bioRxiv Channel: Chan Zuckerberg Biohub
https://biorxiv.org
This feed contains articles for bioRxiv Channel "Chan Zuckerberg Biohub"
bioRxivbioRxiv
https://biorxiv.org
<![CDATA[
T-cell receptor sequencing of early stage breast cancer tumors identifies altered clonal structure of the T-cell repertoire
]]>
https://biorxiv.org/cgi/content/short/172494v1?rss=1"
Beausang, J. F.Wheeler, A. J.Chan, N. H.Hanft, V. R.Dirbas, F. M.Jeffrey, S. S.Quake, S. R.2017-08-04doi:10.1101/172494Cold Spring Harbor Laboratory Press2017-08-04
<![CDATA[
Stochastic Simulation Of Dopamine Neuromodulation For Implementation Of Fluorescent Neurochemical Probes In The Striatal Extracellular Space
]]>
https://biorxiv.org/cgi/content/short/144436v1?rss=1"
Beyene, A.McFarlane, I. R.Pinals, R.Landry, M.2017-05-31doi:10.1101/144436Cold Spring Harbor Laboratory Press2017-05-31
<![CDATA[
Decoding directional genetic dependencies through orthogonal CRISPR/Cas screens
]]>
https://biorxiv.org/cgi/content/short/120170v1?rss=1"
Boettcher, M.Tian, R.Blau, J.Markegard, E.Wu, D.Biton, A.Zaitlen, N.McCormick, F.Kampmann, M.McManus, M. T.2017-03-25doi:10.1101/120170Cold Spring Harbor Laboratory Press2017-03-25
<![CDATA[
Directed evolution of TurboID for efficient proximity labeling in living cells and organisms
]]>
https://biorxiv.org/cgi/content/short/196980v1?rss=1"
Branon, T. C.Bosch, J. A.Sanchez, A. D.Udeshi, N. D.Svinkina, T.Carr, S. A.Feldman, J. L.Perrimon, N.Ting, A. Y.2017-10-02doi:10.1101/196980Cold Spring Harbor Laboratory Press2017-10-02
<![CDATA[
An Open-Source, Programmable Pneumatic Setup for Operation and Automated Control of Single- and Multi-Layer Microfluidic Devices
]]>
https://biorxiv.org/cgi/content/short/173468v1?rss=1"
Brower, K.Puccinelli, R.Markin, C.Shimko, T.Longwell, S.Cruz, B.Gomez-Sjoberg, R.Fordyce, P. M.2017-08-13doi:10.1101/173468Cold Spring Harbor Laboratory Press2017-08-13
<![CDATA[
Nonivasive prenatal diagnosis of single-gene disorders using droplet digital PCR
]]>
https://biorxiv.org/cgi/content/short/179804v1?rss=1"
Camunas-Soler, J.Lee, H.Hudgins, L.Hintz, S. R.Blumenfeld, Y. J.El-Sayed, Y. Y.Quake, S. R.2017-08-23doi:10.1101/179804Cold Spring Harbor Laboratory Press2017-08-23
<![CDATA[
Epigenetic maintenance of DNA methylation after evolutionary loss of the de novo methyltransferase
]]>
https://biorxiv.org/cgi/content/short/149385v1?rss=1"
50 MY through a process analogous to Darwinian evolution of the genome.
]]>Catania, S.Dumesic, P. A.Stoddard, C.Cooke, S.Burke, J.Cuomo, C. A.Narlikar, G. J.Madhani, H. D.2017-06-13doi:10.1101/149385Cold Spring Harbor Laboratory Press2017-06-13
<![CDATA[
The centrosomin CM2 domain is a multi-functional binding domain with distinct cell cycle roles
]]>
https://biorxiv.org/cgi/content/short/200204v1?rss=1"
Citron, Y. R.Fagerstrom, C. J.Keszthelyi, B.Huang, B.Rusan, N. M.Kelly, M. J. S.Agard, D. A.2017-10-10doi:10.1101/200204Cold Spring Harbor Laboratory Press2017-10-10
<![CDATA[
Theoretical quantification of interference in the TASEP: Application to mRNA translation shows near-optimality of termination rates
]]>
https://biorxiv.org/cgi/content/short/147017v1?rss=1"
Dao Duc, K.Saleem, Z. H.Song, Y. S.2017-06-07doi:10.1101/147017Cold Spring Harbor Laboratory Press2017-06-07
<![CDATA[
Dynamics Of The Human Antibody Repertoire Following B-cell Depletion In Systemic Sclerosis
]]>
https://biorxiv.org/cgi/content/short/139758v1?rss=1"
de Bourcy, C. F. A.Dekker, C. L.Davis, M. M.Nicolls, M. R.Quake, S. R.2017-05-18doi:10.1101/139758Cold Spring Harbor Laboratory Press2017-05-18
<![CDATA[
PhaMers identifies novel bacteriophage sequences from thermophilic hot springs
]]>
https://biorxiv.org/cgi/content/short/169672v1?rss=1"
Deaton, J.Yu, F.Quake, S.2017-07-28doi:10.1101/169672Cold Spring Harbor Laboratory Press2017-07-28
<![CDATA[
Molecular Recognition of Dopamine with Dual Near Infrared Excitation-Emission Two-Photon Microscopy
]]>
https://biorxiv.org/cgi/content/short/145912v1?rss=1"
Del Bonis-O'Donnell, J. T.Page, R. H.Beyene, A. G.Tindall, E. G.McFarlane, I. R.Landry, M. P.2017-06-04doi:10.1101/145912Cold Spring Harbor Laboratory Press2017-06-04
<![CDATA[
Nanoparticle-Guided Biomolecule Delivery for Transgene Expression and Gene Silencing in Mature Plants
]]>
https://biorxiv.org/cgi/content/short/179549v1?rss=1"
Demirer, G. S.Chang, R.Zhang, H.Chio, L.Landry, M. P.2017-08-22doi:10.1101/179549Cold Spring Harbor Laboratory Press2017-08-22
<![CDATA[
Metagenomic DNA sequencing for the diagnosis of intraocular infections
]]>
https://biorxiv.org/cgi/content/short/109686v1?rss=1"
Doan, T.Acharya, N.Pinsky, B.Sahoo, M.Chow, E.Banaei, N.Budvytiene, I.Cevallos, V.Zhong, L.Zhou, Z.Lietman, T.DeRisi, J. L.2017-02-18doi:10.1101/109686Cold Spring Harbor Laboratory Press2017-02-18
<![CDATA[
Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
]]>
https://biorxiv.org/cgi/content/short/108043v1?rss=1"
Enge, M.Arda, H. E.Mignardi, M.Beausang, J.Bottino, R.Kim, S. K.Quake, S. R.2017-02-13doi:10.1101/108043Cold Spring Harbor Laboratory Press2017-02-13
<![CDATA[
Improved Split Fluorescent Proteins For Endogenous Protein Labeling
]]>
https://biorxiv.org/cgi/content/short/137059v1?rss=1"
Feng, S.Sekine, S.Pessino, V.Li, H.Leonetti, M. D.Huang, B.2017-05-12doi:10.1101/137059Cold Spring Harbor Laboratory Press2017-05-12
<![CDATA[
Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress
]]>
https://biorxiv.org/cgi/content/short/179093v1?rss=1"
Gasch, A. P.Yu, F. B.Hose, J.Escalante, L. E.Place, M.Bacher, R.Kanbar, J.Ciobanu, D.Sandor, L.Grigoriev, I.Kendziorski, C.Quake, S. R.McClean, M. N.2017-08-21doi:10.1101/179093Cold Spring Harbor Laboratory Press2017-08-21
<![CDATA[
The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate butanol production and differentiation
]]>
https://biorxiv.org/cgi/content/short/139873v1?rss=1"
Herman, N.Kim, S.-J.Li, J. S.Cai, W.Koshino, H.Zhang, W.2017-05-18doi:10.1101/139873Cold Spring Harbor Laboratory Press2017-05-18
<![CDATA[
Signatures of Selection in the Human Antibody Repertoire: Selective Sweeps, Competing Subclones, and Neutral Drift
]]>
https://biorxiv.org/cgi/content/short/145052v1?rss=1"
Horns, F.Vollmers, C.Dekker, C. L.Quake, S. R.2017-10-19doi:10.1101/145052Cold Spring Harbor Laboratory Press2017-10-19
<![CDATA[
Quantius: Generic, high-fidelity human annotation of scientific images at 105-clicks-per-hour
]]>
https://biorxiv.org/cgi/content/short/164087v1?rss=1"
Hughes, A.Mornin, J. D.Biswas, S. K.Bauer, D. P.Bianco, S.Gartner, Z. J.2017-07-15doi:10.1101/164087Cold Spring Harbor Laboratory Press2017-07-15
<![CDATA[
A CRISPR-Cas9 Genome Engineering Platform in Primary CD4+ T Cells for the Interrogation of HIV Host Factors
]]>
https://biorxiv.org/cgi/content/short/205500v1?rss=1"
Hultquist, J. F.Hiatt, J.Schumann, K.McGregor, M. J.Roth, T. L.Haas, P.Doudna, J.Marson, A.Krogan, N. J.2017-10-19doi:10.1101/205500Cold Spring Harbor Laboratory Press2017-10-19
<![CDATA[
Structural Basis of Mitochondrial Receptor Binding and GTP Driven Conformational Constriction by Dynamin-Related Protein 1
]]>
https://biorxiv.org/cgi/content/short/172809v1?rss=1"
Kalia, R.Wang, R. Y.- R.Yusuf, A.Thomas, P. V.Agard, D. A.Shaw, J. M.Frost, A.2017-08-04doi:10.1101/172809Cold Spring Harbor Laboratory Press2017-08-04
<![CDATA[
Time-gated detection of protein-protein interactions with transcriptional readout
]]>
https://biorxiv.org/cgi/content/short/166462v1?rss=1"
100-fold enrichment of cells experiencing a specific GPCR-arrestin PPI during a short 10-minute light window over cells missing that PPI during the same time window. Due to its high specificity, sensitivity, and generality, PPI-FLARE should be a broadly useful tool for PPI analysis and discovery.
]]>Kim, M. W.Wang, W.Sanchez, M. I.Coukos, R.Von Zastrow, M.Ting, A.2017-07-21doi:10.1101/166462Cold Spring Harbor Laboratory Press2017-07-21
<![CDATA[
Humans are colonized by many uncharacterized and highly divergent microbes
]]>
https://biorxiv.org/cgi/content/short/113746v1?rss=1"
Kowarsky, M. A.Camunas-Soler, J.Kertesz, M.De Vlaminck, I.Koh, L. C. W.Pan, W.Martin, L.Neff, N.Okamoto, J.Wong, R. J.Kharbanda, S.El-Sayed, Y.Blumenfeld, Y.Stevenson, D. K.Shaw, G. M.Wolfe, N. D.Quake, S. R.2017-03-04doi:10.1101/113746Cold Spring Harbor Laboratory Press2017-03-04
<![CDATA[
Strain-Specific Human Natural Killer Cell Recognition of Influenza A Virus
]]>
https://biorxiv.org/cgi/content/short/148528v1?rss=1"
Kronstad, L. M.Seiler, C.Vergara, R.Holmes, S. P.Blish, C. A.2017-06-10doi:10.1101/148528Cold Spring Harbor Laboratory Press2017-06-10
<![CDATA[
Metagenomic Next-Generation Sequencing Detects Pulmonary Pathogens in Hematopoietic Cellular Transplant Patients with Acute Respiratory Illnesses
]]>
https://biorxiv.org/cgi/content/short/102798v1?rss=1"
Langelier, C.Zinter, M. S.Kalantar, K.Yank, G. A.Christenson, S.Odonovan, B.White, C.Wilson, M. R.Sapru, A.Dvorak, C. C.Miller, S.Chiu, C. Y.DeRisi, J. L.2017-01-24doi:10.1101/102798Cold Spring Harbor Laboratory Press2017-01-24
<![CDATA[
Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding
]]>
https://biorxiv.org/cgi/content/short/193904v1?rss=1"
Le, D. D.Shimko, T. C.Aditham, A. K.Keys, A. M.Orenstein, Y.Fordyce, P.2017-09-26doi:10.1101/193904Cold Spring Harbor Laboratory Press2017-09-26
<![CDATA[
Design and specificity of long ssDNA donors for CRISPR-based knock-in
]]>
https://biorxiv.org/cgi/content/short/178905v1?rss=1"
Li, H.Beckman, K. A.Pessino, V.Huang, B.Weissman, J. S.Leonetti, M. D.2017-08-21doi:10.1101/178905Cold Spring Harbor Laboratory Press2017-08-21
<![CDATA[
Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-cell RNA Sequencing
]]>
https://biorxiv.org/cgi/content/short/145045v1?rss=1"
Li, H.Horns, F.Wu, B.Xie, Q.Li, J.Li, T.Luginbuhl, D.Quake, S. R.Luo, L.2017-06-03doi:10.1101/145045Cold Spring Harbor Laboratory Press2017-06-03
<![CDATA[
Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans
]]>
https://biorxiv.org/cgi/content/short/155440v1?rss=1"
Luo, S.Yu, J. A.Li, H.Song, Y. S.2017-06-26doi:10.1101/155440Cold Spring Harbor Laboratory Press2017-06-26
<![CDATA[
Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting
]]>
https://biorxiv.org/cgi/content/short/139352v1?rss=1"
Mavor, D.Barlow, K.Asarnow, D.Birman, Y.Britain, D.Chen, W.Green, E. M.Kenner, L. R.Mensa, B.Morinishi, L. S.Nelson, C. A.Poss, E. M.Suresh, P.Tian, R.Arhar, T.Ary, B. E.Bauer, D. P.Bergman, I. D.Brunetti, R. M.Chio, C. M.Dai, S. A.Dickinson, M. S.Elledge, S.Hendel, N. L.Helsell, C. V. M.Kang, E.Kern, N.Khoroshkin, M. S.Kirkemo, L. L.Lewis, G. R.Lou, K.Marin, W. M.Maxwell, A. M.McTigue, P. F.Meyers-Turnbull, D.Nagy, T. L.Natale, A. M.Oltion, K.Pourmal, S.Reder, G. K.Rettko, N. J.Rohweder, P. J.Schwarz, D. M. C.2017-05-17doi:10.1101/139352Cold Spring Harbor Laboratory Press2017-05-17
<![CDATA[
Aberration-corrected high-NA open-top selective-plane illumination microscopy for biological imaging
]]>
https://biorxiv.org/cgi/content/short/140418v1?rss=1"
McGorty, R.Xie, D.Huang, B.2017-05-20doi:10.1101/140418Cold Spring Harbor Laboratory Press2017-05-20
<![CDATA[
Topical Silver Diamine Fluoride For Dental Caries Arrest In Preschool Children: A Randomized Controlled Trial
]]>
https://biorxiv.org/cgi/content/short/131870v1?rss=1"
Milgrom, P.Horst, J. A.Ludwig, S.Rothen, M.Chaffee, B. W.Lyalina, S.Pollard, K.DeRisi, J. L.Mancl, L.2017-04-29doi:10.1101/131870Cold Spring Harbor Laboratory Press2017-04-29
<![CDATA[
Light-Activated Cell Identification and Sorting (LACIS): A New Method to Identify and Select Edited Clones on a Microfluidic Device
]]>
https://biorxiv.org/cgi/content/short/204693v1?rss=1"
Mocciaro, A.Roth, T.Bennett, H.Soumillon, M.Shah, A.Hiatt, J.Chapman, K.Marson, A.Lavieu, G.2017-10-17doi:10.1101/204693Cold Spring Harbor Laboratory Press2017-10-17
<![CDATA[
Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements
]]>
https://biorxiv.org/cgi/content/short/178269v1?rss=1"
Mumbach, M. R.Satpathy, A. T.Boyle, E. A.Dai, C.Gowen, B. G.Cho, S. W.Nguyen, M. L.Rubin, A. J.Granja, J. M.Kazane, K. R.Wei, Y.Nguyen, T.Greenside, P. G.Corces, M. R.Tycko, J.Simeonov, D. R.Suliman, N.Li, R.Xu, J.Flynn, R. A.Kundaje, A.Khavari, P. A.Marson, A.Corn, J. E.Quertermous, T.Greenleaf, W. J.Chang, H. Y.2017-08-26doi:10.1101/178269Cold Spring Harbor Laboratory Press2017-08-26
<![CDATA[
CRISPulator: A Discrete Simulation Tool For Pooled Genetic Screens
]]>
https://biorxiv.org/cgi/content/short/119131v1?rss=1"
Nagy, T.Kampmann, M.2017-03-22doi:10.1101/119131Cold Spring Harbor Laboratory Press2017-03-22
<![CDATA[
Covalent Protein Labeling By SpyTag-SpyCatcher In Fixed Cells For Super-Resolution Microscopy
]]>
https://biorxiv.org/cgi/content/short/125013v1?rss=1"
Pessino, V.Citron, Y. R.Feng, S.Huang, B.2017-04-06doi:10.1101/125013Cold Spring Harbor Laboratory Press2017-04-06
<![CDATA[
Tau Internalization is Regulated by 6-O Sulfation on Heparan Sulfate Proteoglycans (HSPGs)
]]>
https://biorxiv.org/cgi/content/short/167874v1?rss=1"
Rauch, J.Chen, J. J.Sorum, A. W.Miller, G. M.Sharf, T.See, S. K.Hsieh-Wilson, L. C.Kampmann, M.Kosik, K. S.2017-07-24doi:10.1101/167874Cold Spring Harbor Laboratory Press2017-07-24
<![CDATA[
Correction of autoimmune IL2RA mutations in primary human T cells using non-viral genome targeting
]]>
https://biorxiv.org/cgi/content/short/183418v1?rss=1"
1 kilobase) DNA sequences at specific sites in the genomes of primary human T cells while preserving cell viability and function. We successfully tested the potential therapeutic use of this approach in two settings. First, we corrected a pathogenic IL2RA mutation in primary T cells from multiple family members with monogenic autoimmune disease and demonstrated enhanced signalling function. Second, we replaced the endogenous T cell receptor (TCR) locus with a new TCR redirecting T cells to a cancer antigen. The resulting TCR-engineered T cells specifically recognized the tumour antigen, with concomitant cytokine release and tumour cell killing. Taken together, these studies provide preclinical evidence that non-viral genome targeting will enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells.
]]>Roth, T. L.Yu, R.Shifrut, E.Hiatt, J.Li, H.Schumann, K.Tobin, V.Ferris, A. M.Chen, J.Schickel, J.-N.Pellerin, L.Carmody, D.Alkorta-Aranburu, G.Del Gaudio, D.Cho, M.Matsumoto, H.Morell, M.Mao, Y.Nguyen, D.Quadros, R.Gurumurthy, C.Smith, B.Haugwitz, M.Hughes, S. H.Weissman, J.May, A. P.Kupfer, G.Greeley, S.Bacchetta, R.Meffre, E.Roncarolo, M. G.Romberg, N.Herold, K. C.Leonetti, M. D.Marson, A.2017-08-31doi:10.1101/183418Cold Spring Harbor Laboratory Press2017-08-31
<![CDATA[
A correlation analysis framework for localization-based super-resolution microscopy
]]>
https://biorxiv.org/cgi/content/short/125005v1?rss=1"
Schnitzbauer, J.Wang, Y.Bakalar, M.Chen, B.Nuwal, T.Zhao, S.Huang, B.2017-06-23doi:10.1101/125005Cold Spring Harbor Laboratory Press2017-06-23
<![CDATA[
Silver microwires from treating tooth decay with silver diamine fluoride
]]>
https://biorxiv.org/cgi/content/short/152199v1?rss=1"
Seto, J.Horst, J. A.Parkinson, D. Y.Frachella, J. C.DeRisi, J. L.2017-06-19doi:10.1101/152199Cold Spring Harbor Laboratory Press2017-06-19
<![CDATA[
Super-Resolution Microscopy Reveals That Disruption Of Ciliary Transition Zone Architecture Is A Cause Of Joubert Syndrome
]]>
https://biorxiv.org/cgi/content/short/142042v1?rss=1"
Shi, X.Garcia, G.Van De Weghe, J. C.McGorty, R.Pazour, G. J.Doherty, D.Huang, B.Reiter, J. F.2017-05-25doi:10.1101/142042Cold Spring Harbor Laboratory Press2017-05-25
<![CDATA[
5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages
]]>
https://biorxiv.org/cgi/content/short/162081v1?rss=1"
Song, C.-X.Yin, S.Ma, L.Wheeler, A.Chen, Y.Zhang, Y.Liu, B.Xiong, J.Zhang, W.Hi, J.Zhou, Z.Dong, B.Tian, Z.Jeffrey, S. S.Chua, M.-S.So, S.Li, W.Wei, Y.Diao, J.Xie, D.Quake, S. R.2017-07-12doi:10.1101/162081Cold Spring Harbor Laboratory Press2017-07-12
<![CDATA[
Atg8 is essential specifically for an autophagy-independent function in apicoplast biogenesis in blood-stage malaria parasites
]]>
https://biorxiv.org/cgi/content/short/195578v1?rss=1"
Walczak, M.Ganesan, S. M.Niles, J. C.Yeh, E.2017-10-02doi:10.1101/195578Cold Spring Harbor Laboratory Press2017-10-02
<![CDATA[
Controller for microfluidic large-scale integration
]]>
https://biorxiv.org/cgi/content/short/188615v1?rss=1"
White, J.Streets, A. M.2017-09-14doi:10.1101/188615Cold Spring Harbor Laboratory Press2017-09-14
<![CDATA[
Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
]]>
https://biorxiv.org/cgi/content/short/114496v1?rss=1"
Yu, F.Blainey, P. C.Schulz, F.Woyke, T.Horowitz, M. A.Quake, S. R.2017-03-07doi:10.1101/114496Cold Spring Harbor Laboratory Press2017-03-07
<![CDATA[
Single-cell transcriptional dynamics of flavivirus infection
]]>
https://biorxiv.org/cgi/content/short/203331v1?rss=1"
Zanini, F.Pu, S.-Y.Bekerman, E.Einav, S.Quake, S. R.2017-10-14doi:10.1101/203331Cold Spring Harbor Laboratory Press2017-10-14
<![CDATA[
High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency
]]>
https://biorxiv.org/cgi/content/short/184135v1?rss=1"
Zviran, A.Mor, N.Rais, Y.Gingold, H.Peles, S.Chomsky, E.Viukov, S.Buenrostro, J. D.Weinberger, L.Manor, Y. S.Krupalnik, V.Zerbib, M.Hezroni, H.Jaitin, D. A.Larastiaso, D.Gilad, S.Benjamin, S.Mousa, A.Ayyash, M.Sheban, D.Bayerl, J.Aguilera Castrejon, A.Massarwa, R.Maza, I.Hanna, S.Amit, I.Stelzer, Y.Ulitsky, I.Greenleaf, W. J.Pilpel, Y.Novershtern, N.Hanna, J. H.2017-09-07doi:10.1101/184135Cold Spring Harbor Laboratory Press2017-09-07
<![CDATA[
The Human Cell Atlas
]]>
https://biorxiv.org/cgi/content/short/121202v1?rss=1"
Regev, A.Teichmann, S.Lander, E. S.Amit, I.Benoist, C.Birney, E.Bodenmiller, B.Campbell, P.Carninci, P.Clatworthy, M.Clevers, H.Deplancke, B.Dunham, I.Eberwine, J.Eils, R.Enard, W.Farmer, A.Fugger, L.Gottgens, B.Hacohen, N.Haniffa, M.Hemberg, M.Kim, S. K.Klenerman, P.Kriegstein, A.Lein, E.Linnarsson, S.Lundeberg, J.Majumder, P.Marioni, J.Merad, M.Mhlanga, M.Nawijn, M.Netea, M.Nolan, G.Pe'er, D.Philipakis, A.Ponting, C. P.Quake, S. R.Reik, W.Rozenblatt-Rosen, O.Sanes, J. R.Satija, R.Shumacher, T.Shalek, A. K2017-05-08doi:10.1101/121202Cold Spring Harbor Laboratory Press2017-05-08
<![CDATA[
Meta-analysis of massive parallel reporter assay enables functional regulatory elements prediction
]]>
https://biorxiv.org/cgi/content/short/202002v1?rss=1"
Kreimer, A.Yan, Z.Ahituv, N.Yosef, N.2017-10-11doi:10.1101/202002Cold Spring Harbor Laboratory Press2017-10-11
<![CDATA[
A Noninvasive Molecular Clock for Fetal Development Predicts Gestational Age and Preterm Delivery
]]>
https://biorxiv.org/cgi/content/short/212910v1?rss=1"
Ngo, T. T.Moufarrej, M. N.Rasmussen, M.-L. H.Camunas-Soler, J.Pan, W.Okamoto, J.Neff, N.Liu, K.Wong, R. J.Downes, K.Tibshirani, R.Shaw, G. M.Skotte, L.Stevenson, D. K.Biggio, J. R.Elovitz, M. A.Melbye, M.Quake, S. R.2017-11-01doi:10.1101/212910Cold Spring Harbor Laboratory Press2017-11-01
<![CDATA[
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
]]>
https://biorxiv.org/cgi/content/short/210955v1?rss=1"
Garud, N. R.Good, B. H.Hallatschek, O.Pollard, K. S.2017-10-30doi:10.1101/210955Cold Spring Harbor Laboratory Press2017-10-30
<![CDATA[
Metagenomics for chronic meningitis: clarifying interpretation and diagnosis
]]>
https://biorxiv.org/cgi/content/short/213561v1?rss=1"
Wilson, M. R.O'Donovan, B. D.Gelfand, J. M.Sample, H. A.Chow, F. C.Betjemann, J. P.Shah, M. P.Richie, M. B.Gorman, M. P.Hajj-Ali, R. A.Calabrese, L. H.Zorn, K. C.Greenlee, J. E.Blum, J. H.Green, G.Khan, L. M.Banerji, D.Langelier, C.Bryson-Cahn, C.Harrington, W.Lingappa, J. R.Shanbhag, N. M.Green, A. J.Brew, B. J.Soldatos, A.Strnad, L.Doernberg, S. B.Jay, C. A.Douglas, V.Josephson, S. A.DeRisi, J. L.2017-11-07doi:10.1101/213561Cold Spring Harbor Laboratory Press2017-11-07
<![CDATA[
Anti-phage islands force their target phage to directly mediate island excision and spread
]]>
https://biorxiv.org/cgi/content/short/218164v1?rss=1"
McKitterick, A. C.Seed, K.2017-11-11doi:10.1101/218164Cold Spring Harbor Laboratory Press2017-11-11
<![CDATA[
Flex ddG: Rosetta ensemble-based estimation of changes in protein-protein binding affinity upon mutation
]]>
https://biorxiv.org/cgi/content/short/221689v1?rss=1"
Barlow, K. A.O Conchuir, S.Thompson, S.Suresh, P.Lucas, J. E.Heinonen, M.Kortemme, T.2017-11-17doi:10.1101/221689Cold Spring Harbor Laboratory Press2017-11-17
<![CDATA[
Wide-field dynamic monitoring of immune cell trafficking in murine models of glioblastoma
]]>
https://biorxiv.org/cgi/content/short/220954v1?rss=1"
SoRelle, E. D.Yecies, D. W.Liba, O.Bennett, C. F.Graef, C.-M.Dutta, R.Mitra, S. S.Joubert, L.-M.Cheshier, S. H.Grant, G. A.de la Zerda, A.2017-11-17doi:10.1101/220954Cold Spring Harbor Laboratory Press2017-11-17
<![CDATA[
Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly
]]>
https://biorxiv.org/cgi/content/short/217968v1?rss=1"
Parsa, J.-Y.Boudoukha, S.Burke, J.Homer, C.Madhani, H.2017-11-11doi:10.1101/217968Cold Spring Harbor Laboratory Press2017-11-11
<![CDATA[
Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule
]]>
https://biorxiv.org/cgi/content/short/222257v1?rss=1"
Tsai, J. C.Miller-Vedam, L. E.Anand, A. A.Jaishankar, P.Nguyen, H. C.Renslo, A. R.Frost, A.Walter, P.2017-11-22doi:10.1101/222257Cold Spring Harbor Laboratory Press2017-11-22
<![CDATA[
Spliceosome profiling visualizes the operations of a dynamic RNP in vivo at nucleotide resolution
]]>
https://biorxiv.org/cgi/content/short/224170v1?rss=1"
Burke, J.Longhurst, A.Merkurjev, D.Sales-Lee, J.Rao, B.Moresco, J.Yates, J.Li, J. J.Madhani, H. D.2017-11-22doi:10.1101/224170Cold Spring Harbor Laboratory Press2017-11-22
<![CDATA[
Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans
]]>
https://biorxiv.org/cgi/content/short/227660v1?rss=1"
Steinrücken, M.Spence, J. P.Kamm, J. A.Wieczorek, E.Song, Y. S.2017-12-01doi:10.1101/227660Cold Spring Harbor Laboratory Press2017-12-01
<![CDATA[
Genetic architecture drives seasonal onset of hibernation in the 13-lined ground squirrel
]]>
https://biorxiv.org/cgi/content/short/222307v1?rss=1"
Grabek, K. R.Cooke, T. F.Epperson, L. E.Spees, K. K.Cabral, G. F.Sutton, S. C.Merriman, D. K.Martin, S. L.Bustamante, C. D.2017-12-02doi:10.1101/222307Cold Spring Harbor Laboratory Press2017-12-02
<![CDATA[
Spatial organization and dynamics of RNase E and ribosomes in Caulobacter crescentus
]]>
https://biorxiv.org/cgi/content/short/228122v1?rss=1"
Bayas, C. A.Wang, J.Lee, M. K.Schrader, J. M.Shapiro, L.Moerner, W. E.2017-12-03doi:10.1101/228122Cold Spring Harbor Laboratory Press2017-12-03
<![CDATA[
Combined aptamer and transcriptome sequencing of single cells
]]>
https://biorxiv.org/cgi/content/short/228338v1?rss=1"
Delley, C. L.Liu, L.Sarhan, M. F.Abate, A. R.2017-12-03doi:10.1101/228338Cold Spring Harbor Laboratory Press2017-12-03
<![CDATA[
Matrix-corrected mass spectrometry enables sensitive detection of food allergens and reveals widespread soy contamination of processed foods
]]>
https://biorxiv.org/cgi/content/short/231266v1?rss=1"
Croote, D.Braslavsky, I.Quake, S. R.2017-12-12doi:10.1101/231266Cold Spring Harbor Laboratory Press2017-12-12
<![CDATA[
Identification and quantitative analysis of the major determinants of translation elongation rate variation
]]>
https://biorxiv.org/cgi/content/short/090837v1?rss=1"
Dao Duc, K.Song, Y. S.2016-12-01doi:10.1101/090837Cold Spring Harbor Laboratory Press2016-12-01
<![CDATA[
Three-way clustering of multi-tissue multi-individual gene expression data using constrained tensor decomposition
]]>
https://biorxiv.org/cgi/content/short/229245v1?rss=1"
Wang, M.Fischer, J.Song, Y. S.2017-12-05doi:10.1101/229245Cold Spring Harbor Laboratory Press2017-12-05
<![CDATA[
Geometry of the sample frequency spectrum and the perils of demographic inference
]]>
https://biorxiv.org/cgi/content/short/233908v1?rss=1"
Rosen, Z.Bhaskar, A.Roch, S.Song, Y. S.2017-12-13doi:10.1101/233908Cold Spring Harbor Laboratory Press2017-12-13
<![CDATA[
Transcriptomic characterization of 20 organs and tissues from mouse at single cell resolution creates a Tabula Muris
]]>
https://biorxiv.org/cgi/content/short/237446v1?rss=1"
The Tabula Muris Consortium,Quake, S. R.Wyss-Coray, T.Darmanis, S.2017-12-20doi:10.1101/237446Cold Spring Harbor Laboratory Press2017-12-20
<![CDATA[
Phospho-signal flow from a pole-localized microdomain spatially patterns transcription factor activity
]]>
https://biorxiv.org/cgi/content/short/220293v1?rss=1"
Lasker, K.von Diezmann, A.Ahrens, D. G.Mann, T. H.Moerner, W. E.Shapiro, L.2017-12-20doi:10.1101/220293Cold Spring Harbor Laboratory Press2017-12-20
<![CDATA[
Upper Limit for Angular Compounding Speckle Reduction
]]>
https://biorxiv.org/cgi/content/short/239350v1?rss=1"
Winetraub, Y.Wu, C.Chu, S.de la Zerda, A.2017-12-24doi:10.1101/239350Cold Spring Harbor Laboratory Press2017-12-24
<![CDATA[
Identification of Pre-Existing Adaptive Immunity to Cas9 Proteins in Humans
]]>
https://biorxiv.org/cgi/content/short/243345v1?rss=1"
Charlesworth, C. T.Deshpande, P. S.Dever, D. P.Dejene, B.Gomez-Ospina, N.Mantri, S.Pavel-Dinu, M.Camarena, J.Weinberg, K. I.Porteus, M. H.2018-01-05doi:10.1101/243345Cold Spring Harbor Laboratory Press2018-01-05
<![CDATA[
Real time genetic compensation operationally defines the dynamic demands of feedback control
]]>
https://biorxiv.org/cgi/content/short/244020v1?rss=1"
Harrigan, P.Madhani, H.El-Samad, H.2018-01-07doi:10.1101/244020Cold Spring Harbor Laboratory Press2018-01-07
<![CDATA[
Size-dependent segregation controls macrophage phagocytosis of antibody-opsonized targets
]]>
https://biorxiv.org/cgi/content/short/250373v1?rss=1"
10 nm from the target surface. Increasing antigen height allows for co-localization of Fc receptors and the inhibitory phosphatase CD45 at the cell-cell interface, which reduces Fc receptor phosphorylation, and inhibits phagocytosis. Our work shows that close contact between macrophage and target cell is a requirement for efficient phagocytosis, suggesting that therapeutic antibodies should target short antigens in order to trigger Fc receptor activation through size-dependent physical segregation.
]]>Bakalar, M. H.Joffe, A. M.Schmid, E.Son, S.Podolski, M.Fletcher, D. A.2018-01-19doi:10.1101/250373Cold Spring Harbor Laboratory Press2018-01-19
<![CDATA[
High-resolution wide-field human brain tumor margin detection and in vivo murine neuroimaging
]]>
https://biorxiv.org/cgi/content/short/252080v1?rss=1"
Yecies, D.Liba, O.SoRelle, E.Dutta, R.Yuan, E.Vogel, H.Grant, G.de la Zerda, A.2018-01-22doi:10.1101/252080Cold Spring Harbor Laboratory Press2018-01-22
<![CDATA[
Complexity-Aware Simple Modeling
]]>
https://biorxiv.org/cgi/content/short/248419v1?rss=1"
nView larger version (28K):norg.highwire.dtl.DTLVardef@1cc6c8borg.highwire.dtl.DTLVardef@1ea1eb3org.highwire.dtl.DTLVardef@185a0b4org.highwire.dtl.DTLVardef@1f9c6b9_HPS_FORMAT_FIGEXP M_FIG Graphical abstractnnC_FIG
]]>Gomez-Schiavon, M.El-Samad, H.2018-01-16doi:10.1101/248419Cold Spring Harbor Laboratory Press2018-01-16
<![CDATA[
Modeling polypharmacy side effects with graph convolutional networks
]]>
https://biorxiv.org/cgi/content/short/258814v1?rss=1"
Zitnik, M.Agrawal, M.Leskovec, J.2018-02-02doi:10.1101/258814Cold Spring Harbor Laboratory Press2018-02-02
<![CDATA[
Activity of Antimicrobial Peptides Decreases with Increased Cell Membrane Crossing Free Energy Cost
]]>
https://biorxiv.org/cgi/content/short/258863v1?rss=1"
Zou, R.Zhu, X.Tu, Y.Wu, J.Landry, M. P.2018-02-01doi:10.1101/258863Cold Spring Harbor Laboratory Press2018-02-01
<![CDATA[
Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors
]]>
https://biorxiv.org/cgi/content/short/256313v1?rss=1"
Ryu, H.Inoue, F.Whalen, S.Williams, A.Kircher, M.Martin, B.Alvarado, B.Samee, M. A. H.Keough, K.Thomas, S.Kriegstein, A.Shendure, J.Pollen, A.Ahituv, N.Pollard, K.2018-01-29doi:10.1101/256313Cold Spring Harbor Laboratory Press2018-01-29
<![CDATA[
Gut microbiome transition across a lifestyle gradient in Himalaya
]]>
https://biorxiv.org/cgi/content/short/253450v1?rss=1"
nView larger version (108K):norg.highwire.dtl.DTLVardef@68f595org.highwire.dtl.DTLVardef@d33792org.highwire.dtl.DTLVardef@e56314org.highwire.dtl.DTLVardef@1cbbba2_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Jha, A. R.Davenport, E. R.Gautam, Y.Bhandari, D.Tandukar, S.Ng, K.Holmes, S.Gautam, G. P.Sherchand, J. B.Bustamante, C.Sonnenburg, J.2018-01-27doi:10.1101/253450Cold Spring Harbor Laboratory Press2018-01-27
<![CDATA[
Conservation of conformational dynamics across prokaryotic actins
]]>
https://biorxiv.org/cgi/content/short/260208v1?rss=1"
Ng, N.Shi, H.Colavin, A.Huang, K.2018-02-05doi:10.1101/260208Cold Spring Harbor Laboratory Press2018-02-05
<![CDATA[
Selection-free, high frequency genome editing by homologous recombination of human pluripotent stem cells using Cas9 RNP and AAV6
]]>
https://biorxiv.org/cgi/content/short/252163v1?rss=1"
Martin, R.Ikeda, K.Uchida, N.Cromer, M. K.Nishimura, T.Dever, D. P.Camarena, J.Bak, R.Lausten, A.Jakobsen, M. R.Wiebking, V.Sebastiano, V.Nakauchi, H.Porteus, M. H.2018-01-23doi:10.1101/252163Cold Spring Harbor Laboratory Press2018-01-23
<![CDATA[
A first-in-class inhibitor of parasite FtsH disrupts plastid biogenesis in human pathogens
]]>
https://biorxiv.org/cgi/content/short/108910v1?rss=1"
Amberg-Johnson, K.Ganesan, S. M.Lorenzi, H. A.Niles, J. C.Yeh, E.2017-02-15doi:10.1101/108910Cold Spring Harbor Laboratory Press2017-02-15
<![CDATA[
A Specific Non-Bisphosphonate Inhibitor Of The Bifunctional Farnesyl/Geranylgeranyl Diphosphate Synthase In Malaria Parasites
]]>
https://biorxiv.org/cgi/content/short/134338v1?rss=1"
Gisselberg, J. E.Herrera, Z.Orchard, L.Llinas, M.Yeh, E.2017-05-04doi:10.1101/134338Cold Spring Harbor Laboratory Press2017-05-04
<![CDATA[
Cell size regulation through tunable geometric localization of the bacterial actin cytoskeleton
]]>
https://biorxiv.org/cgi/content/short/229286v1?rss=1"
Colavin, A.Shi, H.Huang, K. C.2017-12-04doi:10.1101/229286Cold Spring Harbor Laboratory Press2017-12-04
<![CDATA[
NuMA Targets Dynein to Microtubule Minus-Ends at Mitosis
]]>
https://biorxiv.org/cgi/content/short/148692v1?rss=1"
Hueschen, C.Kenny, S. J.Xu, K.Dumont, S.2017-06-11doi:10.1101/148692Cold Spring Harbor Laboratory Press2017-06-11
<![CDATA[
Remodeling of ER-exit sites initiates a membrane supply pathway forautophagosome biogenesis
]]>
https://biorxiv.org/cgi/content/short/168518v1?rss=1"
Ge, L.Zhang, M.Kenny, S.Liu, D.Maeda, M.Saito, K.Marthur, A.Xu, K.Schekman, R.2017-07-25doi:10.1101/168518Cold Spring Harbor Laboratory Press2017-07-25
<![CDATA[
CRISPR-Tag: an Efficient DNA Tagging System in Living Cells
]]>
https://biorxiv.org/cgi/content/short/280495v1?rss=1"
Chen, B.Zou, W.Huang, B.2018-03-12doi:10.1101/280495Cold Spring Harbor Laboratory Press2018-03-12
<![CDATA[
The proteome of the malaria plastid organelle, a key anti-parasitic target
]]>
https://biorxiv.org/cgi/content/short/265967v1?rss=1"
Boucher, M. J.Ghosh, S.Zhang, L.Lal, A.Jang, S. W.Ju, A.Zhang, S.Wang, X.Ralph, S. A.Zou, J.Elias, J. E.Yeh, E.2018-02-14doi:10.1101/265967Cold Spring Harbor Laboratory Press2018-02-14
<![CDATA[
Ultra-fast cellular contractions in the epithelium of T. adhaerens and the "active cohesion" hypothesis
]]>
https://biorxiv.org/cgi/content/short/258103v1?rss=1"
Armon, S.Bull, M. S.Aranda-Diaz, A. J.Prakash, M.2018-02-16doi:10.1101/258103Cold Spring Harbor Laboratory Press2018-02-16
<![CDATA[
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks
]]>
https://biorxiv.org/cgi/content/short/267211v1?rss=1"
Chan, J.Perrone, V.Spence, J. P.Jenkins, P. A.Mathieson, S.Song, Y. S.2018-02-18doi:10.1101/267211Cold Spring Harbor Laboratory Press2018-02-18
<![CDATA[
Most regulatory interactions are not in linkage disequilibrium
]]>
https://biorxiv.org/cgi/content/short/272245v1?rss=1"
Whalen, S.Pollard, K. S.2018-02-26doi:10.1101/272245Cold Spring Harbor Laboratory Press2018-02-26
<![CDATA[
High Numerical Aperture Epi-illumination Selective Plane Illumination Microscopy
]]>
https://biorxiv.org/cgi/content/short/273359v1?rss=1"
1.06. We demonstrated multicolor and fast volumetric imaging of live cells and single-molecule super-resolution microscopy using our system.
]]>Yang, B.Wang, Y.Feng, S.Pessino, V.Stuurman, N.Huang, B.2018-02-28doi:10.1101/273359Cold Spring Harbor Laboratory Press2018-02-28
<![CDATA[
Robotic automation of droplet microfluidics
]]>
https://biorxiv.org/cgi/content/short/278556v1?rss=1"
Tran, T. M.Kim, S. C.Abate, A. R.2018-03-07doi:10.1101/278556Cold Spring Harbor Laboratory Press2018-03-07
<![CDATA[
Vms1p is a release factor for the Ribosome-associated Quality control Complex
]]>
https://biorxiv.org/cgi/content/short/301341v1?rss=1"
Rendon, O. Z.Fredrickson, E. K.Howard, C. J.Vranken, J. V.Fogarty, S.Tolley, N. D.Kalia, R.Osuna, B. A.Shen, P. S.Hill, C. P.Frost, A.Rutter, J.2018-04-14doi:10.1101/301341Cold Spring Harbor Laboratory Press2018-04-14
<![CDATA[
Taking sharper pictures of malaria with CAMERAs: Combined Antibodies to Measure Exposure Recency Assays
]]>
https://biorxiv.org/cgi/content/short/299446v1?rss=1"
Greenhouse, B.Smith, D. L.Rodriguez-Barraquer, I.Mueller, I.Drakeley, C.2018-04-11doi:10.1101/299446Cold Spring Harbor Laboratory Press2018-04-11
<![CDATA[
Cell cycle-controlled clearance of the CcrM DNA methyltransferase by Lon is dependent on DNA-facilitated proteolysis and substrate polar sequestration
]]>
https://biorxiv.org/cgi/content/short/293738v1?rss=1"
Zhou, X.Shapiro, L.2018-04-03doi:10.1101/293738Cold Spring Harbor Laboratory Press2018-04-03
<![CDATA[
Bayesian Inference for a Generative Model of Transcriptome Profiles from Single-cell RNA Sequencing
]]>
https://biorxiv.org/cgi/content/short/292037v1?rss=1"
Lopez, R.Regier, J.Cole, M. B.Jordan, M.Yosef, N.2018-03-30doi:10.1101/292037Cold Spring Harbor Laboratory Press2018-03-30
<![CDATA[
Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children
]]>
https://biorxiv.org/cgi/content/short/291864v1?rss=1"
Zinter, M. S.Dvorak, C. C.Mayday, M. Y.Iwanaga, K.Ly, N. P.McGarry, M. E.Church, G. D.Faricy, L. E.Rowan, C. M.Hume, J. R.Steiner, M. E.Crawford, E. D.Langelier, C.Kalantar, K.Chow, E. D.Miller, S.Shimano, K.Melton, A.Yanik, G. A.Sapru, A.DeRisi, J. L.2018-03-29doi:10.1101/291864Cold Spring Harbor Laboratory Press2018-03-29
<![CDATA[
Probing the Acyl Carrier Protein-Enzyme Interactions within Terminal Alkyne Biosynthetic Machinery
]]>
https://biorxiv.org/cgi/content/short/291195v1?rss=1"
Su, M.Zhu, X.Zhang, W.2018-03-29doi:10.1101/291195Cold Spring Harbor Laboratory Press2018-03-29
<![CDATA[
Asymmetrically Positioned Flagellar Control Units Regulate Human Sperm Rotation
]]>
https://biorxiv.org/cgi/content/short/290122v1?rss=1"
Miller, M.Kenny, S.Mannowetz, N.Mansell, S.Wojcik, M.Mendoza, S.Zucker, R.Xu, K.Lishko, P. V.2018-03-27doi:10.1101/290122Cold Spring Harbor Laboratory Press2018-03-27
<![CDATA[
Low-Cost Touchscreen Driven Programmable Dual Syringe Pump for Life Science Applications
]]>
https://biorxiv.org/cgi/content/short/288290v1?rss=1"
Garcia, V. E.Liu, J.DeRisi, J.2018-03-25doi:10.1101/288290Cold Spring Harbor Laboratory Press2018-03-25
<![CDATA[
Efficiently inferring the demographic history of many populations with allele count data
]]>
https://biorxiv.org/cgi/content/short/287268v1?rss=1"
Kamm, J. A.Terhorst, J.Durbin, R.Song, Y. S.2018-03-23doi:10.1101/287268Cold Spring Harbor Laboratory Press2018-03-23
<![CDATA[
Chromatin features constrain structural variation across evolutionary timescales
]]>
https://biorxiv.org/cgi/content/short/285205v1?rss=1"
Fudenberg, G.Pollard, K.2018-03-19doi:10.1101/285205Cold Spring Harbor Laboratory Press2018-03-19
<![CDATA[
Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection
]]>
https://biorxiv.org/cgi/content/short/284992v1?rss=1"
Zylberberg, M.Van Hemert, C.Handel, C. M.DeRisi, J.2018-03-19doi:10.1101/284992Cold Spring Harbor Laboratory Press2018-03-19
<![CDATA[
Oblique plane single-molecule localization microscopy for thick samples
]]>
https://biorxiv.org/cgi/content/short/289686v1?rss=1"
Kim, J.Wojcik, M.Wang, Y.Xu, K.Zhang, X.2018-03-27doi:10.1101/289686Cold Spring Harbor Laboratory Press2018-03-27
<![CDATA[
Discovering novel calcineurin inhibitors through quantitative mapping of protein-peptide affinity landscapes
]]>
https://biorxiv.org/cgi/content/short/306779v1?rss=1"
Nguyen, H. Q.Roy, J.Harink, B.Damle, N.Baxter, B.Brower, K.Kortemme, T.Thorn, K.Cyert, M.Fordyce, P. M.2018-04-23doi:10.1101/306779Cold Spring Harbor Laboratory Press2018-04-23
<![CDATA[
Particle-templated emulsification for microfluidics-free digital biology
]]>
https://biorxiv.org/cgi/content/short/304923v1?rss=1"
Hatori, M. N.Kim, S. C.Abate, A. R.2018-04-19doi:10.1101/304923Cold Spring Harbor Laboratory Press2018-04-19
<![CDATA[
Design and analysis of a Proportional-Integral-Derivative controller with biological molecules
]]>
https://biorxiv.org/cgi/content/short/303545v1?rss=1"
Chevalier, M.Gomez-Schiavon, M.Ng, A.El-Samad, H.2018-04-18doi:10.1101/303545Cold Spring Harbor Laboratory Press2018-04-18
<![CDATA[
Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California
]]>
https://biorxiv.org/cgi/content/short/301556v1?rss=1"
Retallack, H.Okihiro, M. S.Britton, E.Van Sommeran, S.DeRisi, J. L.2018-04-15doi:10.1101/301556Cold Spring Harbor Laboratory Press2018-04-15
<![CDATA[
Claudin-4 Reconstituted in Unilamellar Vesicles is Sufficient to Form Tight Interfaces that Partition Membrane Proteins
]]>
https://biorxiv.org/cgi/content/short/309856v1?rss=1"
Belardi, B.Son, S.Vahey, M. D.Wang, J.Hou, J.Fletcher, D. A.2018-04-27doi:10.1101/309856Cold Spring Harbor Laboratory Press2018-04-27
<![CDATA[
Isonitrile Formation by a Non-heme Iron(II)-dependent Oxidase/Decarboxylase
]]>
https://biorxiv.org/cgi/content/short/308460v1?rss=1"
Harris, N. C.Born, D. A.Cai, W.Huang, Y.Martin, J.Khalaf, R.Drennan, C. L.Zhang, W.2018-04-25doi:10.1101/308460Cold Spring Harbor Laboratory Press2018-04-25
<![CDATA[
High-throughput chromatin accessibility profiling at single-cell resolution
]]>
https://biorxiv.org/cgi/content/short/310284v1?rss=1"
Mezger, A.Klemm, S.Mann, I.Brower, K.Mir, A.Bostick, M.Farmer, A.Fordyce, P.Linnarsson, S.Greenleaf, W.2018-04-28doi:10.1101/310284Cold Spring Harbor Laboratory Press2018-04-28
<![CDATA[
Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period
]]>
https://biorxiv.org/cgi/content/short/313346v1?rss=1"
Angermeyer, A.Das, M. M.Singh, D. V.Seed, K. D.2018-05-02doi:10.1101/313346Cold Spring Harbor Laboratory Press2018-05-02
<![CDATA[
Prioritizing network communities
]]>
https://biorxiv.org/cgi/content/short/315903v1?rss=1"
Zitnik, M.Sosic, R.Leskovec, J.2018-05-07doi:10.1101/315903Cold Spring Harbor Laboratory Press2018-05-07
<![CDATA[
Network Enhancement: a general method to denoise weighted biological networks
]]>
https://biorxiv.org/cgi/content/short/317941v1?rss=1"
Wang, B.Pourshafeie, A.Zitnik, M.Zhu, J.Bustamante, C.Batzoglou, S.Leskovec, J.2018-05-09doi:10.1101/317941Cold Spring Harbor Laboratory Press2018-05-09
<![CDATA[
CDK19 is a Regulator of Triple-Negative Breast Cancer Growth
]]>
https://biorxiv.org/cgi/content/short/317776v1?rss=1"
Hsieh, R. W.Kuo, A. H.Scheeren, F. A.Zarnegar, M. A.Sikandar, S. S.Antony, J.Heitink, L. S.Periyakoil, D.Kalisky, T.Sim, S.Qian, D.Malhotra, S. V.Somlo, G.Dirbas, F. M.Jadhav, A.Newman, A. M.Clarke, M. F.2018-05-10doi:10.1101/317776Cold Spring Harbor Laboratory Press2018-05-10
<![CDATA[
Mobile-CRISPRi: Enabling Genetic Analysis of Diverse Bacteria
]]>
https://biorxiv.org/cgi/content/short/315499v1?rss=1"
Peters, J. M.Koo, B.-M.Patino, R.Heussler, G. E.Hearne, C. C.Inclan, Y.Hawkins, J. S.Lu, C. H. S.Harden, M. M.Osadnik, H.Peters, J. E.Engel, J. N.Dutton, R. J.Grossman, A. D.Gross, C. A.Rosenberg, O. S.2018-05-05doi:10.1101/315499Cold Spring Harbor Laboratory Press2018-05-05
<![CDATA[
Secretion of redox-active metabolites as a general strategy for iron acquisition in plants
]]>
https://biorxiv.org/cgi/content/short/168104v1?rss=1"
Rajniak, J.Giehl, R. F.Chang, E.Murgia, I.von Wiren, N.Sattely, E. S.2017-07-25doi:10.1101/168104Cold Spring Harbor Laboratory Press2017-07-25
<![CDATA[
N-hydroxy-pipecolic acid is a mobile signal that induces systemic disease resistance in Arabidopsis
]]>
https://biorxiv.org/cgi/content/short/288449v1?rss=1"
Chen, Y. C.Holmes, E.Rajniak, J.Kim, J.-G.Tang, S.Fischer, C.Mudgett, M. B.Sattely, E.2018-03-25doi:10.1101/288449Cold Spring Harbor Laboratory Press2018-03-25
<![CDATA[
Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics
]]>
https://biorxiv.org/cgi/content/short/128843v1?rss=1"
Street, K.Risso, D.Fletcher, R. B.Das, D.Ngai, J.Yosef, N.Purdom, E.Dudoit, S.2017-04-19doi:10.1101/128843Cold Spring Harbor Laboratory Press2017-04-19
<![CDATA[
Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq
]]>
https://biorxiv.org/cgi/content/short/235382v1?rss=1"
Cole, M. B.Risso, D.Wagner, A.DeTomaso, D.Ngai, J.Purdom, E.Dudoit, S.Yosef, N.2017-12-16doi:10.1101/235382Cold Spring Harbor Laboratory Press2017-12-16
<![CDATA[
Connectivity Problems on Heterogeneous Graphs
]]>
https://biorxiv.org/cgi/content/short/300012v1?rss=1"
0, and that this bound is tight. Moving beyond the worst case, we explore a special set of instances where the reference graph grows monotonically between conditions, and show that this problem admits substantially improved approximation algorithms. We also developed an integer linear programming solver for the general problem and demonstrate its ability to reach optimality with instances from the human protein interaction network.nnConclusionOur results demonstrate that in contrast to most connectivity problems studied in computational biology, accounting for multiplicity of biological conditions adds considerable complexity, which we propose to address with a new solver. Importantly, our results extend to several network connectivity problems that are commonly used in computational biology, such as Prize-Collecting Steiner Tree, and provide insight into the theoretical guarantees for their applications in a multiple condition setting.nnAvailabilityOur solver for the general condition Steiner network problem is available at https://github.com/YosefLab/condition_connectivity_problems
]]>Wu, J.Khodaverdian, A.Weitz, B.Yosef, N.2018-04-13doi:10.1101/300012Cold Spring Harbor Laboratory Press2018-04-13
<![CDATA[
Super-resolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact C. elegans tissue
]]>
https://biorxiv.org/cgi/content/short/112599v1?rss=1"
Kohler, S.Wojcik, M.Xu, K.Dernburg, A. F.2017-02-28doi:10.1101/112599Cold Spring Harbor Laboratory Press2017-02-28
<![CDATA[
Hsp90 dictates viral sequence space by balancing the evolutionary tradeoffs between protein stability, aggregation and translation rate
]]>
https://biorxiv.org/cgi/content/short/208462v1?rss=1"
Geller, R.Pechmann, S.Acevedo, A.Andino, R.Frydman, J.2017-10-24doi:10.1101/208462Cold Spring Harbor Laboratory Press2017-10-24
<![CDATA[
Therapeutic importance of timely immunophenotyping of breast cancer in a resource-constrained setting: a retrospective hospital-based cohort study
]]>
https://biorxiv.org/cgi/content/short/198721v1?rss=1"
Lopez Pineda, A.Rodriguez Moran, M. F.Alvarez Aguilar, C.Fuentes Valle, S. M.Acosta Rosales, R.Bustamante, C. D.2017-10-06doi:10.1101/198721Cold Spring Harbor Laboratory Press2017-10-06
<![CDATA[
Neolithization of North Africa involved the migration of people from both the Levant and Europe
]]>
https://biorxiv.org/cgi/content/short/191569v1?rss=1"
Fregel, R.Mendez, F. L.Bokbot, Y.Martin-Socas, D.Camalich-Massieu, M. D.Avila-Arcos, M. C.Underhill, P. A.Shapiro, B.Wojcik, G. L.Rasmussen, M.Soares, A. E. R.Kapp, J.Sockell, A.Rodriguez-Santos, F. J.Mikdad, A.Santana, J.Trujillo-Mederos, A.Bustamante, C. D.2017-09-21doi:10.1101/191569Cold Spring Harbor Laboratory Press2017-09-21
<![CDATA[
Genomic insights into the domestication of the chocolate tree, Theobroma cacao L.
]]>
https://biorxiv.org/cgi/content/short/223438v1?rss=1"
Cornejo, O. E.Yee, M.-C.Dominguez, V.Andrews, M.Sockell, A.Strandberg, E.Livingstone, D.Stack, C.Romero, A.Umaharan, P.Royaert, S.Tawari, N. R.Pauline, N.Schnell, R.Wilbert, P.Mockaitis, K.Bustamante, C. D.Motamayor, J. C.2017-11-22doi:10.1101/223438Cold Spring Harbor Laboratory Press2017-11-22
<![CDATA[
A high-density carbon fiber neural recording array technology
]]>
https://biorxiv.org/cgi/content/short/320937v1?rss=1"
Massey, T. L.Santacruz, S. R.Hou, J. F.Pister, K. S.Carmena, J. M.Maharbiz, M. M.2018-05-13doi:10.1101/320937Cold Spring Harbor Laboratory Press2018-05-13
<![CDATA[
Links between environment, diet, and the hunter-gatherer microbiome
]]>
https://biorxiv.org/cgi/content/short/319673v1?rss=1"
Fragiadakis, G. K.Smits, S. A.Sonnenburg, E. D.Van Treuren, W.Reid, G.Knight, R.Manjurano, A.Changalucha, J.Dominguez-Bello, M. G.Leach, J.Sonnenburg, J. L.2018-05-15doi:10.1101/319673Cold Spring Harbor Laboratory Press2018-05-15
<![CDATA[
Viral Taxonomy Derived From Evolutionary Genome Relationships
]]>
https://biorxiv.org/cgi/content/short/322511v1?rss=1"
Dougan, T.Quake, S. R.2018-05-15doi:10.1101/322511Cold Spring Harbor Laboratory Press2018-05-15
<![CDATA[
Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs
]]>
https://biorxiv.org/cgi/content/short/323105v1?rss=1"
10-fold dynamic range in response to two different small-molecule ligands. Since our system acts directly on each target-specific sgRNA, it enables new applications that require differential and opposing temporal control of multiple genes.
]]>Kundert, K.Lucas, J. E.Watters, K. E.Fellmann, C.Ng, A. H.Heineike, B. M.Fitzsimmons, C. M.Oakes, B. L.Savage, D. F.El-Samad, H.Doudna, J. A.Kortemme, T.2018-05-15doi:10.1101/323105Cold Spring Harbor Laboratory Press2018-05-15
<![CDATA[
Integration of cell cycle signals by multi-PAS domain kinases
]]>
https://biorxiv.org/cgi/content/short/323444v1?rss=1"
Mann, T. H.Shapiro, L.2018-05-16doi:10.1101/323444Cold Spring Harbor Laboratory Press2018-05-16
<![CDATA[
Gold Nanoprisms as Optical Coherence Tomography Contrast Agents in the Second Near Infrared Window for Enhanced Angiography in Live Animals
]]>
https://biorxiv.org/cgi/content/short/322545v1?rss=1"
Si, P.Yuan, E.Liba, O.Winetraub, Y.Yousefi, S.SoRelle, E.Yecies, D.Dutta, R.de la Zerda, A.2018-05-16doi:10.1101/322545Cold Spring Harbor Laboratory Press2018-05-16
<![CDATA[
Strain-level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes
]]>
https://biorxiv.org/cgi/content/short/324566v1?rss=1"
Olm, M. R.West, P. T.Brooks, B.Firek, B. A.Baker, R.Morowitz, M. J.Banfield, J. F.2018-05-17doi:10.1101/324566Cold Spring Harbor Laboratory Press2018-05-17
<![CDATA[
Human IgE producing B cells have a unique transcriptional program and generate high affinity, allergen-specific antibodies
]]>
https://biorxiv.org/cgi/content/short/327866v1?rss=1"
Croote, D.Darmanis, S.Nadeau, K. C.Quake, S. R.2018-05-22doi:10.1101/327866Cold Spring Harbor Laboratory Press2018-05-22
<![CDATA[
Evidence for Alternative Complement Cascade Activation in Primary CNS Vasculitis
]]>
https://biorxiv.org/cgi/content/short/329862v1?rss=1"
Mandel-Brehm, C.Retallack, H.Knudsen, G. M.Yamana, A.Hajj-Ali, R. A.Calabrese, L. H.Tihan, T.Sample, H. A.Zorn, K. C.Gorman, M. P.Madan Cohen, J.Sreih, A. G.Marcus, J. F.Josephson, S. A.Douglas, V. C.Gelfand, J. M.Wilson, M. R.DeRisi, J. L.2018-05-24doi:10.1101/329862Cold Spring Harbor Laboratory Press2018-05-24
<![CDATA[
Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria
]]>
https://biorxiv.org/cgi/content/short/328856v1?rss=1"
Matheus Carnevali, P. B.Schulz, F.Castelle, C. J.Kantor, R.Shih, P.Sharon, I.Santini, J.Olm, M.Amano, Y.Thomas, B. C.Anantharaman, K.Burstein, D.Becraft, E. D.Stepanauskas, R.Woyke, T.Banfield, J. F.2018-05-25doi:10.1101/328856Cold Spring Harbor Laboratory Press2018-05-25
<![CDATA[
Low fidelity assembly of influenza A virus promotes escape from host cells
]]>
https://biorxiv.org/cgi/content/short/332650v1?rss=1"
Vahey, M. D.Fletcher, D. A.2018-05-28doi:10.1101/332650Cold Spring Harbor Laboratory Press2018-05-28
<![CDATA[
Leveraging genetic variants for personalized and allele-specific sgRNA design
]]>
https://biorxiv.org/cgi/content/short/342923v1?rss=1"
2,500 human genomes to identify optimized pairs of sgRNAs that can be used for human therapeutic editing in large populations in the future.
]]>Keough, K. C.Lyalina, S.Olvera, M. P.Whalen, S.Conklin, B. R.Pollard, K. S.2018-06-08doi:10.1101/342923Cold Spring Harbor Laboratory Press2018-06-08
<![CDATA[
Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race
]]>
https://biorxiv.org/cgi/content/short/381962v1?rss=1"
McKitterick, A.LeGault, K.Angermeyer, A.Alam, M.Seed, K.2018-08-01doi:10.1101/381962Cold Spring Harbor Laboratory Press2018-08-01
<![CDATA[
Biological capacities clearly define a major subdivision in Domain Bacteria
]]>
https://biorxiv.org/cgi/content/short/335083v1?rss=1"
Meheust, R.Burstein, D.Castelle, C. J.Banfield, J. F.2018-05-30doi:10.1101/335083Cold Spring Harbor Laboratory Press2018-05-30
<![CDATA[
RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix
]]>
https://biorxiv.org/cgi/content/short/341107v1?rss=1"
1500 tertiary assemblies with differing helical sequences and compared calculations to independent measurements from a high-throughput experimental platform. The blind predictions accounted for thermodynamic effects from changing helix sequence and length with unexpectedly tight accuracies (RMSD of 0.34 and 0.77 kcal/mol, respectively). These comparisons lead to a detailed picture of how RNA base pair steps fluctuate within complex assemblies and suggest a new route toward predicting RNA tertiary structure formation and energetics.
]]>Yesselman, J. D.Denny, S. K.Bisaria, N.Herschlag, D.Greenleaf, W. J.Das, R.2018-06-06doi:10.1101/341107Cold Spring Harbor Laboratory Press2018-06-06
<![CDATA[
Repurposing the quinoline antibiotic nitroxoline to treat infections caused by the brain-eating amoeba Balamuthia mandrillaris
]]>
https://biorxiv.org/cgi/content/short/331785v1?rss=1"
Laurie, M. T.White, C. V.Retallack, H.Wu, W.Moser, M. S.Sakanari, J.Ang, K.Wilson, C.Arkin, M. R.DeRisi, J. L.2018-06-06doi:10.1101/331785Cold Spring Harbor Laboratory Press2018-06-06
<![CDATA[
Usp16 modulates Wnt signaling in primary tissues through Cdkn2a regulation
]]>
https://biorxiv.org/cgi/content/short/326272v1?rss=1"
Adorno, M.Nicolis di Robilant, B.Sikandar, S.Haro Acosta, V.Antony, J.Heller, C.Clarke, M.2018-06-08doi:10.1101/326272Cold Spring Harbor Laboratory Press2018-06-08
<![CDATA[
Integrating Host Response and Unbiased Microbe Detection for Lower Respiratory Tract Infection Diagnosis in Critically Ill Adults
]]>
https://biorxiv.org/cgi/content/short/341149v1?rss=1"
Langelier, C.Kalantar, K. L.Moazed, F.Wilson, M. R.Crawford, E.Deiss, T.Belzer, A.Bolourchi, S.Caldera, S.Fung, M.Jauregui, A.Malcolm, K.Lyden, A.Khan, L.Vessel, K.Quan, J.Zinter, M.Chiu, C. Y.Chow, E. D.Wilson, J.Miller, S.Matthay, M. A.Pollard, K. S.Christenson, S.Calfee, C. S.DeRisi, J. L.2018-06-11doi:10.1101/341149Cold Spring Harbor Laboratory Press2018-06-11
<![CDATA[
CD38 is a key regulator of enhanced NK cell immune responses during pregnancy through its role in immune synapse formation
]]>
https://biorxiv.org/cgi/content/short/349084v1?rss=1"
Le Gars, M.Seiler, C.Kay, A.Bayless, N.Starosvetsky, E.Moore, L.Shen-Orr, S.Aziz, N.Dekker, C.Khatri, P.Swan, G.Davis, M.Holmes, S.Blish, C.2018-06-16doi:10.1101/349084Cold Spring Harbor Laboratory Press2018-06-16
<![CDATA[
Single cell RNAseq provides a molecular and cellular cartography of changes to the human endometrium through the menstrual cycle
]]>
https://biorxiv.org/cgi/content/short/350538v1?rss=1"
Wang, W.Vilella, F.Moreno, I.Pan, W.Simon, C.Quake, S. R.2018-06-19doi:10.1101/350538Cold Spring Harbor Laboratory Press2018-06-19
<![CDATA[
Ultralarge Modulation of Single Wall Carbon Nanotube Fluorescence Mediated by Neuromodulators Adsorbed on Arrays of Oligonucleotide Rings
]]>
https://biorxiv.org/cgi/content/short/351627v1?rss=1"
Beyene, A. G.Alizadehmojarad, A. A.Dorlhiac, G.Streets, A. M.Kral, P.Vukovic, L.Landry, M. P.2018-06-20doi:10.1101/351627Cold Spring Harbor Laboratory Press2018-06-20
<![CDATA[
Megaphage infect Prevotella and variants are widespread in gut microbiomes
]]>
https://biorxiv.org/cgi/content/short/356790v1?rss=1"
540 kb in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phage. We refer to these as Lak phage. CRISPR spacer targeting indicates that the Lak phage infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed, and up to 35 putative tRNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in relative abundance of phage sub-populations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phage are widespread in gut communities that contain Prevotella species, especially in individuals in the developing world, and conclude that megaphage, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.
]]>Devoto, A. E.Santini, J. M.Olm, M. R.Anantharaman, K.Munk, P.Tung, J.Archie, E. A.Turnbaugh, P. J.Seed, K. D.Blekhman, R.Aarestrup, F. M.Thomas, B. C.Banfield, J. F.2018-06-27doi:10.1101/356790Cold Spring Harbor Laboratory Press2018-06-27
<![CDATA[
Differences in the path to exit the ribosome across the three domains of life
]]>
https://biorxiv.org/cgi/content/short/357970v1?rss=1"
Dao Duc, K.Batra, S. S.Bhattacharya, N.Cate, J. H. D.Song, Y. S.2018-06-28doi:10.1101/357970Cold Spring Harbor Laboratory Press2018-06-28
<![CDATA[
Imaging Striatal Dopamine Release Using a Non-Genetically Encoded Near-Infrared Fluorescent Catecholamine Nanosensor
]]>
https://biorxiv.org/cgi/content/short/356543v1?rss=1"
Beyene, A. G.Delevich, K.Del Bonis ODonnell, J. T.Piekarski, D. J.Lin, W. C.Thomas, A. W.Yang, S. J.Kosillo, P.Yang, D.Wilbrecht, L.Landry, M. P.2018-07-03doi:10.1101/356543Cold Spring Harbor Laboratory Press2018-07-03
<![CDATA[
Early transcriptional responses after dengue vaccination mirror the response to natural infection and predict neutralizing antibody titers
]]>
https://biorxiv.org/cgi/content/short/314377v1?rss=1"
200 versus 21 post-vaccination; 3,210 versus 286 transcripts with significant fold-change), but shared gene modules were induced in the same sequence. The abundance of 131 transcripts on days 8 and 9 post-vaccination was strongly correlated with NAb titers measured 6 weeks post-vaccination.nnConclusionsLAV dengue vaccination elicits early transcriptional responses that mirror those found in symptomatic natural infection and provide candidate early markers of protection against DENV infection.nnClinical Trial Registration Number: NCT00831012 (available at clinicaltrials.gov)nnSummary: Interferon- and cell cycle-associated gene transcript abundance levels in the peripheral blood of dengue vaccine recipients on days 8 and 9 post-vaccination were associated with dengue neutralizing antibody titers on day 42, and mirrored responses in primary dengue infection, suggesting the possibility of predicting protective immunity.
]]>Popper, S. J.Strouts, F. R.Lindow, J. C.Cheng, H. K.Montoya, M.Balmaseda, A.Durbin, A. P.Whitehead, S. S.Harris, E.Kirkpatrick, B. D.Relman, D. A.2018-05-06doi:10.1101/314377Cold Spring Harbor Laboratory Press2018-05-06
<![CDATA[
A smartphone-based tool for rapid, portable, and automated wide-field retinal imaging
]]>
https://biorxiv.org/cgi/content/short/364265v1?rss=1"
Kim, T.Myers, F.Reber, C.Loury, P.Loumou, P.Webster, D.Echanique, C.Li, P.Davila, J.Maamari, R.Switz, N.Keenan, J.Woodward, M.Paulus, Y.Margolis, T.Fletcher, D.2018-07-07doi:10.1101/364265Cold Spring Harbor Laboratory Press2018-07-07
<![CDATA[
Self-assembling Manifolds in Single-cell RNA Sequencing Data
]]>
https://biorxiv.org/cgi/content/short/364166v1?rss=1"
Tarashansky, A. J.Xue, Y.Quake, S. R.Wang, B.2018-07-07doi:10.1101/364166Cold Spring Harbor Laboratory Press2018-07-07
<![CDATA[
Smart bone plates can monitor fracture healing
]]>
https://biorxiv.org/cgi/content/short/366039v1?rss=1"
Lin, M. C.Hu, D.Marmor, M.Herfat, S. T.Bahney, C. S.Maharbiz, M. M.2018-07-10doi:10.1101/366039Cold Spring Harbor Laboratory Press2018-07-10
<![CDATA[
Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
]]>
https://biorxiv.org/cgi/content/short/266700v1?rss=1"
Goltsman, D. S. A.Sun, C. L.Proctor, D. M.DiGiulio, D. B.Robaczewska, A.Thomas, B. C.Shaw, G. M.Stevenson, D. K.Holmes, S. P.Banfield, J. F.Relman, D. A.2018-02-18doi:10.1101/266700Cold Spring Harbor Laboratory Press2018-02-18
<![CDATA[
Multi-omics analysis of AML cells treated with azacitidine reveals highly variable cell surface proteome remodeling
]]>
https://biorxiv.org/cgi/content/short/369322v1?rss=1"
Leung, K. K.Nguyen, A.Shi, T.Tang, L.Ni, X.Escoubet, L.MacBeth, K. J.DiMartino, J.Wells, J. A.2018-07-14doi:10.1101/369322Cold Spring Harbor Laboratory Press2018-07-14
<![CDATA[
High-resolution mapping of cancer cell networks using co-functional interactions
]]>
https://biorxiv.org/cgi/content/short/369751v1?rss=1"
300 whole genome CRISPR screens, we report ~1 million pairs of correlated "co-functional" genes that provide finer-scale information about cell compartments, biological pathways, and protein complexes than traditional gene sets. Lastly, we employed a gene community detection approach to implicate core genes for cancer growth and compress signal from functionally related genes in the same community into a single score. This work establishes new algorithms for probing cancer cell networks and motivates the acquisition of further CRISPR screen data across diverse genotypes and cell types to further resolve the complexity of cell signaling processes.
]]>Boyle, E. A.Pritchard, J. K.Greenleaf, W. J.2018-07-16doi:10.1101/369751Cold Spring Harbor Laboratory Press2018-07-16
<![CDATA[
Massively parallel characterization of regulatory dynamics during neural induction
]]>
https://biorxiv.org/cgi/content/short/370452v1?rss=1"
Inoue, F.Kreimer, A.Ashuach, T.Ahituv, N.Yosef, N.2018-07-16doi:10.1101/370452Cold Spring Harbor Laboratory Press2018-07-16
<![CDATA[
The Genetic Basis for the Cooperative Bioactivation of Plant Lignans by a Human Gut Bacterial Consortium
]]>
https://biorxiv.org/cgi/content/short/357640v1?rss=1"
Bess, E. N.Bisanz, J. E.Spanogiannopoulos, P.Ang, Q. Y.Bustion, A.Kitamura, S.Alba, D. L.Wolan, D. W.Koliwad, S. K.Turnbaugh, P. J.2018-06-27doi:10.1101/357640Cold Spring Harbor Laboratory Press2018-06-27
<![CDATA[
Live imaging of Aiptasia larvae, a model system for studying coral bleaching, using a simple microfluidic device
]]>
https://biorxiv.org/cgi/content/short/370478v1?rss=1"
10 hours. We visualized algal migration within Aiptasia larvae and observed algal expulsion under an environmental stressor. To our knowledge, this device is the first to enable live imaging of cnidarian larvae and their algal symbionts and, in further implementation, could provide important insights into the cellular mechanisms of coral bleaching under different environmental stressors. The device is simple to use, requires minimal external equipment and no specialized training to operate, and can easily be adapted to study a variety of large, motile organisms.
]]>Van Treuren, W.Brower, K.Labanieh, L.Hunt, D.Lensch, S.Cruz, B.Cartwright, H. N.Tran, C.Fordyce, P. M.2018-07-19doi:10.1101/370478Cold Spring Harbor Laboratory Press2018-07-19
<![CDATA[
DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors
]]>
https://biorxiv.org/cgi/content/short/352484v1?rss=1"
McGinnis, C. S.Murrow, L. M.Gartner, Z. J.2018-06-20doi:10.1101/352484Cold Spring Harbor Laboratory Press2018-06-20
<![CDATA[
Information-rich localization microscopy through machine learning
]]>
https://biorxiv.org/cgi/content/short/373878v1?rss=1"
Kim, T.Moon, S.Xu, K.2018-07-22doi:10.1101/373878Cold Spring Harbor Laboratory Press2018-07-22
<![CDATA[
A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota
]]>
https://biorxiv.org/cgi/content/short/375360v1?rss=1"
Kalantar, K.Moazed, F.Christenson, S.Wilson, J.Deiss, T.Belzer, A.Vessell, K.Jauregui, A.Boulourchi, S.DeRisi, J. L.Calfee, C.Langelier, C.2018-07-24doi:10.1101/375360Cold Spring Harbor Laboratory Press2018-07-24
<![CDATA[
SymSim: simulating multi-faceted variability in single cell RNA sequencing
]]>
https://biorxiv.org/cgi/content/short/378646v1?rss=1"
Zhang, X.Xu, C.Yosef, N.2018-07-28doi:10.1101/378646Cold Spring Harbor Laboratory Press2018-07-28
<![CDATA[
An actuated neural probe architecture for reducing gliosis-induced recording degradation
]]>
https://biorxiv.org/cgi/content/short/380006v1?rss=1"
Massey, T. L.Kuo, L. S.Fan, J. L.Maharbiz, M. M.2018-07-30doi:10.1101/380006Cold Spring Harbor Laboratory Press2018-07-30
<![CDATA[
Host cell metabolism contributes to delayed-death kinetics of apicoplast inhibitors in Toxoplasma gondii
]]>
https://biorxiv.org/cgi/content/short/384123v1?rss=1"
Amberg-Johnson, K.Yeh, E.2018-08-03doi:10.1101/384123Cold Spring Harbor Laboratory Press2018-08-03
<![CDATA[
Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function
]]>
https://biorxiv.org/cgi/content/short/384776v1?rss=1"
Shifrut, E.Carnevale, J.Tobin, V.Roth, T. L.Woo, J. M.Bui, C.Li, P. J.Diolaiti, M.Ashworth, A.Marson, A.2018-08-03doi:10.1101/384776Cold Spring Harbor Laboratory Press2018-08-03
<![CDATA[
Etiology of fever in Ugandan children: identification of microbial pathogens using metagenomic next-generation sequencing and IDseq, a platform for unbiased metagenomic analysis
]]>
https://biorxiv.org/cgi/content/short/385005v1?rss=1"
Ramesh, A.Nakielny, S.Hsu, J.Kyohere, M.Byaruhanga, O.de Bourcy, C.Egger, R.Dimitrov, B.Juan, Y.-F.Sheu, J.Wang, J.Kalantar, K.Langelier, C.Ruel, T.Mpimbaza, A.Wilson, M. R.Rosenthal, P. J.DeRisi, J. L.2018-08-04doi:10.1101/385005Cold Spring Harbor Laboratory Press2018-08-04
<![CDATA[
The ESCRT-III proteins IST1 and CHMP1B assemble around nucleic acids
]]>
https://biorxiv.org/cgi/content/short/386532v1?rss=1"
Talledge, N.McCullough, J.Wenzel, D.Nguyen, H. C.Lalonde, M. S.Bajorek, M.Skalicky, J.Frost, A.Sundquist, W. I.2018-08-07doi:10.1101/386532Cold Spring Harbor Laboratory Press2018-08-07
<![CDATA[
MULTI-seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
]]>
https://biorxiv.org/cgi/content/short/387241v1?rss=1"
McGinnis, C. S.Patterson, D. M.Winkler, J.Hein, M. Y.Srivastava, V.Conrad, D. N.Murrow, L. M.Weissman, J. S.Werb, Z.Chow, E. D.Gartner, Z. J.2018-08-08doi:10.1101/387241Cold Spring Harbor Laboratory Press2018-08-08
<![CDATA[
Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection
]]>
https://biorxiv.org/cgi/content/short/388181v1?rss=1"
Zanini, F.Robinson, M.Croote, D.Sahoo, M. K.Sanz, A. M.Ortiz-Lasso, E.Albornoz, L. L.Suarez, F. R.Montoya, J. G.Pinsky, B. A.Quake, S.Einav, S.2018-08-09doi:10.1101/388181Cold Spring Harbor Laboratory Press2018-08-09
<![CDATA[
Lateral gene transfer shapes the distribution of RuBisCO among Candidate Phyla Radiation bacteria and DPANN archaea
]]>
https://biorxiv.org/cgi/content/short/386292v1?rss=1"
Jaffe, A. L.Castelle, C. J.Dupont, C. L.Banfield, J. F.2018-08-07doi:10.1101/386292Cold Spring Harbor Laboratory Press2018-08-07
<![CDATA[
Reconstructing B cell receptor sequences from short-read single cell RNA-sequencing with BRAPeS
]]>
https://biorxiv.org/cgi/content/short/389999v1?rss=1"
Afik, S.Yosef, N.2018-08-10doi:10.1101/389999Cold Spring Harbor Laboratory Press2018-08-10
<![CDATA[
Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens
]]>
https://biorxiv.org/cgi/content/short/391417v1?rss=1"
Berghuis, B. A.Yu, F. B.Schulz, F.Blainey, P. C.Woyke, T.Quake, S.2018-08-14doi:10.1101/391417Cold Spring Harbor Laboratory Press2018-08-14
<![CDATA[
Modeling Spatial Correlation of Transcripts With Application to Developing Pancreas
]]>
https://biorxiv.org/cgi/content/short/391433v1?rss=1"
Liu, R.Mignardi, M.Jones, R.Enge, M.Kim, S. K.Quake, S. R.Zou, J.2018-08-14doi:10.1101/391433Cold Spring Harbor Laboratory Press2018-08-14
<![CDATA[
Systematic characterization of genome editing in primary T cells reveals proximal genomic insertions and enables machine learning prediction of CRISPR-Cas9 DNA repair outcomes
]]>
https://biorxiv.org/cgi/content/short/404947v1?rss=1"
Leenay, R. T.Aghazadeh, A.Hiatt, J.Tse, D.Hulquist, J.Krogan, N.Wu, Z.Marson, A.May, A. P.Zou, J.2018-08-31doi:10.1101/404947Cold Spring Harbor Laboratory Press2018-08-31
<![CDATA[
Local membrane charge regulates β2 adrenergic receptor coupling to Gi
]]>
https://biorxiv.org/cgi/content/short/400408v1?rss=1"
Strohman, M. J.Maeda, S.Hilger, D.Masureel, M.Du, Y.Kobilka, B. K.2018-08-25doi:10.1101/400408Cold Spring Harbor Laboratory Press2018-08-25
<![CDATA[
Depletion of microbiome-derived molecules in the host using Clostridium genetics
]]>
https://biorxiv.org/cgi/content/short/401489v1?rss=1"
Guo, C.-J.Allen, B.Hiam, K.Dodd, D.van Treuren, W.Higginbottom, S.Fischer, C.Sonnenburg, J.Spitzer, M.Fischbach, M.2018-08-27doi:10.1101/401489Cold Spring Harbor Laboratory Press2018-08-27
<![CDATA[
A mutagenesis screen for essential plastid biogenesis genes in human malaria parasites
]]>
https://biorxiv.org/cgi/content/short/401570v1?rss=1"
Tang, Y.Meister, T. R.Walczak, M.Pulkoski-Gross, M.Hari, S. B.Sauer, R. T.Amberg-Johnson, K.Yeh, E.2018-08-27doi:10.1101/401570Cold Spring Harbor Laboratory Press2018-08-27
<![CDATA[
An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs)
]]>
https://biorxiv.org/cgi/content/short/402560v1?rss=1"
Harink, B.Nguyen, H.Thorn, K.Fordyce, P.2018-08-28doi:10.1101/402560Cold Spring Harbor Laboratory Press2018-08-28
<![CDATA[
Single-cell transcriptomics identifies drivers of local inflammation in multiple sclerosis
]]>
https://biorxiv.org/cgi/content/short/403527v1?rss=1"
Schafflick, D.Cole, M.Hartlehnert, M.Lautwein, T.Buscher, K.Wolbert, J.Meuth, S. G.Stettner, M.Kleinschnitz, C.Kuhlmann, T.Gross, C. C.Wiendl, H.Yosef, N.Meyer zu Horste, G.2018-08-29doi:10.1101/403527Cold Spring Harbor Laboratory Press2018-08-29
<![CDATA[
Functional Interpretation of Single-Cell Similarity Maps
]]>
https://biorxiv.org/cgi/content/short/403055v1?rss=1"
DeTomaso, D.Jones, M.Subramaniam, M.Ashuach, T.Ye, C. J.Yosef, N.2018-08-29doi:10.1101/403055Cold Spring Harbor Laboratory Press2018-08-29
<![CDATA[
FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences
]]>
https://biorxiv.org/cgi/content/short/426338v1?rss=1"
Quan, J.Langelier, C.Kuchta, A.Batson, J.Teyssier, N.Lyden, A.Caldera, S.McGeever, A.Dimitrov, B.King, R.Wilheim, J.Murphy, M.Pesce Ares, L.Travisano, K. A.Sit, R.Amato, R.Mumbengegwi, D. R.Smith, J. L.Bennett, A.Gosling, R.Mourani, P. M.Calfee, C. S.Neff, N. F.Chow, E. D.Kim, P. S.Greenhouse, B.DeRisi, J. L.Crawford, E. D.2018-09-27doi:10.1101/426338Cold Spring Harbor Laboratory Press2018-09-27
<![CDATA[
Printed Droplet Microfluidics for on demand dispensing of picoliter droplets and cells
]]>
https://biorxiv.org/cgi/content/short/167163v1?rss=1"
Cole, R. H.Tang, S.-Y.Siltanen, C. A.Shahi, P.Zhang, J. Q.Poust, S.Gartner, Z. J.Abate, A. R.2017-07-21doi:10.1101/167163Cold Spring Harbor Laboratory Press2017-07-21
<![CDATA[
High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq
]]>
https://biorxiv.org/cgi/content/short/416966v1?rss=1"
Liu, L.Dalal, C.Heineike, B.Abate, A.2018-09-15doi:10.1101/416966Cold Spring Harbor Laboratory Press2018-09-15
<![CDATA[
Coupled active systems encode emergent behavioral dynamics of the unicellular predator Lacrymaria olor
]]>
https://biorxiv.org/cgi/content/short/406595v1?rss=1"
Coyle, S. M.Flaum, E.Li, H.Krishnamurthy, D.Prakash, M.2018-09-03doi:10.1101/406595Cold Spring Harbor Laboratory Press2018-09-03
<![CDATA[
CHEMOMETRIC APPROACHES FOR DEVELOPING INFRARED NANOSENSORS TO IMAGE ANTHRACYCLINES
]]>
https://biorxiv.org/cgi/content/short/407650v1?rss=1"
Del Bonis-O Donnell, J. T.Pinals, R.Jeong, S.Thakrar, A.Wolfinger, R.Landry, M. P.2018-09-04doi:10.1101/407650Cold Spring Harbor Laboratory Press2018-09-04
<![CDATA[
Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort
]]>
https://biorxiv.org/cgi/content/short/412890v1?rss=1"
Sprockett, D.Fischer, N.Boneh, R. S.Turner, D.Kierkus, J.Sladek, M.Escher, J.Wine, E.Yerushalmi, B.Dias, J. A.Shaoul, R.Kori, M.Snapper, S.Holmes, S.Bousvaros, A.Levine, A.Relman, D. A.2018-09-10doi:10.1101/412890Cold Spring Harbor Laboratory Press2018-09-10
<![CDATA[
The Plasmodium falciparum cytoplasmic translation apparatus: a promising therapeutic target not yet exploited by clinically approved antimalarials.
]]>
https://biorxiv.org/cgi/content/short/415513v1?rss=1"
Sheridan, C. M.Garcia, V. E.Ahyong, V.DeRisi, J. L.2018-09-12doi:10.1101/415513Cold Spring Harbor Laboratory Press2018-09-12
<![CDATA[
Evidence that disruption of apicoplast protein import in malaria parasites evades delayed-death growth inhibition
]]>
https://biorxiv.org/cgi/content/short/422618v1?rss=1"
Boucher, M. J.Yeh, E.2018-09-21doi:10.1101/422618Cold Spring Harbor Laboratory Press2018-09-21
<![CDATA[
phylogenize: a web tool to identify microbial genes underlying environment associations
]]>
https://biorxiv.org/cgi/content/short/425231v1?rss=1"
Bradley, P. H.Pollard, K. S.2018-09-24doi:10.1101/425231Cold Spring Harbor Laboratory Press2018-09-24
<![CDATA[
Collective intercellular communication through ultra-fast hydrodynamic trigger waves
]]>
https://biorxiv.org/cgi/content/short/428573v1?rss=1"
Mathijssen, A.Culver, J.Bhamla, M. S.Prakash, M.2018-09-26doi:10.1101/428573Cold Spring Harbor Laboratory Press2018-09-26
<![CDATA[
A mouse tissue atlas of small non-coding RNA
]]>
https://biorxiv.org/cgi/content/short/430561v1?rss=1"
Isakova, A.Quake, S.2018-09-29doi:10.1101/430561Cold Spring Harbor Laboratory Press2018-09-29
<![CDATA[
Mapping the complex paracrine response to hormones in the human breast at single-cell resolution
]]>
https://biorxiv.org/cgi/content/short/430611v1?rss=1"
Murrow, L. M.Weber, R. J.Caruso, J.McGinnis, C. S.Borowsky, A. D.Desai, T. A.Thomson, M.Tlsty, T. D.Gartner, Z. J.2018-09-29doi:10.1101/430611Cold Spring Harbor Laboratory Press2018-09-29
<![CDATA[
Miniaturization and optimization of 384-well compatible metagenomic sequencing library preparation
]]>
https://biorxiv.org/cgi/content/short/440156v1?rss=1"
Mayday, M. Y.Khan, L. M.Chow, E. D.Zinter, M. S.DeRisi, J. L.2018-10-10doi:10.1101/440156Cold Spring Harbor Laboratory Press2018-10-10
<![CDATA[
The key parameters that govern translation efficiency
]]>
https://biorxiv.org/cgi/content/short/440693v1?rss=1"
Erdmann-Pham, D. D.Dao Duc, K.Song, Y. S.2018-10-11doi:10.1101/440693Cold Spring Harbor Laboratory Press2018-10-11
<![CDATA[
On-ratio PDMS bonding for multilayer microfluidic device fabrication
]]>
https://biorxiv.org/cgi/content/short/450544v1?rss=1"
Lai, A.Altemose, N.White, J. A.Streets, A. M.2018-10-23doi:10.1101/450544Cold Spring Harbor Laboratory Press2018-10-23
<![CDATA[
Bright split red fluorescent proteins with enhanced complementation efficiency for the tagging of endogenous proteins and visualization of synapses
]]>
https://biorxiv.org/cgi/content/short/454041v1?rss=1"
Feng, S.Varshney, A.Coto Villa, D.Modavi, C.Kohler, J.Farah, F.Ali, N.Mueller, J. D.VanHoven, M.Huang, B.2018-10-25doi:10.1101/454041Cold Spring Harbor Laboratory Press2018-10-25
<![CDATA[
Evolution of resilience in protein interactomes across the tree of life
]]>
https://biorxiv.org/cgi/content/short/454033v1?rss=1"
Zitnik, M.Sosic, R.Feldman, M. W.Leskovec, J.2018-10-26doi:10.1101/454033Cold Spring Harbor Laboratory Press2018-10-26
<![CDATA[
Atlas of Subcellular RNA Localization Revealed by APEX-seq
]]>
https://biorxiv.org/cgi/content/short/454470v1?rss=1"
Fazal, F. M.Han, S.Kaewsapsak, P.Parker, K. R.Xu, J.Boettiger, A. N.Chang, H. Y.Ting, A. Y.2018-10-26doi:10.1101/454470Cold Spring Harbor Laboratory Press2018-10-26
<![CDATA[
Directed evolution of split APEX peroxidase
]]>
https://biorxiv.org/cgi/content/short/452888v1?rss=1"
Han, Y.Martell, J.Branon, T.Boassa, D.Shechner, D.Ellisman, M.Ting, A.2018-10-25doi:10.1101/452888Cold Spring Harbor Laboratory Press2018-10-25
<![CDATA[
A direct selection strategy for isolating aptamers with pH-sensitive binding activity
]]>
https://biorxiv.org/cgi/content/short/460063v1?rss=1"
Gordon, C. K. L.Eisenstein, M.Soh, H. T.2018-11-01doi:10.1101/460063Cold Spring Harbor Laboratory Press2018-11-01
<![CDATA[
Chiral twisting in cytoskeletal polymers regulates filament size and orientation
]]>
https://biorxiv.org/cgi/content/short/459974v1?rss=1"
Shi, H.Quint, D.Gopinathan, A.Huang, K. C.2018-11-01doi:10.1101/459974Cold Spring Harbor Laboratory Press2018-11-01
<![CDATA[
Multicolor fluorescent imaging by space-constrained computational hyperspectral imaging
]]>
https://biorxiv.org/cgi/content/short/458869v1?rss=1"
Wang, Y.Yang, B.Feng, S.Pessino, V.Huang, B.2018-11-01doi:10.1101/458869Cold Spring Harbor Laboratory Press2018-11-01
<![CDATA[
Deformed Alignment of Super-Resolution Images for Semi-flexible Structures in 3D
]]>
https://biorxiv.org/cgi/content/short/461913v1?rss=1"
Shi, X.Garcia, G.Wang, Y.Reiter, J. F.Huang, B.2018-11-05doi:10.1101/461913Cold Spring Harbor Laboratory Press2018-11-05
<![CDATA[
Spectrin is a mechanoresponsive protein shaping the architecture of intercellular invasion
]]>
https://biorxiv.org/cgi/content/short/154831v1?rss=1"
Duan, R.Kim, J. H.Shilagardi, K.Schiffhauer, E.Son, S.Lee, D.Li, S.Thomas, C.Luo, T.Fletcher, D. A.Robinson, D. N.Chen, E. H.2017-06-23doi:10.1101/154831Cold Spring Harbor Laboratory Press2017-06-23
<![CDATA[
Tissue Folding by Mechanical Compaction of the Mesenchyme
]]>
https://biorxiv.org/cgi/content/short/164020v1?rss=1"
Hughes, A. J.Miyazaki, H.Coyle, M. C.Zhang, J.Laurie, M. T.Chu, D.Vavrusova, Z.Schneider, R. A.Klein, O. D.Gartner, Z. J.2017-07-15doi:10.1101/164020Cold Spring Harbor Laboratory Press2017-07-15
<![CDATA[
Quantification of anti-parasite and anti-disease immunity to malaria as a function of age and exposure
]]>
https://biorxiv.org/cgi/content/short/191197v1?rss=1"
Rodriguez-Barraquer, I.Arinaitwe, E.Jagannathan, P.Kamya, M.Rosenthal, P.Rek, J.Dorsey, G.Nankabirwa, J.Staedke, S. G.Kilama, M.Drakeley, C.Ssewanyan, I.Smith, D. L.Greenhouse, B.2017-09-20doi:10.1101/191197Cold Spring Harbor Laboratory Press2017-09-20
<![CDATA[
Large-scale, quantitative protein assays on a high-throughput DNA sequencing chip
]]>
https://biorxiv.org/cgi/content/short/342808v1?rss=1"
Layton, C. J.McMahon, P. L.Greenleaf, W. J.2018-06-08doi:10.1101/342808Cold Spring Harbor Laboratory Press2018-06-08
<![CDATA[
Nonparametric analysis of contributions to variance in genomics and epigenomics data
]]>
https://biorxiv.org/cgi/content/short/314112v1?rss=1"
Moskowitz, D. M.Greenleaf, W. J.2018-05-04doi:10.1101/314112Cold Spring Harbor Laboratory Press2018-05-04
<![CDATA[
Single-embryo and single-blastomere immunoblotting reports protein expression heterogeneity in early-stage preimplantation embryos
]]>
https://biorxiv.org/cgi/content/short/357731v1?rss=1"
Rosas, E.Modzelewski, A. J.He, L.Herr, A. E.2018-06-28doi:10.1101/357731Cold Spring Harbor Laboratory Press2018-06-28
<![CDATA[
C. albicans white and opaque cells exhibit distinct spectra of organ colonization in standard mouse models of infection
]]>
https://biorxiv.org/cgi/content/short/461293v1?rss=1"
Takagi, J.Singh-Babak, S. D.Lohse, M. B.Dalal, C. K.Johnson, A. D.2018-11-07doi:10.1101/461293Cold Spring Harbor Laboratory Press2018-11-07
<![CDATA[
Intrinsic cooperativity potentiates parallel cis-regulatory evolution
]]>
https://biorxiv.org/cgi/content/short/301234v1?rss=1"
Sorrells, T. R.Johnson, A. N.Howard, C. J.Britton, C. S.Fowler, K. R.Feigerle, J. T.Weil, P. A.Johnson, A. D.2018-04-14doi:10.1101/301234Cold Spring Harbor Laboratory Press2018-04-14
<![CDATA[
Live-Cell Imaging Reveals Enhancer-dependent Sox2 Transcription in the Absence of Enhancer Proximity
]]>
https://biorxiv.org/cgi/content/short/409672v1?rss=1"
Alexander, J. M.Guan, J.Huang, B.Lomvardas, S.Weiner, O. D.2018-09-05doi:10.1101/409672Cold Spring Harbor Laboratory Press2018-09-05
<![CDATA[
Co-translational protein targeting facilitates centrosomal recruitment of PCNT during centrosome maturation
]]>
https://biorxiv.org/cgi/content/short/241083v1?rss=1"
Sepulveda, G.Antkowiak, M.Brust-Mascher, I.Mahe, K.Ou, T.Castro, N.Christensen, L. N.Cheung, L.Yoon, D.Huang, B.Jao, L.-E.2017-12-30doi:10.1101/241083Cold Spring Harbor Laboratory Press2017-12-30
<![CDATA[
Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH
]]>
https://biorxiv.org/cgi/content/short/101444v1?rss=1"
Guan, J.Liu, H.Shi, X.Feng, S.Huang, B.2017-01-18doi:10.1101/101444Cold Spring Harbor Laboratory Press2017-01-18
<![CDATA[
Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I
]]>
https://biorxiv.org/cgi/content/short/408757v1?rss=1"
Gomez-Ospina, N.Scharenberg, S. G.Mostrel, N.Bak, R. O.Mantri, S.Quadros, R. M.Gurumurthy, C. B.Lee, C.Bao, G.Aurelian, L.Porteus, M.2018-09-04doi:10.1101/408757Cold Spring Harbor Laboratory Press2018-09-04
<![CDATA[
Gene Correction for SCID-X1 in Long-Term Hematopoietic Stem Cells
]]>
https://biorxiv.org/cgi/content/short/397463v1?rss=1"
Pavel-Dinu, M.Wiebking, V.Dejene, B. T.Srifa, W.Mantri, S.Nicolas, C.Lee, C.Bao, G.Kildebeck, E. J.Punjya, N.Sindhu, C.Inlay, M. A.Saxena, N.DeRavin, S. S.Malech, H.Roncarolo, M. G.Weinberg, K. I.Porteus, M.2018-08-22doi:10.1101/397463Cold Spring Harbor Laboratory Press2018-08-22
<![CDATA[
Low-cost, sub-micron resolution, wide-field computational microscopy using opensource hardware
]]>
https://biorxiv.org/cgi/content/short/460055v1?rss=1"
Aidukas, T.Eckert, R.Harvey, A. R.Waller, L.Konda, P. C.2018-11-02doi:10.1101/460055Cold Spring Harbor Laboratory Press2018-11-02
<![CDATA[
Spatiotemporal dissection of the cell cycle regulated human proteome
]]>
https://biorxiv.org/cgi/content/short/543231v1?rss=1"
Mahdessian, D.Sullivan, D.Danielsson, F.Arif, M.Zhang, C.Akesson, L.Gnann, C.Schutten, R.Thul, P.Carja, O.Ayoglu, B.Mardinoglu, A.Ponten, F.Uhen, M.Lindskog, C.Lundberg, E.2019-02-07doi:10.1101/543231Cold Spring Harbor Laboratory Press2019-02-07
<![CDATA[
Hypotonic stress induces fast, reversible degradation of the vimentin cytoskeleton via intracellular calcium release
]]>
https://biorxiv.org/cgi/content/short/607416v1?rss=1"
Pan, L.Zhang, P.Hu, F.Yan, R.He, M.Li, W.Xu, J.Xu, K.2019-04-13doi:10.1101/607416Cold Spring Harbor Laboratory Press2019-04-13
<![CDATA[
Rapid discovery of synthetic DNA sequences to rewrite endogenous T cell circuits
]]>
https://biorxiv.org/cgi/content/short/604561v1?rss=1"
Roth, T. L.Li, P. J.Nies, J.Yu, R.Nguyen, M. L. T.Lee, Y.Apathy, R.Truong, A.Hiatt, J.Wu, D.Nguyen, D. N.Goodman, D.Bluestone, J. A.Roybal, K.Shifrut, E.Marson, A.2019-04-12doi:10.1101/604561Cold Spring Harbor Laboratory Press2019-04-12
<![CDATA[
The evolutionary advantage of cultural memory on heterogeneous contact networks
]]>
https://biorxiv.org/cgi/content/short/466524v1?rss=1"
Carja, O.Creanza, N.2018-11-09doi:10.1101/466524Cold Spring Harbor Laboratory Press2018-11-09
<![CDATA[
Cell-free DNA Reveals Potential Zoonotic Reservoirs in Non-Human Primates
]]>
https://biorxiv.org/cgi/content/short/481093v1?rss=1"
Kowarsky, M.De Vlaminck, I.Okamoto, J.Neff, N. F.LeBreton, M.Nwobegabay, J.Tamoufe, U.Ledoux, J. D.Tafon, B.Kiyang, J.Saylors, K.Wolfe, N. D.Quake, S. R.2018-11-29doi:10.1101/481093Cold Spring Harbor Laboratory Press2018-11-29
<![CDATA[
Structural basis of eIF2B-catalyzed GDP exchange and phosphoregulation by the integrated stress response
]]>
https://biorxiv.org/cgi/content/short/504654v1?rss=1"
Anand, A. A.Kenner, L. R.Nguyen, H. C.Myasnikov, A. G.Klose, C. J.McGeever, L. A.Tsai, J. C.Miller-Vedam, L. E.Walter, P.Frost, A.2018-12-22doi:10.1101/504654Cold Spring Harbor Laboratory Press2018-12-22
<![CDATA[
A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells
]]>
https://biorxiv.org/cgi/content/short/506188v1?rss=1"
Fonseca, J. P.Bonny, A. R.Kumar, G. R.Ng, A. H.Town, J.Wu, Q. C.Aslankoohi, E.Chen, S. Y.Harrigan, P.Osimiri, L. C.Kistler, A. L.El-Samad, H.2018-12-26doi:10.1101/506188Cold Spring Harbor Laboratory Press2018-12-26
<![CDATA[
MPRAnalyze - A statistical framework for Massively Parallel Reporter Assays
]]>
https://biorxiv.org/cgi/content/short/527887v1?rss=1"
Ashuach, T.Fischer, D. S.Kreimer, A.Ahituv, N.Theis, F. J.Yosef, N.2019-01-23doi:10.1101/527887Cold Spring Harbor Laboratory Press2019-01-23
<![CDATA[
Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage
]]>
https://biorxiv.org/cgi/content/short/530204v1?rss=1"
Li, Z.-R.Li, J.Cai, W.Lai, J.McKinnie, S.Zhang, W.-P.Moore, B.Zhang, W.Qian, P.-Y.2019-01-24doi:10.1101/530204Cold Spring Harbor Laboratory Press2019-01-24
<![CDATA[
Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations
]]>
https://biorxiv.org/cgi/content/short/532168v1?rss=1"
Spence, J. P.Song, Y. S.2019-01-28doi:10.1101/532168Cold Spring Harbor Laboratory Press2019-01-28
<![CDATA[
Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models
]]>
https://biorxiv.org/cgi/content/short/532895v1?rss=1"
Xu, C.Lopez, R.Mehlman, E.Regier, J.Jordan, M. I.Yosef, N.2019-01-29doi:10.1101/532895Cold Spring Harbor Laboratory Press2019-01-29
<![CDATA[
A tunable microfluidic device enables cargo encapsulation by cell- or organelle-sized lipid vesicles comprising asymmetric lipid monolayers
]]>
https://biorxiv.org/cgi/content/short/534586v1?rss=1"
Romanov, V.McCullough, J.Sharma, A.Vershinin, M.Gale, B. K.Frost, A.2019-01-29doi:10.1101/534586Cold Spring Harbor Laboratory Press2019-01-29
<![CDATA[
Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota
]]>
https://biorxiv.org/cgi/content/short/538132v1?rss=1"
Aranda-Diaz, A.Obadia, B.Thomsen, T.Hallberg, Z. F.Guvener, Z. T.Huang, K. C.Ludington, W. B.2019-02-01doi:10.1101/538132Cold Spring Harbor Laboratory Press2019-02-01
<![CDATA[
Continuous, Topologically Guided Protein Crystallization Controls Bacterial Surface Layer Self-Assembly
]]>
https://biorxiv.org/cgi/content/short/538397v1?rss=1"
Comerci, C. J.Herrmann, J.Yoon, J.Jabbarpour, F.Zhou, X.Nomellini, J. F.Smit, J.Shapiro, L.Wakatsuki, S.Moerner, W. E.2019-02-01doi:10.1101/538397Cold Spring Harbor Laboratory Press2019-02-01
<![CDATA[
DNA Nanostructures Coordinate Gene Silencing in Mature Plants
]]>
https://biorxiv.org/cgi/content/short/538678v1?rss=1"
Zhang, H.Demirer, G. S.Zhang, H.Ye, T.Goh, N. S.Aditham, A. J.Cunningham, F. J.Fan, C.Landry, M.2019-02-02doi:10.1101/538678Cold Spring Harbor Laboratory Press2019-02-02
<![CDATA[
Microbial biogeography and ecology of the mouth and implications for periodontal diseases
]]>
https://biorxiv.org/cgi/content/short/541052v1?rss=1"
Proctor, D.Shelef, K.Gonzalez, A.Long, C.Dethlefsen, L.Burns, A.Loomer, P.Armitage, G.Ryder, M.Millman, M.Knight, R.Holmes, S.Relman, D. A.2019-02-08doi:10.1101/541052Cold Spring Harbor Laboratory Press2019-02-08
<![CDATA[
Diet induces reproducible alterations in the mouse and human gut microbiome
]]>
https://biorxiv.org/cgi/content/short/541797v1?rss=1"
Bisanz, J. E.Upadhyay, V.Turnbaugh, J. A.Ly, K.Turnbaugh, P. J.2019-02-05doi:10.1101/541797Cold Spring Harbor Laboratory Press2019-02-05
<![CDATA[
Optogenetic control reveals differential promoter interpretation of transcription factor nuclear translocation dynamics
]]>
https://biorxiv.org/cgi/content/short/548255v1?rss=1"
Chen, S. Y.Osimiri, L. C.Chevalier, M. W.Bugaj, L. J.Ng, A. H.Stewart-Ornstein, J.Neves, L. T.El-Samad, H.2019-02-13doi:10.1101/548255Cold Spring Harbor Laboratory Press2019-02-13
<![CDATA[
A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards
]]>
https://biorxiv.org/cgi/content/short/551978v1?rss=1"
Lind, A.Lai, Y. Y. Y.Mostovoy, Y.Holloway, A. K.Iannucci, A.Mak, A. C.Fondi, M.Orlandini, V.Eckalbar, W. L.Milan, M.Rovatsos, M.Kichigin, I. G.Makunin, A. I.Trifonov, V.Schijlen, E.Kratochvil, L.Fani, R.Jessop, T. S.Patarnello, T.Hicks, J. W.Ryder, O. A.Mendelson, J. R.Ciofi, C.Kwok, P.-Y. A.Pollard, K. S.Bruneau, B.2019-02-15doi:10.1101/551978Cold Spring Harbor Laboratory Press2019-02-15
<![CDATA[
High-Fidelity Nanopore Sequencing of Ultra-Short DNA Sequences
]]>
https://biorxiv.org/cgi/content/short/552224v1?rss=1"
Wilson, B. D.Eisenstein, M.Soh, H. T.2019-02-16doi:10.1101/552224Cold Spring Harbor Laboratory Press2019-02-16
<![CDATA[
Pancreas patch-seq links physiologic dysfunction in diabetes to single-cell transcriptomic phenotypes
]]>
https://biorxiv.org/cgi/content/short/555110v1?rss=1"
Camunas-Soler, J.Dai, X.Hang, Y.Bautista, A.Lyon, J.Suzuki, K.Kim, S. K.Quake, S. R.MacDonald, P. E.2019-02-20doi:10.1101/555110Cold Spring Harbor Laboratory Press2019-02-20
<![CDATA[
Nucleic Acid Cleavage with a Hyperthermophilic Cas9 from an Unculturable Ignavibacterium
]]>
https://biorxiv.org/cgi/content/short/555169v1?rss=1"
Schmidt, S. T.Yu, F. B.Blainey, P. C.May, A. P.Quake, S. R.2019-02-20doi:10.1101/555169Cold Spring Harbor Laboratory Press2019-02-20
<![CDATA[
Functional Enrichment and Analysis of Antigen-Specific Memory B Cell Antibody Repertoires in PBMCs
]]>
https://biorxiv.org/cgi/content/short/557769v1?rss=1"
Waltari, E.McGeever, A.Kim, P. S.McCutcheon, K. M.2019-02-22doi:10.1101/557769Cold Spring Harbor Laboratory Press2019-02-22
<![CDATA[
Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors
]]>
https://biorxiv.org/cgi/content/short/558676v1?rss=1"
Olm, M. R.Bhattacharya, N.Crits-Christoph, A.Firek, B. A.Baker, R.Song, Y. S.Morowitz, M. J.Banfield, J. F.2019-02-22doi:10.1101/558676Cold Spring Harbor Laboratory Press2019-02-22
<![CDATA[
Super-resolution displacement mapping of unbound single molecules reveals nanoscale heterogeneities in intracellular diffusivity
]]>
https://biorxiv.org/cgi/content/short/559484v1?rss=1"
Xiang, L.Chen, K.Yan, R.Li, W.Xu, K.2019-02-25doi:10.1101/559484Cold Spring Harbor Laboratory Press2019-02-25
<![CDATA[
Nanotubes effectively deliver siRNA to intact plant cells and protect siRNA against nuclease degradation
]]>
https://biorxiv.org/cgi/content/short/564427v1?rss=1"
Demirer, G. S.Zhang, H.Goh, N. S.Chang, R.Landry, M. P.2019-03-01doi:10.1101/564427Cold Spring Harbor Laboratory Press2019-03-01
<![CDATA[
Afucosylated maternal anti-dengue IgGs are a biomarker for susceptibility to dengue disease in their infants
]]>
https://biorxiv.org/cgi/content/short/565259v1?rss=1"
Thulin, N. K.Brewer, R. C.Sherwood, R.Bournazos, S.Edwards, K. G.Ramadoss, N. S.Taubenberger, J. K.Memoli, M.Jagannathan, P.Zhang, S.Libraty, D. H.Wang, T. T.2019-03-06doi:10.1101/565259Cold Spring Harbor Laboratory Press2019-03-06
<![CDATA[
Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding
]]>
https://biorxiv.org/cgi/content/short/571588v1?rss=1"
Becker, W. R.Jarmoskaite, I.Kappel, K.Vaidyanathan, P. P.Denny, S. K.Das, R.Greenleaf, W. J.Herschlag, D.2019-03-08doi:10.1101/571588Cold Spring Harbor Laboratory Press2019-03-08
<![CDATA[
Clades of huge phage from across Earth’s ecosystems
]]>
https://biorxiv.org/cgi/content/short/572362v1?rss=1"
Al-Shayeb, B.Sachdeva, R.Chen, L.-X.Ward, F.Munk, P.Devoto, A.Castelle, C. J.Olm, M. R.Bouma-Gregson, K.Amano, Y.He, C.Meheust, R.Brooks, B.Thomas, A.Lavy, A.Matheus-Carnevali, P.Sun, C.Goltsman, D.Borton, M. A.Nelson, T. C.Kantor, R.Jaffe, A. L.Keren, R.Farag, I. F.Lei, S.Finstad, K.Amundson, R.Anantharaman, K.Zhou, J.Probst, A. J.Power, M. E.Tringe, S. G.Li, W.-J.Wrighton, K.Harrison, S.Morowitz, M.Relman, D. A.Doudna, J. A.Lehours, A.-C.Warren, L.Cate, J. H.Santini, J. M.Banfield, J. F.2019-03-11doi:10.1101/572362Cold Spring Harbor Laboratory Press2019-03-11
<![CDATA[
The ER membrane protein complex is important for the biogenesis of flavivirus polyproteins
]]>
https://biorxiv.org/cgi/content/short/572602v1?rss=1"
Ngo, A. M.Shurtleff, M. J.Popova, K. D.Kulsuptrakul, J.Weissman, J. S.Puschnik, A. S.2019-03-09doi:10.1101/572602Cold Spring Harbor Laboratory Press2019-03-09
<![CDATA[
A role for liquid-liquid phase separation in ESCRT-mediated nuclear envelope reformation.
]]>
https://biorxiv.org/cgi/content/short/577460v1?rss=1"
von Appen, A.Lajoie, D.Johnson, I. E.Trnka, M.Pick, S. M.Burlingame, A. L.Ullman, K. S.Frost, A.2019-03-14doi:10.1101/577460Cold Spring Harbor Laboratory Press2019-03-14
<![CDATA[
A non-Dicer RNase III and four other novel factors required for RNAi-mediated transposon suppression in the human pathogenic yeast C. neoformans
]]>
https://biorxiv.org/cgi/content/short/577924v1?rss=1"
Burke, J. E.Longhurst, A. D.Natarajan, P.Rao, B.Liu, S. J.Sales-Lee, J.Mortensen, Y.Moresco, J.Diedrich, J. K.Yates, J. R.Madhani, H. D.2019-03-14doi:10.1101/577924Cold Spring Harbor Laboratory Press2019-03-14
<![CDATA[
The \"sewing machine\" for minimally invasive neural recording
]]>
https://biorxiv.org/cgi/content/short/578542v1?rss=1"
Hanson, T. L.Diaz-Botia, C. A.Kharazia, V.Maharbiz, M. M.Sabes, P. N.2019-03-14doi:10.1101/578542Cold Spring Harbor Laboratory Press2019-03-14
<![CDATA[
Unbiased metagenomic sequencing for pediatric meningitis in Bangladesh reveals neuroinvasive Chikungunya virus outbreak and other unrealized pathogens
]]>
https://biorxiv.org/cgi/content/short/579532v1?rss=1"
99% identical to each other and to a Bangladeshi strain only previously recognized to cause systemic illness in 2017. CHIKV qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital (n=472) revealed 17 additional CHIKV meningitis cases. Orthogonal molecular confirmation of each mNGS-identified infection, case-based clinical data, and follow-up of patients substantiated the key findings.nnUsing mNGS, we obtained a microbiological diagnosis for 40% of idiopathic meningitis cases and identified a previous unappreciated pediatric CHIKV meningitis outbreak. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis and facilitate informed policy decisions.
]]>Saha, S.Ramesh, A.Kalantar, K. L.Malaker, R.Hasanuzzaman, M.Khan, L. M.Mayday, M. Y.Sajib, M. S. I.Li, L. M.Langelier, C.Rahman, H.Crawford, E. D.Tato, C. M.Islam, M.Juan, Y.-F.Bourcy, C. d.Dimitrov, B.Wang, J.Tang, J.Sheu, J.Egger, R.Carvalho, T. R. D.Wilson, M. R.Saha, S.DeRisi, J.2019-03-15doi:10.1101/579532Cold Spring Harbor Laboratory Press2019-03-15
<![CDATA[
Separations-Encoded Microparticles For Single-Cell Western Blotting
]]>
https://biorxiv.org/cgi/content/short/580233v1?rss=1"
Gumuscu, B.Herr, A.2019-03-16doi:10.1101/580233Cold Spring Harbor Laboratory Press2019-03-16
<![CDATA[
Luciferase-LOV BRET enables versatile and specific transcriptional readout of cellular protein-protein interactions
]]>
https://biorxiv.org/cgi/content/short/580845v1?rss=1"
Kim, C. K.Cho, K. F.Kim, M. W.Ting, A. Y.2019-03-18doi:10.1101/580845Cold Spring Harbor Laboratory Press2019-03-18
<![CDATA[
Two accessory proteins govern MmpL3 mycolic acid transport in mycobacteria
]]>
https://biorxiv.org/cgi/content/short/581447v1?rss=1"
Fay, A.Czudnochowski, N.Rock, J.Johnson, J.Krogan, N.Rosenberg, O.Glickman, M.2019-03-27doi:10.1101/581447Cold Spring Harbor Laboratory Press2019-03-27
<![CDATA[
The menstrual cycle is a primary contributor to cyclic variation in women’s mood, behavior, and vital signs
]]>
https://biorxiv.org/cgi/content/short/583153v1?rss=1"
Pierson, E.Althoff, T.Thomas, D.Hillard, P.Leskovec, J.2019-03-20doi:10.1101/583153Cold Spring Harbor Laboratory Press2019-03-20
<![CDATA[
Live-cell Imaging Analysis of Antimycin-Type Depsipeptides via Bioorthogonal Stimulated Raman Scattering Microscopy
]]>
https://biorxiv.org/cgi/content/short/583252v1?rss=1"
Seidel, J. A.Miao, Y.Porterfield, W.Cai, W.Zhu, X.Kim, S.-J.Hu, F.Bhattarai-Kline, S.Min, W.Zhang, W.2019-03-21doi:10.1101/583252Cold Spring Harbor Laboratory Press2019-03-21
<![CDATA[
Single-shot autofocus microscopy using deep learning
]]>
https://biorxiv.org/cgi/content/short/587485v1?rss=1"
Pinkard, H.Phillips, Z.Babakhani, A.Fletcher, D. A.Waller, L.2019-03-23doi:10.1101/587485Cold Spring Harbor Laboratory Press2019-03-23
<![CDATA[
Discrete and Continuous Cell Identities of the Adult Murine Striatum
]]>
https://biorxiv.org/cgi/content/short/591396v1?rss=1"
Stanley, G.Gokce, O.Malenka, R. C.Sudhof, T. C.Quake, S. R.2019-03-27doi:10.1101/591396Cold Spring Harbor Laboratory Press2019-03-27
<![CDATA[
A Cas9 nanoparticle system with truncated Cas9 target sequences on DNA repair templates enhances genome targeting in diverse human immune cell types
]]>
https://biorxiv.org/cgi/content/short/591719v1?rss=1"
Nguyen, D. N.Roth, T. L.Li, J.Chen, P. A.Mamedov, M. M.Vo, L. T.Tobin, V.Apathy, R.Goodman, D.Shifrut, E.Bluestone, J. A.Puck, J. M.Szoka, F. C.Marson, A.2019-03-28doi:10.1101/591719Cold Spring Harbor Laboratory Press2019-03-28
<![CDATA[
Coordinating Receptor Expression and Wiring Specificity in Olfactory Receptor Neurons
]]>
https://biorxiv.org/cgi/content/short/594895v1?rss=1"
Li, H.Li, T.Horns, F.Li, J.Xie, Q.Xu, C.Wu, B.Kebschull, J.Vacek, D.Xie, A.Luginbuhl, D.Quake, S.Luo, L.2019-03-31doi:10.1101/594895Cold Spring Harbor Laboratory Press2019-03-31
<![CDATA[
Unusual metabolism and hypervariation in the genome of a Gracilibacteria (BD1-5) from an oil degrading community
]]>
https://biorxiv.org/cgi/content/short/595074v1?rss=1"
Sieber, C. M. K.Paul, B. G.Castelle, C. J.Hu, P.Tringe, S. G.Valentine, D. L.Andersen, G. L.Banfield, J. F.2019-04-01doi:10.1101/595074Cold Spring Harbor Laboratory Press2019-04-01
<![CDATA[
Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil
]]>
https://biorxiv.org/cgi/content/short/597468v1?rss=1"
Starr, E. P.Nuccio, E. E.Pett-Ridge, J.Banfield, J. F.Firestone, M. K.2019-04-04doi:10.1101/597468Cold Spring Harbor Laboratory Press2019-04-04
<![CDATA[
Tuning the affinity of tandem calponin homology domains
]]>
https://biorxiv.org/cgi/content/short/598359v1?rss=1"
Harris, A. R.Belardi, B.Jreij, P.Wei, K.Bausch, A.Fletcher, D. A.2019-04-04doi:10.1101/598359Cold Spring Harbor Laboratory Press2019-04-04
<![CDATA[
RNAi screen reveals a role for PACSIN2 and caveolins during bacterial cell-to-cell spread
]]>
https://biorxiv.org/cgi/content/short/599795v1?rss=1"
Sanderlin, A.Vondrak, C.Scricco, A.Fedrigo, I.Ahyong, V.Lamason, R.2019-04-04doi:10.1101/599795Cold Spring Harbor Laboratory Press2019-04-04
<![CDATA[
Trans-synaptic Fish-lips Signaling Prevents Misconnections between Non-synaptic Partner Olfactory Neurons
]]>
https://biorxiv.org/cgi/content/short/600064v1?rss=1"
Xie, Q.Wu, B.Li, J.Li, H.Luginbuhl, D.Xu, C.Wang, X.Luo, L.2019-04-04doi:10.1101/600064Cold Spring Harbor Laboratory Press2019-04-04
<![CDATA[
Perturbation of the human gut microbiome by a non-antibiotic drug contributes to the resolution of autoimmune disease
]]>
https://biorxiv.org/cgi/content/short/600155v1?rss=1"
Nayak, R. R.Alexander, M.Stapleton-Grey, K.Ubeda, C.Scher, J. U.Turnbaugh, P. J.2019-04-05doi:10.1101/600155Cold Spring Harbor Laboratory Press2019-04-05
<![CDATA[
Sentinel Case of Candida auris in the Western United States Following Prolonged Occult Colonization in a Returned Traveler from India
]]>
https://biorxiv.org/cgi/content/short/601559v1?rss=1"
Woodworth, M. H.Dynerman, D.Crawford, E. D.Li, L. M.Doernberg, S. B.Ramirez, L.Serpa, P. H.Nichols, A.Lyden, A.Tato, C. M.Miller, S.Derisi, J. L.Langelier, C.2019-04-12doi:10.1101/601559Cold Spring Harbor Laboratory Press2019-04-12
<![CDATA[
Scale-free Vertical Tracking Microscopy: Towards Bridging Scales in Biological Oceanography
]]>
https://biorxiv.org/cgi/content/short/610246v1?rss=1"
Krishnamurthy, D.Li, H.Benoit du Rey, F.Cambournac, P.Larson, A.Prakash, M.2019-04-15doi:10.1101/610246Cold Spring Harbor Laboratory Press2019-04-15
<![CDATA[
Revealing architectural order with polarized light imaging and deep neural networks
]]>
https://biorxiv.org/cgi/content/short/631101v1?rss=1"
Guo, S.-M.Krishnan, A. P.Folkesson, J.Ivanov, I.Chhun, B.Cho, N.Leonetti, M.Mehta, S. B.2019-05-09doi:10.1101/631101Cold Spring Harbor Laboratory Press2019-05-09
<![CDATA[
Global ecotypes in the ubiquitous marine clade SAR86
]]>
https://biorxiv.org/cgi/content/short/635185v1?rss=1"
Hoarfrost, A.Nayfach, S.Ladau, J.Yooseph, S.Arnosti, C.Dupont, C. L.Pollard, K.2019-05-10doi:10.1101/635185Cold Spring Harbor Laboratory Press2019-05-10
<![CDATA[
A Novel Chromatin-Opening Element for Stable Long-term Transgene Expression
]]>
https://biorxiv.org/cgi/content/short/626713v1?rss=1"
Rudina, S. S.Smolke, C. D.2019-05-03doi:10.1101/626713Cold Spring Harbor Laboratory Press2019-05-03
<![CDATA[
Click-PD: A Quantitative Method for Base-Modified Aptamer Discovery
]]>
https://biorxiv.org/cgi/content/short/626572v1?rss=1"
Gordon, C. K. L.Wu, D. T.Feagin, T. A.Pusuluri, A.Csordas, A. T.Eisenstein, M.Hawker, C. J.Niu, J.Soh, H. T.2019-05-03doi:10.1101/626572Cold Spring Harbor Laboratory Press2019-05-03
<![CDATA[
Modulating pathogenesis with Mobile-CRISPRi
]]>
https://biorxiv.org/cgi/content/short/618637v1?rss=1"
Rosenberg, O.Qu, J.-X.Prasad, N. K.Peters, J.Looney, M.Yu, M.Lyden, A.Chen, S.Crawford, E.Silvis, M.2019-04-25doi:10.1101/618637Cold Spring Harbor Laboratory Press2019-04-25
<![CDATA[
Brain endothelial cells are exquisite sensors of age-related circulatory cues
]]>
https://biorxiv.org/cgi/content/short/617258v1?rss=1"
Chen, M. B.Yousef, H.Yang, A. C.Lee, D.Lehallier, B.Schaum, N.Quake, S. R.Wyss-Coray, T.2019-04-24doi:10.1101/617258Cold Spring Harbor Laboratory Press2019-04-24
<![CDATA[
Weakly supervised classification of rare aortic valve malformations using unlabeled cardiac MRI sequences
]]>
https://biorxiv.org/cgi/content/short/339630v1?rss=1"
Fries, J. A.Varma, P.Chen, V.Xiao, K.Tejeda, H.Priyanka, S.Dunnmon, J.Chubb, H.Maskatia, S.Fiterau, M.Delp, S.Ashley, E.Re, C.Priest, J.2018-06-05doi:10.1101/339630Cold Spring Harbor Laboratory Press2018-06-05
<![CDATA[
Compromised function of an ESCRT complex promotes endolysosomal escape of tau seeds and propagation of tau aggregation
]]>
https://biorxiv.org/cgi/content/short/637785v1?rss=1"
Chen, J. J.Nathaniel, D. L.Raghavan, P.Nelson, M.Tian, R.Tse, E.Hong, J. Y.See, S. K.Mok, S.-A.Southworth, D. R.Grinberg, L. T.Gestwicki, J. E.Leonetti, M. D.Kampmann, M.2019-05-15doi:10.1101/637785Cold Spring Harbor Laboratory Press2019-05-15
<![CDATA[
Genome replication dynamics of a bacteriophage and its satellite reveal strategies for parasitism and viral restriction
]]>
https://biorxiv.org/cgi/content/short/639039v1?rss=1"
Barth, Z.Silvas, T.Angermeyer, A.Seed, K.2019-05-17doi:10.1101/639039Cold Spring Harbor Laboratory Press2019-05-17
<![CDATA[
Methods Matter -- Standard Production Platforms For Recombinant AAV Can Produce Chemically And Functionally Distinct Vectors
]]>
https://biorxiv.org/cgi/content/short/640169v1?rss=1"
Rumachik, N. G.Malaker, S. A.Poweleit, N.Maynard, L. H.Adams, C. M.Leib, R. D.Cirolia, G.Thomas, D.Stamnes, S.Holt, K.Sinn, P.May, A. P.Paulk, N. K.2019-05-17doi:10.1101/640169Cold Spring Harbor Laboratory Press2019-05-17
<![CDATA[
Computational design of a modular protein sense/response system
]]>
https://biorxiv.org/cgi/content/short/648485v1?rss=1"
Glasgow, A. A.Huang, Y.-M.Mandell, D. J.Thompson, M.Ritterson, R.Loshbaugh, A. L.Pellegrino, J.Krivacic, C.Pache, R. A.Barlow, K. A.Ollikainen, N.Jeon, D.Kelly, M. J. S.Fraser, J. S.Kortemme, T.2019-05-24doi:10.1101/648485Cold Spring Harbor Laboratory Press2019-05-24
<![CDATA[
Consistent metagenome-derived metrics verify and define bacterial species boundaries
]]>
https://biorxiv.org/cgi/content/short/647511v1?rss=1"
Olm, M. R.Crits-Christoph, A.Diamond, S.Lavy, A.Matheus Carnevali, P. B.Banfield, J. F.2019-05-24doi:10.1101/647511Cold Spring Harbor Laboratory Press2019-05-24
<![CDATA[
Persistent Features of Intermittent Transcription
]]>
https://biorxiv.org/cgi/content/short/650895v1?rss=1"
Wilkinson, M.Darmanis, S.Pisco, A. O.Huber, G.2019-05-27doi:10.1101/650895Cold Spring Harbor Laboratory Press2019-05-27
<![CDATA[
Graphene-enabled, spatially controlled electroporation of adherent cells for live-cell super-resolution microscopy
]]>
https://biorxiv.org/cgi/content/short/642868v1?rss=1"
Moon, S.Li, W.Xu, K.2019-05-27doi:10.1101/642868Cold Spring Harbor Laboratory Press2019-05-27
<![CDATA[
Gold Nanobipyramids as Second Near Infrared Optical Coherence Tomography Contrast Agents for Multiplexed In Vivo Lymphangiography
]]>
https://biorxiv.org/cgi/content/short/656744v1?rss=1"
Si, P.Shevidi, S.Yuan, E.Yuan, K.Lautman, Z.Jeffrey, S. S.Sledge, G. W.de la Zerda, A.2019-05-31doi:10.1101/656744Cold Spring Harbor Laboratory Press2019-05-31
<![CDATA[
micrIO: An Open-Source Autosampler and Fraction Collector for Automated Microfluidic Input-Output
]]>
https://biorxiv.org/cgi/content/short/655324v1?rss=1"
Longwell, S. A.Fordyce, P. M.2019-06-02doi:10.1101/655324Cold Spring Harbor Laboratory Press2019-06-02
<![CDATA[
A single-parasite transcriptional landscape of asexual development in Toxoplasma gondii
]]>
https://biorxiv.org/cgi/content/short/656165v1?rss=1"
5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
]]>Xue, Y.Theisen, T. C.Ferrel, A.Rastogi, S.Quake, S. R.Boothroyd, J. C.2019-06-03doi:10.1101/656165Cold Spring Harbor Laboratory Press2019-06-03
<![CDATA[
Structural insights into ligand efficacy and activation of the glucagon receptor
]]>
https://biorxiv.org/cgi/content/short/660837v1?rss=1"
Hilger, D.Krishna Kumar, K.Hu, H.Pedersen, M. F.Giehm, L.Mathiesen, J. M.Skiniotis, G.Kobilka, B. K.2019-06-05doi:10.1101/660837Cold Spring Harbor Laboratory Press2019-06-05
<![CDATA[
The murine transcriptome reveals global aging nodes with organ-specific phase and amplitude
]]>
https://biorxiv.org/cgi/content/short/662254v1?rss=1"
Schaum, N.Lehallier, B.Hahn, O.Hosseinzadeh, S.Lee, S. E.Sit, R.Lee, D. P.Losada, P. M.Zardeneta, M. E.Palovics, R.Fehlmann, T.Webber, J.McGeever, A.Zhang, H.Berdnik, D.Tan, W.Zee, A.Tan, M.The Tabula Muris Consortium,Pisco, A.Karkanias, J.Neff, N. F.Keller, A.Darmanis, S.Quake, S. R.Wyss-Coray, T.2019-06-07doi:10.1101/662254Cold Spring Harbor Laboratory Press2019-06-07
<![CDATA[
Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing
]]>
https://biorxiv.org/cgi/content/short/653337v1?rss=1"
Crawford, E. D.Kamm, J.Miller, S.Li, L.Caldera, S.Lyden, A. D.Yokoe, D.Nichols, A.Ramirez-Avila, L.Tran, N. K.Barnhard, S.Conner, P. M.Nambiar, A.Zinter, M. S.Moayeri, M.Hayakawa Serpa, P.Prince, B. C.Quan, J.Sit, R.Tan, M.Phelps, M.DeRisi, J. S.Tato, C. M.Langelier, C.2019-05-30doi:10.1101/653337Cold Spring Harbor Laboratory Press2019-05-30
<![CDATA[
A Single Cell Transcriptomic Atlas Characterizes Aging Tissues in the Mouse
]]>
https://biorxiv.org/cgi/content/short/661728v1?rss=1"
The Tabula Muris Consortium,Pisco, A. O.Schaum, N.McGeever, A.Karkanias, J.Neff, N. F.Darmanis, S.Wyss-Coray, T.Quake, S. R.2019-06-08doi:10.1101/661728Cold Spring Harbor Laboratory Press2019-06-08
<![CDATA[
Decoding commensal-host communication through genetic engineering of Staphylococcus epidermidis
]]>
https://biorxiv.org/cgi/content/short/664656v1?rss=1"
Chen, Y. E.Bouladoux, N.Hurabielle, C.Mattke, A.Belkaid, Y. A.Fischbach, M. A.2019-06-10doi:10.1101/664656Cold Spring Harbor Laboratory Press2019-06-10
<![CDATA[
Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis
]]>
https://biorxiv.org/cgi/content/short/666230v1?rss=1"
Schubert, R. D.Hawes, I.Ramachandran, P. S.Ramesh, A.Crawford, E. D.Pak, J. E.Wu, W.Cheung, C. K.O'Donovan, B. D.Tato, C. M.Lyden, A.Tan, M.Sit, R.Sowa, G.Sample, H. A.Zorn, K. C.Banerji, D.Khan, L. M.Bove, R.Hauser, S. L.Gelfand, A. A.Johnson-Kerner, B.Nash, K.Krishnamoorthy, K. S.Chitnis, T.Ding, J. Z.McMillan, H. J.Chiu, C. Y.Briggs, B.Glaser, C. A.Yen, C.Chu, V.Wadford, D. A.Dominguez, S. R.Ng, T. F. F.Marine, R. L.Lopez, A. S.Nix, W. A.Soldatos, A.Gorman, M.Benson, L.Messacar, K.Konopka-Anstadt, J. L.Ob2019-06-10doi:10.1101/666230Cold Spring Harbor Laboratory Press2019-06-10
<![CDATA[
Terasaki Spiral Ramps and Intracellular Diffusion
]]>
https://biorxiv.org/cgi/content/short/675165v1?rss=1"
Huber, G.Wilkinson, M.2019-06-19doi:10.1101/675165Cold Spring Harbor Laboratory Press2019-06-19
<![CDATA[
High Throughput Evolution of Near Infrared Serotonin Nanosensors
]]>
https://biorxiv.org/cgi/content/short/673152v1?rss=1"
Jeong, S.Yang, D.Beyene, A. G.Best, A.Landry, M.2019-06-18doi:10.1101/673152Cold Spring Harbor Laboratory Press2019-06-18
<![CDATA[
Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions
]]>
https://biorxiv.org/cgi/content/short/674291v1?rss=1"
Loshbaugh, A. L.Kortemme, T.2019-06-17doi:10.1101/674291Cold Spring Harbor Laboratory Press2019-06-17
<![CDATA[
Motility induced fracture reveals a ductile to brittle crossover in the epithelial tissues of a simple animal
]]>
https://biorxiv.org/cgi/content/short/676866v1?rss=1"
Prakash, V.Bull, M. S.Prakash, M.2019-06-19doi:10.1101/676866Cold Spring Harbor Laboratory Press2019-06-19
<![CDATA[
Evaluating Protein Transfer Learning with TAPE
]]>
https://biorxiv.org/cgi/content/short/676825v1?rss=1"
Rao, R.Bhattacharya, N.Thomas, N.Duan, Y.Chen, X.Canny, J.Abbeel, P.Song, Y. S.2019-06-20doi:10.1101/676825Cold Spring Harbor Laboratory Press2019-06-20
<![CDATA[
Inference of complex population histories using whole-genome sequences from multiple populations
]]>
https://biorxiv.org/cgi/content/short/026591v1?rss=1"
Matthias SteinrückenJohn A. KammYun S. Song2015-09-16doi:10.1101/026591Cold Spring Harbor Laboratory Press2015-09-16
<![CDATA[
Wide distribution of phage that infect freshwater SAR11 bacteria
]]>
https://biorxiv.org/cgi/content/short/672428v1?rss=1"
Chen, L.-X.Zhao, Y.McMahon, K. D.Mori, J. F.Jessen, G. L.Nelson, T. C.Warren, L. A.Banfield, J. F.2019-06-15doi:10.1101/672428Cold Spring Harbor Laboratory Press2019-06-15
<![CDATA[
Viral satellites exploit phage proteins to escape degradation of the bacterial host chromosome
]]>
https://biorxiv.org/cgi/content/short/671271v1?rss=1"
McKitterick, A.Hays, S.Alam, M.Seed, K.2019-06-14doi:10.1101/671271Cold Spring Harbor Laboratory Press2019-06-14
<![CDATA[
Deep Learning Interpretation of Echocardiograms
]]>
https://biorxiv.org/cgi/content/short/681676v1?rss=1"
Ghorbani, A.Ouyang, D.Abid, A.He, B.Chen, J. H.Harrington, R. A.Liang, D. H.Ashley, E. A.Zou, J. Y.2019-06-24doi:10.1101/681676Cold Spring Harbor Laboratory Press2019-06-24
<![CDATA[
Mapping gene regulatory networks of primary CD4+ T cells using single-cell genomics and genome engineering
]]>
https://biorxiv.org/cgi/content/short/678060v1?rss=1"
Gate, R. E.Kim, M. C.Lu, A.Lee, D.Shifrut, E.Subramaniam, M.Marson, A.Ye, C. J.2019-06-21doi:10.1101/678060Cold Spring Harbor Laboratory Press2019-06-21
<![CDATA[
Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption
]]>
https://biorxiv.org/cgi/content/short/684670v1?rss=1"
Jeong, S.Pinals, R. L.Dharmadhikari, B.Song, H.Kalluri, A.Debnath, D.Qi, W.Ham, M.-H.Patra, P.Landry, M.2019-06-27doi:10.1101/684670Cold Spring Harbor Laboratory Press2019-06-27
<![CDATA[
Independent Control of the Thermodynamic and Kinetic Properties of Aptamer Switches
]]>
https://biorxiv.org/cgi/content/short/688275v1?rss=1"
Wilson, B. D.Hariri, A. A.Thompson, I. A. P.Eisenstein, M.Soh, H. T.2019-07-02doi:10.1101/688275Cold Spring Harbor Laboratory Press2019-07-02
<![CDATA[
Label-retention expansion microscopy
]]>
https://biorxiv.org/cgi/content/short/687954v1?rss=1"
Shi, X.Li, Q.Dai, Z.Tran, A.Feng, S.Ramirez, A. D.Lin, Z.Wang, X.Chow, T. T.Seiple, I. B.Huang, B.2019-07-01doi:10.1101/687954Cold Spring Harbor Laboratory Press2019-07-01
<![CDATA[
CRISPR-based platform for multimodal genetic screens in human iPSC-derived neurons
]]>
https://biorxiv.org/cgi/content/short/513309v1?rss=1"
Tian, R.Gachechiladze, M. A.Ludwig, C. H.Laurie, M. T.Hong, J. Y.Nathaniel, D.Prabhu, A. V.Fernandopulle, M. S.Patel, R.Ward, M. E.Kampmann, M.2019-01-07doi:10.1101/513309Cold Spring Harbor Laboratory Press2019-01-07
<![CDATA[
High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications
]]>
https://biorxiv.org/cgi/content/short/695429v1?rss=1"
Stojkovic, V.Myasnikov, A.Young, I.Frost, A.Fraser, J.Fujmori, D.2019-07-07doi:10.1101/695429Cold Spring Harbor Laboratory Press2019-07-07
<![CDATA[
Mapping Vector Field of Single Cells
]]>
https://biorxiv.org/cgi/content/short/696724v1?rss=1"
Qiu, X.Zhang, Y.Yang, D.Hosseinzadeh, S.Wang, L.Yuan, R.Xu, S.Ma, Y.Replogle, J.Darmanis, S.Xing, J.Weissman, J.2019-07-09doi:10.1101/696724Cold Spring Harbor Laboratory Press2019-07-09
<![CDATA[
A single cell framework for multi-omic analysis of disease identifies malignant regulatory signatures in mixed phenotype acute leukemia
]]>
https://biorxiv.org/cgi/content/short/696328v1?rss=1"
Granja, J. M.Klemm, S.McGinnis, L. M.Kathiria, A. S.Mezger, A.Parks, B.Gars, E.Liedtke, M.Zheng, G. X.Chang, H. Y.Majeti, R.Greenleaf, W. J.2019-07-09doi:10.1101/696328Cold Spring Harbor Laboratory Press2019-07-09
<![CDATA[
HLA upregulation during dengue virus infection suppresses the natural killer cell response
]]>
https://biorxiv.org/cgi/content/short/698803v1?rss=1"
McKechnie, J. L.Beltran, D.Pitti, A.Saenz, L.Arauz, A. B.Vergara, R.Harris, E.Lanier, L. L.Blish, C. A.Lopez-Verges, S.2019-07-11doi:10.1101/698803Cold Spring Harbor Laboratory Press2019-07-11
<![CDATA[
Cytoplasmic protein granules organize kinase-mediated RAS signaling
]]>
https://biorxiv.org/cgi/content/short/704312v1?rss=1"
Tulpule, A.Guan, J.Neel, D. S.Lin, Y. P.Heslin, A.Allegakoan, H.Perati, S.Ramirez, A. D.Shi, X.Yang, B.Feng, S.Huang, B.Bivona, T. G.2019-07-16doi:10.1101/704312Cold Spring Harbor Laboratory Press2019-07-16
<![CDATA[
μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells
]]>
https://biorxiv.org/cgi/content/short/706903v1?rss=1"
Altemose, N.Maslan, A.Lai, A.White, J. A.Streets, A. M.2019-07-18doi:10.1101/706903Cold Spring Harbor Laboratory Press2019-07-18
<![CDATA[
Transcriptional program of memory B cell activation, broadly binding anti-influenza antibodies, and bystander activation after vaccination revealed by single-cell transcriptomics
]]>
https://biorxiv.org/cgi/content/short/709337v1?rss=1"
Horns, F.Dekker, C. L.Quake, S. R.2019-07-22doi:10.1101/709337Cold Spring Harbor Laboratory Press2019-07-22
<![CDATA[
Limits and constraints on mechanisms of cell-cycle regulation imposed by cell size-homeostasis measurements
]]>
https://biorxiv.org/cgi/content/short/720292v1?rss=1"
Willis, L.Jonsson, H.Huang, K. C.2019-07-30doi:10.1101/720292Cold Spring Harbor Laboratory Press2019-07-30
<![CDATA[
Biosurfactant production maintains viability in anoxic conditions by depolarizing the membrane in Bacillus subtilis
]]>
https://biorxiv.org/cgi/content/short/720532v1?rss=1"
100-fold less viable than 3610. We discovered that the higher viability in 3610 was due to its ability to produce the antibacterial compound surfactin, as surfactin addition rescued 168 viability and also increased yield in aerobic growth. We further demonstrate that surfactin strongly depolarizes the B. subtilis membrane, and that other known membrane-potential disruptors restore viability to 168. These findings highlight the importance of surfactin for survival during oxygen-depleted conditions and demonstrate that antimicrobials normally considered harmful can instead benefit cells in stressful conditions when the terminal electron acceptor in respiration is limiting.
]]>Arjes, H. A.Vo, L.Dunn, C. M.Willis, L.DeRosa, C. A.Fraser, C. L.Kearns, D. B.Huang, K.2019-07-30doi:10.1101/720532Cold Spring Harbor Laboratory Press2019-07-30
<![CDATA[
Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs
]]>
https://biorxiv.org/cgi/content/short/717686v1?rss=1"
Ng, K. M.Aranda-Diaz, A.Tropini, C.Frankel, M. R.Van Treuren, W. W.O'Laughlin, C.Merrill, B. D.Yu, F. B.Pruss, K. M.Oliveira, R. A.Higginbottom, S. K.Neff, N. F.Fischbach, M. A.Xavier, K. B.Sonnenburg, J. L.Huang, K. C.2019-08-08doi:10.1101/717686Cold Spring Harbor Laboratory Press2019-08-08
<![CDATA[
Facile discovery of isonitrile natural products via tetrazine based click reactions
]]>
https://biorxiv.org/cgi/content/short/711853v1?rss=1"
Huang, Y.Cai, W.Del Rio Flores, A.Twiff, F. F.Zhang, W.2019-07-26doi:10.1101/711853Cold Spring Harbor Laboratory Press2019-07-26
<![CDATA[
Super-resolution microscopy unveils FIP200-scaffolded, cup-shaped organization of mammalian autophagic initiation machinery
]]>
https://biorxiv.org/cgi/content/short/712828v1?rss=1"
Kenny, S.Chen, X.Ge, L.Xu, K.2019-07-31doi:10.1101/712828Cold Spring Harbor Laboratory Press2019-07-31
<![CDATA[
Mitochondrial dysfunction is signaled to the integrated stress response by OMA1, DELE1 and HRI
]]>
https://biorxiv.org/cgi/content/short/715896v1?rss=1"
Guo, X.Aviles, G.Liu, Y.Tian, R.Unger, B. A.Lin, Y.-H. T.Wiita, A. P.Xu, K.Correia, M. A.Kampmann, M.2019-07-26doi:10.1101/715896Cold Spring Harbor Laboratory Press2019-07-26
<![CDATA[
Systematic identification of engineered methionines and oxaziridines for efficient, stable, and site-specific antibody bioconjugation
]]>
https://biorxiv.org/cgi/content/short/748160v1?rss=1"
Elledge, S. K.Tran, H. L.Christian, A. H.Steri, V.Hann, B.Toste, F. D.Chang, C. J.Wells, J. A.2019-08-28doi:10.1101/748160Cold Spring Harbor Laboratory Press2019-08-28
<![CDATA[
Biphasic Response of Protein Kinase A to Cyclic Adenosine Monophosphate Triggers Distinct Epithelial Phenotypes
]]>
https://biorxiv.org/cgi/content/short/747030v1?rss=1"
Fonseca, J. P.Aslankoohi, E.El-Samad, H.2019-08-28doi:10.1101/747030Cold Spring Harbor Laboratory Press2019-08-28
<![CDATA[
A molecular cell atlas of the human lung from single cell RNA sequencing
]]>
https://biorxiv.org/cgi/content/short/742320v1?rss=1"
Travaglini, K. J.Nabhan, A. N.Penland, L.Sinha, R.Gillich, A.Sit, R. V.Chang, S.Conley, S. D.Mori, Y.Seita, J.Berry, G. J.Shrager, J. B.Metzger, R. J.Kuo, C. S.Neff, N.Weissman, I. L.Quake, S. R.Krasnow, M. A.2019-08-27doi:10.1101/742320Cold Spring Harbor Laboratory Press2019-08-27
<![CDATA[
A metabolic pathway for bile acid dehydroxylation by the gut microbiome
]]>
https://biorxiv.org/cgi/content/short/758557v1?rss=1"
Funabashi, M.Grove, T.Pascal, V.Varma, Y.McFadden, M.Brown, L.Guo, C.Medema, M. H.Almo, S.Fischbach, M. A.2019-09-05doi:10.1101/758557Cold Spring Harbor Laboratory Press2019-09-05
<![CDATA[
An exploration of ambigrammatic sequences in narnaviruses
]]>
https://biorxiv.org/cgi/content/short/761890v1?rss=1"
3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.
]]>DeRisi, J. L.Huber, G.Kistler, A.Retallack, H.Wilkinson, M.Yllanes, D.2019-09-09doi:10.1101/761890Cold Spring Harbor Laboratory Press2019-09-09
<![CDATA[
Model-driven generation of artificial yeast promoters
]]>
https://biorxiv.org/cgi/content/short/748616v1?rss=1"
0.79) predictive accuracies on multiple sequence-activity prediction tasks. We developed model-guided design strategies which yielded large, sequence-diverse sets of novel promoters exhibiting activities similar to current best-in-class sequences. In addition to providing large sets of new promoters, our results show the value of model-guided design as an approach for generating useful DNA parts.
]]>Smolke, C.Kotopka, B.2019-08-28doi:10.1101/748616Cold Spring Harbor Laboratory Press2019-08-28
<![CDATA[
Corona exchange dynamics on carbon nanotubes by multiplexed fluorescence monitoring
]]>
https://biorxiv.org/cgi/content/short/761296v1?rss=1"
Pinals, R. L.Yang, D.Lui, A.Cao, W.Landry, M. P.2019-09-08doi:10.1101/761296Cold Spring Harbor Laboratory Press2019-09-08
<![CDATA[
Enhancing natural killer cell function with gp41-targeting bispecific antibodies to combat HIV infection
]]>
https://biorxiv.org/cgi/content/short/760280v1?rss=1"
Ramadoss, N. S.Zhao, N. Q.Richardson, B. A.Grant, P. M.Kim, P. S.Blish, C. A.2019-09-08doi:10.1101/760280Cold Spring Harbor Laboratory Press2019-09-08
<![CDATA[
A viral fusogen hijacks the actin cytoskeleton to drive cell-cell fusion
]]>
https://biorxiv.org/cgi/content/short/761502v1?rss=1"
10 nm) ectodomains that undergo conformational changes to bring apposing membranes in close contact prior to fusion. Here we report that a viral fusogen with a short (<2 nm) ectodomain, the reptilian orthoreovirus p14, accomplishes the same task by hijacking the actin cytoskeleton. We show that the cytoplasmic domain of p14 triggers N-WASP-mediated assembly of a branched actin network, directly coupling local force generation with a short membrane-disruptive ectodomain. This work reveals that overcoming energetic barriers to cell-cell fusion does not require conformational changes of tall fusogens but can instead be driven by harnessing the host cytoskeleton.nnImpact StatementA viral fusogen drives cell-cell fusion by hijacking the actin machinery to directly couple actin assembly with a short fusogenic ectodomain.
]]>Chan, K. M. C.Son, S.Schmid, E. M.Fletcher, D. A.2019-09-08doi:10.1101/761502Cold Spring Harbor Laboratory Press2019-09-08
<![CDATA[
Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon
]]>
https://biorxiv.org/cgi/content/short/779074v1?rss=1"
Sprockett, D. D.Martin, M.Costello, E. K.Burns, A. R.Holmes, S. P.Gurven, M.Relman, D. A.2019-09-23doi:10.1101/779074Cold Spring Harbor Laboratory Press2019-09-23
<![CDATA[
Muntjac chromosome evolution and architecture
]]>
https://biorxiv.org/cgi/content/short/772343v1?rss=1"
Mudd, A. B.Bredeson, J. V.Baum, R.Hockemeyer, D.Rokhsar, D. S.2019-09-18doi:10.1101/772343Cold Spring Harbor Laboratory Press2019-09-18
<![CDATA[
Linked optical and gene expression profiling of single cells at high throughput
]]>
https://biorxiv.org/cgi/content/short/766683v1?rss=1"
Zhang, J. Q.Siltanen, C. A.Liu, L.Chang, K.-C.Gartner, Z. J.Abate, A. R.2019-09-12doi:10.1101/766683Cold Spring Harbor Laboratory Press2019-09-12
<![CDATA[
A diet-dependent enzyme from the human gut microbiome promotes Th17 accumulation and colitis
]]>
https://biorxiv.org/cgi/content/short/766899v1?rss=1"
Alexander, M.Ang, Q. Y.Turnbaugh, P. J.2019-09-12doi:10.1101/766899Cold Spring Harbor Laboratory Press2019-09-12
<![CDATA[
A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery
]]>
https://biorxiv.org/cgi/content/short/786319v1?rss=1"
Tang, S.Kim, P. S.2019-09-29doi:10.1101/786319Cold Spring Harbor Laboratory Press2019-09-29
<![CDATA[
Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics
]]>
https://biorxiv.org/cgi/content/short/790642v1?rss=1"
Durham, N. D.Agrawal, A.Waltari, E.Croote, D.Zanini, F.Fouch, M.Davidson, E.Smith, O.Carabajal, E.Pak, J. E.Doranz, B. J.Robinson, M.Sanz, A. M.Albornoz, L. L.Rosso, F.Einav, S.Quake, S. R.McCutcheon, K. M.Goo, L.2019-10-02doi:10.1101/790642Cold Spring Harbor Laboratory Press2019-10-02
<![CDATA[
Ubiquitination modulates a protein energy landscape site-specifically with consequences for proteasomal degradation
]]>
https://biorxiv.org/cgi/content/short/843631v1?rss=1"
Carroll, E. C.Greene, E. R.Martin, A.Marqusee, S.2019-11-15doi:10.1101/843631Cold Spring Harbor Laboratory Press2019-11-15
<![CDATA[
Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria
]]>
https://biorxiv.org/cgi/content/short/780593v1?rss=1"
Shiver, A. L.Culver, R.Deutschbauer, A. M.Huang, K.2019-09-30doi:10.1101/780593Cold Spring Harbor Laboratory Press2019-09-30
<![CDATA[
Persistent transcriptional programs are associated with remote memory in diverse cells of the medial prefrontal cortex
]]>
https://biorxiv.org/cgi/content/short/784413v1?rss=1"
Chen, M. B.Jiang, X.Quake, S. R.Sudhof, T. C.2019-09-26doi:10.1101/784413Cold Spring Harbor Laboratory Press2019-09-26
<![CDATA[
A T cell behavioral manifold couples speed and turning to create heterogeneity in vivo
]]>
https://biorxiv.org/cgi/content/short/785964v1?rss=1"
Jerison, E. R.Quake, S. R.2019-09-27doi:10.1101/785964Cold Spring Harbor Laboratory Press2019-09-27
<![CDATA[
Molecular Cross-Validation for Single-Cell RNA-seq
]]>
https://biorxiv.org/cgi/content/short/786269v1?rss=1"
Batson, J.Royer, L. A.Webber, J. T.2019-09-30doi:10.1101/786269Cold Spring Harbor Laboratory Press2019-09-30
<![CDATA[
Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite
]]>
https://biorxiv.org/cgi/content/short/790493v1?rss=1"
Hays, S. G.Seed, K.2019-10-02doi:10.1101/790493Cold Spring Harbor Laboratory Press2019-10-02
<![CDATA[
A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells
]]>
https://biorxiv.org/cgi/content/short/791947v1?rss=1"
Gayoso, A.Lopez, R.Steier, Z. R.Regier, J.Streets, A. M.Yosef, N.2019-10-07doi:10.1101/791947Cold Spring Harbor Laboratory Press2019-10-07
<![CDATA[
GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control
]]>
https://biorxiv.org/cgi/content/short/792994v1?rss=1"
Hickey, K. L.Dickson, K.Cogan, J. Z.Replogle, J. M.Schoof, M.D'Orazio, K. N.Sinha, N. K.Frost, A.Green, R.Kostova, K. K.Weissman, J. S.2019-10-03doi:10.1101/792994Cold Spring Harbor Laboratory Press2019-10-03
<![CDATA[
Detecting Zero-Inflated Genes in Single-Cell Transcriptomics Data
]]>
https://biorxiv.org/cgi/content/short/794875v1?rss=1"
Clivio, O.Lopez, R.Regier, J.Gayoso, A.Jordan, M. I.Yosef, N.2019-10-07doi:10.1101/794875Cold Spring Harbor Laboratory Press2019-10-07
<![CDATA[
Membrane constriction and thinning by sequential ESCRT-III polymerization
]]>
https://biorxiv.org/cgi/content/short/798181v1?rss=1"
Nguyen, H. C.Talledge, N.McCullough, J.Sharma, A.Moss, F. R.Iwasa, J. H.Vershinin, M. D.Sundquist, W. I.Frost, A.2019-10-11doi:10.1101/798181Cold Spring Harbor Laboratory Press2019-10-11
<![CDATA[
Predicting 3D genome folding from DNA sequence
]]>
https://biorxiv.org/cgi/content/short/800060v1?rss=1"
Fudenberg, G.Kelley, D. R.Pollard, K. S.2019-10-10doi:10.1101/800060Cold Spring Harbor Laboratory Press2019-10-10
<![CDATA[
Inference of Single-Cell Phylogenies from Lineage Tracing Data
]]>
https://biorxiv.org/cgi/content/short/800078v1?rss=1"
Jones, M. G.Khodaverdian, A.Quinn, J. J.Chan, M. M.Hussmann, J. A.Wang, R.Xu, C.Weissman, J. S.Yosef, N.2019-10-10doi:10.1101/800078Cold Spring Harbor Laboratory Press2019-10-10
<![CDATA[
A large inner membrane pore defines the ESX translocon
]]>
https://biorxiv.org/cgi/content/short/800169v1?rss=1"
Poweleit, N.Czudnochowski, N.Nakagawa, R.Murphy, K. C.Sassetti, C. M.Rosenberg, O.2019-10-10doi:10.1101/800169Cold Spring Harbor Laboratory Press2019-10-10
<![CDATA[
Molecular and Morphological Signatures of Chordate Development: Two Distinct Pathways, One Tunicate
]]>
https://biorxiv.org/cgi/content/short/801589v1?rss=1"
Kowarsky, M.Anselmi, C.Hotta, K.Burighel, P.Zaniolo, G.Caicci, F.Rosental, B.Neff, N. F.Ishizuka, K. J.Palmeri, K. J.Okamoto, J.Gordon, T.Weissman, I. L.Quake, S. R.Manni, L.Voskoboynik, A.2019-10-14doi:10.1101/801589Cold Spring Harbor Laboratory Press2019-10-14
<![CDATA[
Optimized double emulsion flow cytometry with high-throughput single droplet isolation
]]>
https://biorxiv.org/cgi/content/short/803460v1?rss=1"
70% efficiency. In addition, we establish complete downstream recovery of nucleic acids from single, sorted double emulsion droplets, an advance in droplet sorting comparable with the capabilities of single-cell FACS. This work resolves several hurdles in the field of high-throughput droplet analysis and paves the way for a variety of new droplet assays, including rare variant isolation and multiparameter single-cell analysis, marrying the full power of flow cytometry with droplet microfluidics.
]]>Brower, K. K.Carswell-Crumpton, C.Klemm, S.Cruz, B.Kim, G.Calhoun, S. G.Nichols, L.Fordyce, P. M.2019-10-15doi:10.1101/803460Cold Spring Harbor Laboratory Press2019-10-15
<![CDATA[
Deconstructing the structural conservation of distantly related bacterial nucleoid-associated proteins using functional chimeras
]]>
https://biorxiv.org/cgi/content/short/804138v1?rss=1"
Lourenco, R.Saurabh, S.Herrmann, J.Wakatsuki, S.Shapiro, L.2019-10-13doi:10.1101/804138Cold Spring Harbor Laboratory Press2019-10-13
<![CDATA[
The Development, Function, and Plasticity of the Immune Macroenvironment in Cancer
]]>
https://biorxiv.org/cgi/content/short/805473v1?rss=1"
Allen, B. M.Hiam, K. J.Burnett, C. E.Venida, A.DeBarge, R.Carmi, Y.Spitzer, M. H.2019-10-16doi:10.1101/805473Cold Spring Harbor Laboratory Press2019-10-16
<![CDATA[
A weak link with actin organizes tight junctions to control epithelial permeability
]]>
https://biorxiv.org/cgi/content/short/805689v1?rss=1"
Belardi, B.Hamkins-Indik, T.Harris, A. R.Fletcher, D. A.2019-10-16doi:10.1101/805689Cold Spring Harbor Laboratory Press2019-10-16
<![CDATA[
3D projection electrophoresis for single-cell immunoblotting
]]>
https://biorxiv.org/cgi/content/short/805770v1?rss=1"
2.5 cells/s (70X faster than serial sampling) and perform 25 immunoblots/mm2 device area (>10X increase over previous immunoblots). A straightforward device for parallel single-cell immunoblotting, projection electrophoresis promises to advance integration of protein-level profiles into the emerging single-cell atlas of genomic and transcriptomic profiles.
]]>Grist, S. M.Mourdoukoutas, A. P.Herr, A. E.2019-10-16doi:10.1101/805770Cold Spring Harbor Laboratory Press2019-10-16
<![CDATA[
Precise regulation of the relative rates of surface area and volume synthesis in dynamic environments
]]>
https://biorxiv.org/cgi/content/short/806885v1?rss=1"
Shi, H.Hu, Y.Huang, K. C.2019-10-17doi:10.1101/806885Cold Spring Harbor Laboratory Press2019-10-17
<![CDATA[
Accurate and Complete Genomes from Metagenomes
]]>
https://biorxiv.org/cgi/content/short/808410v1?rss=1"
Chen, L.-X.Anantharaman, K.Shaiber, A.Eren, A. M.Banfield, J. F.2019-10-17doi:10.1101/808410Cold Spring Harbor Laboratory Press2019-10-17
<![CDATA[
Unifying single-cell annotations based on the Cell Ontology
]]>
https://biorxiv.org/cgi/content/short/810234v1?rss=1"
Wang, S.Pisco, A. O.Karkanias, J.Altman, R. B.2019-10-20doi:10.1101/810234Cold Spring Harbor Laboratory Press2019-10-20
<![CDATA[
Directed evolution improves the catalytic efficiency of TEV protease
]]>
https://biorxiv.org/cgi/content/short/811570v1?rss=1"
Sanchez Lopez, M. I.Ting, A. Y.2019-10-21doi:10.1101/811570Cold Spring Harbor Laboratory Press2019-10-21
<![CDATA[
A Chromatin Accessibility Atlas of the Developing Human Telencephalon
]]>
https://biorxiv.org/cgi/content/short/811620v1?rss=1"
Markenscoff-Papadimitriou, E.Whalen, S.Przytycki, P.Thomas, R.Binyameen, F.Nowakowski, T. J.Sanders, S. J.State, M. W.Pollard, K. S.Rubenstein, J. L.2019-10-21doi:10.1101/811620Cold Spring Harbor Laboratory Press2019-10-21
<![CDATA[
Cell-Surface Proteomic Profiling in the Fly Brain Uncovers New Wiring Regulators
]]>
https://biorxiv.org/cgi/content/short/819037v1?rss=1"
Li, J.Han, S.Li, H.Udeshi, N. D.Svinkina, T.Mani, D. R.Xu, C.Guajardo, R.Xie, Q.Li, T.Luginbuhl, D. J.Wu, B.McLaughlin, C. N.Xie, A.Kaewsapsak, P.Quake, S. R.Carr, S. A.Ting, A. Y.Luo, L.2019-10-25doi:10.1101/819037Cold Spring Harbor Laboratory Press2019-10-25
<![CDATA[
Drug resistant gut bacteria mimic a host mechanism for anticancer drug clearance
]]>
https://biorxiv.org/cgi/content/short/820084v1?rss=1"
Spanogiannopoulos, P.Bradley, P. H.Melamed, J.Malig, Y. N. A.Lam, K. N.Gerona, R. R.Pollard, K. S.Turnbaugh, P.2019-10-25doi:10.1101/820084Cold Spring Harbor Laboratory Press2019-10-25
<![CDATA[
northstar: leveraging cell atlases to identify healthy and neoplastic cells in transcriptomes from human tumors
]]>
https://biorxiv.org/cgi/content/short/820928v1?rss=1"
Zanini, F.Berghuis, B. A.Jones, R. C.Nicolis di Robilant, B.Nong, R. Y.Norton, J.Clarke, M. F.Quake, S. R.2019-10-27doi:10.1101/820928Cold Spring Harbor Laboratory Press2019-10-27
<![CDATA[
Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives
]]>
https://biorxiv.org/cgi/content/short/821132v1?rss=1"
Zou, L.Spanogiannopoulos, P.Chien, H.-C.Pieper, L. M.Cai, W.Khuri, N.Pottel, J.Vora, B.Ni, Z.Tsakalozou, E.Zhang, W.Shoichet, B. K.Giacomini, K. M.Turnbaugh, P. J.2019-10-28doi:10.1101/821132Cold Spring Harbor Laboratory Press2019-10-28
<![CDATA[
Deep functional synthesis: a machine learning approach to gene functional enrichment
]]>
https://biorxiv.org/cgi/content/short/824086v1?rss=1"
Wang, S.Ma, J.Fong, S.Rensi, S.Han, J.Peng, J.Pratt, D.Altman, R.Ideker, T.2019-11-13doi:10.1101/824086Cold Spring Harbor Laboratory Press2019-11-13
<![CDATA[
CRISPR-based screens uncover determinants of immunotherapy response and potential combination therapy strategies
]]>
https://biorxiv.org/cgi/content/short/833707v1?rss=1"
Ramkumar, P.Tian, R.Seyler, M.Leong, J. T.Choudhry, P.Hechler, T.Shah, N.Wong, S. W.Martin, T. G.Wolf, J. L.Roybal, K. T.Pahl, A.Taunton, J.Wiita, A. P.Kampmann, M.2019-11-07doi:10.1101/833707Cold Spring Harbor Laboratory Press2019-11-07
<![CDATA[
Design of Ceramic Packages for Acoustically Coupled Implantable Medical Devices
]]>
https://biorxiv.org/cgi/content/short/836312v1?rss=1"
Shen, K.Maharbiz, M. M.2019-11-11doi:10.1101/836312Cold Spring Harbor Laboratory Press2019-11-11
<![CDATA[
Surface Modification Effects on Single-Walled Carbon Nanotubes for Multimodal Optical Applications
]]>
https://biorxiv.org/cgi/content/short/837278v1?rss=1"
Chio, L.Pinals, R. L.Goh, N. S.Murali, A.Landry, M. P.2019-11-12doi:10.1101/837278Cold Spring Harbor Laboratory Press2019-11-12
<![CDATA[
Deep profiling reveals substantial heterogeneity of integration outcomes in CRISPR knock-in experiments
]]>
https://biorxiv.org/cgi/content/short/841098v1?rss=1"
Canaj, H.Hussmann, J. A.Li, H.Beckman, K. A.Goodrich, L.Cho, N. H.Li, Y. J.Santos, D. A.McGeever, A.Stewart, E. M.Pessino, V.Mandegar, M. A.Huang, C.Gan, L.Panning, B.Huang, B.Weissman, J. S.Leonetti, M. D.2019-11-13doi:10.1101/841098Cold Spring Harbor Laboratory Press2019-11-13
<![CDATA[
Modulating the cellular context broadly reshapes the mutational landscape of a model enzyme
]]>
https://biorxiv.org/cgi/content/short/848010v1?rss=1"
Thompson, S.Zhang, Y.Ingle, C.Reynolds, K. A.Kortemme, T.2019-11-20doi:10.1101/848010Cold Spring Harbor Laboratory Press2019-11-20
<![CDATA[
A Spectral De-mixing Model for Triplex In Vivo Imaging of Optical Coherence Tomography Contrast Agents
]]>
https://biorxiv.org/cgi/content/short/846170v1?rss=1"
Yuan, E.Si, P.Shevidi, S.de la Zerda, A.2019-11-18doi:10.1101/846170Cold Spring Harbor Laboratory Press2019-11-18
<![CDATA[
Semi-supervised identification of cell populations in single-cell ATAC-seq
]]>
https://biorxiv.org/cgi/content/short/847657v1?rss=1"
Przytycki, P. F.Pollard, K. S.2019-11-19doi:10.1101/847657Cold Spring Harbor Laboratory Press2019-11-19
<![CDATA[
Heterogeneity and targeted therapy-induced adaptations in lung cancer revealed by longitudinal single-cell RNA sequencing
]]>
https://biorxiv.org/cgi/content/short/2019.12.08.868828v1?rss=1"
Maynard, A.McCoach, C. E.Rotow, J. K.Harris, L.Haderk, F.Kerr, L. D.Yu, E. A.Schenk, E. L.Tan, W.Zee, A.Tan, M.Gui, P.Lea, T.Wu, W.Urisman, A.Jones, K.Sit, R.Kolli, P. K.Seeley, E.Gesthalter, Y.Le, D. D.Yamauchi, K. A.Naeger, D. M.Thomas, N. J.Gupta, A.Gonzalez, M.Do, H.Tan, L.Gomez-Sjoberg, R.Gubens, M.Jahan, T.Kratz, J. R.Jablons, D.Neff, N.Doebele, R. C.Weissman, J.Blakely, C. M.Darmanis, S.Bivona, T. G.2019-12-13doi:10.1101/2019.12.08.868828Cold Spring Harbor Laboratory Press2019-12-13
<![CDATA[
A minimal CRISPR-Cas3 system for genome engineering
]]>
https://biorxiv.org/cgi/content/short/860999v1?rss=1"
Csorgo, B.Leon, L. M.Chau-Ly, I. J.Vasquez-Rifo, A.Berry, J. D.Mahendra, C.Crawford, E.Lewis, J. D.Bondy-Denomy, J.2019-12-03doi:10.1101/860999Cold Spring Harbor Laboratory Press2019-12-03
<![CDATA[
Combined use of metagenomic sequencing and host response profiling for the diagnosis of suspected sepsis.
]]>
https://biorxiv.org/cgi/content/short/854182v1?rss=1"
Cheng, H. K.Tan, S. K.Sweeney, T. E.Jeganathan, P.Briese, T.Khadka, V.Strouts, F.Thair, S.Dalai, S.Hitchcock, M.Multani, A.Aronson, J.Andermann, T.Yu, A.Yang, S.Holmes, S.Lipkin, W. I.Khatri, P.Relman, D. A.2019-11-25doi:10.1101/854182Cold Spring Harbor Laboratory Press2019-11-25
<![CDATA[
Characterization of the impact of daclizumab beta on circulating natural killer cells by mass cytometry
]]>
https://biorxiv.org/cgi/content/short/865477v1?rss=1"
Ranganath, T.Simpson, L. J.Seiler, C.Ferreira, A.-M.Vendrame, E.Zhao, N. Q.Fontenot, J. D.Holmes, S. P.Blish, C. A.2019-12-05doi:10.1101/865477Cold Spring Harbor Laboratory Press2019-12-05
<![CDATA[
Paralogs in the PKA regulon traveled different evolutionary routes to divergent expression in budding yeast.
]]>
https://biorxiv.org/cgi/content/short/860981v1?rss=1"
Heineike, B. M.El-Samad, H.2019-12-02doi:10.1101/860981Cold Spring Harbor Laboratory Press2019-12-02
<![CDATA[
Nanotopography enhances dynamic remodeling of tight junction proteins through cytosolic complexes
]]>
https://biorxiv.org/cgi/content/short/858118v1?rss=1"
Huang, X.Shi, X.Hansen, M. E.Nemeth, C. L.Celli, A.Huang, B.Mauro, T.Koval, M.Desai, T.2019-11-28doi:10.1101/858118Cold Spring Harbor Laboratory Press2019-11-28
<![CDATA[
A CRISPR screen identifies UFMylation and TRAMP-like complexes required for hepatitis A virus infection
]]>
https://biorxiv.org/cgi/content/short/2019.12.15.877100v1?rss=1"
Puschnik, A. S.Kulsuptrakul, J.Wang, R.Meyers, N. L.Ott, M.2019-12-16doi:10.1101/2019.12.15.877100Cold Spring Harbor Laboratory Press2019-12-16
<![CDATA[
Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular sensors
]]>
https://biorxiv.org/cgi/content/short/2019.12.16.877183v1?rss=1"
Andreasson, J.Gotrik, M.Wu, M. J.Wayment-Steele, H.Kladwang, W.Portela, F.Wellington-Oguri, R.Players, E.Das, R.Greenleaf, W.2019-12-16doi:10.1101/2019.12.16.877183Cold Spring Harbor Laboratory Press2019-12-16
<![CDATA[
Loss of Tsc1 from striatal direct pathway neurons impairs endocannabinoid-LTD and enhances motor routine learning
]]>
https://biorxiv.org/cgi/content/short/2019.12.15.877126v1?rss=1"
Benthall, K. N.Cording, K. R.Agopyan-Miu, A. H. C. W.Chen, E. Y.Bateup, H. S.2019-12-16doi:10.1101/2019.12.15.877126Cold Spring Harbor Laboratory Press2019-12-16
<![CDATA[
Single cell epigenomic atlas of the developing human brain and organoids
]]>
https://biorxiv.org/cgi/content/short/2019.12.30.891549v1?rss=1"
75,000 cells from eight distinct areas of developing human forebrain using single cell ATAC-seq (scATACseq). We identified thousands of loci that undergo extensive cell type-specific changes in accessibility during corticogenesis. Chromatin state profiling also reveals novel distinctions between neural progenitor cells from different cortical areas not seen in transcriptomic profiles and suggests a role for retinoic acid signaling in cortical arealization. Comparison of the cell type-specific chromatin landscape of cerebral organoids to primary developing cortex found that organoids establish broad cell type-specific enhancer accessibility patterns similar to the developing cortex, but lack many putative regulatory elements identified in homologous primary cell types. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.
]]>Ziffra, R. S.Kim, C. N.Wilfert, A.Haeussler, M.Casella, A. M.Przytycki, P. F.Kreimer, A.Pollard, K. S.Ament, S. A.Eichler, E. E.Ahituv, N.Nowakowski, T. J.2019-12-31doi:10.1101/2019.12.30.891549Cold Spring Harbor Laboratory Press2019-12-31
<![CDATA[
Antigen responsive CD4+ T cell clones contribute to the HIV-1 latent reservoir
]]>
https://biorxiv.org/cgi/content/short/2020.01.10.902155v1?rss=1"
Mendoza, P.Jackson, J. R.Oliveira, T.Gaebler, C.Ramos, V.Caskey, M.Jankovic, M.Nussenzweig, M. C.Cohn, L. B.2020-01-11doi:10.1101/2020.01.10.902155Cold Spring Harbor Laboratory Press2020-01-11
<![CDATA[
Protein sequence design with a learned potential
]]>
https://biorxiv.org/cgi/content/short/2020.01.06.895466v1?rss=1"
Anand, N.Eguchi, R. R.Derry, A.Altman, R. B.Huang, P.2020-01-07doi:10.1101/2020.01.06.895466Cold Spring Harbor Laboratory Press2020-01-07
<![CDATA[
ATP hydrolysis by the SNF2 domain of the ultraspecific maintenance methylase Dnmt5 drives recognition and modification of hemimethylated DNA
]]>
https://biorxiv.org/cgi/content/short/2020.01.05.895227v1?rss=1"
Dumesic, P. A.Stoddard, C. I.Catania, S.Narlikar, G. J.Madhani, H.2020-01-06doi:10.1101/2020.01.05.895227Cold Spring Harbor Laboratory Press2020-01-06
<![CDATA[
Biophysical basis of cellular multi-specificity encoded in a model molecular switch
]]>
https://biorxiv.org/cgi/content/short/2020.01.04.893909v1?rss=1"
Perica, T.Mathy, C. J. P.Xu, J.Jang, G. M.Zhang, Y.Kaake, R.Ollikainen, N.Braberg, H.Swaney, D. L.Kelly, M. J. S.Krogan, N. J.Kortemme, T.2020-01-06doi:10.1101/2020.01.04.893909Cold Spring Harbor Laboratory Press2020-01-06
<![CDATA[
Lactoferrin Reverses Methotrexate Driven Epithelial Barrier Defect by Inhibiting TGF-β Mediated Epithelial to Mesenchymal Transition
]]>
https://biorxiv.org/cgi/content/short/2019.12.23.878207v1?rss=1"
Wallach, T.Srivastava, V.Reyes, E.Klein, O. D.Gartner, Z. J.2019-12-26doi:10.1101/2019.12.23.878207Cold Spring Harbor Laboratory Press2019-12-26
<![CDATA[
The rise of diversity in metabolic platforms across the Candidate Phyla Radiation
]]>
https://biorxiv.org/cgi/content/short/2019.12.18.881540v1?rss=1"
Jaffe, A. L.Castelle, C. J.Matheus Carnevali, P. B.Gribaldo, S.Banfield, J.2019-12-19doi:10.1101/2019.12.18.881540Cold Spring Harbor Laboratory Press2019-12-19
<![CDATA[
Coverage-dependent bias creates the appearance of binary splicing in single cells
]]>
https://biorxiv.org/cgi/content/short/2019.12.19.883256v1?rss=1"
Buen Abad Najar, C. F.Yosef, N.Lareau, L. F.2019-12-20doi:10.1101/2019.12.19.883256Cold Spring Harbor Laboratory Press2019-12-20
<![CDATA[
Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
]]>
https://biorxiv.org/cgi/content/short/2019.12.21.886093v1?rss=1"
Roodgar, M.Good, B. H.Garud, N. R.Martis, S.Avula, M.Zhou, W.Lancaster, S.Lee, H.Babveyh, A.Nesamoney, S.Pollard, K. S.Snyder, M. P.2019-12-23doi:10.1101/2019.12.21.886093Cold Spring Harbor Laboratory Press2019-12-23
<![CDATA[
Mouse Aging Cell Atlas Analysis Reveals Global and Cell Type Specific Aging Signatures
]]>
https://biorxiv.org/cgi/content/short/2019.12.23.887604v1?rss=1"
Zhang, M. J.Pisco, A. O.Darmanis, S.Zou, J.2019-12-27doi:10.1101/2019.12.23.887604Cold Spring Harbor Laboratory Press2019-12-27
<![CDATA[
Adaption of a Conventional ELISA to a 96-well ELISA-Array for Measuring the Antibody Responses to Influenza virus proteins, viruses and vaccines
]]>
https://biorxiv.org/cgi/content/short/2019.12.20.885285v1?rss=1"
Waltari, E.Carabajal, E.Sanyal, M.Friedland, N.McCutcheon, K. M.2019-12-23doi:10.1101/2019.12.20.885285Cold Spring Harbor Laboratory Press2019-12-23
<![CDATA[
Molecular height measurement by cell surface optical profilometry (CSOP)
]]>
https://biorxiv.org/cgi/content/short/2019.12.31.892075v1?rss=1"
Son, S.Takatori, S.Belardi, B.Podolski, M.Bakalar, M. H.Fletcher, D. A.2020-01-01doi:10.1101/2019.12.31.892075Cold Spring Harbor Laboratory Press2020-01-01
<![CDATA[
Protein Corona Composition and Dynamics on Carbon Nanotubes in Blood Plasma and Cerebrospinal Fluid
]]>
https://biorxiv.org/cgi/content/short/2020.01.13.905356v1?rss=1"
Pinals, R. L.Yang, D.Rosenberg, D. J.Chaudhary, T.Crothers, A. R.Iavarone, A. T.Hammel, M.Landry, M. P.2020-01-14doi:10.1101/2020.01.13.905356Cold Spring Harbor Laboratory Press2020-01-14
<![CDATA[
Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by PhIP-Seq
]]>
https://biorxiv.org/cgi/content/short/2020.01.20.913186v1?rss=1"
Vazquez, S. E.Ferre, E. M. N.Scheel, D. W.Sunshine, S.Miao, B.Mandel-Brehm, C.Quandt, Z.Chan, A. Y.Cheng, M.German, M. S.Lionakis, M. S.DeRisi, J. L.Anderson, M. S.2020-01-21doi:10.1101/2020.01.20.913186Cold Spring Harbor Laboratory Press2020-01-21
<![CDATA[
Single-cell metabolic analysis by mass cytometry reveals distinct transitional states of CD8 T cell differentiation
]]>
https://biorxiv.org/cgi/content/short/2020.01.21.911545v1?rss=1"
Levine, L. S.Hiam, K. J.Marquez, D. M.Tenvooren, I.Contreras, D. C.Rathmell, J. C.Spitzer, M. H.2020-01-22doi:10.1101/2020.01.21.911545Cold Spring Harbor Laboratory Press2020-01-22
<![CDATA[
InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains
]]>
https://biorxiv.org/cgi/content/short/2020.01.22.915579v1?rss=1"
1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born via cesarean section harbored Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital versus maternal microbiomes. Genomic loci showing diversity within an infant included variants found in other infants, possibly reflecting inoculation from diverse hospital-associated sources. InStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.
]]>Olm, M. R.Crits-Christoph, A.Bouma-Gregson, K.Firek, B.Morowitz, M.Banfield, J.2020-01-23doi:10.1101/2020.01.22.915579Cold Spring Harbor Laboratory Press2020-01-23
<![CDATA[
Continuous detection of glucose and insulin in live animals
]]>
https://biorxiv.org/cgi/content/short/2020.01.22.916106v1?rss=1"
Poudineh, M.Maikawa, C. L.Yue Ma, E.Pan, J.Mamerow, D.Han, Y.Baker, S. w.Beirami, A.Eisenstein, M.Kim, S.Vuckovic, J.Appel, E. A.Soh, H. T.2020-01-23doi:10.1101/2020.01.22.916106Cold Spring Harbor Laboratory Press2020-01-23
<![CDATA[
In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity
]]>
https://biorxiv.org/cgi/content/short/2020.01.23.912717v1?rss=1"
Wagner, A.Wang, C.DeTomaso, D.Avila-Pacheco, J.Zaghouani, S.Fessler, J.Akama-Garren, E.Pierce, K.Ron-Harel, N.Douglas, V. P.Haigis, M.Sobel, R. A.Clish, C.Regev, A.Kuchroo, V. K.Yosef, N.2020-01-24doi:10.1101/2020.01.23.912717Cold Spring Harbor Laboratory Press2020-01-24
<![CDATA[
Host-derived Circular RNAs Display Proviral Activities in Hepatitis C Virus - Infected Cells
]]>
https://biorxiv.org/cgi/content/short/2020.01.24.917971v1?rss=1"
Chen, T.-C.Tallo-Parra, M.Kadener, S.Böttcher, R.Perez-Vilaro, G.Boonchuen, P.Somboonwiwat, K.Diez, J.Sarnow, P.2020-01-24doi:10.1101/2020.01.24.917971Cold Spring Harbor Laboratory Press2020-01-24
<![CDATA[
Pharmaceutical-grade Rigosertib is a Microtubule-destabilizing Agent
]]>
https://biorxiv.org/cgi/content/short/2020.01.28.923235v1?rss=1"
99.9% purity) results in qualitatively indistinguishable phenotypes as treatment with commercially obtained rigosertib across multiple assays. The two compounds have indistinguishable chemical-genetic interactions with genes involved in modulating the microtubule network (KIF2C and TACC3), both destabilize microtubules in cells and in vitro, and both show substantially reduced toxicity in cell lines expressing a rationally-designed mutant of tubulin (L240F TUBB mutant), in which the rigosertib binding site in tubulin is mutated. Importantly, the specificity of the L240F TUBB mutant for microtubule-destabilizing agents, which is disputed by Reddy and co-workers, was recently confirmed by an independent research group (Patterson et al., 2019). We conclude that rigosertib kills cancer cells by destabilizing microtubules, in agreement with our original findings.
]]>Jost, M.Chen, Y.Gilbert, L. A.Horlbeck, M. A.Krenning, L.Menchon, G.Rai, A.Cho, M. Y.Stern, J. J.Prota, A. E.Kampmann, M.Akhmanova, A.Steinmetz, M. O.Tanenbaum, M. E.Weissman, J. S.2020-01-29doi:10.1101/2020.01.28.923235Cold Spring Harbor Laboratory Press2020-01-29
<![CDATA[
Mapping of the nucleolar proteome reveals spatiotemporal organization related to intrinsic protein disorder
]]>
https://biorxiv.org/cgi/content/short/2020.01.30.923003v1?rss=1"
Stenstrom, L.Mahdessian, D.Gnann, C.Leonetti, M.Uhlen, M.Cuylen-Haering, S.Thul, P.Lundberg, E.2020-01-30doi:10.1101/2020.01.30.923003Cold Spring Harbor Laboratory Press2020-01-30
<![CDATA[
Poecivirus is present in individuals with beak deformities in seven species of North American birds
]]>
https://biorxiv.org/cgi/content/short/2020.02.03.927442v1?rss=1"
Zylberberg, M.Van Hemert, C.Handel, C. M.Liu, R.DeRisi, J.2020-02-04doi:10.1101/2020.02.03.927442Cold Spring Harbor Laboratory Press2020-02-04
<![CDATA[
Re-evaluating the conventional wisdom about binding assays
]]>
https://biorxiv.org/cgi/content/short/2020.02.03.932392v1?rss=1"
Wilson, B. D.Soh, H. T.2020-02-03doi:10.1101/2020.02.03.932392Cold Spring Harbor Laboratory Press2020-02-03
<![CDATA[
Hubble2D6: A deep learning approach for predicting drug metabolic activity
]]>
https://biorxiv.org/cgi/content/short/684357v1?rss=1"
McInnes, G.Dalton, R.Sangkuhl, K.Whirl-Carrillo, M.Lee, S.-b.Altman, R. B.Woodahl, E. L.2019-06-27doi:10.1101/684357Cold Spring Harbor Laboratory Press2019-06-27
<![CDATA[
Differential Impacts on Host Transcription by ROP and GRA Effectors from the Intracellular Parasite Toxoplasma gondii
]]>
https://biorxiv.org/cgi/content/short/2020.02.04.934570v1?rss=1"
Rastogi, S.Xue, Y.Quake, S. R.Boothroyd, J. C.2020-02-05doi:10.1101/2020.02.04.934570Cold Spring Harbor Laboratory Press2020-02-05
<![CDATA[
Identifying Informative Gene Modules Across Modalities of Single Cell Genomics
]]>
https://biorxiv.org/cgi/content/short/2020.02.06.937805v1?rss=1"
DeTomaso, D.Yosef, N.2020-02-07doi:10.1101/2020.02.06.937805Cold Spring Harbor Laboratory Press2020-02-07
<![CDATA[
Binding affinity and conformational preferences influence kinetic stability of short oligonucleotides on carbon nanotubes
]]>
https://biorxiv.org/cgi/content/short/2020.02.08.939918v1?rss=1"
View larger version (22K):
org.highwire.dtl.DTLVardef@6483e6org.highwire.dtl.DTLVardef@10f9e60org.highwire.dtl.DTLVardef@66c8c3org.highwire.dtl.DTLVardef@68ff4_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Alizadehmojarad, A.Zhou, X.Beyene, A. G.Chacon, K.Sung, Y.Landry, M. P.Vukovic, L.2020-02-10doi:10.1101/2020.02.08.939918Cold Spring Harbor Laboratory Press2020-02-10
<![CDATA[
Measuring aptamer folding energy using a molecular clamp
]]>
https://biorxiv.org/cgi/content/short/2020.02.10.941203v1?rss=1"
Qu, H.Ma, Q.Wang, L.Mao, Y.Eisenstein, M.Soh, H. T.Zheng, L.2020-02-10doi:10.1101/2020.02.10.941203Cold Spring Harbor Laboratory Press2020-02-10
<![CDATA[
Form and function: diverse homeostatic and immunomodulatory roles of immune cells in the developing lung revealed at single cell resolution
]]>
https://biorxiv.org/cgi/content/short/2020.02.10.942359v1?rss=1"
Domingo-Gonzalez, R.Zanini, F.Che, X.Liu, M.Jones, R. C.Swift, M. A.Quake, S. R.Cornfield, D. N.Alvira, C. M.2020-02-11doi:10.1101/2020.02.10.942359Cold Spring Harbor Laboratory Press2020-02-11
<![CDATA[
Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine Pathway
]]>
https://biorxiv.org/cgi/content/short/2020.01.23.911966v1?rss=1"
Wang, C.Wagner, A.Fessler, J.Avila-Pacheco, J.Karminski, J.Thakore, P.Zaghouani, S.Pierce, K.Bod, L.Schnell, A.DeTomaso, D.Ron-Harel, N.Haigis, M.Puleston, D.Pearce, E.Soleimani, M.Sobel, R.Clish, C.Regev, A.Yosef, N.Kuchroo, V.2020-01-23doi:10.1101/2020.01.23.911966Cold Spring Harbor Laboratory Press2020-01-23
<![CDATA[
Single mosquito metatranscriptomics recovers mosquito species, blood meal sources, and microbial cargo, including viral dark matter
]]>
https://biorxiv.org/cgi/content/short/2020.02.10.942854v1?rss=1"
Batson, J.Kistler, A.Dudas, G.Li, L.Ratnasari, K.Haas-Stapleton, E.Logan, P.Retallack, H.2020-02-13doi:10.1101/2020.02.10.942854Cold Spring Harbor Laboratory Press2020-02-13
<![CDATA[
No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells
]]>
https://biorxiv.org/cgi/content/short/2020.02.12.946509v1?rss=1"
McGinnis, C. S.Siegel, D. A.Xie, G.Stone, M.Gartner, Z. J.Roan, N. R.Lee, S. A.2020-02-13doi:10.1101/2020.02.12.946509Cold Spring Harbor Laboratory Press2020-02-13
<![CDATA[
Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation
]]>
https://biorxiv.org/cgi/content/short/2020.02.13.942896v1?rss=1"
90%) and affiliate phylogenetically with those of coexisting bacterial methanotrophs, and their abundance patterns correlate with the abundances of these bacteria, supporting host-phage relationships. We suggest that phage PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contribute to growth on methane. Transcriptomics data from one system showed that the phage-associated pmoC genes are actively expressed in situ. Augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this powerful greenhouse gas into the environment.
]]>Chen, L.-X.Meheust, R.Crits-Christoph, A.McMahon, K. D.Colenbrander Nelson, T.Warren, L. A.Banfield, J.2020-02-14doi:10.1101/2020.02.13.942896Cold Spring Harbor Laboratory Press2020-02-14
<![CDATA[
The interaction of crossover formation and the dynamic architecture of the synaptonemal complex during meiosis
]]>
https://biorxiv.org/cgi/content/short/2020.02.16.947804v1?rss=1"
Köhler, S.Wojcik, M.Xu, K.Dernburg, A.2020-02-16doi:10.1101/2020.02.16.947804Cold Spring Harbor Laboratory Press2020-02-16
<![CDATA[
μCB-seq: Microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells
]]>
https://biorxiv.org/cgi/content/short/2020.02.18.954974v1?rss=1"
Chen, T. N.Gupta, A. N.Zalavadia, M. D.Streets, A.2020-02-20doi:10.1101/2020.02.18.954974Cold Spring Harbor Laboratory Press2020-02-20
<![CDATA[
The transcriptional landscape of Venezuelan equine encephalitis virus infection
]]>
https://biorxiv.org/cgi/content/short/2020.02.18.955393v1?rss=1"
Yao, Z.Zanini, F.Kumar, S.Panpradist, N.Muniz, A.Quake, S. R.Einav, S.2020-02-19doi:10.1101/2020.02.18.955393Cold Spring Harbor Laboratory Press2020-02-19
<![CDATA[
Biased localization of actin binding proteins by actin filament conformation
]]>
https://biorxiv.org/cgi/content/short/2020.02.21.959791v1?rss=1"
Harris, A. R.Jreij, P.Belardi, B.Bausch, A.Fletcher, D. A.2020-02-22doi:10.1101/2020.02.21.959791Cold Spring Harbor Laboratory Press2020-02-22
<![CDATA[
Mapping proteolytic neo-N termini at the surface of living cells
]]>
https://biorxiv.org/cgi/content/short/2020.02.23.961904v1?rss=1"
Weeks, A. M.Byrnes, J. R.Lui, I.Wells, J. A.2020-02-24doi:10.1101/2020.02.23.961904Cold Spring Harbor Laboratory Press2020-02-24
<![CDATA[
Discovering novel cell types across heterogeneous single-cell experiments
]]>
https://biorxiv.org/cgi/content/short/2020.02.25.960302v1?rss=1"
Brbic, M.Zitnik, M.Wang, S.Pisco, A. O.Altman, R. B.Darmanis, S.Leskovec, J.2020-02-26doi:10.1101/2020.02.25.960302Cold Spring Harbor Laboratory Press2020-02-26
<![CDATA[
Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome
]]>
https://biorxiv.org/cgi/content/short/2020.02.25.964536v1?rss=1"
Tessema, S. K.Hathaway, N. J.Teyssier, N. B.Murphy, M.Aydemir, O.Duarte, E. M.Simone, W.Colborn, J.Saute, F.Crawford, E.Aide, P.Bailey, J. A.Greenhouse, B.2020-02-26doi:10.1101/2020.02.25.964536Cold Spring Harbor Laboratory Press2020-02-26
<![CDATA[
CRISPR Screen in Regulatory T Cells Reveals Ubiquitination Modulators of Foxp3
]]>
https://biorxiv.org/cgi/content/short/2020.02.26.966911v1?rss=1"
Cortez, J. T.Montauti, E.Shifrut, E.Zhang, Y.Shaked, O.Xu, Y.Roth, T.Simeonov, D.Zhang, Y.Chen, S.Li, Z.Vogel, I. A.Prator, G. Y.Zhang, B.Lee, Y.Sun, Z.Ifergan, I.Van Gool, F.Bluestone, J. A.Marson, A.Fang, D.2020-02-27doi:10.1101/2020.02.26.966911Cold Spring Harbor Laboratory Press2020-02-27
<![CDATA[
Joint profiling of proteins and DNA in single cells reveals extensive proteogenomic decoupling in leukemia
]]>
https://biorxiv.org/cgi/content/short/2020.02.26.967133v1?rss=1"
Demaree, B.Delley, C. L.Vasudevan, H. N.Peretz, C. A. C.Ruff, D.Smith, C. C.Abate, A. R.2020-02-28doi:10.1101/2020.02.26.967133Cold Spring Harbor Laboratory Press2020-02-28
<![CDATA[
RNA-protein interaction mapping via MS2 or Cas13-based APEX targeting
]]>
https://biorxiv.org/cgi/content/short/2020.02.27.968297v1?rss=1"
Han, S.Zhao, B. S.Myers, S. A.Carr, S. A.He, C.Ting, A. Y.2020-02-28doi:10.1101/2020.02.27.968297Cold Spring Harbor Laboratory Press2020-02-28
<![CDATA[
Charge-Altering Releasable Transporters enable specific phenotypic manipulation of resting primary natural killer cells
]]>
https://biorxiv.org/cgi/content/short/2020.02.28.970491v1?rss=1"
Wilk, A. J.Benner, N. L.Vergara, R.Haabeth, O. A. W.Levy, R.Waymouth, R. M.Wender, P. A.Blish, C. A.2020-03-03doi:10.1101/2020.02.28.970491Cold Spring Harbor Laboratory Press2020-03-03
<![CDATA[
Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
]]>
https://biorxiv.org/cgi/content/short/2020.03.02.968818v1?rss=1"
Manning, J. E.Bohl, J. A.Lay, S.Chea, S.Ly, S.Sengdoeurn, Y.Heng, S.Vuthy, C.Kalantar, K.Ahyong, V.Tan, M.Sheu, J.Tato, C. M.DeRisi, J.Baril, L.Dussart, P.Duong, V.Karlsson, E. A.2020-03-05doi:10.1101/2020.03.02.968818Cold Spring Harbor Laboratory Press2020-03-05
<![CDATA[
Ageing compromises mouse thymus function and remodels epithelial cell differentiation
]]>
https://biorxiv.org/cgi/content/short/2020.03.02.973008v1?rss=1"
Ponting, C. P.Baran-Gale, J.Morgan, M. D.Maio, S.Dhalla, F.Calvo-Asensio, I.Deadman, M.Handel, A. E.Maynard, A.Chen, S.Green, F.Sit, R.Neff, N.Darmanis, S.Tan, W.May, A. P.Marioni, J. C.Holländer, G. A.2020-03-03doi:10.1101/2020.03.02.973008Cold Spring Harbor Laboratory Press2020-03-03
<![CDATA[
Bacteroides thetaiotaomicron-infecting bacteriophage isolates inform sequence-based host range prediction
]]>
https://biorxiv.org/cgi/content/short/2020.03.04.977157v1?rss=1"
Hryckowian, A. J.Merrill, B. D.Porter, N. T.Van Treuren, W.Nelson, E. J.Garlena, R. A.Russell, D. A.Martens, E. C.Sonnenburg, J. L.2020-03-05doi:10.1101/2020.03.04.977157Cold Spring Harbor Laboratory Press2020-03-05
<![CDATA[
Differentiation drives widespread rewiring of the neural stem cell chaperone network
]]>
https://biorxiv.org/cgi/content/short/2020.03.05.976068v1?rss=1"
Vonk, W. I. M.Rainbolt, T. K.Dolan, P. T.Webb, A. E.Brunet, A.Frydman, J.2020-03-06doi:10.1101/2020.03.05.976068Cold Spring Harbor Laboratory Press2020-03-06
<![CDATA[
Fronto-striatal projections regulate approach-avoidance conflict
]]>
https://biorxiv.org/cgi/content/short/2020.03.05.979708v1?rss=1"
Loewke, A. C.Minerva, A. R.Nelson, A. B.Kreitzer, A. C.Gunaydin, L. A.2020-03-06doi:10.1101/2020.03.05.979708Cold Spring Harbor Laboratory Press2020-03-06
<![CDATA[
Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota
]]>
https://biorxiv.org/cgi/content/short/2020.03.06.976126v1?rss=1"
1,000 different families of putative metabolic gene clusters. Analysis of the enzyme content of these gene clusters suggests that they encode pathways with a wide range of predicted substrate classes, including saccharides, amino acids/peptides and lipids. Altogether, these results indicate a potentially important role of this protein superfamily in the human gut, and our dataset provides significant opportunities for the discovery of novel pathways that may have significant effects on human health.
]]>Pascal Andreu, V.Fischbach, M. A.Medema, M. H.2020-03-06doi:10.1101/2020.03.06.976126Cold Spring Harbor Laboratory Press2020-03-06
<![CDATA[
High-Throughput Stool Metaproteomics: Method and Application to Human Specimens
]]>
https://biorxiv.org/cgi/content/short/2020.03.06.981712v1?rss=1"
Gonzalez, C. G.Wastyk, H. C.Topf, M.Gardner, C. D.Sonnenburg, J. L.Elias, J. E.2020-03-08doi:10.1101/2020.03.06.981712Cold Spring Harbor Laboratory Press2020-03-08
<![CDATA[
Split-TurboID enables contact-dependent proximity labeling in cells
]]>
https://biorxiv.org/cgi/content/short/2020.03.11.988022v1?rss=1"
100 endogenous proteins, including many not previously linked to ER-mitochondria contacts. We validated eight novel candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially-specific proximity labeling in cells.
]]>Cho, K. F.Branon, T. C.Rajeev, S.Svinkina, T.Udeshi, N. D.Thoudam, T.Kwak, C.Rhee, H.-W.Lee, I.-K.Carr, S. A.Ting, A. Y.2020-03-12doi:10.1101/2020.03.11.988022Cold Spring Harbor Laboratory Press2020-03-12
<![CDATA[
A family of viral satellites manipulates invading virus gene expression and affects cholera toxin mobilization
]]>
https://biorxiv.org/cgi/content/short/2020.03.12.988147v1?rss=1"
Barth, Z. K.Netter, Z.Angermeyer, A.Bhardwaj, P.Seed, K.2020-03-12doi:10.1101/2020.03.12.988147Cold Spring Harbor Laboratory Press2020-03-12
<![CDATA[
Efficient Generation of Isogenic Primary Human Myeloid Cells using CRISPR-Cas9 Ribonucleoproteins
]]>
https://biorxiv.org/cgi/content/short/2020.03.13.991414v1?rss=1"
Hiatt, J.Cavero, D. A.McGregor, M. J.Gordon, D. E.Zheng, W.Budzik, J. M.Roth, T. L.Haas, K. M.Rathore, U.Meyer-Franke, A.Bouzidi, M. S.Hultquist, J. F.Wojcechowskyj, J. A.Fontaine, K. A.Pillai, S. K.Cox, J. S.Ernst, J. D.Krogan, N. J.Marson, A.2020-03-15doi:10.1101/2020.03.13.991414Cold Spring Harbor Laboratory Press2020-03-15
<![CDATA[
Differential encoding in prefrontal cortex projection neuron classes across cognitive tasks
]]>
https://biorxiv.org/cgi/content/short/2020.03.14.991018v1?rss=1"
Lui, J. H.Nguyen, N. D.Grutzner, S. M.Darmanis, S.Peixoto, D.Wagner, M. J.Allen, W. E.Kebschull, J. M.Richman, E. B.Ren, J.Newsome, W. T.Quake, S. R.Luo, L.2020-03-14doi:10.1101/2020.03.14.991018Cold Spring Harbor Laboratory Press2020-03-14
<![CDATA[
Rational Design of Aptamer Switches with Programmable pH Response
]]>
https://biorxiv.org/cgi/content/short/2020.03.14.992040v1?rss=1"
Thompson, I. A. P.Zheng, L.Eisenstein, M.Soh, H. T.2020-03-16doi:10.1101/2020.03.14.992040Cold Spring Harbor Laboratory Press2020-03-16
<![CDATA[
Single-cell transcriptomic analysis of the adult mouse spinal cord
]]>
https://biorxiv.org/cgi/content/short/2020.03.16.992958v1?rss=1"
Blum, J.Nakayama, L.Klemm, S.Kathiria, A.Guttenplan, K.Hoang, P.Shadrach, J.Kaltschmidt, J.Greenleaf, W.Gitler, A. D.2020-03-17doi:10.1101/2020.03.16.992958Cold Spring Harbor Laboratory Press2020-03-17
<![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[
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
]]>
https://biorxiv.org/cgi/content/short/2020.03.22.002386v1?rss=1"
Gordon, D. E.Jang, G. M.Bouhaddou, M.Xu, J.Obernier, K.O'Meara, M. J.Guo, J. Z.Swaney, D. L.Tummino, T. A.Huttenhain, R.Kaake, R.Richards, A. L.Tutuncuoglu, B.Foussard, H.Batra, J.Haas, K.Modak, M.Kim, M.Haas, P.Polacco, B. J.Braberg, H.Fabius, J. M.Eckhardt, M.Soucheray, M.Brewer, M.Cakir, M.McGregor, M. J.Li, Q.Naing, Z. Z. C.Zhou, Y.Peng, S.Kirby, I. T.Melnyk, J. E.Chorba, J. S.Lou, K.Dai, S. A.Shen, W.Shi, Y.Zhang, Z.Barrio-Hernandez, I.Memon, D.Hernandez-Armenta, C.Mathy, C. J. P.Perica, T.Pilla, K. B.2020-03-22doi:10.1101/2020.03.22.002386Cold Spring Harbor Laboratory Press2020-03-22
<![CDATA[
FcRn, but not FcgRs, drives maternal-fetal transplacental transport of human IgGantibodies
]]>
https://biorxiv.org/cgi/content/short/2020.03.22.999243v1?rss=1"
Borghi, S.Bournazos, S.Thulin, N.Li, C.Gajewski, A.Sherwood, R.Zhang, S.Harris, E.Jagannathan, P.Wang, L.-X.Ravetch, J. V.Wang, T. T.2020-03-25doi:10.1101/2020.03.22.999243Cold Spring Harbor Laboratory Press2020-03-25
<![CDATA[
Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics
]]>
https://biorxiv.org/cgi/content/short/2020.03.23.004093v1?rss=1"
West, P. T.Peters, S. L.Olm, M. R.Yu, F. B.Lou, Y. C.Firek, B. A.Baker, R.Johnson, A. D.Morowitz, M. J.Hettich, R. L.Banfield, J. F.2020-03-25doi:10.1101/2020.03.23.004093Cold Spring Harbor Laboratory Press2020-03-25
<![CDATA[
Human microglia upregulate cytokine signatures and accelerate maturation of neural networks
]]>
https://biorxiv.org/cgi/content/short/2020.03.24.006874v1?rss=1"
Schmunk, G.Chang, K. N.Soliman, S. S.Keefe, M. G.Bogdanoff, D.Tejera, D.Ziffra, R. S.Shin, D.Allen, D. E.Chhun, B. B.McGinnis, C. S.Winkler, E. A.Abla, A. A.Chang, E. F.Gartner, Z. J.Mehta, S. B.Piao, X.Hengen, K. B.Nowakowski, T. J.2020-03-25doi:10.1101/2020.03.24.006874Cold Spring Harbor Laboratory Press2020-03-25
<![CDATA[
Inter-domain dynamics drive cholesterol transport by NPC1 and NPC1L1 proteins
]]>
https://biorxiv.org/cgi/content/short/2020.03.26.009217v1?rss=1"
Saha, P.Shumate, J. L.Caldwell, J. G.Elghobashi-Meinhardt, N.Lu, A.Zhang, L.Olsson, N.Elias, J. E.Pfeffer, S. R.2020-03-29doi:10.1101/2020.03.26.009217Cold Spring Harbor Laboratory Press2020-03-29
<![CDATA[
SCITO-seq: single-cell combinatorial indexed cytometry sequencing
]]>
https://biorxiv.org/cgi/content/short/2020.03.27.012633v1?rss=1"
Hwang, B.Lee, D. S.Tamaki, W.Sun, Y.Ogorodnikov, A.Hartoularos, G.Winters, A.Song, Y. S.Chow, E. D.Spitzer, M. H.Ye, C. J.2020-03-30doi:10.1101/2020.03.27.012633Cold Spring Harbor Laboratory Press2020-03-30
<![CDATA[
Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans
]]>
https://biorxiv.org/cgi/content/short/2020.03.30.016329v1?rss=1"
Summers, D. K.Perry, D. S.Rao, B.Madhani, H. D.2020-03-30doi:10.1101/2020.03.30.016329Cold Spring Harbor Laboratory Press2020-03-30
<![CDATA[
Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding
]]>
https://biorxiv.org/cgi/content/short/2020.05.01.072884v1?rss=1"
Newberry, R. W.Arhar, T.Costello, J.Hartoularos, G. C.Maxwell, A. M.Naing, Z. Z. C.Pittman, M.Reddy, N. R.Schwarz, D. M. C.Wassarman, D. R.Wu, T. S.Barrero, D.Caggiano, C.Catching, A.Cavazos, T. B.Estes, L. S.Faust, B.Fink, E. A.Goldman, M. A.Gomez, Y. K.Gordon, M. G.Gunsalus, L. M.Hoppe, N.Jaime-Garza, M.Johnson, M. C.Jones, M. G.Kung, A. F.Lopez, K. E.Lumpe, J.Martyn, C.McCarthy, E. E.Miller-Vedam, L. E.Navarro, E. J.Palar, A.Pellegrino, J.Saylor, W.Stephens, C. A.Strickland, J.Torosyan, H.Wankowicz, S. A.Wong, D2020-05-03doi:10.1101/2020.05.01.072884Cold Spring Harbor Laboratory Press2020-05-03
<![CDATA[
Discovery of disease treatment mechanisms through the multiscale interactome
]]>
https://biorxiv.org/cgi/content/short/2020.04.30.069690v1?rss=1"
Ruiz, C.Zitnik, M.Leskovec, J.2020-05-02doi:10.1101/2020.04.30.069690Cold Spring Harbor Laboratory Press2020-05-02
<![CDATA[
ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis
]]>
https://biorxiv.org/cgi/content/short/2020.04.28.066498v1?rss=1"
Granja, J. M.Corces, M. R.Pierce, S. E.Bagdatli, S. T.Choudhry, H.Chang, H.Greenleaf, W.2020-04-29doi:10.1101/2020.04.28.066498Cold Spring Harbor Laboratory Press2020-04-29
<![CDATA[
A transient role of primary cilia in controlling direct versus indirect neurogenesis in the developing cerebral cortex
]]>
https://biorxiv.org/cgi/content/short/2020.04.28.065615v1?rss=1"
Theil, T.Hasenpusch-Theil, K.Laclef, C.Colligan, M.Fitzgerald, E.Howe, K.Carroll, E.Abrams, S.Reiter, J. F.Schneider-Maunoury, S.2020-04-28doi:10.1101/2020.04.28.065615Cold Spring Harbor Laboratory Press2020-04-28
<![CDATA[
PlanktonScope: Affordable modular imaging platform for citizen oceanography
]]>
https://biorxiv.org/cgi/content/short/2020.04.23.056978v1?rss=1"
Pollina, T.Larson, A.Lombard, F.Li, H.Colin, S.Vargas, C. d.Prakash, M.2020-04-23doi:10.1101/2020.04.23.056978Cold Spring Harbor Laboratory Press2020-04-23
<![CDATA[
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
]]>
https://biorxiv.org/cgi/content/short/2020.04.19.049254v1?rss=1"
Muus, C.Luecken, M. D.Eraslan, G.Waghray, A.Heimberg, G.Sikkema, L.Kobayashi, Y.Vaishnav, E. D.Subramanian, A.Smillie, C.Jagadeesh, K.Duong, E. T.Fiskin, E.Torlai Triglia, E.Ansari, M.Cai, P.Lin, B.Buchanan, J.Chen, S.Shu, J.Haber, A. L.Chung, H.Montoro, D. T.Adams, T.Aliee, H.Allon, S. J.Andrusivova, Z.Angelidis, I.Ashenberg, O.Bassler, K.Becavin, C.Benhar, I.Bergenstrahle, J.Bergenstrahle, L.Bolt, L.Braun, E.Bui, L. T.Chaffin, M.Chichelnitskiy, E.Chiou, J.Conlon, T. M.Cuoco, M. S.Deprez, M.Fischer, D. S.G2020-04-20doi:10.1101/2020.04.19.049254Cold Spring Harbor Laboratory Press2020-04-20
<![CDATA[
Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates
]]>
https://biorxiv.org/cgi/content/short/2020.04.16.045302v1?rss=1"
Damas, J.Hughes, G. M.Keough, K. C.Painter, C. A.Persky, N. S.Corbo, M.Hiller, M.Koepfli, K.-P.Pfenning, A. R.Zhao, H.Genereux, D. P.Swofford, R.Pollard, K. S.Ryder, O. A.Nweeia, M. T.Lindblad-Toh, K.Teeling, E. C.Karlsson, E. K.Lewin, H. A.2020-04-18doi:10.1101/2020.04.16.045302Cold Spring Harbor Laboratory Press2020-04-18
<![CDATA[
Continuous lineage recording reveals rapid, multidirectional metastasis in a lung cancer xenograft model in mouse
]]>
https://biorxiv.org/cgi/content/short/2020.04.16.045245v1?rss=1"
Quinn, J. J.Jones, M. G.Okimoto, R. A.Yosef, N.Bivona, T. G.Weissman, J. S.2020-04-17doi:10.1101/2020.04.16.045245Cold Spring Harbor Laboratory Press2020-04-17
<![CDATA[
The folding and unfolding behavior of ribonuclease H on the ribosome
]]>
https://biorxiv.org/cgi/content/short/2020.04.16.044867v1?rss=1"
Jensen, M. K.Samelson, A. J.Steward, A.Clarke, J.Marqusee, S.2020-04-18doi:10.1101/2020.04.16.044867Cold Spring Harbor Laboratory Press2020-04-18
<![CDATA[
Expanding the space of protein geometries by computational design of de novo fold families
]]>
https://biorxiv.org/cgi/content/short/2020.04.14.041772v1?rss=1"
Pan, X.Thompson, M.Zhang, Y.Lin, L.Fraser, J. S.Kelly, M. J. S.Kortemme, T.2020-04-15doi:10.1101/2020.04.14.041772Cold Spring Harbor Laboratory Press2020-04-15
<![CDATA[
Oleic acid Induces Tissue Resident FoxP3 Regulatory T cell Lineage Stability and Suppressive Functions
]]>
https://biorxiv.org/cgi/content/short/2020.04.14.041525v1?rss=1"
Pompura, S. L.Wagner, A.Kitz, A.LaPerche, J.Yosef, N.Dominguez-Villar, M.Hafler, D. A.2020-04-15doi:10.1101/2020.04.14.041525Cold Spring Harbor Laboratory Press2020-04-15
<![CDATA[
Treated HIV Infection Alters Phenotype But Not HIV-specific Function of Peripheral Blood Natural Killer Cells
]]>
https://biorxiv.org/cgi/content/short/2020.04.12.038604v1?rss=1"
Zhao, N. Q.Ferreira, A.-M.Grant, P. M.Holmes, S.Blish, C. A.2020-04-13doi:10.1101/2020.04.12.038604Cold Spring Harbor Laboratory Press2020-04-13
<![CDATA[
Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments
]]>
https://biorxiv.org/cgi/content/short/2020.04.10.036442v1?rss=1"
Chen, Z.Shaw, A.Wilson, H.Woringer, M.Darzacq, X.Marqusee, S.Wang, Q.Bustamante, C.2020-04-11doi:10.1101/2020.04.10.036442Cold Spring Harbor Laboratory Press2020-04-11
<![CDATA[
Immune factor of bacterial origin protects ticks against host microbial commensals
]]>
https://biorxiv.org/cgi/content/short/2020.04.10.036376v1?rss=1"
Hayes, B. M.Radkov, A. D.Yarza, F.Flores, S.Kim, J. R.Zhao, Z.Lexa, K. W.Marnin, L.Biboy, J.Bowcutt, V.Vollmer, W.Pedra, J. H.Chou, S.2020-04-11doi:10.1101/2020.04.10.036376Cold Spring Harbor Laboratory Press2020-04-11
<![CDATA[
Stress-Induced Transient Cell Cycle Arrest Coordinates Metabolic Resource Allocation to Balance Adaptive Tradeoffs
]]>
https://biorxiv.org/cgi/content/short/2020.04.08.033035v1?rss=1"
Bonny, A. R.Kochanowski, K.Diether, M.El-Samad, H.2020-04-10doi:10.1101/2020.04.08.033035Cold Spring Harbor Laboratory Press2020-04-10
<![CDATA[
A Single-Objective Light-Sheet Microscope with 200 nm-Scale Resolution.
]]>
https://biorxiv.org/cgi/content/short/2020.04.07.030569v1?rss=1"
Sapoznik, E.Chang, B.-J.Ju, R. J.Welf, E. S.Broadbent, D.Carisey, A. F.Stehbens, S. J.Lee, K.-m.Marin, A.Hanker, A. B.Schmidt, J. C.Arteaga, C. L.Yang, B.Kruithoff, R.Millett-Sikking, A.York, A. G.Dean, K. M.Fiolka, R. P.2020-04-08doi:10.1101/2020.04.07.030569Cold Spring Harbor Laboratory Press2020-04-08
<![CDATA[
IDseq - An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring
]]>
https://biorxiv.org/cgi/content/short/2020.04.07.030551v1?rss=1"
Kalantar, K. L.Carvalho, T.de Bourcy, C. F. A.Dimitrov, B.Dingle, G.Egger, R.Han, J.Holmes, O. B.Juan, Y.King, R.Kislyuk, A.Mariano, M.Reyenoso, L. V.Rissato Cruz, D.Sheu, J.Tang, J.Wang, J.Zhang, M. A.Zhong, E.Ahyong, V.Lay, S.Chea, S.Bohl, J. A.Manning, J. E.Tato, C. M.DeRisi, J. L.2020-04-09doi:10.1101/2020.04.07.030551Cold Spring Harbor Laboratory Press2020-04-09
<![CDATA[
Optical Aberration Correction via Phase Diversity and Deep Learning
]]>
https://biorxiv.org/cgi/content/short/2020.04.05.026567v1?rss=1"
Krishnan, A. P.Belthangady, C.Nyby, C.Lange, M.Yang, B.Royer, L. A.2020-04-06doi:10.1101/2020.04.05.026567Cold Spring Harbor Laboratory Press2020-04-06
<![CDATA[
Adaptive actin organization counteracts elevated membrane tension to ensure robust endocytosis
]]>
https://biorxiv.org/cgi/content/short/2020.04.05.026559v1?rss=1"
Kaplan, C.Kenny, S. J.Chen, S.Schoeneberg, J.Sitarska, E.Diz-Munoz, A.Xu, K.Drubin, D. G.2020-04-06doi:10.1101/2020.04.05.026559Cold Spring Harbor Laboratory Press2020-04-06
<![CDATA[
Molecular characterization of selectively vulnerable neurons in Alzheimer's Disease
]]>
https://biorxiv.org/cgi/content/short/2020.04.04.025825v1?rss=1"
Leng, K.Li, E.Eser, R.Piergies, A.Sit, R.Tan, M.Neff, N.Li, S. H.Diehl Rodriguez, R.Suemoto, C. K.Paraizo Leite, R. E.Pasqualucci, C. A.Seeley, W. W.Spina, S.Heinsen, H.Grinberg, L. T.Kampmann, M. T.2020-04-05doi:10.1101/2020.04.04.025825Cold Spring Harbor Laboratory Press2020-04-05
<![CDATA[
A negative feedback loop mediated by the NR4A family of nuclear hormone receptors restrains expansion of B cells that receive signal one in the absence of signal two
]]>
https://biorxiv.org/cgi/content/short/2020.03.31.017434v1?rss=1"
Tan, C.Hiwa, R.Mueller, J. L.Vykunta, V.Hibiya, K.Noviski, M.Huizar, J.Brooks, J. F.Garcia, J.Heyn, C.Li, Z.Marson, A.Zikherman, J.2020-04-01doi:10.1101/2020.03.31.017434Cold Spring Harbor Laboratory Press2020-04-01
<![CDATA[
Bacterial evolution in high osmolarity environments
]]>
https://biorxiv.org/cgi/content/short/2020.05.07.081752v1?rss=1"
Cesar, S.Anjur-Dietrich, M.Yu, B.Li, E.Rojas, E.Neff, N.Cooper, T. F.Huang, K. C.2020-05-08doi:10.1101/2020.05.07.081752Cold Spring Harbor Laboratory Press2020-05-08
<![CDATA[
Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells
]]>
https://biorxiv.org/cgi/content/short/2020.05.08.083337v1?rss=1"
Gayoso, A.Steier, Z.Lopez, R.Regier, J.Nazor, K. L.Streets, A.Yosef, N.2020-05-10doi:10.1101/2020.05.08.083337Cold Spring Harbor Laboratory Press2020-05-10
<![CDATA[
Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries
]]>
https://biorxiv.org/cgi/content/short/2020.05.09.086264v1?rss=1"
Zhou, J.Li, S.Leung, K. K.ODonovan, B. K.Zou, J.DeRisi, J.Wells, J. A.2020-05-10doi:10.1101/2020.05.09.086264Cold Spring Harbor Laboratory Press2020-05-10
<![CDATA[
Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals
]]>
https://biorxiv.org/cgi/content/short/2020.05.13.092619v1?rss=1"
1:5000. Antibody cloning revealed expanded clones of RBD-specific memory B cells expressing closely related antibodies in different individuals. Despite low plasma titers, antibodies to three distinct epitopes on RBD neutralized at half-maximal inhibitory concentrations (IC50s) as low as single digit ng/mL. Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.
]]>Robbiani, D. F.Gaebler, C.Muecksch, F.Cetrulo Lorenzi, J.Wang, Z.Cho, A.Agudelo, M.Barnes, C.Finkin, S.Hagglof, T.Oliveira, T.Viant, C.Hurley, A.Millard, K.Kost, R.Cipolla, M.Gazumyan, A.Gordon, K.Bianchini, F.Chen, S.Ramos, V.Patel, R.Dizon, J.Shimeliovich, I.Mendoza, P.Hartweger, H.Nogueira, L.Pack, M.Horowitz, J.Schmidt, F.Weisblum, Y.Hoffmann, H.-H.Michailidis, E.Ashbrook, A.Waltari, E. F.Pak, J.Huey-Tubman, K.Koranda, N.Hoffman, P.West, A.Rice, C.Hatziioannou, T.Bjorkman, P.Bieniasz, P.Caskey, M.Nuss2020-05-15doi:10.1101/2020.05.13.092619Cold Spring Harbor Laboratory Press2020-05-15
<![CDATA[
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale
]]>
https://biorxiv.org/cgi/content/short/2020.05.14.086363v1?rss=1"
Matheus Carnevali, P. B.Lavy, A.Thomas, A. D.Crits-Christoph, A.Diamond, S.Meeheust, R.Olm, M. R.Sharrar, A.Lei, S.Dong, W.Falco, N.Bouskill, N.Newcomer, M.Nico, P.Wainwright, H.Dwivedi, D.Williams, K. H.Hubbard, S.Banfield, J. F.2020-05-15doi:10.1101/2020.05.14.086363Cold Spring Harbor Laboratory Press2020-05-15
<![CDATA[
Huge and variable diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
]]>
https://biorxiv.org/cgi/content/short/2020.05.14.094862v1?rss=1"
He, C. Y.Keren, R.Whittaker, M.Farag, I. F.Doudna, J. A.Cate, J. H.Banfield, J. F.2020-05-15doi:10.1101/2020.05.14.094862Cold Spring Harbor Laboratory Press2020-05-15
<![CDATA[
Polarized endosome dynamics engage cytosolic Par-3 and dynein during asymmetric division
]]>
https://biorxiv.org/cgi/content/short/2020.05.15.098012v1?rss=1"
Zhao, X.Tong, K.Chen, x.Yang, B.Li, Q.Dai, Z.Shi, X.Seiple, I.Huang, B.Guo, S.2020-05-16doi:10.1101/2020.05.15.098012Cold Spring Harbor Laboratory Press2020-05-16
<![CDATA[
Trimeric SARS-CoV-2 Spike interacts with dimeric ACE2 with limited intra-Spike avidity
]]>
https://biorxiv.org/cgi/content/short/2020.05.21.109157v1?rss=1"
Lui, I.Zhou, X. X.Lim, S. A.Elledge, S.Solomon, P.Rettko, N. J.Zha, B. S.Kirkemo, L. L.Gramespacher, J. A.Liu, J.Muecksch, F.Lorenzi, J. C. C.Schmidt, F.Weisblum, Y.Robbiani, D. F.Nussenzweig, M. C.Hatziioannou, T.Bieniasz, P. D.Rosenberg, O.Leung, K. K.Wells, J. A.2020-05-21doi:10.1101/2020.05.21.109157Cold Spring Harbor Laboratory Press2020-05-21
<![CDATA[
TuNR: Orthogonal Control of Mean and Variability of Endogenous Genes in a Human Cell Line
]]>
https://biorxiv.org/cgi/content/short/2020.05.23.112979v1?rss=1"
Bonny, A. R.Fonseca, J. P.Park, J. E.El-Samad, H.2020-05-24doi:10.1101/2020.05.23.112979Cold Spring Harbor Laboratory Press2020-05-24
<![CDATA[
Single cell analysis of human site-specific melanocyte differentiation and the decoding of developmental programs in melanoma
]]>
https://biorxiv.org/cgi/content/short/2020.05.25.115287v1?rss=1"
Belote, R. L.Le, D.Maynard, A.Lang, U. E.Sinclair, A.Planells-Palop, V.Baskin, L. S.Tward, A. D.Darmanis, S.Judson-Torres, R. L.2020-05-28doi:10.1101/2020.05.25.115287Cold Spring Harbor Laboratory Press2020-05-28
<![CDATA[
Combinatorial Polyacrylamide Hydrogels for Preventing Biofouling on Implantable Biosensors
]]>
https://biorxiv.org/cgi/content/short/2020.05.25.115675v1?rss=1"
Chan, D.Chien, J.-C.Axpe, E.Blankemeier, L.Baker, S. W.Swaminathan, S.Piunova, V. A.Zubarev, D. Y.Soh, H. T.Appel, E. A.2020-05-28doi:10.1101/2020.05.25.115675Cold Spring Harbor Laboratory Press2020-05-28
<![CDATA[
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
]]>
https://biorxiv.org/cgi/content/short/2020.05.28.121541v1?rss=1"
Bassler, K.Fujii, W.Kapellos, T. S.Horne, A.Reiz, B.Dudkin, E.Luecken, M.Reusch, N.Osei-Sarpong, C.Warnat-Herresthal, S.Wagner, A.Bonaguro, L.Guenther, P.Pizarro, C.Schreiber, T.Becker, M.Haendler, K.Wohnhaas, C. T.Baumgartner, F.Koehler, M.Theis, H.Kraut, M.Wadsworth, M. H.Hughes, T. K.Ferreira, H. J. G.Schulte-Schrepping, J.Hinkley, E.Kaltheuner, I. H.Geyer, M.Thiele, C.Shalek, A. K.Feisst, A.Thomas, D.Dickten, H.Beyer, M.Baum, P.Yosef, N.Aschenbrenner, A. C.Ulas, T.Hasenauer, J.Theis, F. J.Skowasch, D.Schult2020-05-30doi:10.1101/2020.05.28.121541Cold Spring Harbor Laboratory Press2020-05-30
<![CDATA[
Latrophilin-2 repels Teneurin-3+ hippocampal axons during target selection
]]>
https://biorxiv.org/cgi/content/short/2020.05.28.122242v1?rss=1"
Pederick, D. T.Lui, J. H.Gingrich, E. C.Xu, C.Liu, Y.He, Z.Quake, S. R.Luo, L.2020-05-29doi:10.1101/2020.05.28.122242Cold Spring Harbor Laboratory Press2020-05-29
<![CDATA[
A multiplexed, automated evolution pipeline enablesscalable discovery and characterization of biosensors
]]>
https://biorxiv.org/cgi/content/short/2020.05.29.117960v1?rss=1"
Townshend, B.Xiang, J.Manzanarez, G.Hayden, E. J.Smolke, C. D.2020-05-31doi:10.1101/2020.05.29.117960Cold Spring Harbor Laboratory Press2020-05-31
<![CDATA[
SiCTeC: an inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging
]]>
https://biorxiv.org/cgi/content/short/2020.05.29.123158v1?rss=1"
Knapp, B. D.Zhu, L.Huang, K. C.2020-06-01doi:10.1101/2020.05.29.123158Cold Spring Harbor Laboratory Press2020-06-01
<![CDATA[
SiCTeC: an inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging
]]>
https://biorxiv.org/cgi/content/short/2020.05.29.123166v1?rss=1"
Knapp, B. D.Zhu, L.Huang, K. C.2020-06-01doi:10.1101/2020.05.29.123166Cold Spring Harbor Laboratory Press2020-06-01
<![CDATA[
Towards Mycobacterium tuberculosis detection at the point-of-care: a brighter solvatochromic probe permits the detection of mycobacteria within minutes
]]>
https://biorxiv.org/cgi/content/short/2020.05.29.124008v1?rss=1"
Kamariza, M.Keyser, S. G. L.Utz, A.Knapp, B.Ahn, G.Cambier, C. J.Chen, T.Huang, K. C.Bertozzi, C.2020-05-30doi:10.1101/2020.05.29.124008Cold Spring Harbor Laboratory Press2020-05-30
<![CDATA[
Accurate prediction of genetic circuit behavior requires multidimensional characterization of parts
]]>
https://biorxiv.org/cgi/content/short/2020.05.30.122077v1?rss=1"
Dods, G.Gomez-Schiavon, M.El-Samad, H.Ng, A. H.2020-05-31doi:10.1101/2020.05.30.122077Cold Spring Harbor Laboratory Press2020-05-31
<![CDATA[
Single cell profiling of total RNA using Smart-seq-total
]]>
https://biorxiv.org/cgi/content/short/2020.06.02.131060v1?rss=1"
Isakova, A.Neff, N.Quake, S.2020-06-03doi:10.1101/2020.06.02.131060Cold Spring Harbor Laboratory Press2020-06-03
<![CDATA[
CaaX-like protease of cyanobacterial origin is required for complex plastid biogenesis in malaria parasites
]]>
https://biorxiv.org/cgi/content/short/2020.06.02.130229v1?rss=1"
Meister, T. R.Tang, Y.Pulkoski-Gross, M. J.Yeh, E.2020-06-03doi:10.1101/2020.06.02.130229Cold Spring Harbor Laboratory Press2020-06-03