, L.Fisher-Ward, C. L.Awan, A. R.Flower, M.Davies, B.Isaacs, A. M.Fisher, E. M.Cunningham, T. J.2025-02-06doi:10.1101/2025.02.06.636691Cold Spring Harbor Laboratory Press2025-02-06
<![CDATA[
Functional specialisation of multisensory temporal integration in the mouse superior colliculus
]]>
https://biorxiv.org/cgi/content/short/2025.02.11.637674v1?rss=1"
Bianchini, G.Razafindrahaba, I.Moglie, M. J.Konstantinou, G.Cano-Ferrer, X.Imbert, A.Iacaruso, F.2025-02-12doi:10.1101/2025.02.11.637674Cold Spring Harbor Laboratory Press2025-02-12
<![CDATA[
Enhancing the efficiency of oncolytic vaccinia virus for ovarian cancer treatment
]]>
https://biorxiv.org/cgi/content/short/2025.02.04.636413v1?rss=1"
Drymiotou, S.Queval, C. J.Tyson, K. E.Sheach, L. A.Postigo, A.Rosa, I. D.Howell, M.McNeish, I. A.Way, M.2025-02-04doi:10.1101/2025.02.04.636413Cold Spring Harbor Laboratory Press2025-02-04
<![CDATA[
Subunit specialisation in AAA+ proteins and substrate unfolding during transcription complex remodelling
]]>
https://biorxiv.org/cgi/content/short/2025.02.15.638424v1?rss=1"
Gao, F.Ye, F.Buck, M.Zhang, X.2025-02-16doi:10.1101/2025.02.15.638424Cold Spring Harbor Laboratory Press2025-02-16
<![CDATA[
Phosphatase specificity influences phosphorylation timing of CDK substrates during the cell cycle
]]>
https://biorxiv.org/cgi/content/short/2025.02.21.639482v1?rss=1"
Zeisner, T. U.Auchynnikava, T.Nurse, P.2025-02-22doi:10.1101/2025.02.21.639482Cold Spring Harbor Laboratory Press2025-02-22
<![CDATA[
Dissecting PADI6 function defines oocyte cytoplasmic lattices as regulatory hubs for fundamental cellular processes
]]>
https://biorxiv.org/cgi/content/short/2025.02.21.639491v1?rss=1"
Williams, J. P. C.Auchynnikava, T.McCarthy, A.Ojarikre, O. A.Bertran, M. T.Weston, A. E.Leonce, D.Olsen, J.Niakan, K. K.Skehel, M.Turner, J. M. A.Walport, L. J.2025-02-22doi:10.1101/2025.02.21.639491Cold Spring Harbor Laboratory Press2025-02-22
<![CDATA[
3D spatial transcriptomics reveals the molecular domain structure of the mouse olfactory bulb
]]>
https://biorxiv.org/cgi/content/short/2025.02.19.639192v1?rss=1"
Klimpert, N.Kollo, M.Brann, D. H.Tan, C.Barry, D.Ma, Y.Schaefer, A. T.Fleischmann, A.2025-02-24doi:10.1101/2025.02.19.639192Cold Spring Harbor Laboratory Press2025-02-24
<![CDATA[
Cryptosporidium modifies intestinal microvilli through an exported virulence factor
]]>
https://biorxiv.org/cgi/content/short/2025.02.25.639898v1?rss=1"
Rodrigues, E.Pallett, M. A.Straker, L. C.Mkandawire, T. T.Sala, K.Collinson, L.Sateriale, A.2025-02-25doi:10.1101/2025.02.25.639898Cold Spring Harbor Laboratory Press2025-02-25
<![CDATA[
Dynamic Modeling of Cell Cycle Arrest Through Integrated Single-Cell and Mathematical Modelling Approaches
]]>
https://biorxiv.org/cgi/content/short/2025.02.20.639240v1?rss=1"
Cortes-Rios, J.Rodriguez-Fernandez, M.Sorger, P. K.Fröhlich, F.2025-02-26doi:10.1101/2025.02.20.639240Cold Spring Harbor Laboratory Press2025-02-26
<![CDATA[
Retroelement co-option disrupts the cancer transcriptional programme
]]>
https://biorxiv.org/cgi/content/short/2025.02.21.639580v1?rss=1"
Loong, J.Thompson, R.Hall, C.Doglio, L.Pape, J.Kassiotis, G.2025-02-27doi:10.1101/2025.02.21.639580Cold Spring Harbor Laboratory Press2025-02-27
<![CDATA[
Biochemical reconstitution of sister chromatid cohesion establishment during DNA replication
]]>
https://biorxiv.org/cgi/content/short/2025.02.25.640040v1?rss=1"
Minamino, M.Diffley, J.Uhlmann, F.2025-02-28doi:10.1101/2025.02.25.640040Cold Spring Harbor Laboratory Press2025-02-28
<![CDATA[
Salmonella effector kinase SteC is activated by host-mediated phosphorylation
]]>
https://biorxiv.org/cgi/content/short/2025.03.01.640964v1?rss=1"
Pillay, T. D.Lemetais, B.Huber, J.Diaz Del Olmo, I.Li, Y.Masino, L.Maslen, S.Liu, M.Esposito, D.Hinton, J. C. D.Yu, X.-J.Thurston, T. L. M.Rittinger, K.2025-03-02doi:10.1101/2025.03.01.640964Cold Spring Harbor Laboratory Press2025-03-02
<![CDATA[
A human induced pluripotent stem cell toolbox for studying sex chromosome effects
]]>
https://biorxiv.org/cgi/content/short/2025.02.28.640277v1?rss=1"
Meleckyte, R.Varsally, W.Zohren, J.Eriksson, J.Incitti, T.Starnes, L.Pointon, A.Hicks, R.Powell, B. E.Turner, J.2025-03-03doi:10.1101/2025.02.28.640277Cold Spring Harbor Laboratory Press2025-03-03
<![CDATA[
Molecular and cellular signatures differentiate Parkinson's disease from Parkinson's disease with dementia
]]>
https://biorxiv.org/cgi/content/short/2025.03.04.641379v1?rss=1"
Fairbrother-Browne, A.Grant-Peters, M.Brenton, J. W.Nelvagal, H.Reynolds, R. H.Lim, Y. M.Gustavsson, E. K.Macpherson, H.Montgomery, K.Evans, J. R.Hicks, A. R.Chiraki, N.Curless, T.Real, R.Xenakis, T.Houlden, H.Morris, H. R.Gandhi, S.Wood, N. W.Hardy, J.Jaunmuktane, Z.Ryten, M.2025-03-04doi:10.1101/2025.03.04.641379Cold Spring Harbor Laboratory Press2025-03-04
<![CDATA[
CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing
]]>
https://biorxiv.org/cgi/content/short/2025.03.02.641068v1?rss=1"
3000 intramolecular RNA structures of which > 400 are proximal to splice sites. Antisense oligonucleotide (ASO) disruption of several such structures that sequester splice sites has a major impact on alternative splicing outcomes, even though the ASOs do not directly disrupt splice sites. ASO disruption of novel regulatory elements that we designate "RNA kinetic switches", modified alternative splicing of NISCH Exon 18, GAK Exon 7 and MEGF8 Exon 14 in a way that depends on the rate of transcription elongation. We propose that these switches mediate kinetic coupling via effects of transcription speed on folding of nascent RNA structures that modulate alternative splicing, and that many nascent RNA structures can thereby serve as new targets for splice modifying ASOs.
Significance StatementAlternative splicing (AS) of mRNAs is a major regulator of gene expression that is frequently disrupted is disease. AS is affected by the speed of RNA polymerase II that synthesizes mRNA precursors, but how such kinetic coupling works is not well understood. We developed a method, CAR-SPLASH, to capture RNA structures in nascent RNA chains by cross-linking with psoralen. CAR-SPLASH identified novel structural regulatory elements we call "RNA kinetic switches" that control AS in a way that depends on the speed of transcription. RNA kinetic switches are new targets for splice modifying antisense oligonucleotides that could have therapeutic value.
]]>Shenasa, H.Fong, N.Erickson, B.Iosub, I.Ule, J.Bentley, D.2025-03-06doi:10.1101/2025.03.02.641068Cold Spring Harbor Laboratory Press2025-03-06
<![CDATA[
Mechanism of DNA-protein crosslink bypass by CMG helicase
]]>
https://biorxiv.org/cgi/content/short/2025.03.06.641852v1?rss=1"
Kyaw, M. T.Xie, S.de Lamo Peitz, E.Yardimci, H.2025-03-06doi:10.1101/2025.03.06.641852Cold Spring Harbor Laboratory Press2025-03-06
<![CDATA[
Predictable Engineering of Signal-DependentCis-Regulatory Elements
]]>
https://biorxiv.org/cgi/content/short/2025.03.07.642002v1?rss=1"
Cornwall-Scoones, J.Benzinger, D.Yu, T.Pezzotta, A.Sagner, A.Gerontogianni, L.Bernadet, S.Finnie, E.Boezio, G. L. M.Stuart, H. T.Melchionda, M.Inge, O. C. K.Dumitrascu, B.Briscoe, J.Delas, M. J.2025-03-07doi:10.1101/2025.03.07.642002Cold Spring Harbor Laboratory Press2025-03-07
<![CDATA[
Mechanical fracturing of the extracellular matrix patterns the vertebrate heart
]]>
https://biorxiv.org/cgi/content/short/2025.03.07.641942v1?rss=1"
Jin Ji, C. C.Santos-Olivan, D.Ramel, M.-C.Sanchez-Posada, J.Paizakis, P.Andrews, T. G.Noel, E. S.Torres-Sanchez, A.Priya, R.2025-03-07doi:10.1101/2025.03.07.641942Cold Spring Harbor Laboratory Press2025-03-07
<![CDATA[
DEK::NUP214 acts as an XPO1-dependent transcriptional activator of essential leukemia genes
]]>
https://biorxiv.org/cgi/content/short/2025.03.05.641116v1?rss=1"
500 compounds) revealed that t(6;9) cases display a selective response to XPO1 inhibitors (Selinexor & Eltanexor) and a distinct transcriptomic signature characterized by the overexpression of FOXC1 and HOX genes that are key leukemia mediators. CUT&RUN experiments demonstrated the direct binding of DEK::NUP214 to the promoters of FOXC1 and HOXA/B clusters. Strikingly, the expression of these genes and the binding of DEK::NUP214 to their regulatory regions were selectively reduced upon XPO1 inhibition in t(6;9) cells. Altogether, these results identified a novel function of DEK::NUP214 as an XPO1-dependent transcriptional activator of key leukemia drivers and provide a rationale to explore the use of XPO1 inhibitors in this patient population.
]]>Kaya, F.Bewicke-Copley, F.Miettinen, J. J.Casado, P.Leddy, E.Deniz, O.Lavallee, V.-P.Philippe, C.Zheng, J.Grebien, F.Khan, N.Krizsan, S.Saad, J.Nolin-Lapalme, A.Lemieux, S.Audemard, E. O.Matthews, J.Grantham, M.Di Bella, D.Wennerberg, K.Parsons, A.Rio-Machin, A.Gribben, J.Cavenagh, J. D.Freeman, S. D.Bodor, C.Sauvageau, G.Wang, J.Llamas-Sillero, P.Cazier, J.-B.Taussig, D. C.Bonnet, D.Cutillas, P. R.Heckman, C.Fitzgibbon, J.Rouault-Pierre, K.2025-03-07doi:10.1101/2025.03.05.641116Cold Spring Harbor Laboratory Press2025-03-07
<![CDATA[
Granulocyte Derived Resistin Inhibits Monocyte Maturation and Induces Immune Suppression in CMML
]]>
https://biorxiv.org/cgi/content/short/2025.03.03.640303v1?rss=1"
Hull, N. J.Cant, R.Guest, L. A.Wang, Y.-H.Gurashi, K.Paredes, R.Huerga Encabo, H.Lin, C.-C.Tien, H.-F.Sellers, R.Sahoo, S.Bonnet, D.Selimoglu-Buet, D.Solary, E.Wiseman, D. H.Batta, K.2025-03-07doi:10.1101/2025.03.03.640303Cold Spring Harbor Laboratory Press2025-03-07
<![CDATA[
Engineering Cortical Networks: An Open Platform for Controlled Human Circuit Formation and Synaptic Analysis In vitro
]]>
https://biorxiv.org/cgi/content/short/2025.03.07.642064v1?rss=1"
Suklai, P.Minckley, T. F.Hagemann, C.Faber, K.Norkett, R.Guetta, L.OToole, K.Geary, B.Devine, M. J.Serio, A.2025-03-10doi:10.1101/2025.03.07.642064Cold Spring Harbor Laboratory Press2025-03-10
<![CDATA[
PhotoNeuro: A compact photodetector for synchronization of visual stimulus presentation during behavioral experiments in neuroscience.
]]>
https://biorxiv.org/cgi/content/short/2025.03.22.644703v1?rss=1"
Cano Ferrer, X.Moglie, M. J.Konstantinou, G.Blot, A.Bianchini, G.Imbert, A.Znamenskiy, P.Iacaruso, M. F.2025-03-24doi:10.1101/2025.03.22.644703Cold Spring Harbor Laboratory Press2025-03-24
<![CDATA[
Mapping and quantifying nascent transcript start sites using TT-TSS-seq
]]>
https://biorxiv.org/cgi/content/short/2025.03.25.645230v1?rss=1"
Elgood Hunt, E.Vivori, C.van Werven, F.2025-03-27doi:10.1101/2025.03.25.645230Cold Spring Harbor Laboratory Press2025-03-27
<![CDATA[
DNA supercoiling impacts alternative transcription start site selection in yeast
]]>
https://biorxiv.org/cgi/content/short/2025.03.25.645220v1?rss=1"
Elgood Hunt, E.Vivori, C.van Werven, F.2025-03-26doi:10.1101/2025.03.25.645220Cold Spring Harbor Laboratory Press2025-03-26
<![CDATA[
PRMT activity promotes global 3' UTR shortening in proliferating cells
]]>
https://biorxiv.org/cgi/content/short/2025.03.06.641848v1?rss=1"
Griffith, L.Capitanchik, C.Moore, S.Farcas, A.Gwynne, M.Pedna, M.Jones, D. M.Chakrabarti, A. M.Lagos, D.Urosevic, J.Lynch, J. T.Ule, J.2025-03-10doi:10.1101/2025.03.06.641848Cold Spring Harbor Laboratory Press2025-03-10
<![CDATA[
The evolution of gene regulation in mammalian cerebellum development
]]>
https://biorxiv.org/cgi/content/short/2025.03.14.643248v1?rss=1"
Sarropoulos, I.Sepp, M.Yamada, T.Schaefer, P. S. L.Trost, N.Schmidt, J.Schneider, C.Drummer, C.Missbach, S.Taskiran, I. I.Hecker, N.Bravo Gonzalez-Blas, C.Kempynck, N.Froemel, R.Joshi, P.Leushkin, E.Arnskoetter, F.Leiss, K.Okonechnikov, K.Lisgo, S.Palkovits, M.Paabo, S.Cardoso-Moreira, M.Kutscher, L. M.Behr, R.Pfister, S. M.Aerts, S.Kaessmann, H.2025-03-16doi:10.1101/2025.03.14.643248Cold Spring Harbor Laboratory Press2025-03-16
<![CDATA[
Autologous human iPSC-derived Alveolus-on-Chip reveals early pathological events of M. tuberculosis infection
]]>
https://biorxiv.org/cgi/content/short/2025.03.14.643230v1?rss=1"
Luk, C. H.Conway, G.Goh, K. J.Fearns, A.Rodriguez-Hernandez, I.D'Antuono, R.Day, N. J.Athanasiadi, N.Pellegrino, E.Hobi, N.Stucki, J.Gutierrez, M. G.2025-03-17doi:10.1101/2025.03.14.643230Cold Spring Harbor Laboratory Press2025-03-17
<![CDATA[
Population activity of mossy fibre axon input to the cerebellar cortex during behaviours
]]>
https://biorxiv.org/cgi/content/short/2025.03.23.644738v1?rss=1"
Ros, H.Xie, Y.Sadeh, S.Silver, R. A.2025-03-24doi:10.1101/2025.03.23.644738Cold Spring Harbor Laboratory Press2025-03-24
<![CDATA[
Two distinct cytokine response clusters identified in healthcare workers with apparent resistance to infection with Mycobacterium tuberculosis despite sustained occupational exposure
]]>
https://biorxiv.org/cgi/content/short/2025.03.27.643001v1?rss=1"
Balfour, A.Masina, N.Queiroz, A.Andrade, B.Fukutani, E.Bekiswa, A.Lewinsohn, D.Lewinsohn, D.Goliath, R.Wilkinson, K. A.Schutz, C.Meintjes, G.Shey, M. S.2025-03-28doi:10.1101/2025.03.27.643001Cold Spring Harbor Laboratory Press2025-03-28
<![CDATA[
Structural Basis of CSN-mediated SCF Deneddylation
]]>
https://biorxiv.org/cgi/content/short/2025.03.25.645352v1?rss=1"
Enchev, R. I.Ding, S.Clapperton, J. A.Maeots, M.-E.Kunzelmann, S.Shaaban, M.2025-03-26doi:10.1101/2025.03.25.645352Cold Spring Harbor Laboratory Press2025-03-26
<![CDATA[
The ubiquitin E3 ligase Huwe1 facilitates viral and self RNA sensing by RIG-I-like receptors
]]>
https://biorxiv.org/cgi/content/short/2025.03.27.645708v1?rss=1"
Oosenbrug, T.Gravekamp, D.Pinto-Fernandez, A.Crotta, S.Finsterbusch, K.van der Kooij, S. B.ter Haar, L. R.Asschert, Y.Kleian, G. F. E.Kessler, B. M.Wack, A.van der Veen, A. G.2025-04-01doi:10.1101/2025.03.27.645708Cold Spring Harbor Laboratory Press2025-04-01
<![CDATA[
An intercellular metabolic relay for brain sparingin Drosophila
]]>
https://biorxiv.org/cgi/content/short/2025.04.02.645514v1?rss=1"
Franchet, A.Jin, Y.Newell, C. L.Girard, V.Maniere, G.Grosjean, Y.Barrington, C.MacRae, J. I.Gilmore, I. S.Gould, A. P.2025-04-03doi:10.1101/2025.04.02.645514Cold Spring Harbor Laboratory Press2025-04-03
<![CDATA[
Why do we have so many excitatory neurons?
]]>
https://biorxiv.org/cgi/content/short/2024.09.24.614724v1?rss=1"
Wang, Q.Cardona, A.Zlatic, M.Vogelstein, J.Priebe, C.2024-09-24doi:10.1101/2024.09.24.614724Cold Spring Harbor Laboratory Press2024-09-24
<![CDATA[
VP-CLEM-Kit: An accessible pipeline for visual proteomics using super resolution volume correlative light and electron microscopy (SR-vCLEM)
]]>
https://biorxiv.org/cgi/content/short/2025.04.08.647770v1?rss=1"
Lumkwana, D.Lightley, J.Vesga, A. G.de Folter, J.Domart, M.-C.Maclachlan, C.Kumar, S.Evans, J. R.Peddie, C.Burrell, A.Yoshimura, A.Mangali, A.Vahrjmeijer, N.Bhaga, M.Smit, C.Titze, B.Horrocks, M. H.Cobra Straker, L.Garcia, E.Jones, M. L.Mclean, A.Roufosse, C.Loos, B.Gandhi, S.Strange, A.Henriques, R.French, P. M.Collinson, L.2025-04-10doi:10.1101/2025.04.08.647770Cold Spring Harbor Laboratory Press2025-04-10
<![CDATA[
Chronobot: Deep learning guided time-resolved cryo-EM captures molecular choreography of RecA in homology search
]]>
https://biorxiv.org/cgi/content/short/2025.04.21.649820v1?rss=1"
Mäeots, M.-E.Tupin, S.Esfahani, N. M. M.Molina, J. B. R.Clapperton, J. A.Amin, A.Imbert, A.Enchev, R. I.2025-04-22doi:10.1101/2025.04.21.649820Cold Spring Harbor Laboratory Press2025-04-22
<![CDATA[
Structure-Function Mapping of Olfactory Bulb Circuits with Synchrotron X-ray Nanotomography
]]>
https://biorxiv.org/cgi/content/short/2025.04.24.650439v1?rss=1"
80,000 cell nuclei in individual experiments, and delineate several hundred functionally imaged projection neurons and their detailed morphology, including up to 20 M/TCs per individual glomerulus ("sister" cells). In over 2400 sister cell pairs, we consistently find that odour response amplitudes to a panel of 47 monomolecular odours are conserved between sister cells, with, however, distinct responses to individual odours. Responses correlated with anatomical features such as cell body position and lateral dendritic arborisation. Thus, sister cells neither simply relay glomerular inputs nor are they dominated by network activity. Instead, they show a "balanced diversity" in their responses, enabling efficient encoding of odour stimuli whilst retaining the overall structure of odour space. Thus, synchrotron X-ray tomography can reliably link subcellular anatomy to function in a non-destructive way across the mm3 scale. With recent advances in X-ray optics9 and the emergence of 4th generation synchrotrons10,11, it becomes conceivable to extend this highly accessible approach to entire brain regions with increasing resolution.
]]>Zhang, Y.Bosch, C.Ackels, T.Laugros, A.Bonnin, A.Livingstone, J.Waltenberg, C.Berning, M.Tootoonian, S.Kollo, M.Nathansen, A.Rzepka, N.Cloetens, P.Pacureanu, A.Schaefer, A.2025-04-27doi:10.1101/2025.04.24.650439Cold Spring Harbor Laboratory Press2025-04-27
<![CDATA[
Chromosome-Specific Aneuploidy Engineering via dCas9-Induced Centromeric Chromatin Relaxation
]]>
https://biorxiv.org/cgi/content/short/2025.04.25.650684v1?rss=1"
FENG, H.Deng, D.Dahiya, R.Wang, L.Zeng, J.Tan, B. J. Y.Byrne, F.Shepherd, S. T. C.Wang, J.Johnson, S. C.Harrod, A.Lane, K. A.Fendler, A.Cattin, A.-L.Tippu, Z.Nie, M.Zhao, Y.Wang, R.Ai, W.Bouricha, O.Barber, T.Dovga, Y.Xu, Y.Xu, Y.Devito, L. G.Healy, L.Sun, Z.Shen, W.Wang, H.Lim, E. S.OToole, S. M.Akker, S.Drake, W. M.Jin, H.Downs, J. A.McClelland, S. E.Diffley, J. F. C.Ly, P.Turajlic, S.2025-04-27doi:10.1101/2025.04.25.650684Cold Spring Harbor Laboratory Press2025-04-27
<![CDATA[
VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment
]]>
https://biorxiv.org/cgi/content/short/2025.04.25.650693v1?rss=1"
Calderon, R. I.Sah, N.Huang, M.Kittle, R. H.Shaik, W.Chousal, J. N.Kallol, S.Bui, T.Morey, R.Mitre, A.Fogarty, N. M. E.Gerri, C.Zheng, C.DeHoff, P. M.Home, P.Niakan, K.Cook-Andersen, H.Fisch, K. M.Paul, S.Soncin, F.2025-04-29doi:10.1101/2025.04.25.650693Cold Spring Harbor Laboratory Press2025-04-29
<![CDATA[
Diverse Genomic Landscape of Swine Influenza A Virus in England (2014 - 2021)
]]>
https://biorxiv.org/cgi/content/short/2025.04.28.650978v1?rss=1"
Mollett, B. C.Byrne, A. M. P.Everett, H. E.Reid, S. M.Williamson, S.Anderson, T. K.James, J.Banyard, A. C.Brown, I. H.Lewis, N. S.2025-04-30doi:10.1101/2025.04.28.650978Cold Spring Harbor Laboratory Press2025-04-30
<![CDATA[
Distinct druggable biological processes in early-onset prostate cancer
]]>
https://biorxiv.org/cgi/content/short/2025.04.25.650707v1?rss=1"
Schmidt, S.Jarai, Z.Larkeryd, A.Ozer, B.Karlsson, Q.Campbell, J.Merson, S.Dennis, N.Hazell, S.Mitsopoulos, C.Cooper, C.ICGC-UK, T.Consortium, T.Russell, K.Workman, P.Eeles, R.Al-Lazikani, B.2025-04-29doi:10.1101/2025.04.25.650707Cold Spring Harbor Laboratory Press2025-04-29
<![CDATA[
PEtab.jl: Advancing the Efficiency and Utility of Dynamic Modelling
]]>
https://biorxiv.org/cgi/content/short/2025.04.30.651378v1?rss=1"
Cvijovic, M.Persson, S.Frohlich, F.Grein, S.Lomna, T.Ognissanti, D.Hassselgren, V.Hasenauer, J.2025-05-04doi:10.1101/2025.04.30.651378Cold Spring Harbor Laboratory Press2025-05-04
<![CDATA[
A single cell ATAC-seq atlas uncovers dynamic changes in chromatin accessibility during cell fate specification at the neural plate border
]]>
https://biorxiv.org/cgi/content/short/2025.05.03.652017v1?rss=1"
Harmrud, E.Leese, J.Thiery, A. P.Buzzi, A. L.Vigilante, A.Briscoe, J.Streit, A.2025-05-05doi:10.1101/2025.05.03.652017Cold Spring Harbor Laboratory Press2025-05-05
<![CDATA[
A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain
]]>
https://biorxiv.org/cgi/content/short/2025.05.02.651738v1?rss=1"
Brann, D. H.Tsukahara, T.Tau, C.Kalloor, D.Lubash, R.Thamarai Kannan, L.Klimpert, N.Kollo, M.Escamilla-Del-Arenal, M.Bintu, B.Bozza, T.Datta, S. R.2025-05-08doi:10.1101/2025.05.02.651738Cold Spring Harbor Laboratory Press2025-05-08
<![CDATA[
Sex-dependent neural plasticity in response to damage
]]>
https://biorxiv.org/cgi/content/short/2025.05.05.652027v1?rss=1"
Recatala-Martinez, M.Bosch, M.Gaspar, P.Mineo, A.Rios, S.Miguel-Aliaga, I.Morey, M.2025-05-09doi:10.1101/2025.05.05.652027Cold Spring Harbor Laboratory Press2025-05-09
<![CDATA[
Mycobacterium tuberculosis partitions the Krebs cycle to persist under iron starvation
]]>
https://biorxiv.org/cgi/content/short/2025.05.12.653400v1?rss=1"
Serafini, A.Garza-Garcia, A.Sorze, D.de Carvalho, L. P. S.Manganelli, R.2025-05-12doi:10.1101/2025.05.12.653400Cold Spring Harbor Laboratory Press2025-05-12
<![CDATA[
Conformational dynamics of the bacterial E3 ligase SspH1
]]>
https://biorxiv.org/cgi/content/short/2025.05.12.653404v1?rss=1"
Kennedy, C. R.Esposito, D.House, D.Rittinger, K.2025-05-15doi:10.1101/2025.05.12.653404Cold Spring Harbor Laboratory Press2025-05-15
<![CDATA[
AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI
]]>
https://biorxiv.org/cgi/content/short/2025.05.12.653464v1?rss=1"
Cunha, I.Panconi, L.Bauer, S.Gestin, M.Latron, E.Sahai, E.Le Marois, A.Griffie, J.2025-05-14doi:10.1101/2025.05.12.653464Cold Spring Harbor Laboratory Press2025-05-14
<![CDATA[
Physiological febrile heat stress increases cytoadhesion through increased protein trafficking of Plasmodium falciparum surface proteins into the red blood cell
]]>
https://biorxiv.org/cgi/content/short/2025.05.14.653932v1?rss=1"
Jones, D.Belda, H.Fuchs, G.Anaguano, D.Nofal, S. D.Treeck, M.2025-05-14doi:10.1101/2025.05.14.653932Cold Spring Harbor Laboratory Press2025-05-14
<![CDATA[
A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity
]]>
https://biorxiv.org/cgi/content/short/2025.05.13.653495v1?rss=1"
de Jong, G.Memi, F.Gracia, T.Lazareva, O.Gould, O.Aivazidis, A.Dave, M.Zhang, Q.Jensen, M.Rifaioglu, A. S.Barros-Silva, J. D.Eckert, S.Zhou, D.Wood, Y.Tuck, E.Er, S.Marshall, H.Roberts, K.Trinh, A. L.Rai, S.Shaw, T.Oszlanczi, A.Powell, H.Petryszak, R.Katsirea, Z.Mamun, I.Mulas, I.Quaegebeur, A.Briggs, M.Makarchuk, S.Cox, J.Lee, J. T. H.Rueda, L.Saraswat, M.Bulstrode, H.Young, A.Patel, M.Porter, T.Prigmore, E.Mall, M.Saez-Rodriguez, J.Briscoe, J.Rowitch, D. H.Mair, R.Behjati, S.Stegle, O.Bayraktar, O. A.2025-05-14doi:10.1101/2025.05.13.653495Cold Spring Harbor Laboratory Press2025-05-14
<![CDATA[
Mice discriminate odour source distance via sub-sniff temporal features of odour plumes
]]>
https://biorxiv.org/cgi/content/short/2025.05.14.653752v1?rss=1"
Marin, A. C.Harris, J. J.Dasgupta, D.Erskine, A.Warner, T. P. A.Schaefer, A. T.Ackels, T.2025-05-17doi:10.1101/2025.05.14.653752Cold Spring Harbor Laboratory Press2025-05-17
<![CDATA[
Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data
]]>
https://biorxiv.org/cgi/content/short/2025.05.28.656648v1?rss=1"
Fontaine, M.Vives, M. J. D.Saez, M.Maizels, R.Finnie, E.Briscoe, J.Rand, D. A.2025-05-28doi:10.1101/2025.05.28.656648Cold Spring Harbor Laboratory Press2025-05-28
<![CDATA[
Targeting Neutrophil Extracellular Traps to inhibit Colon Cancer Tumor Necrosis and Metastasis
]]>
https://biorxiv.org/cgi/content/short/2025.05.30.657122v1?rss=1"
Gazzara, E.Adrover, J. M.Lui, A.Han, S.Aminzada, Z.Bhandari, N.Sivetz, N.Shirue, V. S.Shergill, B. S.Curtis, M. B.George, S. C.Cicala, A.Rishi, A.Chung, C.Devoe, C.Huang, H.Weiss, M.Lou, E.Tuveson, D. A.Beyaz, S.Westcott, P. M. K.Egeblad, M.Gholami, S.2025-06-03doi:10.1101/2025.05.30.657122Cold Spring Harbor Laboratory Press2025-06-03
<![CDATA[
C9orf72 polyGA knock-in mice exhibit mild motor and proteomic changes consistent with ALS/FTD
]]>
https://biorxiv.org/cgi/content/short/2025.05.30.656994v1?rss=1"
Milioto, C.Carcole, M.Zanovello, M.Ahmed, M.Nirujogi, R. S.Biggs, D.Katona, E.Glaria, I.Santos, A.Devoy, A.Fratta, P.Alessi, D. R.Davies, B.Greensmith, L.Fisher, E.Isaacs, A. M.2025-06-02doi:10.1101/2025.05.30.656994Cold Spring Harbor Laboratory Press2025-06-02
<![CDATA[
Lysosomal stress induces amyloid-β aggregate release and reactive transformation in human astrocytes
]]>
https://biorxiv.org/cgi/content/short/2025.05.27.656416v1?rss=1"
Goldsworthy, S.Fertan, E.Dyal, P.Domoney, S.Livesey, F.Klenerman, D.Patani, R.Hung, C.2025-06-01doi:10.1101/2025.05.27.656416Cold Spring Harbor Laboratory Press2025-06-01
<![CDATA[
Beneficial and detrimental consequences of AHR activation in intestinal infection
]]>
https://biorxiv.org/cgi/content/short/2025.05.28.656570v1?rss=1"
Diaz, O. P.zhou, L.Barrington, C.Lindquist, D.Graelmann, F.Wincent, E.Stockinger, B.2025-06-01doi:10.1101/2025.05.28.656570Cold Spring Harbor Laboratory Press2025-06-01
<![CDATA[
The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis
]]>
https://biorxiv.org/cgi/content/short/2025.05.27.656346v1?rss=1"
Roeselova, A.Shivakumaraswamy, S.Jurkeviciute, G.He, J.-Z.Auburger, J.Schmitt, J.Kramer, G.Bukau, B.Enchev, R. I.Balchin, D.2025-05-30doi:10.1101/2025.05.27.656346Cold Spring Harbor Laboratory Press2025-05-30
<![CDATA[
The penetrant chordoid glioma PRKCA mutation is an oncogenic gain-of-function kinase inactivation eliciting early onset chondrosarcoma in mice.
]]>
https://biorxiv.org/cgi/content/short/2025.05.28.656646v1?rss=1"
Calleja, v.Henry, J. C.Cobbaut, M.Sewell, J.Rizzoti, K.Houghton, F.Boeing, S.Anyanwu, N.Varsani-Brown, S.Snoeks, T.Suarez-Bonnet, A.Priestnall, S. L.McDonald, N. Q.Cameron, A. J.Parker, P. J.2025-05-29doi:10.1101/2025.05.28.656646Cold Spring Harbor Laboratory Press2025-05-29
<![CDATA[
MitoTracker transfers from astrocytes to neurons independently of mitochondria
]]>
https://biorxiv.org/cgi/content/short/2025.05.27.655523v1?rss=1"
Hole, K. L.Norkett, R.Russell, E.Strom, M.Howden, J. H.Corbett, N. J.Brownlees, J.Devine, M. J.2025-05-28doi:10.1101/2025.05.27.655523Cold Spring Harbor Laboratory Press2025-05-28
<![CDATA[
RAD51AP1 is a versatile RAD51 modulator
]]>
https://biorxiv.org/cgi/content/short/2025.05.24.655746v1?rss=1"
Kuhlen, L.Argunhan, B.Liang, P.Zhong, J.Masino, L.Zhang, X.2025-05-24doi:10.1101/2025.05.24.655746Cold Spring Harbor Laboratory Press2025-05-24
<![CDATA[
Protein Kinase C δ: a critical hub regulating macrophage immunomodulatory functions during Mycobacterium tuberculosis infection
]]>
https://biorxiv.org/cgi/content/short/2025.05.19.653976v1?rss=1"
Hazra, R.Ozturk, M.Peton, N.Ganief, T.Poswayo, S. K.Rousseau, R. P.Naidoo, S.Jones, S.-S.Savulescu, A. F.Moseki, R.Abhimanyu, A.Plessis, N. D.Blackburn, J.Mhlanga, M. M.Kahn, C. R.Brombacher, F.Wilkinson, R. J.Parihar, S. P.2025-05-23doi:10.1101/2025.05.19.653976Cold Spring Harbor Laboratory Press2025-05-23
<![CDATA[
Substrate heterogeneity promotes cancer cell dissemination
]]>
https://biorxiv.org/cgi/content/short/2025.05.20.655037v1?rss=1"
Dunajova, Z.Tasciyan, S.Majek, J.Merrin, J.Sahai, E.Sixt, M.Hannezo, E.2025-05-23doi:10.1101/2025.05.20.655037Cold Spring Harbor Laboratory Press2025-05-23
<![CDATA[
CRITICAL ROLE OF ADULT-BORN DENTATE GRANULE NEURONS IN PATTERN COMPLETION
]]>
https://biorxiv.org/cgi/content/short/2025.05.15.654267v1?rss=1"
roullet, p.Koehl, M.Delage, P.Guillemot, F.Abrous, N.2025-05-20doi:10.1101/2025.05.15.654267Cold Spring Harbor Laboratory Press2025-05-20
<![CDATA[
The blood-brain barrier regulates brain tumour growth specifically via the SLC36 amino acid transporter Pathetic in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2025.05.15.654179v1?rss=1"
Dong, Q.AlvarezOchoa, E.Kosakamoto, H.Obata, F.Alexandre, C.Cheng, L.2025-05-20doi:10.1101/2025.05.15.654179Cold Spring Harbor Laboratory Press2025-05-20
<![CDATA[
A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics
]]>
https://biorxiv.org/cgi/content/short/2025.06.06.658228v1?rss=1"
Autorino, C.Khoromskaia, D.Harari, L.Floris, E.Booth, H.Pallares-Cartes, C.Petrasiunaite, V.Dorrity, M.Corominas-Murtra, B.Hadjivasiliou, Z.Petridou, N.2025-06-06doi:10.1101/2025.06.06.658228Cold Spring Harbor Laboratory Press2025-06-06
<![CDATA[
MRTF-dependent cytoskeletal dynamics drive efficient cell cycle progression
]]>
https://biorxiv.org/cgi/content/short/2025.06.06.657372v1?rss=1"
Nielsen, J. C.Benito-Jardon, M.Petrela, N. C.Diring, J.Bellamy, S.Treisman, R.2025-06-07doi:10.1101/2025.06.06.657372Cold Spring Harbor Laboratory Press2025-06-07
<![CDATA[
Multimodal profiling unveils a reversible basal-like breast cancer cell state resistant to AKT inhibition
]]>
https://biorxiv.org/cgi/content/short/2025.06.06.658331v1?rss=1"
Ratcliffe, C. D. H.Sparks, H.Boezio, G. L. M.Alexandrov, Y.Jenkins, R. P.Le Marois, A.Soro-Barrio, P.Lee, R.Strohbuecker, S.Joshi, S.Ellis, J. K.Fortier, A.-M.Gustafsson, N.Cunha, A. C.Park, M.MacRae, J. I.Serio, A.Briscoe, J.Riddell, A.Barry, S. T.Dunsby, C.Sahai, E.2025-06-07doi:10.1101/2025.06.06.658331Cold Spring Harbor Laboratory Press2025-06-07
<![CDATA[
Cross-species comparative connectomics reveals the evolution of an olfactory circuit
]]>
https://biorxiv.org/cgi/content/short/2025.06.11.659158v1?rss=1"
Roberts, R.Giez, C.Dhawan, S.Pang, S.Randel, N.Zhiyuan, L.Gong, H.Dekens, L.DiFrisco, J.Xu, C. S.Hess, H.Zlatic, M.Cardona, A.Prieto-Godino, L. L.2025-06-11doi:10.1101/2025.06.11.659158Cold Spring Harbor Laboratory Press2025-06-11
<![CDATA[
SARS-CoV-2 envelope protein induces LC3 lipidation via the V-ATPase-ATG16L1 axis
]]>
https://biorxiv.org/cgi/content/short/2025.06.12.659257v1?rss=1"
Figueras-Novoa, C.Timimi, L. J.Marcassa, E.Taveira-Marques, R.Adams, L.Jiang, M.Wu, M. Y.Montaner, B.Ng, K.De Lorenzo, G.Furnon, W.Cowton, V. M.Upfold, N.Kassiotis, G.Harvey, R.Patel, A. H.Howell, M.Ulferts, R.Beale, R.2025-06-13doi:10.1101/2025.06.12.659257Cold Spring Harbor Laboratory Press2025-06-13
<![CDATA[
Overnight circuit remodelling drives juvenile alloparental care
]]>
https://biorxiv.org/cgi/content/short/2025.06.13.659524v1?rss=1"
Jamieson, B. B.Chen, M. X.Liang, S.El Rasheed, L. S. H.Chattey, G. M. K.Kohl, J.2025-06-15doi:10.1101/2025.06.13.659524Cold Spring Harbor Laboratory Press2025-06-15
<![CDATA[
VISIBLE: An imaging-driven system for sampling, biofabrication, and manipulation of complex biological models
]]>
https://biorxiv.org/cgi/content/short/2025.06.12.659321v1?rss=1"
Joshi, S.Moreno-Gonzalez, C.Suklai, P.Carraro, E.Ratcliffe, C. D. H.Boezio, G. L. M.Konstantinou, G.Hagemann, C.Kavanagh, T.Ameer-Beg, S.Imbert, A.Sahai, E.Tedesco, F. S.Serio, A.2025-06-17doi:10.1101/2025.06.12.659321Cold Spring Harbor Laboratory Press2025-06-17
<![CDATA[
Anti-activin treatment increases T cell infiltration in breast and pancreatic tumours and promotes survival in a SMAD4-null mouse pancreatic cancer model
]]>
https://biorxiv.org/cgi/content/short/2025.06.13.659133v1?rss=1"
McCluney, S.Park, D.Miller, D. S.Mehic, M.Bloxham, R. D.De Vries, E.Wang, X.Boeing, S.D'Antonio, L.Wieteska, L.Pyeatt, G.Strohbuecker, S.Chakravarty, P.Maia De Oliveira, T.Wilcockson, R.Hyvonen, M.Hunt, J.Hill, C. S.2025-06-17doi:10.1101/2025.06.13.659133Cold Spring Harbor Laboratory Press2025-06-17
<![CDATA[
The evolution of gene regulatory programs controlling gonadal development in primates
]]>
https://biorxiv.org/cgi/content/short/2025.06.17.659946v1?rss=1"
Trost, N.Fallahshahroudi, A.Sarropoulos, I.Schneider, C.Schmidt, J.Mbengue, N.Wolff, E.Drummer, C.Frömel, R.Lisgo, S.Murat, F.Sepp, M.Cardoso-Moreira, M.Behr, R.Kaessmann, H.2025-06-19doi:10.1101/2025.06.17.659946Cold Spring Harbor Laboratory Press2025-06-19
<![CDATA[
Advanced human iPSC-based modelling of LMNA-related congenital muscular dystrophy enables development of targeted genetic therapies for muscle laminopathies
]]>
https://biorxiv.org/cgi/content/short/2025.06.22.660928v1?rss=1"
View larger version (15K):
org.highwire.dtl.DTLVardef@134276forg.highwire.dtl.DTLVardef@108f44forg.highwire.dtl.DTLVardef@dfa04eorg.highwire.dtl.DTLVardef@1956a90_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LILMNA-mutant iPSCs undergo efficient skeletal myogenesis upon transgene-free, small molecule-based lineage-directed differentiation
C_LIO_LIL-CMD iPSCs recapitulate hallmark disease-associated nuclear phenotypes and show a pro-inflammatory transcriptional profile
C_LIO_LIDisease modelling platforms based on iPSC-derived skeletal muscle cells enable comparative testing of gene editing strategies
C_LIO_LICRISPR-edited L-CMD iPSC-derived myogenic cells show amelioration of disease-associated readouts
C_LI
]]>Moore, D. P.Steele-Stallard, H. B.Pinton, L.Lionello, V. M.Rossi, L.Aghaeipour, A.Jalal, S.Wong, C. T. Y.Clara-Hwang, A.Bonne, G.Zammit, P. S.Tedesco, F. S.2025-06-23doi:10.1101/2025.06.22.660928Cold Spring Harbor Laboratory Press2025-06-23
<![CDATA[
Sensitizing Immune-Refractory Ovarian Tumors via p53 Mutation-Tailored Immunotherapy
]]>
https://biorxiv.org/cgi/content/short/2025.06.23.661120v1?rss=1"
Chatterjee, R.Simoni-Nieves, A.Truong, A.Lindzen, M.Ozmen, F.Cherry, C.Zwicky, P.Mukherjee, S.Selvadurai, B.-R.Salame, T. M.Gupta, N.Giri, S.Kramarski, L.Avraham, Y.Weizman, E.Ozmen, T.Noronha, A.Chakrabarti, P.Ramesh-Kumar, D.Downward, J.Dahan, R.Amit, I.Velculescu, V.Brenton, J.Mills, G.Oren, M.Yarden, Y.2025-06-27doi:10.1101/2025.06.23.661120Cold Spring Harbor Laboratory Press2025-06-27
<![CDATA[
The adaptive molecular landscape of reprogrammed telomeric sequences
]]>
https://biorxiv.org/cgi/content/short/2025.06.24.661269v1?rss=1"
D'Angiolo, M.Barre, B. P.Khaiwal, S.Muenzner, J.Hallin, J.De Chiara, M.Tellini, N.Warringer, J.Ralser, M.Gilson, E.Liti, G.2025-06-27doi:10.1101/2025.06.24.661269Cold Spring Harbor Laboratory Press2025-06-27
<![CDATA[
An optimised computational approach for the identification of somatic structural variants in cancer
]]>
https://biorxiv.org/cgi/content/short/2025.07.01.662575v1?rss=1"
Waise, S.Mensah, N.Lesluyes, T.Demeulemeester, J.Flanagan, A. M.Pillay, N.Van Loo, P.2025-07-02doi:10.1101/2025.07.01.662575Cold Spring Harbor Laboratory Press2025-07-02
<![CDATA[
Lonafarnib Partially Reverses Cardiac Senescence in Human and Mouse Progeria Models via Autophagy Activation
]]>
https://biorxiv.org/cgi/content/short/2025.06.27.661680v1?rss=1"
Monteiro, L. M.Pitrez, P. R.Correira-Santos, S.Dark, N.Santinha, D.Aveleira, C.Townsend, M.Taylor, J.Nissan, X.Sardao, V.Cortes, L.Mitter, R.Marino, A.Sousa-Soares, C.Ribeiro, R.Smith, J. C.Logarinho, E.Ori, A.Bernardo, A. S.Ferreira, L.2025-07-02doi:10.1101/2025.06.27.661680Cold Spring Harbor Laboratory Press2025-07-02
<![CDATA[
Metabolic control of enteroendocrine cell fate through a redox state sensor CtBP
]]>
https://biorxiv.org/cgi/content/short/2025.06.30.662346v1?rss=1"
View larger version (32K):
org.highwire.dtl.DTLVardef@3baaeorg.highwire.dtl.DTLVardef@d505edorg.highwire.dtl.DTLVardef@178361dorg.highwire.dtl.DTLVardef@128e210_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Rovenko, B. M.Moisio, K.Biehler, C.Girych, M.Hallasaari, A.Deniz, O.Bluhm, S.Viitanen, A.Kokki, K.Fabris, G.Yang, Y.Cracan, V.Miguel-Aliaga, I.Hietakangas, V.2025-07-02doi:10.1101/2025.06.30.662346Cold Spring Harbor Laboratory Press2025-07-02
<![CDATA[
Control of CDK activity and the cell cycle by CKS proteins
]]>
https://biorxiv.org/cgi/content/short/2025.07.04.663185v1?rss=1"
Curran, J. F.Basu, S.Auchynnikava, T.Nurse, P.2025-07-07doi:10.1101/2025.07.04.663185Cold Spring Harbor Laboratory Press2025-07-07
<![CDATA[
Kandinsky: enabling neighbourhood analysis of spatial omics data for functional insights on cell ecosystems
]]>
https://biorxiv.org/cgi/content/short/2025.07.10.664141v1?rss=1"
Andrei, P.Grieco, M.Acha-Sagredo, A.Dhami, P.Fung, K.Rodriguez-Justo, M.Cereda, M.Ciccarelli, F. D.2025-07-16doi:10.1101/2025.07.10.664141Cold Spring Harbor Laboratory Press2025-07-16
<![CDATA[
A new material constant of DNA is the major determinant of looping dynamics
]]>
https://biorxiv.org/cgi/content/short/2025.07.10.664086v1?rss=1"
kBT) internal energy barriers. The salt-independence of this dissipation also rules out long range electrostatic interactions as its origins. Instead our findings point to a complex local energy landscape for bending and a potential previously unappreciated role of water binding DNA constraining its local mobility. Our findings radically change our understanding of DNA dynamics and reveal DNA as a viscoelastic semiflexible polymer with dramatically slower dynamics compared to an ideal elastic rod. This work establishes bending friction as a fundamental material property that must underpin any model of DNA dynamics in biology, physics, and nanotechnology.
]]>Pobegalov, G.Molodtsov, M.Khatri, B. S.2025-07-16doi:10.1101/2025.07.10.664086Cold Spring Harbor Laboratory Press2025-07-16
<![CDATA[
Differential chromatin response to retinoic acid in neuroblastoma according to type of ATRX mutation
]]>
https://biorxiv.org/cgi/content/short/2025.07.14.664731v1?rss=1"
Lorenzi, F.Shipley, M.Deane, L.Goldstone, R.Tandon, V.Martins da Costa, B.Greenslade, K.Barker, K.Nemati, F.Bellini, A.Schleiermacher, G.Chesler, L.Guillemot, F.George, S. L.2025-07-18doi:10.1101/2025.07.14.664731Cold Spring Harbor Laboratory Press2025-07-18
<![CDATA[
A Paracrine-to-Autocrine Shunt of GREM1 Fuels Colorectal Cancer Metastasis via ACVR1C
]]>
https://biorxiv.org/cgi/content/short/2025.07.11.664267v1?rss=1"
Zhou, H.Jin, Q.Fu, Z.Yang, Y.Gao, Y.Wang, N.Zhao, B.Gui, L.Li, J.Zhu, Z.Zhang, Y.He, Y.Zhang, Y.Luo, S.Fu, L.Wu, X.Zhang, J.Shen, X.Wang, T.Jiang, Y.Li, N.2025-07-16doi:10.1101/2025.07.11.664267Cold Spring Harbor Laboratory Press2025-07-16
<![CDATA[
Barcoded Rabies In Situ Connectomics for high-throughput reconstruction of neural circuits
]]>
https://biorxiv.org/cgi/content/short/2025.07.16.665048v1?rss=1"
1000 neurons uniquely. To minimize the probability of barcode transmission between starter neurons, we developed a strategy to tightly control their density. We then applied BRISC to map inputs of single neurons in the primary visual cortex (V1). Using in situ sequencing, we read out the expression of viral barcodes in rabies-infected neurons, while preserving spatial information. We then matched barcode sequences between starter and presynaptic neurons, mapping the inputs of 385 neurons and identifying 7,814 putative synaptic connections. The resulting connectivity matrix revealed layer- and cell-type-specific local connectivity rules and topographic organization of long-range inputs to V1. These results show that BRISC can simultaneously resolve the synaptic connectivity of hundreds of neurons while preserving spatial information, enabling reconstruction of neural circuits at an unprecedented scale.
]]>Becalick, A.Blot, A.Strom, M.Znamenskiy, P.2025-07-20doi:10.1101/2025.07.16.665048Cold Spring Harbor Laboratory Press2025-07-20
<![CDATA[
Boundary constraints can determine pattern emergence
]]>
https://biorxiv.org/cgi/content/short/2025.07.21.665949v1?rss=1"
Loo, Y. T.Chen, J.Harrison, R.Rito, T.Theis, S.Charras, G.Briscoe, J.Saunders, T. E.2025-07-22doi:10.1101/2025.07.21.665949Cold Spring Harbor Laboratory Press2025-07-22
<![CDATA[
Hippocampal circuit-specific enhancement of GABA-inhibition caused by discrete gene regions in a Down syndrome model
]]>
https://biorxiv.org/cgi/content/short/2025.07.21.665861v1?rss=1"
Hannan, S. B.Lana-Elola, E.Scales, S. W.Fisher, E. M. C.Tybulewicz, V. L. J.Smart, T. G.2025-07-24doi:10.1101/2025.07.21.665861Cold Spring Harbor Laboratory Press2025-07-24
<![CDATA[
Topographic alignment of auditory inputs to the visual cortex
]]>
https://biorxiv.org/cgi/content/short/2025.07.29.667237v1?rss=1"
Egea-Weiss, A.Turner-Bridger, B.Viduolyte, A.Marianelli, E.Znamenskiy, P.Iacaruso, M. F.2025-07-31doi:10.1101/2025.07.29.667237Cold Spring Harbor Laboratory Press2025-07-31
<![CDATA[
Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites
]]>
https://biorxiv.org/cgi/content/short/2025.07.29.667472v1?rss=1"
Downes, K. W.Flood, J. R.Nans, A.Van der Verren, S.Audhya, A.Zanetti, G.2025-07-30doi:10.1101/2025.07.29.667472Cold Spring Harbor Laboratory Press2025-07-30
<![CDATA[
Integrative modeling of seasonal influenza evolution via AI-powered antigenic cartography
]]>
https://biorxiv.org/cgi/content/short/2025.08.04.668423v1?rss=1"
Ito, J.Kawakubo, S.Unno, H.Strange, A.Lytras, S.Okumura, K.Lilley, A.Harvey, R.Lewis, N.Sato, K.2025-08-04doi:10.1101/2025.08.04.668423Cold Spring Harbor Laboratory Press2025-08-04
<![CDATA[
Extracting biological structure and heterogeneity from the nano to the macro scale
]]>
https://biorxiv.org/cgi/content/short/2025.08.06.668903v1?rss=1"
Rosten, E.Stedman, D.Chu, L.-Y.Wickramanayake, K.Littlejohn, G.Baxter, K. J.McConnell, G.Culley, S.Ch'ng, Q.Leterrier, C.Bates, M.Molodtsov, M.Cox, S.2025-08-07doi:10.1101/2025.08.06.668903Cold Spring Harbor Laboratory Press2025-08-07
<![CDATA[
Reconstructing Waddington's Landscape from Data
]]>
https://biorxiv.org/cgi/content/short/2025.08.11.669575v1?rss=1"
Cislo, D. J.Delas, M. J.Briscoe, J.Siggia, E. D.2025-08-13doi:10.1101/2025.08.11.669575Cold Spring Harbor Laboratory Press2025-08-13
<![CDATA[
Inactivation of Airborne Pathogen Surrogates by Triethylene Glycol
]]>
https://biorxiv.org/cgi/content/short/2025.08.08.669335v1?rss=1"
Desai, G.Goldman, E.Jordan, W.Balarashti, J.Caravanos, J.Edgar, R. S.Grignard, E.Ramachandran, G.Mainelis, G.2025-08-08doi:10.1101/2025.08.08.669335Cold Spring Harbor Laboratory Press2025-08-08
<![CDATA[
In situ cryo-electron tomography of vaccinia virus exit from infected cells
]]>
https://biorxiv.org/cgi/content/short/2025.08.20.671218v1?rss=1"
Hernandez-Gonzalez, M.Nans, A.Calcraft, T.Rosenthal, P. B.Way, M.2025-08-20doi:10.1101/2025.08.20.671218Cold Spring Harbor Laboratory Press2025-08-20
<![CDATA[
Developmental changes in the carotid body transcriptome accompanying the maturation of chemosensitivity
]]>
https://biorxiv.org/cgi/content/short/2025.08.21.671502v1?rss=1"
Hodson, E. J.Sugimoto, Y.Manamperige, R. S.Ford, S. G.Botting-Lawford, K. J.Niu, Y.Nathan, J. A.Giussani, D. A.Ratcliffe, P. J.2025-08-25doi:10.1101/2025.08.21.671502Cold Spring Harbor Laboratory Press2025-08-25
<![CDATA[
α-Synuclein driven cell susceptibility in Parkinson's disease
]]>
https://biorxiv.org/cgi/content/short/2025.08.19.670819v1?rss=1"
Breiter, J. C.Beckwith, J. S.Brock, E. E.Lachica, J.Toomey, C. E.Fu, B.Ryten, M.Weiss, L. E.Wood, N. W.Gandhi, S.Vendruscolo, M.Lee, S. F.2025-08-23doi:10.1101/2025.08.19.670819Cold Spring Harbor Laboratory Press2025-08-23
<![CDATA[
Balanced contractility and adhesion drive polarization in a minimal elastic actomyosin network
]]>
https://biorxiv.org/cgi/content/short/2025.08.26.672435v1?rss=1"
Messi, Z.Raynaud, F.Goehring, N. W.Verkhovsky, A. B.2025-08-29doi:10.1101/2025.08.26.672435Cold Spring Harbor Laboratory Press2025-08-29
<![CDATA[
Multiomic analysis reveals developmental dynamics of the human heart in health and disease
]]>
https://biorxiv.org/cgi/content/short/2024.04.29.591736v1?rss=1"
Cranley, J.Kanemaru, K.Bayraktar, S.Knight-Schrijver, V.Pett, J. P.Polanski, K.Dabrowska, M.Mulas, I.Richardson, L.Semprich, C.Kapuge, R.Perera, S.He, X.Ho, S. Y.Yayon, N.Tuck, L.Roberts, K.Palmer, J.Davaapil, H.Gambardella, L.Patel, M.Tyser, R.Sinha, S.Teichmann, S.2024-04-29doi:10.1101/2024.04.29.591736Cold Spring Harbor Laboratory Press2024-04-29
<![CDATA[
Microglial activation and alpha-synuclein oligomers drive the early inflammatory phase of Parkinson's disease
]]>
https://biorxiv.org/cgi/content/short/2025.08.25.671921v1?rss=1"
Evans, J. R.Grant-Peters, M.Beckwith, J. S.Toomey, C. E.Popovic, R.Breiter, J. C.Brenton, J. W.Fairbrother-Browne, A.Strohbuecker, S.Lachica, J.Rodriguez-Lopez, M.Brock, E. E.Fu, B.Nahidiazar, L.Lopez-Garcia, P.Ferguson, R.Saleeb, R. S.Lucas-Clarke, H.Penverne, A.D'Sa, K.Pang, C. W.Horrocks, M. H.Vendruscolo, M.Wood, N.Lee, S. F.Ryten, M.Gandhi, S.2025-08-28doi:10.1101/2025.08.25.671921Cold Spring Harbor Laboratory Press2025-08-28
<![CDATA[
Plasmodium ARK1 regulates spindle formation during atypical mitosis and forms a divergent chromosomal passenger complex
]]>
https://biorxiv.org/cgi/content/short/2025.08.27.672654v1?rss=1"
Nagar, A.Yanase, R.Zeeshan, M.Ferguson, D. J. P.Abel, S.Pashley, S. L.Mishra, A.Eze, A.Rea, E.Brady, D.Bottrill, A. R.Vaughan, S.Le Roch, K. G.Guttery, D. S.Holder, A. A.Tromer, E. C.Sharma, P.Tewari, R.2025-08-27doi:10.1101/2025.08.27.672654Cold Spring Harbor Laboratory Press2025-08-27
<![CDATA[
Critical point drying of brain tissue for X-ray phase contrast imaging
]]>
https://biorxiv.org/cgi/content/short/2025.09.02.673701v1?rss=1"
Khan, S.Albers, J.Vorobyev, A.Zhang, Y.Reichmann, J.Svetlove, A.de Marco, F.Denisova, K.Yang, Y.Seichepine, F.Douglas, J. O.Duke, E.Cloetens, P.Pacureanu, A.Schaefer, A.Bosch, C.2025-09-07doi:10.1101/2025.09.02.673701Cold Spring Harbor Laboratory Press2025-09-07
<![CDATA[
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025
]]>
https://biorxiv.org/cgi/content/short/2025.09.06.674661v1?rss=1"
Kikawa, C.Huddleston, J.Loes, A. N.Turner, S. A.Lee, J.Barr, I. G.Cowling, B. J.Englund, J. A.Greninger, A. L.Harvey, R.Hasegawa, H.Ho, F.Lacombe, K.Leung, N. H.Lewis, N. S.Peck, H.Watanabe, S.Smith, D. J.Bedford, T.Bloom, J. D.2025-09-06doi:10.1101/2025.09.06.674661Cold Spring Harbor Laboratory Press2025-09-06
<![CDATA[
Lactate Blocks Tertiary Lymphoid Structure Formation by Inhibiting B Cell Chemotaxis
]]>
https://biorxiv.org/cgi/content/short/2025.08.30.673054v1?rss=1"
Calado, D. P.Boulat, V.Alberts, E.Driscoll, P. C.Hung, M. S.Cunha, A.Quist, J.Liu, F.Brundin, C. A.Bhalla, A.Avalle, L.Rosekilly, J.Ryan, L.Gillett, C.Strom, M.Poli, V.MacRae, J. I.Grigoriadis, A.2025-09-04doi:10.1101/2025.08.30.673054Cold Spring Harbor Laboratory Press2025-09-04
<![CDATA[
Streptococcus pneumoniae accessory capsular genes modulate fitness, pathogenicity and immune evasion
]]>
https://biorxiv.org/cgi/content/short/2025.09.11.675585v1?rss=1"
Chan, J. M.Flynn, H. R.Kim, S.Demetriou, H.Ramos-Sevillano, E.Alsari, A.Roalfe, L.Ercoli, G.Kalizang'oma, A.Brown, C.Chaguza, C.French, N.Brown, J. S.Goldblatt, D.de Carvalho, L. P. S.Heyderman, R.2025-09-15doi:10.1101/2025.09.11.675585Cold Spring Harbor Laboratory Press2025-09-15
<![CDATA[
Investigations into fission yeast chromosome size determinants
]]>
https://biorxiv.org/cgi/content/short/2025.09.15.676266v1?rss=1"
Wu, P.-S.Fallesen, T.Uhlmann, F.2025-09-15doi:10.1101/2025.09.15.676266Cold Spring Harbor Laboratory Press2025-09-15
<![CDATA[
Immunogenicity and Efficacy of Digitally Immune Optimised H1N1 Vaccine Candidates in Swine and Murine Animal Models
]]>
https://biorxiv.org/cgi/content/short/2025.09.12.675937v1?rss=1"
Del Rosario, J. M. M.van Diemen, P. M.Frost, S.vishwanath, s.Sujit, S. B.Ashokan, S. K.Mollett, B. C.Ramsay, A. M.Simpson, B.Asbach, B.Carnell, G. W.Chan, A.Tonks, P.Temperton, N. J.Davies, M.McCauley, J. W.Kinsley, R.Wagner, R.Everett, H. E.Heeney, J. L.2025-09-14doi:10.1101/2025.09.12.675937Cold Spring Harbor Laboratory Press2025-09-14
<![CDATA[
SLFN11 restricts escape from telomere crisis to prevent alternative lengthening of telomeres
]]>
https://biorxiv.org/cgi/content/short/2025.09.10.675313v1?rss=1"
Segura-Bayona, S.Borel, V.Stanage, T. H.Maric, M.Walter, M.Oliveira, R. A.Li, S.Idilli, A. I.Peritore, M.Hewitt, G.Hekkelman, M.Snell, D. M.Jones, S. T.Cheshire, C.Elezi, A.Chakravarty, P.Mitter, R.Mikolajczak, A.Gee, H. E.Nye, E.O'Sullivan, R. J.Singhi, A. D.Brummelkamp, T. R.Cesare, A. J.Boulton, S. J.2025-09-10doi:10.1101/2025.09.10.675313Cold Spring Harbor Laboratory Press2025-09-10
<![CDATA[
TDP-43 loss of function drives aberrant splicing in Parkinson's disease
]]>
https://biorxiv.org/cgi/content/short/2025.09.04.673943v1?rss=1"
500 post-mortem human brain samples from individuals with and without PD to show that splicing alterations are frequently detected. Differentially spliced genes were significantly more enriched for those causally-implicated in both PD and ALS than genes that were differentially expressed. Furthermore, we observed a strong association between these splicing alterations and dysfunction of the RNA-binding protein (RBP), TAR DNA-binding protein 43 (TDP-43). Strikingly, genes and exon junctions affected by TDP-43 knockdown overlapped significantly with those dysregulated across brain regions in PD. In brains from individuals with the LRRK2 c.6055G>A (p.G2019S) mutation, the most common genetic cause of PD, we also observed significant enrichment of TDP-43-dependent splicing changes. This finding was corroborated in human pluripotent stem cell-derived midbrain dopaminergic neurons and a LRRK2 p.G2019S knock-in mouse model, where reduced nuclear TDP-43 levels evidenced the well-recognised loss-of-function mechanism contributing to splicing dysregulation. By leveraging our RNA-based analyses we predicted TDP-43-dependent novel peptide sequences and validated their existence within human LRRK2 mutation mDNs, while also demonstrating an overall loss of protein and mRNA expression in mis-spliced genes. Collectively, our findings reveal that PD is marked by extensive splicing dysregulation dependent on TDP-43, making TDP-43 a promising new therapeutic target in PD.
]]>Brenton, J. W.Follett, J.Nirujogi, R.Toomey, C. E.Lopez-Garcia, P.Evans, J. R.Lee, Y. J.Syed, K. M.Rocamora Perez, G.Fairbrother-Browne, A.D'Sa, K.Grant-Peters, M.Lachica, J.Hicks, A. R.Wagen, A. Z.O'Callaghan, B.Macpherson, H.Montgomery, K.-a.Busquets, O.Reynolds, R. H.Garcia Ruiz, S.Cao, T.Chen, Z.Plun-Favreau, H.Wong, P. C.Farrer, M.Lashley, T.Soldner, F.Hockemeyer, D.Alessi, D.Wood, N. W.Hardy, J.Rio, D. C.Jaunmuktane, Z.Gustavsson, E. K.Gandhi, S.Ryten, M.2025-09-09doi:10.1101/2025.09.04.673943Cold Spring Harbor Laboratory Press2025-09-09
<![CDATA[
Chaperone AIP Couples mTORC1 Activation and Catabolic Metabolism During Neonatal Development
]]>
https://biorxiv.org/cgi/content/short/2025.09.18.677011v1?rss=1"
Korbonits, M.Wang, X.Barry, S.Lim, C. T.Suleyman, O.De Tito, S.Uddin, N. B.Vignola, M. L.Hall, C.Perna, L.Chapple, P.Henson, S.Morales, V.Bianchi, K.Edvardsson, V. O.Ragnarsson, K. A.Kristinsdottir, V. E.Debeer, A.Sleyp, Y.Zinchenko, R. A.Anderson, G.Duchen, M.Singh, K.Chung, C.-Y.Yuan, Y.Patel, S.Aksoy, E.Borovikov, A.Bjornsson, H. T.Van Esch, H.Czibik, G.Tooze, S.Brennan, C. H.Haworth, O.2025-09-18doi:10.1101/2025.09.18.677011Cold Spring Harbor Laboratory Press2025-09-18
<![CDATA[
Mechanisms for cross-neutralisation of diverse bat sarbecoviruses
]]>
https://biorxiv.org/cgi/content/short/2025.09.17.674891v1?rss=1"
Upadhyay, A.Seow, J.Alguel, Y.Newman, J.Thakur, N.Hay, A.Tam, J. C. H.Nans, A.Orton, R.Bailey, D.Cherepanov, P.Doores, K. J.2025-09-17doi:10.1101/2025.09.17.674891Cold Spring Harbor Laboratory Press2025-09-17
<![CDATA[
Morphogen and juxtacrine signalling dynamically integrate to specify cell fates with single-cell resolution
]]>
https://biorxiv.org/cgi/content/short/2025.09.15.676088v1?rss=1"
Donoghue, A.Mosby, L.Lago-Baldaia, I.Hodgetts, T.Ursu, E.Erten, Z.Hadjivasiliou, Z.Fernandes, V. M.2025-09-17doi:10.1101/2025.09.15.676088Cold Spring Harbor Laboratory Press2025-09-17
<![CDATA[
Conserved Aberrant Developmental Trajectories of Human and Mouse SBMA Motor Neurons
]]>
https://biorxiv.org/cgi/content/short/2025.09.17.674754v1?rss=1"
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]]>Devine, H.Roberts, M. J.Ziff, O. J.Hanna, M. G.Greensmith, L.Patani, R.Malik, B.2025-09-17doi:10.1101/2025.09.17.674754Cold Spring Harbor Laboratory Press2025-09-17
<![CDATA[
Characterisation of LAMP1- and LAMP2A-positive organelles in neurons
]]>
https://biorxiv.org/cgi/content/short/2025.09.17.676809v1?rss=1"
Abouward, R.Abdelhafid, A. M.Wilkins, O. G.Lee, S.-Y.Ibrahim, F.Skehel, M.Ting, A.Birsa, N.Ule, J.Schiavo, G.2025-09-17doi:10.1101/2025.09.17.676809Cold Spring Harbor Laboratory Press2025-09-17
<![CDATA[
Cell migration sculpts evolutionary dynamics favouring therapy resistance in lung cancer
]]>
https://biorxiv.org/cgi/content/short/2025.09.15.675999v1?rss=1"
Bhargava, A.Fu, X.Bailey, S.Naito, Y.Mohammadi, H.Hynds, R. E.Hooper, S.Biswas, D.Le Marois, A.Kumar, S.Alexandrov, Y.French, P. M.McGinty, J.Bates, P. A.Swanton, C.Sahai, E.2025-09-16doi:10.1101/2025.09.15.675999Cold Spring Harbor Laboratory Press2025-09-16
<![CDATA[
Distinct ATRX functions cooperate with 9-1-1 and CST complexesto safeguard replication and telomere integrity
]]>
https://biorxiv.org/cgi/content/short/2025.09.22.677761v1?rss=1"
Segura-Bayona, S.Maric, M.Takaki, T.Manova, Z.Li, S.Stanage, T. H.Idilli, A. I.Hewitt, G.Ruis, P.Millar, R.Patel, H.Howell, S.Kotsantis, P.Howell, M.Boulton, S. J.2025-09-22doi:10.1101/2025.09.22.677761Cold Spring Harbor Laboratory Press2025-09-22
<![CDATA[
Systems-level feedback loops maintain gene expression homeostasis following RNA polymerase II dosage perturbation
]]>
https://biorxiv.org/cgi/content/short/2025.09.18.677100v1?rss=1"
Olthof, A. M.Gonzalez, M. N.Poulsen, N. B.Moreno, N. N.Bautu, T.Cugusi, S.Svejstrup, J.2025-09-18doi:10.1101/2025.09.18.677100Cold Spring Harbor Laboratory Press2025-09-18
<![CDATA[
Peptide molecular glues select between BET paralogues by exploiting allosteric sites and conformational dynamics
]]>
https://biorxiv.org/cgi/content/short/2025.09.24.678353v1?rss=1"
Patel, K.Mohanty, B.Norman, A.Franck, C.Pachl, P.Yang, L.Jing, X.Reid, X. J.Walshe, J. L.Solomon, P.Tran, D. H.Ford, D.Low, J. K. K.Wilkinson-White, L.Passioura, T.Payne, R. J.Suga, H.Walport, L. J.Mackay, J. P.2025-09-24doi:10.1101/2025.09.24.678353Cold Spring Harbor Laboratory Press2025-09-24
<![CDATA[
Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context
]]>
https://biorxiv.org/cgi/content/short/2025.09.26.678648v1?rss=1"
750-fold over multicolor labeling and enable morphology reconstruction with intrinsic error correction. We acquired a [~]10 million {micro}m3 volume of mouse hippocampal area CA2/3, multiplexed across 23 barcode antigen and synaptic marker channels. By combining barcodes with shape information, we achieve an 8x increase in automatic tracing accuracy of genetically labelled neurons. We demonstrate PRISM supports automatic proofreading across micron-scale spatial gaps and reconnects neurites across discontinuities spanning hundreds of microns. Using PRISMs molecular annotation capability, we map the distribution of synapses onto traced neural morphology, characterizing challenging synaptic structures such as thorny excrescences (TEs), and discovering a size correlation among spatially proximal TEs on the same dendrite. PRISM thus supports selfcorrecting neuron reconstruction with molecular context.
]]>Park, S. Y.Sheridan, A.An, B.Jarvis, E.Lyudchik, J.Patton, W.Axup, J. Y.Chan, S. W.Damstra, H. G. J.Leible, D.Leung, K. S.Magno, C. A.Meeran, A.Michalska, J. M.Rieger, F.Wang, C.Wu, M.Church, G. M.Funke, J.Huffman, T.Leeper, K. G. C.Truckenbrodt, S.Winnubst, J.Kornfeld, J. M. R.Boyden, E. S.Rodriques, S. G.Payne, A. C.2025-09-28doi:10.1101/2025.09.26.678648Cold Spring Harbor Laboratory Press2025-09-28
<![CDATA[
CLONAL SELECTION SUPPORTED BY SINGLE CELL DNA SEQUENCING REVEALS HORMONAL ADAPTATION AND RESISTANCE IN LOCALLY ADVANCED BREAST CANCER DURING NEOADJUVANT AROMATASE INHIBITION
]]>
https://biorxiv.org/cgi/content/short/2025.09.24.678208v1?rss=1"
O'Mahony, D. G.Lesluyes, T.Brorson, I. S.Vernhoff, P.Sokolova, K.Aure, M. R.Alnaes, G. G.Hooen, R. M.Sundaram, A. Y.Theesfeld, C.Geisler, S. B.Sauer, T.Bahrami, N.Parulkar, R.Tahiri, A.Luders, T.Troyanskaya, O.Vaske, C.Van Loo, P.Geisler, J.Kristensen, V. N.2025-09-26doi:10.1101/2025.09.24.678208Cold Spring Harbor Laboratory Press2025-09-26
<![CDATA[
Splenic granulopoiesis and S100A9 drive resistance to checkpoint inhibitors conferred by liver metastases
]]>
https://biorxiv.org/cgi/content/short/2025.09.30.679035v1?rss=1"
Lee, R.Hooper, S.Pallett, L.Diniz, M.Mckinnon-Snell, T.Ramsden, Z.Rabas, N.Boeing, S.Kennedy, O.Buttercase, C.Aidoo-Micah, G.Price, G.Macfarlane, S. C.Bailey, S.Davies, J.Mathur, A.Pistocchi, G.Carminati, A.Gupta, A.Serra, P.Davidson, B. R.Pollok, J.-M.Papayannopoulos, V.Malanchi, I.Lorigan, P.Maini, M. K.Sahai, E.2025-10-01doi:10.1101/2025.09.30.679035Cold Spring Harbor Laboratory Press2025-10-01
<![CDATA[
Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates
]]>
https://biorxiv.org/cgi/content/short/2025.10.06.677012v1?rss=1"
Davi, V.Parutto, P.Crapart, C.Zhang, Y.Konno, T.Chambers, J.Franklin, J. P.Maddison, D.Awadelkareem, M. A.Devine, M. J.Koslover, E.Avezov, E.2025-10-07doi:10.1101/2025.10.06.677012Cold Spring Harbor Laboratory Press2025-10-07
<![CDATA[
Apicortin defines the Plasmodium apical conoid body during transmission but is dispensable for the parasite life cycle
]]>
https://biorxiv.org/cgi/content/short/2025.10.01.678762v1?rss=1"
Zeeshan, M.Mishra, A.Pashley, S. L.Markus, R.Brady, D.Holder, A. A.Moores, C.Tewari, R.2025-10-03doi:10.1101/2025.10.01.678762Cold Spring Harbor Laboratory Press2025-10-03
<![CDATA[
Rapid expansion of podoplanin-positive fibroblasts following radiation limits the anti-tumour CD8+ T-cell response to radiotherapy.
]]>
https://biorxiv.org/cgi/content/short/2025.10.07.680949v1?rss=1"
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]]>Wilkins, A. C.Makris, S.Green, M.Hooper, S.Mikolajczak, A.Giangreco, G.Allanki, S.Nye, E.Connick, E.Mitter, R.Cooper, S.Durie, E.Pedersen, M.Burley, A.O'Fee, K.O'Leary, B.Shewring, D.Ramsden, Z.Melcher, A.Harrington, K.Somaiah, N.Acton, S. E.Sahai, E.2025-10-07doi:10.1101/2025.10.07.680949Cold Spring Harbor Laboratory Press2025-10-07
<![CDATA[
DNMT3A-R882 mutations intrinsically drive dysfunctional neutropoiesis from human haematopoietic stem cells
]]>
https://biorxiv.org/cgi/content/short/2025.10.08.679225v1?rss=1"
Mantica, G.Vedi, A.Tuval, A.Huerga Encabo, H.Hayler, D.Krzywon, A.Mitchell, E.Dunn, W. G.Biezuner, T.Bastos, H. P.Sham, K.Santoro, A.Lee, J.Williams, N.Danin, A.Chapal, N.Moskovitz, Y.Arruda, A.Fiorillo, E.Orru, V.Marongiu, M.McKinney, E.Cucca, F.Collin, M.Minden, M.Campbell, P.Vassiliou, G. S.Fabre, M. A.Nangalia, J.Bonnet, D.Shlush, L.Laurenti, E.2025-10-08doi:10.1101/2025.10.08.679225Cold Spring Harbor Laboratory Press2025-10-08
<![CDATA[
Continuous evolution of a halogenase enzyme with improved solubility and activity for sustainable bioproduction
]]>
https://biorxiv.org/cgi/content/short/2025.10.08.681035v1?rss=1"
Pulschen, A. A.Booth, J.Satanowski, A.Soudy, C.Caro-Astorga, J.Ather, O.Patel, N.Alidoust, A.Aoudjane, S.Nematollahi, L.DeBenedictis, E.2025-10-08doi:10.1101/2025.10.08.681035Cold Spring Harbor Laboratory Press2025-10-08
<![CDATA[
Cell cycle oscillations in a polarity network facilitate state switching by morphogenetic cues
]]>
https://biorxiv.org/cgi/content/short/2025.10.12.681824v1?rss=1"
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]]>Ng, K.Sebaa, H.Hirani, N.Chizh, A.Messi, Z.Bland, T.Sugioka, K.Goehring, N. W.2025-10-13doi:10.1101/2025.10.12.681824Cold Spring Harbor Laboratory Press2025-10-13
<![CDATA[
Extensive and differential platinum chemotherapy mutagenesis in children
]]>
https://biorxiv.org/cgi/content/short/2025.10.12.681852v1?rss=1"
Wenger, A.Lee-Six, H.Dave, M.Layeghifard, M.Lawson, A. R. J.Abascal, F.Nicola, P. A.Treger, T. D.Ogbonnah, T.Parks, C.Oliver, T. R. W.Kennedy, J.Hodder, A.Anderson, N. D.Silva, F. L. T.Trinh, M. K.Dowe, T.Habarwaa, M.Sun, J. J.Assia-Zamora, S.Cortes-Cerisuelo, M.Jassem, W.Town, C.Dhawan, A.Jain, V.Straathof, K.Deheragoda, M.Martincorena, I.Palm, L.Hutchinson, J. C.Coorens, T. H. H.Trayers, C.Heaton, N.Shlien, A.Zen, Y.Rouhani, F. J.Behjati, S.2025-10-14doi:10.1101/2025.10.12.681852Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
Ecological cues orchestrate concerted courtship in a Drosophila host specialist
]]>
https://biorxiv.org/cgi/content/short/2025.10.13.681913v1?rss=1"
Brand, P.Keller, K.Coleman, R. T.Eghbali, N. B.Zylka, S.Prieto-Godino, L. L.Ruta, V.2025-10-14doi:10.1101/2025.10.13.681913Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
The origin and molecular evolution of the mammalian liver cell architecture
]]>
https://biorxiv.org/cgi/content/short/2025.10.14.682049v1?rss=1"
Yuan, X.Rodriguez-Montes, L.Zaremba, B.Trost, N.Schneider, C.Schmidt, J.Berki, B.Ibberson, D.Leushkin, E.Nickel, B.Palkovits, M.Truman, R. W.Barsh, G.Lees, J.Fallahshahroudi, A.Grützner, F.Tzika, A. C.Milinkovitch, M. C.Pääbo, S.Cardoso-Moreira, M.Kaessmann, H.2025-10-14doi:10.1101/2025.10.14.682049Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
The SNCA A53T mutation sensitizes human neurons and microglia to ferroptosis
]]>
https://biorxiv.org/cgi/content/short/2025.10.13.682089v1?rss=1"
Mahoney-Sanchez, L.Clarke-Lucas, H.Penverne, A.Evans, J. R.D'Sa, K.Strohbuecker, S.Lopex Garcia, P.Cosker, K.Soltic, D.O'Callaghan, B. J.Griffiths, A.Pintchovski, S. A.Plun-Favreau, H.Hallqvist, J.Mills, K.Gandhi, S.2025-10-14doi:10.1101/2025.10.13.682089Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
Autoantibody origins in lupus and in relapse post CAR-T therapy
]]>
https://biorxiv.org/cgi/content/short/2025.10.20.683393v1?rss=1"
Grenov, A.Yoon, J.Snell, D. M.Mikolajczak, A.Wang, H.Gurel, E.Rodriguez-Ronchel, A.Yegen, G.Lee, L.Artim Esen, B.Rahman, A.Maciocia, P.Vinuesa, C.2025-10-20doi:10.1101/2025.10.20.683393Cold Spring Harbor Laboratory Press2025-10-20
<![CDATA[
Inhibition of neutrophil degranulation by Nexinhib20 delays the development of radiation-induced pulmonary fibrosis
]]>
https://biorxiv.org/cgi/content/short/2025.10.22.684057v1?rss=1"
Ruhland, S.Nikolatou, K.Bridgeman, V. L.Rizou, T.Sahai, E.Bordoloi, J.Nolan, E.Elosegui-Artola, A.Malanchi, I.2025-10-23doi:10.1101/2025.10.22.684057Cold Spring Harbor Laboratory Press2025-10-23
<![CDATA[
Cancer-driven neutrophil priming couples systemic epithelial regenerative programs with pre-metastatic niche formation
]]>
https://biorxiv.org/cgi/content/short/2025.10.20.683483v1?rss=1"
Rabas, N.Bridgeman, V.Hennequart, M.Rodrigues, F. S.Farias, A.Ferreira, R. M. M.Axarlis, K.Nduka, O.Chakravarty, P.Legrave, N.Furlani, I.Malanchi, I.2025-10-21doi:10.1101/2025.10.20.683483Cold Spring Harbor Laboratory Press2025-10-21
<![CDATA[
Post-infection pig and ferret antisera show similar antigenic profiles for human influenza A(H1N1pdm09) viruses
]]>
https://biorxiv.org/cgi/content/short/2025.10.30.685573v1?rss=1"
Harvey, R.Cayol, T.Paudyal, B.Lilley, A.Carr, C.Hatton, C.Briggs, E.Daniels, R. S.Richardson, S.Peacock, T. P.Lewis, N. S.Brown, I.Mccauley, J.Tchilian, E.2025-10-31doi:10.1101/2025.10.30.685573Cold Spring Harbor Laboratory Press2025-10-31
<![CDATA[
Regulation of cell proliferation by a novel feedback system on Cdk function
]]>
https://biorxiv.org/cgi/content/short/2025.10.28.685054v1?rss=1"
Ryan, J. R.Leray, B.Jain, A.Coehlo, N.Domingo-Sananes, M. R.Aspert, T.Charvin, G.Krockenberger, M.Chica Blaguera, N.Lopez Aviles, S.Takacs, L.Uhlmann, F.Yang, L.Yue, J.-X.Liti, G.Cochard, V.Chevreux, G.Sugiyama, H.Goto, Y.Aoki, K.Wu, P.-Y. J.Mackereth, C. D.Tyson, J.Novak, B.Coudreuse, D.2025-10-29doi:10.1101/2025.10.28.685054Cold Spring Harbor Laboratory Press2025-10-29
<![CDATA[
Transcript-Capture sequencing enriches mRNA of Mycobacterium tuberculosis from host samples
]]>
https://biorxiv.org/cgi/content/short/2025.10.28.685133v1?rss=1"
200-fold increase in bacterial mRNA reads from mixed samples and allows analysis of the complete bacterial transcriptome from clinical samples. We apply Transcript-Capture to models of tuberculosis (TB) infection as well as sputum samples from TB patients. TB patients exhibit unexplained heterogeneity in disease progression, and the activity of Mycobacterium tuberculosis (Mtb) has been proposed to affect treatment response. By applying Transcript-Capture to sputum samples collected from TB patients we generate the first complete in vivo bacterial transcriptome of Mtb via NGS. Mtb from patient sputa shows upregulation of genes involved in host lipid utilization and zinc limitation, as well as a similar gene expression profile to Mtb log phase growth in vitro. Applying Transcript-Capture to clinical sputa provides a snapshot of bacterial activity directly from human patients and can be used to investigate the physiological state of bacteria surviving in vivo.
GRAPHICAL ABSTRACT
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/685133v1_ufig1.gif" ALT="Figure 1">
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]]>Lamont, E. I.Jones, R. M.Assadi, J.Morrison, R.Song, T.Yu, X.Wiener, D. M.Via, L. E.Winter, J.Ma, S. I.Wilkinson, R. J.Barry, C. E.Sherman, D. R.2025-10-28doi:10.1101/2025.10.28.685133Cold Spring Harbor Laboratory Press2025-10-28
<![CDATA[
Leveraging death of drug-sensitive cancer cells to promote immune-mediated bystander killing of subclones of drug-resistant tumor cells
]]>
https://biorxiv.org/cgi/content/short/2025.10.27.684825v1?rss=1"
Tomaschko, M.Ng, K.Moore, C.Pillsbury, C. E.Rana, S.Campbell, J.Mukherjee, S.Mikolajczak, A.Anastasiou, P.de Castro, A.Alonso de la Vega, A.de Carne Trecesson, S.Goehring, N.Molina-Arcas, M.Downward, J.2025-10-28doi:10.1101/2025.10.27.684825Cold Spring Harbor Laboratory Press2025-10-28
<![CDATA[
SERINC5 Is the Primary Target of Retroviral Antagonists Among Human SERINC Paralogs and Requires a Tri-Cysteine Motif for Its Counteraction by HIV-1 Nef
]]>
https://biorxiv.org/cgi/content/short/2025.10.27.684794v1?rss=1"
Bertelli, C.Rosa, A.Vanzo, T.Chande, A.Serwa, R.Tate, E. W.Cherepanov, P. P.Pizzato, M.2025-10-27doi:10.1101/2025.10.27.684794Cold Spring Harbor Laboratory Press2025-10-27
<![CDATA[
Multicellular Calcium Waves in Cancer-Associated Fibroblasts Regulate Neuronal Mimicry and Anisotropy Leading to Immune Exclusion
]]>
https://biorxiv.org/cgi/content/short/2025.10.23.684281v1?rss=1"
View larger version (35K):
org.highwire.dtl.DTLVardef@938ee5org.highwire.dtl.DTLVardef@18a9c48org.highwire.dtl.DTLVardef@11a5982org.highwire.dtl.DTLVardef@ea6a79_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Giangreco, G.Ramsden, Z.Rullan, A.Hooper, S.Novo, D.Castro, J. L.Chakravarty, P.Milan, M.Mohammadi, H.Llop, S.Juarez, M.Schneider-Luftman, D.Oliva, M.Alemany, L.Angelova, M.Olow, A.Yu, X.Hobson, P.Harrington, K. J.Sahai, E.2025-10-24doi:10.1101/2025.10.23.684281Cold Spring Harbor Laboratory Press2025-10-24
<![CDATA[
Cooperative and antagonistic interactions between sub-clones favour the co-existence of multiple resistance mechanisms in melanoma
]]>
https://biorxiv.org/cgi/content/short/2025.10.23.684170v1?rss=1"
Schlegelmilch, K.Hollek, V.Hooper, S.Giangreco, G.Bailey, S.Macfarlane, S.Carminati, A.Bowes, A.Strohbuecker, S.Fu, X.Sahai, E.2025-10-24doi:10.1101/2025.10.23.684170Cold Spring Harbor Laboratory Press2025-10-24
<![CDATA[
Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
]]>
https://biorxiv.org/cgi/content/short/2025.10.24.684328v1?rss=1"
Boezio, G. L. M.Depotter, J. R. L.Frith, T. J. R.Radley, A.Strohbuecker, S.Cunha, A. C.Howell, M.Briscoe, J.2025-10-24doi:10.1101/2025.10.24.684328Cold Spring Harbor Laboratory Press2025-10-24
<![CDATA[
Spillover of H5 influenza viruses to vampire bats at the marine-terrestrial interface
]]>
https://biorxiv.org/cgi/content/short/2025.11.09.686930v1?rss=1"
Tu, I.-T.Lynggaard, C.Adams, L.Walsh, S. K.Chen, H.Raveendran, S.Turnbull, M. L.Griffiths, M. E.Ribeiro, R.Perez, J. G.Bazan, W. V.Tello, C.Zariquiey, C.Rodriguez, K. P.Risco, M.Mamani, I. Q.Chavez, W.Villafuerte, R. Z.Manuttupa, J. C.Castro Namuche, J. P.Moreira-Soto, A.Drexler, J. F.Delhon, G.Faust, C.Cardenas-Alayza, S.Hutchinson, E.Murcia, P. R.Palmarini, M.Bohmann, K.Harvey, R.Streicker, D. G.2025-11-11doi:10.1101/2025.11.09.686930Cold Spring Harbor Laboratory Press2025-11-11
<![CDATA[
Inhibiting epithelial cell extrusion and inflammation synergistically reverses asthmatic airway remodelling
]]>
https://biorxiv.org/cgi/content/short/2025.11.10.687569v1?rss=1"
Bagley, D. C.Russell, T.Martinez-Nunez, R. T.Marcotti, S.Rosenblatt, J.2025-11-11doi:10.1101/2025.11.10.687569Cold Spring Harbor Laboratory Press2025-11-11
<![CDATA[
Topological defects drive influenza glycoprotein lattice assembly on spherical membranes
]]>
https://biorxiv.org/cgi/content/short/2025.11.06.686978v1?rss=1"
Liu, Z. B.Halldorsson, S.Calcraft, T.Calder, L. J.Rosenthal, P. B.2025-11-07doi:10.1101/2025.11.06.686978Cold Spring Harbor Laboratory Press2025-11-07
<![CDATA[
Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes
]]>
https://biorxiv.org/cgi/content/short/2025.11.06.686945v1?rss=1"
Gomez-Gil, E.Guerra, P.Gu, Y.Foo, S.Billard, B.Balogh, G.Peter, M.Oliferenko, S.2025-11-07doi:10.1101/2025.11.06.686945Cold Spring Harbor Laboratory Press2025-11-07
<![CDATA[
A structural and regulatory framework for Atg9-containing vesicle formation and their Atg1-dependent remodelling during autophagy initiation
]]>
https://biorxiv.org/cgi/content/short/2025.11.06.685569v1?rss=1"
Oeo-Santos, C.Knüpling, E.Davis, C.Meng, X.Maslen, S.Kunzelmann, S.D'Antuono, R.Olerinyova, A.Auchynnikava, T.Skehel, M.Schreiber, A.2025-11-06doi:10.1101/2025.11.06.685569Cold Spring Harbor Laboratory Press2025-11-06
<![CDATA[
PMGen: From Peptide-MHC Prediction to Neoantigen Generation
]]>
https://biorxiv.org/cgi/content/short/2025.11.14.688404v1?rss=1"
Asgary, A. H.Aleyasin, A.Mehl, J. A.Ludewig, B.Mishto, M.Liepe, J.Soeding, J.2025-11-14doi:10.1101/2025.11.14.688404Cold Spring Harbor Laboratory Press2025-11-14
<![CDATA[
Siglec-engaging immunosuppressive sialoglycans are upregulated in prostate cancer and are targetable to suppress bone metastasis
]]>
https://biorxiv.org/cgi/content/short/2025.11.12.687981v1?rss=1"
Peng, Z.Hodgson, K.Fisher, M.Mei, S.Orozco-Moreno, M.Cao, L.Kemp, M.Gatlin, W.Donald, L.Zeng, F.Lawson, M. A.Ungar, D.Sykes, D. B.Elliott, D. J.Peng, L.Schumann, B.Wang, N.Munkley, J.2025-11-13doi:10.1101/2025.11.12.687981Cold Spring Harbor Laboratory Press2025-11-13
<![CDATA[
Pathogenic Keratinocyte States and Fibroblast Niches Define the Tissue Microenvironment in Severe Hidradenitis Suppurativa
]]>
https://biorxiv.org/cgi/content/short/2025.11.11.682326v1?rss=1"
Du-Harpur, X.Ganier, C.Mazin, P.Cheshire, C.Rashidghamat, E.Luscombe, N. M.Lynch, M. D.Watt, F. M.2025-11-12doi:10.1101/2025.11.11.682326Cold Spring Harbor Laboratory Press2025-11-12
<![CDATA[
WNT inhibition primes the transcriptional landscape of mesoderm to initiate a phased ventricular cardiomyocyte specification programme
]]>
https://biorxiv.org/cgi/content/short/2025.11.11.687613v1?rss=1"
Velecela, V.Bassil, A.Fawcett, E.Smith, E.Konstantopoulos, D.Salmen, F.Bernardo, A. S.Hoppler, S. S.2025-11-12doi:10.1101/2025.11.11.687613Cold Spring Harbor Laboratory Press2025-11-12
<![CDATA[
PETRA: Prime editing of transcribed regulatory elements to assay expression
]]>
https://biorxiv.org/cgi/content/short/2025.11.18.689114v1?rss=1"
Reyes, M. A.Herger, M.Cubitt, L.Findlay, G. M.2025-11-18doi:10.1101/2025.11.18.689114Cold Spring Harbor Laboratory Press2025-11-18
<![CDATA[
Human airway epithelia clear rhinovirus-infected cells using two waves of cell extrusion
]]>
https://biorxiv.org/cgi/content/short/2025.11.18.689008v1?rss=1"
Fore, F.Bagley, D. C.Martinez-Nunez, R. T.Aniscenko, J.Johnston, S.Rosenblatt, J.2025-11-18doi:10.1101/2025.11.18.689008Cold Spring Harbor Laboratory Press2025-11-18
<![CDATA[
A divergent Plasmodium NEK4 acts as a key regulator driving the early events of meiosis
]]>
https://biorxiv.org/cgi/content/short/2025.11.21.689802v1?rss=1"
Yanase, R.Hair, M.Zeeshan, M.Ferguson, D. J. P.Brady, D.Pasquarello, C.Bottrill, A.Bhanvadia, S.Neal, A.Tromer, E. C.Le Roch, K. G.Hainard, A.Holder, A. A.Vaughan, S.Guttery, D. S.Tewari, R.2025-11-23doi:10.1101/2025.11.21.689802Cold Spring Harbor Laboratory Press2025-11-23
<![CDATA[
Rv3400 is a phosphoglucomutase required for trehalose metabolism in Mycobacterium tuberculosis
]]>
https://biorxiv.org/cgi/content/short/2025.11.20.689507v1?rss=1"
Liu, Y.Ruecker, N.Faulkner, V.Rachineni, K.Al-Saffar, N.VillacampaTeixeira, P.Dias da Costa, T.Johnson, E.Robertson, B. D.Ehrt, S.Larrouy-Maumus, G.2025-11-20doi:10.1101/2025.11.20.689507Cold Spring Harbor Laboratory Press2025-11-20
<![CDATA[
XIST Drives X-Chromosome Inactivation and Safeguards Female Extraembryonic Cells in Humans
]]>
https://biorxiv.org/cgi/content/short/2025.11.19.689206v1?rss=1"
Panda, A.Carrillo, L.Balaton, B. P.Brouillet, J.Nshemereirwe, S.Bonroy, J.Alfeghaly, C.Facchinello, R.Khodeer, S.Boers, R.Castel, G.London, C.Cazottes, E.Moscatelli, M.Tchinda, R. S.Pham, T. X. A.To, S. K.Allsop, R. N.Wang, Y.Staneva, D.Rugg-Gunn, P.Niakan, K.Gribnau, J.Ouimette, J.-F.Rougeulle, C.Pasque, V.2025-11-19doi:10.1101/2025.11.19.689206Cold Spring Harbor Laboratory Press2025-11-19
<![CDATA[
Oncogenic RAS activity is linked to immune priming and adenosine-driven immune evasion in lung adenocarcinoma
]]>
https://biorxiv.org/cgi/content/short/2025.11.25.690426v1?rss=1"
de Carne Trecesson, S.East, P.Pillsbury, C.Silva dos Santos, M.Cha, H.Colliver, E.Gilmore, T.Rana, S.Moore, C.Lighterness, S.Caswell, D. R.Boumelha, J.Tomaschko, M.Baer, R.Eyles, J.Teixeira, B.Saeed, M.Litchfield, K.Molina-Arcas, M.Lee, S.-H.MacRae, J.Hobson, P.Swanton, C.Downward, J.2025-11-26doi:10.1101/2025.11.25.690426Cold Spring Harbor Laboratory Press2025-11-26
<![CDATA[
SPIN90 modulates the architecture of lamellipodial actin in an ARPC5L dependent fashion.
]]>
https://biorxiv.org/cgi/content/short/2025.12.01.691495v1?rss=1"
Cao, L.Basant, A.Mladenov, M.Kogata, N.Jegou, A.Romet-Lemonne, G.Brasselet, S.Mavrakis, M.Way, M.2025-12-02doi:10.64898/2025.12.01.691495Cold Spring Harbor Laboratory Press2025-12-02
<![CDATA[
The ERCC6L2-MRI-KU complex coordinates NHEJ at staggered DNA double-strand breaks.
]]>
https://biorxiv.org/cgi/content/short/2025.11.28.691009v1?rss=1"
Reichl, P. I.Sonmez, C.Sun, Y.King, A.Davies, B.Wilkinson, A. C.Lottersberger, F.Chapman, J. R.2025-11-28doi:10.1101/2025.11.28.691009Cold Spring Harbor Laboratory Press2025-11-28
<![CDATA[
Tracking gene expression of single mitochondria in live neurons using nanotweezers
]]>
https://biorxiv.org/cgi/content/short/2025.12.10.693488v1?rss=1"
Sahota, A.Nadappuram, B.Allerton, S. C.Lesept, F.Howden, J.Claxton, S.Liu, Y.Aprile, F. A.Kittler, J.Devine, M. J.Edel, J.Ivanov, A.2025-12-13doi:10.64898/2025.12.10.693488Cold Spring Harbor Laboratory Press2025-12-13
<![CDATA[
PD-L2 Regulates Natural Antibody and IL-10 Secretion by B-1 cells
]]>
https://biorxiv.org/cgi/content/short/2025.12.11.693708v1?rss=1"
Amendt, T.Vanes, L.Tybulewicz, V.2025-12-14doi:10.64898/2025.12.11.693708Cold Spring Harbor Laboratory Press2025-12-14
<![CDATA[
Placental insufficiency causes fetal growth restriction in mice lacking Delta-like homologue 1
]]>
https://biorxiv.org/cgi/content/short/2025.12.16.694688v1?rss=1"
Charalambous, M.Vignola, M. L.Esse, R.Scagliotti, V.Servadei, C.Kardasz, D.Marinelli, E.Dent, C.2025-12-18doi:10.64898/2025.12.16.694688Cold Spring Harbor Laboratory Press2025-12-18
<![CDATA[
Mesodermal-specific MECP2 expression in Drosophila induces visceral and skeletal muscle defects rescued by butyrate supplementation
]]>
https://biorxiv.org/cgi/content/short/2025.12.16.694631v1?rss=1"
Consonni, G.Kozluca, M.Gagliani, M. C.Mineo, A.Cortese, K.Miguel-Aliaga, I.Vignoli, A.Borghi, E.Galeone, A.vaccari, t.2025-12-18doi:10.64898/2025.12.16.694631Cold Spring Harbor Laboratory Press2025-12-18
<![CDATA[
Capsid flexibility during Ty1 virus-like particle assembly
]]>
https://biorxiv.org/cgi/content/short/2025.12.17.694965v1?rss=1"
Sibert, B. S.Hannon-Hatfield, A.Nicastro, G.Cottee, M. A.Taylor, I. A.Garfinkel, D. J.Wright, E. R.2025-12-18doi:10.64898/2025.12.17.694965Cold Spring Harbor Laboratory Press2025-12-18
<![CDATA[
BATF3 controls the homeostatic maintenance and function of innate-like γδ T cells
]]>
https://biorxiv.org/cgi/content/short/2025.12.16.694583v1?rss=1"
Papotto, P. H.Hernandez-Garcia, E.Zarco-Cuadrillero, A.Redondo-Urzainqui, A.Parkinson, J. E.Pinheiro, R. G. R.MacDonald, A.Sancho, D.Silva-Santos, B.Allen, J. E.Hayday, A. C.Iborra, S.Munoz-Ruiz, M.2025-12-18doi:10.64898/2025.12.16.694583Cold Spring Harbor Laboratory Press2025-12-18
<![CDATA[
PKN2 regulates cell-junctions to limit colitis and colon tumour formation
]]>
https://biorxiv.org/cgi/content/short/2025.12.15.694339v1?rss=1"
Henry, J. C.Campbell, A. N.Huddar, P.Sewell, J.Menezes, S.Passman, A.Smith, K.McGauran, S.Lin, M.-L.Rosewell, I.Jansen, M.McDonald, N. Q.Graham, T. A.McDonald, S. A.Cameron, A. J.2025-12-17doi:10.64898/2025.12.15.694339Cold Spring Harbor Laboratory Press2025-12-17
<![CDATA[
Humanized Kcnv2 E151X Mouse Captures Hallmarks of KCNV2-Associated Retinal Dystrophy
]]>
https://biorxiv.org/cgi/content/short/2026.01.05.697593v1?rss=1"
Xhaferri, N.Biswas, S.Davies, B.Lindner, M.2026-01-05doi:10.64898/2026.01.05.697593Cold Spring Harbor Laboratory Press2026-01-05
<![CDATA[
Dlx2 reprograms the transcriptome and laminar position of glia-derivedAscl1-induced interneurons
]]>
https://biorxiv.org/cgi/content/short/2026.01.02.697435v1?rss=1"
Cooper, A.Garcia Mora, A.Herrera-Oropeza, G.Beltran Arranz, A.Marichal, N.Shi, Y.Leaman, S.Lozano Gonzalez, K.Strom, M.Fursham, H.Guillemot, F.Berninger, B.2026-01-02doi:10.64898/2026.01.02.697435Cold Spring Harbor Laboratory Press2026-01-02
<![CDATA[
Control of cellular cortical tension and shape by RhoGTPase signalling
]]>
https://biorxiv.org/cgi/content/short/2025.12.15.694413v1?rss=1"
Bohec, P.Khoromskaia, D.Kelkar, M.Ferber, E.Duprez, G.Lavoie, G.Valon, L.Roux, P. P.Salbreux, G.Charras, G.2025-12-17doi:10.64898/2025.12.15.694413Cold Spring Harbor Laboratory Press2025-12-17
<![CDATA[
The Structured RNA-binding Domains and Condensation Capacity of FUS Shape its RNA-binding Landscape and Function.
]]>
https://biorxiv.org/cgi/content/short/2026.01.12.699057v1?rss=1"
Jutzi, D.Alcalde, J.Hutten, S.Tiryaki, F.Davies, B.Plun-Favreau, H.Sibley, C.Dormann, D.Ruepp, M.-D.2026-01-12doi:10.64898/2026.01.12.699057Cold Spring Harbor Laboratory Press2026-01-12
<![CDATA[
Bro1-Mediated Trafficking Couples TOR Signalling to Cellular Metabolism and Longevity
]]>
https://biorxiv.org/cgi/content/short/2026.01.12.698986v1?rss=1"
Ng, K.Kumar, J.Dabrowska, A.Clemente-Ramos, J.Islam, R. A.Xintarakou, O.Freiwald, A.Barthel, N.Ludwig, D.Stamataki, D.Alao, J. P.Thorpe, P.Ralser, M.Mulleder, M.Mole, S. E.Rallis, C.2026-01-12doi:10.64898/2026.01.12.698986Cold Spring Harbor Laboratory Press2026-01-12
<![CDATA[
Genetic sex of enteric neurons enables ovarian relaxin togate maternal gut plasticity
]]>
https://biorxiv.org/cgi/content/short/2026.01.09.698651v1?rss=1"
Silva, B.Tsakani, E.De, J.Kontopoulos, A.Gaspar, P.Hiridjee, A.Rosselli, C.de Juan-Sanz, J.Campusano, J. M.Treiber, C. D.Waddell, S.Miguel-Aliaga, I.Hadjieconomou, D.2026-01-10doi:10.64898/2026.01.09.698651Cold Spring Harbor Laboratory Press2026-01-10
<![CDATA[
Iterative Bump-and-hole engineering creates a bioorthogonal reporter for N-acetylglucosaminyltransferase I
]]>
https://biorxiv.org/cgi/content/short/2026.01.16.699845v1?rss=1"
Liu, Y.Pieters, S.Bineva-Todd, G.Sagiroglugil, M.Burnap, S. A.Hoddle, F.Cioce, A.Ohara, A.Bruemmer, K.Bertozzi, C.Polizzi, K. M.Struwe, W. B.Rovira, C.Schumann, B.2026-01-17doi:10.64898/2026.01.16.699845Cold Spring Harbor Laboratory Press2026-01-17
<![CDATA[
SARS-CoV-2 membrane protein biogenesis
]]>
https://biorxiv.org/cgi/content/short/2026.01.19.700281v1?rss=1"
Ortiz Mateu, J.Pearson, G. J.Rius-Salvador, M.Sedighian, S.Pavlova, A.Alonso-Romero, J.Acosta-Caceres, J. M.Metola, A.Garcia-Murria, M. J.Skehel, J. M.Gumbart, J. C.Carlton, J. C.von Heijne, G.Sanchez-del Pino, M. M.Martinez-Gil, L.Mingarro, I.2026-01-20doi:10.64898/2026.01.19.700281Cold Spring Harbor Laboratory Press2026-01-20
<![CDATA[
Essential function reflected in the phylodynamics of a multigene family: the pir genes of malaria parasites
]]>
https://biorxiv.org/cgi/content/short/2026.01.23.697869v1?rss=1"
Jackson, A. P.Cunningham, D. A.Lin, L.Claro de Oliveira, N. M.Chevalley-Maurel, S. C.Pianta, G.Little, T. S.Mohring, F.Renfree, A. K.Moon, R. W.Langhorne, J. W.Janse, C. J.Franke-Fayard, B. M. D.van Ooij, C.2026-01-23doi:10.64898/2026.01.23.697869Cold Spring Harbor Laboratory Press2026-01-23
<![CDATA[
Ex vivo maturation of the malaria parasite egress protease SERA6 aids pathway dissection and inhibitor development.
]]>
https://biorxiv.org/cgi/content/short/2026.01.29.702321v1?rss=1"
Withers-Martinez, C.Taha, Z.Collins, C. R.Hackett, F.Tan, M. S.Soudy, C.Joshi, D.Redmond, J.Davies, B.Maslen, S.Skehel, M.George, R.Kjaer, S.Blackman, M. J.2026-01-29doi:10.64898/2026.01.29.702321Cold Spring Harbor Laboratory Press2026-01-29
<![CDATA[
ESFS: A Noise-Resilient Framework for Feature Selection and Marker Gene Discovery in Single-Cell Transcriptomics
]]>
https://biorxiv.org/cgi/content/short/2026.01.26.701684v1?rss=1"
Radley, A.Boezio, G.Shand, C.Perez-Carrasco, R.Briscoe, J.2026-01-27doi:10.64898/2026.01.26.701684Cold Spring Harbor Laboratory Press2026-01-27
<![CDATA[
Mapping the molecular landscape of the living brain: integrating spatial transcriptomics and qMRI
]]>
https://biorxiv.org/cgi/content/short/2025.09.24.678316v1?rss=1"
Grant-Peters, M.Thomas, G. E. C.Zarkali, A.Dobreva, I.Weil, R.Ryten, M.2025-09-25doi:10.1101/2025.09.24.678316Cold Spring Harbor Laboratory Press2025-09-25
<![CDATA[
Immune signatures of protection and progression in the airways of recent human tuberculosis household contacts
]]>
https://biorxiv.org/cgi/content/short/2026.01.29.702551v1?rss=1"
Branchett, W. J.Kim, J.-W.Shields, J.Chakravarty, P.Lee, J.Novsarka, I.Slawinski, H.Wilkinson, K. A.Wilkinson, R. J.Kamil, A.Verma, R.Haldar, P.O'Garra, A.2026-02-02doi:10.64898/2026.01.29.702551Cold Spring Harbor Laboratory Press2026-02-02
<![CDATA[
FluNexus: a versatile web platform for antigenic prediction and visualization of influenza A viruses
]]>
https://biorxiv.org/cgi/content/short/2026.01.29.702696v1?rss=1"
Li, X.Zhou, C.Wu, H.Xiao, K.Hao, J.Zhao, D.Zhu, J.Li, Y.Peng, J.Gu, J.Deng, G.Cai, W.Li, M.Liu, Y.Shang, X.Chen, H.Kong, H.2026-01-30doi:10.64898/2026.01.29.702696Cold Spring Harbor Laboratory Press2026-01-30
<![CDATA[
Targeting Myc activates a tissue-specific tumour resolution programme
]]>
https://biorxiv.org/cgi/content/short/2026.02.06.704498v1?rss=1"
Kortlever, R. M.Campos, T.Boeing, S.Uzwyshyn-Jones, K.Perfetto, A.Evan, G. I.2026-02-09doi:10.64898/2026.02.06.704498Cold Spring Harbor Laboratory Press2026-02-09
<![CDATA[
Position Dependent Feedback Drives Scaling and Robustness of Morphogen Gradients
]]>
https://biorxiv.org/cgi/content/short/2026.02.12.705497v1?rss=1"
Mosby, L. S.Hadjivasiliou, Z.2026-02-16doi:10.64898/2026.02.12.705497Cold Spring Harbor Laboratory Press2026-02-16
<![CDATA[
Emergence and antigenic characterisation of influenza A(H3N2) viruses with hemagglutinin substitutions N158K and K189R during the 2024/25 influenza season
]]>
https://biorxiv.org/cgi/content/short/2026.02.10.704996v1?rss=1"
Koel, B.Byrne, A.Turner, S.James, S.Harvey, R.Galiano, M.Carr, C.Lexmond, P.Pronk, M.Liang, R.Boons, G.-J.de Vries, R.Eggink, D.Lewis, N.Smith, D.Meijer, A.Fouchier, R.2026-02-10doi:10.64898/2026.02.10.704996Cold Spring Harbor Laboratory Press2026-02-10
<![CDATA[
Discrete genetic effects of VHL and PBRM1 inactivation co-operate to disrupt epithelial homeostasis and promote ccRCC
]]>
https://biorxiv.org/cgi/content/short/2026.02.18.706657v1?rss=1"
Kurlekar, S.Lima, J. D. C. C.Kupfer, N.Pugh, C. W.Mole, D. R.Adam, J.Ratcliffe, P. J.2026-02-20doi:10.64898/2026.02.18.706657Cold Spring Harbor Laboratory Press2026-02-20
<![CDATA[
Membrane lipid composition and endocytosis modulate Wingless release from secreting cells
]]>
https://biorxiv.org/cgi/content/short/2026.02.12.705585v1?rss=1"
Alvarez-Rodrigo, I.Alexandre, C.Lebarbachon, C.Borg, A.Finley, H.Arahouan, I.Zhao, Y.Di Pietro, F.Kjaer, S.Booth, P.Bauer, R.Jones, E. Y.Bellaiche, Y.Vincent, J.-P.Willnow, D.2026-02-18doi:10.64898/2026.02.12.705585Cold Spring Harbor Laboratory Press2026-02-18
<![CDATA[
Microglia Rank signaling regulates GnRH function and the Hypothalamic-Pituitary-Gonadal axis
]]>
https://biorxiv.org/cgi/content/short/2026.02.18.706528v1?rss=1"
Collado-Sole, A.Borjini, N.Zhai, J.Soria-Alcaide, G.Folgueira, C.Ruiz-Pino, F.Garcia Vilela, C.Lopez, V.Zouaghi, Y.Jacobs, A.Mora-Romero, B.Barranco, A.Yoldi, G.Rizzoti, K.Sabio, G.Perez-Chacon, G.G. Santamaria, P.Antonio Esteban, J.Pascual, A.Fernandez-Chacon, R.Tena-Sempere, M.Pitteloud, N.Gonzalez-Suarez, E.2026-02-18doi:10.64898/2026.02.18.706528Cold Spring Harbor Laboratory Press2026-02-18
<![CDATA[
Co-option of a mouse-specific retrotransposon rewires Ash2l isoform usage to prime developmental promoters
]]>
https://biorxiv.org/cgi/content/short/2026.02.25.707914v1?rss=1"
Elgood Hunt, E.Vivori, C.Mitter, R.Hannah Johnkingsly Jebaraj, J.Agnadottir, V.Delas, J.Serna Morales, E.Frith, T.Skehel, M.Elosegui-Artola, A.Briscoe, J.van Werven, F.2026-02-26doi:10.64898/2026.02.25.707914Cold Spring Harbor Laboratory Press2026-02-26
<![CDATA[
An injectable soft implant for long-acting, reversible, ultra-stable release of therapeutics
]]>
https://biorxiv.org/cgi/content/short/2026.02.25.707913v1?rss=1"
6 months) zero-order drug release from easily administered formulations is a key challenge in improving patient adherence and facilitating access. Herein, we report the design and development of an injectable, biodegradable, long-acting polymeric microparticle-embedded hydrogel platform for prolonged, zero-order release of therapeutics. This "soft implant" is injectable for ease of administration and can be retrieved via a small incision, allowing for discontinuation of therapy if desired. Central to the platform are surface-eroding poly(orthoester) (POE) microparticles, which were molecularly tailored to tune zero-order drug release across a wide range of timeframes. We demonstrate the clinical potential of the "soft implant" using levonorgestrel, a contraceptive agent requiring sustained dosing. In vitro, we observed zero-order release for 300 days, projected for >12 months, with behavior consistent with surface erosion further supported through Raman chemical mapping. In vivo studies confirmed zero-order release for six months, projected to 12 months, from a subcutaneous injection in rats. We envision that our platform could transform therapies that require long-term, regular drug dosing, significantly improving compliance and therapy outcomes.
]]>Stevens, M. M.Kütahya, C.Panariello, L.Najer, A.Rizou, T.Shamsabadi, A.Brachi, G.Peeler, D. J.Zharova, L.Fernandez Debets, T. F. F.Peschke, P.Constantinou, A. P.Xie, R.Cheng, Y.Burdis, R.Suarez-Bonnet, A.Cihova, M.Yeow, J.Schaufelberger, F.Malanchi, I.2026-02-26doi:10.64898/2026.02.25.707913Cold Spring Harbor Laboratory Press2026-02-26
<![CDATA[
iNeurons are sweet, maybe too sweet? Exploring the impact of media composition on PINK1-dependent mitophagy
]]>
https://biorxiv.org/cgi/content/short/2025.04.01.646648v1?rss=1"
O'Callaghan, B.Melandri, D.Soltic, D.Cosker, K.Soutar, M. P. M.Plun-Favreau, H.2025-04-03doi:10.1101/2025.04.01.646648Cold Spring Harbor Laboratory Press2025-04-03
<![CDATA[
Myc inhibition triggers GM-CSF-driven regression of pancreatic tumours
]]>
https://biorxiv.org/cgi/content/short/2026.02.24.707647v1?rss=1"
Campos, T.Kortlever, R. M.Sodir, N. M.Buck, M. D.Stockis, J.Parker, J.Lam, C. M.Patino-Mercau, J. R.Perfetto, A.Edwards, A.Stefan, B.Halim, T. Y.Gerard, E. I.2026-02-25doi:10.64898/2026.02.24.707647Cold Spring Harbor Laboratory Press2026-02-25
<![CDATA[
A stable subgenomic reporter coronavirus enables transcriptional profiling of bystander cells.
]]>
https://biorxiv.org/cgi/content/short/2026.02.27.708290v1?rss=1"
Gilbride, C.Hemsley-Taylor, J.Nunes, C.Penn, R.Boot, J.Pieris, N.Tripathy, R.Yang, Z.Hutchinson, M.Platt, O. K.Ulferts, R.Mitter, R.Strom, M.Santos, N. B.Bauer, D. L.Mears, H. V.2026-03-03doi:10.64898/2026.02.27.708290Cold Spring Harbor Laboratory Press2026-03-03
<![CDATA[
Contribution of cytotoxic CD8 T cells, neutrophils and type 1 interferon signaling to hyperinflammatory pathology in HIV associated TB meningitis
]]>
https://biorxiv.org/cgi/content/short/2026.03.10.710544v1?rss=1"
Barnacle, J. R.Bangani, N.Slawinski, H.Barrington, C.Wilkinson, K. A.Stek, C. J.Lai, R.Meintjes, G.Robertson, B. D.Gengenbacher, M.Davis, A. G.Barber, D. L.O'Garra, A.Wilkinson, R. J.2026-03-10doi:10.64898/2026.03.10.710544Cold Spring Harbor Laboratory Press2026-03-10
<![CDATA[
Meiotic cohesin Rec8 imposes fitness costs on fission yeast gametesfavoring the evolution of parental bias in gene expression
]]>
https://biorxiv.org/cgi/content/short/2026.03.07.710300v1?rss=1"
Martins, C.Booth, H.Salat Canela, C.Hadjivasiliou, Z.Vjestica, A.2026-03-08doi:10.64898/2026.03.07.710300Cold Spring Harbor Laboratory Press2026-03-08
<![CDATA[
A DNA foundation model predicts osteoporosis risk genes without proximity bias
]]>
https://biorxiv.org/cgi/content/short/2026.03.09.707383v1?rss=1"
Regep, C.Kapourani, C.-A.Sofyali, E.Dobrowolska, A.Loukas, G.Anighoro, A.Canale, E.Gross, T.Licciardello, M.Gupta, R.Maciuca, S.Desai, T.Del Vecchio, A.Field, C.Gemayel, K.Javer, A.Zhang, Z.Tsujikawa, R.Inoue, F.Hessel, E.Taylor-King, J.Whittaker, J.Roblin, D.McIntyre, R.Edwards, L.2026-03-12doi:10.64898/2026.03.09.707383Cold Spring Harbor Laboratory Press2026-03-12
<![CDATA[
The phosphoproteomic landscape of the neurological manifestations in tuberous sclerosis complex
]]>
https://biorxiv.org/cgi/content/short/2026.03.10.698104v1?rss=1"
Girodengo, M.Mihaylov, S. R.Klonowska, K.Mantoan Ritter, L.Flynn, H. R.Skehel, M.Bou Farhat, E.Aronica, E.White, M. A.Kwiatkowski, D.Ultanir, S. K.Bateman, J. M.2026-03-12doi:10.64898/2026.03.10.698104Cold Spring Harbor Laboratory Press2026-03-12
<![CDATA[
Inferring state-dependent functional circuit motifs using higher-order interactions analysis
]]>
https://biorxiv.org/cgi/content/short/2026.03.09.710501v1?rss=1"
Rashid Shomali, S.Rasuli, S. N.Shimazaki, H.Sadeh, S.2026-03-11doi:10.64898/2026.03.09.710501Cold Spring Harbor Laboratory Press2026-03-11
<![CDATA[
Myofibers drive postnatal myonuclear accretion through Arp2/3-dependent membrane protrusions
]]>
https://biorxiv.org/cgi/content/short/2026.03.22.713469v1?rss=1"
Sequeira, C.Di Francescantonio, S.Motta, G.Kogata, N.Way, M.Gomes, E. R.2026-03-23doi:10.64898/2026.03.22.713469Cold Spring Harbor Laboratory Press2026-03-23
<![CDATA[
The antipsychotic drug clozapine suppresses autoimmunity driving psychosis-like behavior in mice
]]>
https://biorxiv.org/cgi/content/short/2026.03.28.714971v1?rss=1"
He, L.Feldman, H.Nguyen, T.Bosc, M.Polisetty, V.Kriel, O.Landwehr, A.Borg, A.Subtil, F. T.Khakpour, M.Zhou, J.Kjaer, S.MacCabe, J.Pollak, T. A.Tremblay, M.-E.Vinuesa, C. G.Hayday, A.Schmack, K.2026-03-31doi:10.64898/2026.03.28.714971Cold Spring Harbor Laboratory Press2026-03-31
<![CDATA[
Natural statistics of host odours predict species-specific olfactory behaviours in Drosophilids
]]>
https://biorxiv.org/cgi/content/short/2026.03.27.714575v1?rss=1"
Gong, H.Ziolkowska, Z.Khallaf, M. A.Pop, S.Ayrton, O.Cano-Ferrer, X.MacRae, J.Knaden, M.Arguello, R.Prieto-Godino, L. L.2026-03-31doi:10.64898/2026.03.27.714575Cold Spring Harbor Laboratory Press2026-03-31
<![CDATA[
A genome-wide atlas of meiotic recombination intermediates reveals distinct modes of DNA repair that direct crossovers away from transcriptionally marked genes
]]>
https://biorxiv.org/cgi/content/short/2026.03.26.714455v1?rss=1"
Henfrey, C.Print, E.Zhang, G.Hinch, R.Maudlin, I.Moralli, D.Davies, B.Donnelly, P.Hinch, A. G.2026-03-28doi:10.64898/2026.03.26.714455Cold Spring Harbor Laboratory Press2026-03-28
<![CDATA[
Intravital imaging uncovers remodelling of humanised bone marrow-like niches
]]>
https://biorxiv.org/cgi/content/short/2026.03.24.713949v1?rss=1"
Ratcliffe, C. D. H.Mian, S. A.Giangreco, G.Le Marois, A.Habel, K.Sahai, E.Bonnet, D.2026-03-26doi:10.64898/2026.03.24.713949Cold Spring Harbor Laboratory Press2026-03-26
<![CDATA[
Distinct signaling center and progenitor identity dynamics initiate human forebrain patterning
]]>
https://biorxiv.org/cgi/content/short/2026.03.25.714146v1?rss=1"
Azizi, A.Fakhreddine, D.Hamid, F.Messi, Z.Strohbuecker, S.Guillemot, F.Houart, C.2026-03-25doi:10.64898/2026.03.25.714146Cold Spring Harbor Laboratory Press2026-03-25
<![CDATA[
Structures and molecular mechanisms of RAD54B in modulating homologous recombination
]]>
https://biorxiv.org/cgi/content/short/2026.03.22.713441v1?rss=1"
Liang, P.Tye, S.Ertl da Costa, J.Maharshi, N.Argunhan, B.Khulen, L.Battley, M.McCormack, E.Heyer, W.-D.Lobrich, M.Zhang, X.2026-03-24doi:10.64898/2026.03.22.713441Cold Spring Harbor Laboratory Press2026-03-24
<![CDATA[
Pro-domain-dependent folding and co-receptor-mediated targeting to optimize an antagonistic TGF-β monomer for gene-based delivery
]]>
https://biorxiv.org/cgi/content/short/2026.03.23.713733v1?rss=1"
Wieteska, L.Hinck, C. S.Mukundan, A.Krzysiak, T.van Dinther, M.Vantieghem, T.Maizels, R. M.ten Dijke, P.Hill, C. S.Hinck, A. P.2026-03-24doi:10.64898/2026.03.23.713733Cold Spring Harbor Laboratory Press2026-03-24
<![CDATA[
Diverse lung challenges elicit a conserved monocyte-to-macrophage differentiation blueprint
]]>
https://biorxiv.org/cgi/content/short/2026.03.15.711867v1?rss=1"
Iliakis, C.T'Jonck, W.Mouat, I. C.Bankole, S.Liang, J.Jones, G.-R.Kulikauskaite, J.Burgess, M. O.Janas, P.Crotta, S.Priestnall, S.Suarez-Bonnet, A.Schwarze, J.Wack, A.Bain, C. C.2026-03-17doi:10.64898/2026.03.15.711867Cold Spring Harbor Laboratory Press2026-03-17
<![CDATA[
Decomposing representational drift across wake and sleep
]]>
https://biorxiv.org/cgi/content/short/2026.03.31.715372v1?rss=1"
Harris, J. J.Schaefer, A. T.Kollo, M.2026-04-02doi:10.64898/2026.03.31.715372Cold Spring Harbor Laboratory Press2026-04-02
<![CDATA[
Plasmodium Protein Kinase 2 is required for ookinete to oocyst transition, and parasite transmission by the mosquito.
]]>
https://biorxiv.org/cgi/content/short/2026.03.27.714672v1?rss=1"
Pashley, S. L.Hair, M.Ukegbu, C. V.Zeeshan, M.Mishra, A.Brady, D.Vaughan, S.Pasquarello, C.Holder, A. A.Hainard, A.Guttery, D. S.Christophides, G. K.Vlachou, D.Sharma, P.Tewari, R.2026-04-02doi:10.64898/2026.03.27.714672Cold Spring Harbor Laboratory Press2026-04-02
<![CDATA[
CDKL5 phosphorylates neuronal ELAVL proteins to promote mRNA binding, protein synthesis and visual cortex development
]]>
https://biorxiv.org/cgi/content/short/2026.04.07.716766v1?rss=1"
Mihaylov, S. R.Lopes, A. T.Silvestre, M.Bianchini, G.Flynn, H. R.Huseynova, A.Strohbuecker, S.Griffith, L.Militti, C.Baltussen, L. L.Yuan, X.Morel, G.Claxton, S.Dempster, K.Lee, F. C. Y.Kanca, O.Köhn, M.Skehel, M.Ule, J.Iacaruso, F.Ultanir, S. K.2026-04-07doi:10.64898/2026.04.07.716766Cold Spring Harbor Laboratory Press2026-04-07
<![CDATA[
NucleoNet and DropNet: Generalist deep learning models for instance segmentation of nuclei and lipid droplets from electron microscopy images
]]>
https://biorxiv.org/cgi/content/short/2026.04.02.713930v1?rss=1"
Bhardwaj, A.Dell, C. W.Mikolaj, M. R.Spiers, H.Harned, A.Kuppusamy, B.Liu, P.Wei, D.Sterneck, E.Narayan, K.2026-04-05doi:10.64898/2026.04.02.713930Cold Spring Harbor Laboratory Press2026-04-05
<![CDATA[
BDNF Regulates Pituitary Stem Cell Engagement towards precursor state
]]>
https://biorxiv.org/cgi/content/short/2026.04.02.716194v1?rss=1"
Sochodolsky, K.Khetchoumian, K.Balsalobre, A.Feeley, R. M.Rice, M. E.Chakravarty, P.Lovell-Badge, R.Rizzoti, K.DROUIN, J.2026-04-04doi:10.64898/2026.04.02.716194Cold Spring Harbor Laboratory Press2026-04-04
<![CDATA[
Nonlinear mixed-effect models and tailored parametrization schemes enables integration of single cell and bulk data
]]>
https://biorxiv.org/cgi/content/short/2026.04.06.716803v1?rss=1"
Wang, D.Froehlich, F.Stapor, P.Schaelte, Y.Huth, M.Eils, R.Kallenberger, S.Hasenauer, J.2026-04-09doi:10.64898/2026.04.06.716803Cold Spring Harbor Laboratory Press2026-04-09