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Archive, 2016-11

4 Immunotropic aspect of the Bacillus coagulans probiotic action
Bomko, T.; Nosalskaya, T.; Kabluchko, T.; Lisnyak, Y.; Martynov, A. V.
10.1101/088757 — pharmacology and toxicology — Posted on 2016-11-19
6 Analgesic effects of neurotensin agonists in a rat bone cancer pain model
Dore-Savard, L.; Tetreault, P.; Roux, M.; Martel, M.; Lemire, M.; Belleville, K.; Beaudet, N.; Sarret, P.
10.1101/089169 — pharmacology and toxicology — Posted on 2016-11-24
9 MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data
Friedman, S. H.; Anderson, A. R. A.; Bortz, D. M.; Fletcher, A. G.; Frieboes, H. B.; Ghaffarizadeh, A.; Grimes, D. R.; Hawkins-Daarud, A.; Hoehme, S.; Juarez, E. F.; Kesselman, C.; Merks, R.; Mumenthaler, S. M.; Newton, P. K.; Norton, K.-A.; Rawat, R.; Rockne, R. C.; Ruderman, D.; Scott, J.; Sindi, S. S.; Sparks, J. L.; Swanson, K.; Agus, D. B.; Macklin, P.
10.1101/090456 — systems biology — Posted on 2016-11-30
10 Recurring functional interactions predict network architecture of interictal and ictal states in neocortical epilepsy
Khambhati, A. N.; Bassett, D. S.; Oommen, B. S.; Chen, S. H.; Lucas, T. H.; Davis, K. A.; Litt, B.
10.1101/090662 — neuroscience — Posted on 2016-11-30
11 Temporal anticipation based on memory
Cravo, A. M.; Rohenkohl, G.; Santos, K. M.; Nobre, A. C.
10.1101/090555 — neuroscience — Posted on 2016-11-30
12 Clinical metagenomics of bone and joint infections: a proof of concept study
Ruppe, E.; Lazarevic, V.; Girard, M.; Mouton, W.; Ferry, T.; Laurent, F.; Schrenzel, J.
10.1101/090530 — microbiology — Posted on 2016-11-30
18 Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis
Dong, H.; Dumenil, J.; Lu, F.-H.; Na, L.; Vanhaeren, H.; Naumann, C.; Klecker, M.; Prior, R.; Smith, C.; McKenzie, N.; Saalbach, G.; Chen, L.; Xia, T.; Gonzalez, N.; Seguela, M.; Inze, D.; Dissmeyer, N.; Li, Y.; Bevan, M. W.
10.1101/090563 — plant biology — Posted on 2016-11-30
19 The NCA-1 ion channel functions downstream of Gq and Rho to regulate locomotion in C. elegans
Topalidou, I.; Chen, P.-A.; Cooper, K.; Watanabe, S.; Jorgensen, E. M.; Ailion, M.
10.1101/090514 — genetics — Posted on 2016-11-30
26 The Effect of Compositional Context on Synthetic Gene Networks
Yeung, E.; Dy, A. J.; Martin, K. B.; Ng, A. H.; Del Vecchio, D.; Beck, J. L.; Collins, J. J.; Murray, R. M.
10.1101/083329 — synthetic biology — Posted on 2016-11-30
27 iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data
Groppe, D. M.; Bickel, S.; Dykstra, A. R.; Wang, X.; Megevand, P.; Mercier, M. R.; Lado, F. A.; Mehta, A. D.; Honey, C. J.
10.1101/069179 — neuroscience — Posted on 2016-11-30
28 Mindcontrol: A Web Application for Brain Segmentation Quality Control
Keshavan, A.; Datta, E.; McDonough, I.; Madan, C. R.; Jordan, K.; Henry, R.
10.1101/090431 — bioinformatics — Posted on 2016-11-30
29 Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis
Steinberg, J.; Ritchie, G. R. S.; Roumeliotis, T. I.; Jayasuriya, R. L.; Brooks, R. A.; Binch, A. L. A.; Shah, K. M.; Coyle, R.; Pardo, M.; Le Maitre, C. L.; Ramos, Y. F. M.; Nelissen, R. G. H. H.; Meulenbelt, I.; McCaskie, A. W.; Choudhary, J. S.; Wilkinson, J. M.; Zeggini, E.
10.1101/038067 — systems biology — Posted on 2016-11-30
31 The risk of sustained sexual transmission of Zika is underestimated
Allard, A.; Althouse, B. M.; Hebert-Dufresne, L.; Scarpino, S. V.
10.1101/090324 — epidemiology — Posted on 2016-11-30
32 Neptune: A Bioinformatics Tool for Rapid Discovery of Genomic Variation in Bacterial Populations
Marinier, E.; Zaheer, R.; Berry, C.; Weedmark, K. A.; Domaratzki, M.; Mabon, P.; Knox, N. C.; Reimer, A. R.; Graham, M. R.; The LiDS-NG Consortium, ; Van Domselaar, G.
10.1101/032227 — bioinformatics — Posted on 2016-11-30
37 Mindcontrol: A Web Application for Brain Segmentation Quality Control
Keshavan, A.; Datta, E.; McDonough, I.; Madan, C. R.; Jordan, K.; Henry, R.
10.1101/090431 — bioinformatics — Posted on 2016-11-29
39 NLR signaling network mediates immunity to diverse plant pathogens
Wu, C.-H.; Abd-El-Haliem, A.; Bozkurt, T. O.; Belhaj, K.; Terauchi, R.; Vossen, J. H.; Kamoun, S.
10.1101/090449 — plant biology — Posted on 2016-11-29
45 The evolutionary history of bears is shaped by gene flow across species
Kumar, V.; Lammers, F.; Bidon, T.; Pfenninger, M.; Kolter, L.; Nilsson, M. A.; Janke, A.
10.1101/090126 — evolutionary biology — Posted on 2016-11-29
49 Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin
Vergara, Z.; Sequeira-Mendes, J.; Morata, J.; Henaff, E.; Peiro, R.; Costas, C.; Casacuberta, J. M.; Gutierrez, C.
10.1101/090183 — genomics — Posted on 2016-11-29
50 SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data
Bacher, R.; Chu, L.-F.; Leng, N.; Gasch, A. P.; Thomson, J. A.; Stewart, R. M.; Newton, M.; Kendziorski, C.
10.1101/090167 — genomics — Posted on 2016-11-29
52 Tuning the course of evolution on the biophysical fitness landscape of an RNA virus
Rotem, A.; Serohijos, A.; Chang, C.; Wolfe, J.; Fischer, A.; Mehoke, T.; Zhang, H.; Tao, Y.; Ung, L.; Choi, J.-M.; Kolawole, A.; Koehler, S.; Wu, S.; Thielen, P.; Cui, N.; Demirev, P.; Giacobbi, N.; Julian, T.; Schwab, K.; Lin, J.; Smith, T.; Pipas, J.; Wobus, C.; Feldman, A.; Weitz, D.; Shakhnovich, E.
10.1101/090258 — evolutionary biology — Posted on 2016-11-28
55 Axonal transcriptome of human stem cell derived neurons
Bigler, R. L.; Kamande, J. W.; Dumitru, R.; Niedringhaus, M.; Taylor, A. M.
10.1101/066142 — neuroscience — Posted on 2016-11-28
57 Retrotransposon Activation Contributes to Neurodegeneration in a DrosophilaTDP-43 Model of ALS.
Krug, L.; Chatterjee, N.; Borges-Monroy, R.; Hearn, S.; Liao, W.-W.; Morrill, K.; Prazak, L.; Chang, Y.-H.; Keegan, R. M.; Rozhkov, N.; Theodorou, D.; Hammell, M.; Dubnau, J.
10.1101/090175 — neuroscience — Posted on 2016-11-28
59 SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data
Bacher, R.; Chu, L.-F.; Leng, N.; Gasch, A. P.; Thomson, J. A.; Stewart, R. M.; Newton, M.; Kendziorski, C.
10.1101/090167 — genomics — Posted on 2016-11-28
60 Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin
Vergara, Z.; Sequeira-Mendes, J.; Morata, J.; Henaff, E.; Peiro, R.; Costas, C.; Casacuberta, J. M.; Gutierrez, C.
10.1101/090183 — genomics — Posted on 2016-11-28
69 Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells
Moenke, G.; Christiano, E.; Finzel, A.; Friedrich, D.; Herzel, H.; Falcke, M.; Loewer, A.
10.1101/068668 — cell biology — Posted on 2016-11-28
70 Sphingolipid metabolic flow controls phosphoinositide turnover at thetrans Golgi network
Capasso, S.; Sticco, L.; Rizzo, R.; Pirozzi, M.; Russo, D.; Dathan, N.; Campelo, F.; van Galen, J.; Hausser, A.; Malhotra, V.; Parashuraman, S.; Luini, A.; D'Angelo, G.
10.1101/090142 — cell biology — Posted on 2016-11-28
71 Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer
O'Donnell, T.; Christie, E. L.; Buros, J.; Aksoy, B. A.; Bowtell, D. D. L.; Snyder Charen, A.; Hammerbacher, J.
10.1101/090134 — cancer biology — Posted on 2016-11-28
72 Structure of general-population antibody titer distributions to influenza A virus
Nhat, N. T. D.; Todd, S.; de Bruin, E.; Thao, T. T. N.; Vy, N. H. T.; Quan, T. M.; Vinh, D. N.; van Beek, J.; Anh, P. H.; Lam, H. M.; Hung, N. T.; Thanh, N. T. L.; Huy, H. L. A.; Ha, V. T. H.; Baker, S.; Thwaites, G. E.; Lien, N. T. N.; Hong, T. T. K.; Farrar, J.; Simmons, C. P.; Chau, N. V. V.; Koopmans, M.; Boni, M. F.
10.1101/090076 — epidemiology — Posted on 2016-11-28
74 Global-scale structure of the eelgrass microbiome
Fahimipour, A. K.; Kardish, M. R.; Eisen, J. A.; Lang, J. M.; Green, J. L.; Stachowicz, J. J.
10.1101/089797 — microbiology — Posted on 2016-11-28
77 Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates
Buddenhagen, C.; Lemmon, A. R.; Lemmon, E. M.; Bruhl, J.; Cappa, J.; Clement, W. L.; Donoghue, M.; Edwards, E. J.; Hipp, A. L.; Kortyna, M.; Mitchell, N.; Moore, A.; Prychid, C. J.; Segovia-Salcedo, M. C.; Simmons, M. P.; Soltis, P. S.; Wanke, S.; Mast, A.
10.1101/086298 — evolutionary biology — Posted on 2016-11-28
79 TriPer, an optical probe tuned to the endoplasmic reticulum, tracks H2O2 consumption by glutathione
Melo, E. P.; Lopes, C.; Gollwitzer, P.; Lortz, S.; Lenzen, S.; Mehmeti, I.; Kaminski, C. F.; Ron, D.; Avezov, E.
10.1101/088351 — cell biology — Posted on 2016-11-28
80 Electrical Stimulus Artifact Cancellation and Neural Spike Detection on Large Multi-Electrode Arrays
Mena, G. E.; Grosberg, L. E.; Hottowy, P.; Litke, A.; Cunningham, J.; Chichilnisky, E.; Paninski, L.
10.1101/089912 — neuroscience — Posted on 2016-11-27
88 Widespread allelic heterogeneity in complex traits
Hormozdiari, F.; Zhu, A.; Kichaev, G.; Segre, A. V.; Ju, C. J.- T.; Joo, J. W.; Won, H.; Sankararaman, S.; Pasaniuc, B.; Shifman, S.; Eskin, E.
10.1101/076984 — genetics — Posted on 2016-11-27
90 Ecological Interactions and the Netflix Problem
Desjardins-Proulx, P.; Laigle, I.; Poisot, T.; Gravel, D.
10.1101/089771 — ecology — Posted on 2016-11-27
91 An interaction map of circulating metabolites, immune gene networks and their genetic regulation
Nath, A. P.; Ritchie, S. C.; Byars, S. G.; Fearnley, L. G.; Havulinna, A. S.; Joensuu, A.; Kangas, A. J.; Soininen, P.; Wennerstrom, A.; Milani, L.; Metspalu, A.; Mannisto, S.; Wurtz, P.; Kettunen, J.; Raitoharju, E.; Kahonen, M.; Juonala, M.; Palotie, A.; Ala-Korpela, M.; Ripatti, S.; Lehtimaki, T.; Abraham, G.; Raitakari, O.; Salomaa, V.; Perola, M.; Inouye, M.
10.1101/089839 — genomics — Posted on 2016-11-26
95 Global-scale structure of the eelgrass microbiome
Fahimipour, A. K.; Kardish, M. R.; Eisen, J. A.; Lang, J. M.; Green, J. L.; Stachowicz, J. J.
10.1101/089797 — microbiology — Posted on 2016-11-26
97 PoGo: Jumping from Peptides to Genomic Loci
Schlaffner, C. N.; Pirklbauer, G.; Bender, A.; Choudhary, J. S.
10.1101/079772 — bioinformatics — Posted on 2016-11-26
98 Baseline mutation profiling of 1134 samples of circulating cell-free DNA and blood cells from healthy individuals
Xia, L.; Li, Z.; Zhou, B.; Tian, G.; Zeng, L.; Dai, H.; Deng, F.; Xie, Y.; Lu, S.; Li, X.; Liu, C.; Huang, W.; He, J.
10.1101/089813 — bioinformatics — Posted on 2016-11-26
99 Metabolome Identification by Systematic Stable Isotope Labeling Experiments and False Discovery Analysis with a Target-Decoy Strategy
Jones, D. R.; Wang, X.; Shaw, T.; Cho, J.-H.; Chen, P.-C.; Dey, K. K.; Zhou, S.; Li, Y.; Kim, N. C.; Taylor, J. P.; Kolli, U.; Li, J.; Peng, J.
10.1101/089904 — biochemistry — Posted on 2016-11-26
103 Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.
Sundaramoorthy, R.; Hughes, A. L.; Singh, V.; Wiechens, N.; Ryan, D. P.; El-Mkami, H.; Petoukhov, M.; Svergun, D. I.; Treuutlein, B.; Fischer, M.; Michaelis, J.; Bottcher, B.; Norman, D. G.; Owen-Hughes, T.
10.1101/089581 — molecular biology — Posted on 2016-11-26
105 Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy
Albuquerque, M. A.; Grande, B. M.; Ritch, E.; Jessa, S.; Krzywinski, M. I.; Grewal, J.; Shah, S.; Boutros, P.; Morin, R.
10.1101/089631 — genomics — Posted on 2016-11-26
109 Inference of evolutionary jumps in large phylogenies using Levy processes
Duchen, P.; Leuenberger, C.; Szilagyi, S. M.; Harmon, L.; Eastman, J.; Schweizer, M.; Wegmann, D.
10.1101/089276 — evolutionary biology — Posted on 2016-11-26
114 Coordinate Based Random Effect Size meta-analysis of neuroimaging studies
Tench, C.; Tanasescu, R.; Cottam, W.; Constantinescu, C.; Auer, D.
10.1101/089565 — neuroscience — Posted on 2016-11-25
115 The Semantics of Adjective Noun Phrases in the Human Brain
Fyshe, A.; Sudre, G.; Wehbe, L.; Rafidi, N.; Mitchell, T. M.
10.1101/089615 — neuroscience — Posted on 2016-11-25
116 Robust extraction of spatio-temporal patterns from resting state fMRI
Glomb, K.; Ponce-Alvarez, A.; Gilson, M.; Ritter, P.; Deco, G.
10.1101/089516 — neuroscience — Posted on 2016-11-25
119 Genome-Wide Association Study Reveals First Locus for Anorexia Nervosa and Metabolic Correlations
Duncan, L.; Yilmaz, Z.; Walters, R.; Goldstein, J.; Antilla, V.; Bulik-Sullivan, B.; Ripke, S.; Adan, R.; Alfredsson, L.; Ando, T.; Andreassen, O.; Aschauer, H.; Baker, J.; Barrett, J.; Bencko, V.; Bergen, A.; Berrettini, W.; Birgegard, A.; Boni, C.; Boraska Perica, V.; Brandt, H.; Bughardt, R.; Carlberg, L.; Cassina, M.; Cesta, C.; Cichon, S.; Clementi, M.; Cohen-Woods, S.; Coleman, J.; Cone, R.; Courtet, P.; Crawford, S.; Crow, S.; Crowley, J.; Danner, U.; Davis, O.; de Zaan, M.; Dedoussis, G.; Degortes, D.; DeSocio, J.; Dick, D.; Dikeos, D.; Dina, C.; Ding, B.; Dmitrzak-Weglarz, M.; Docampo
10.1101/088815 — genomics — Posted on 2016-11-25
120 A genetic risk score to guide age-specific, personalized prostate cancer screening
Seibert, T. M.; Fan, C. C.; Wang, Y.; Zuber, V.; Karunamuni, R.; Parsons, J. K.; Eeles, R. A.; Easton, D. F.; Kote-Jarai, Z.; Amin Al Olama, A.; Benlloch Garcia, S.; Muir, K.; Gronberg, H.; Wiklund, F.; Aly, M.; Schleutker, J.; Sipeky, C.; Tammela, T. L.; Nordestgaard, B. G.; Nielsen, S. F.; Weischer, M.; Bisbjerg, R.; Roder, M. A.; Iversen, P.; Key, T. J.; Travis, R. C.; Neal, D. E.; Donovan, J. L.; Hamdy, F. C.; Pharoah, P.; Pashayan, N.; Khaw, K.-T.; Maier, C.; Vogel, W.; Luedeke, M.; Herkommer, K.; Kibel, A. S.; Cybulski, C.; Wokolorczyk, D.; Kluzniak, W.; Cannon-Albright, L.; Brenner, H.;
10.1101/089383 — genetics — Posted on 2016-11-25
122 Physical models of spatial genome organization
Slanina, S.; Aleshchenko, A.; Eidelman, Y.; Andreev, S.
10.1101/089755 — cancer biology — Posted on 2016-11-25
124 INFERENCE OF CELL TYPE COMPOSITION FROM HUMAN BRAIN TRANSCRIPTOMIC DATASETS ILLUMINATES THE EFFECTS OF AGE, MANNER OF DEATH, DISSECTION, AND PSYCHIATRIC DIAGNOSIS
Hagenauer, M. H.; Li, J. Z.; Walsh, D. M.; Vawter, M. P.; Thompson, R. C.; Turner, C. A.; Bunney, W. E.; Myers, R. M.; Barchas, J. D.; Schatzberg, A. F.; Watson, S. J.; Akil, H.
10.1101/089391 — bioinformatics — Posted on 2016-11-25
130 The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination
Williams, E.; Moore, J.; Li, S. W.; Rustici, G.; Tarkowska, A.; Chessel, A.; Leo, S.; Antal, B.; Ferguson, R. K.; Sarkans, U.; Brazma, A.; Carazo-Salas, R. E.; Swedlow, J.
10.1101/089359 — bioinformatics — Posted on 2016-11-24
135 Human demographic history impacts genetic risk prediction across diverse populations
Martin, A. R.; Gignoux, C. R.; Walters, R. K.; Wojcik, G. L.; Neale, B. M.; Gravel, S.; Daly, M. J.; Bustamante, C. D.; Kenny, E. E.
10.1101/070797 — genomics — Posted on 2016-11-24
140 Activating task relevant prior knowledge increases active information storage in content specific brain areas
Brodski-Guerniero, A.; Paasch, G.-F.; Wollstadt, P.; Oezdemir, I.; Lizier, J. T.; Wibral, M.
10.1101/089300 — neuroscience — Posted on 2016-11-23
141 The dynamics of human cognition: increasing global integration coupled with decreasing segregation found using intracortical EEG
Cruzat, J.; Deco, G.; Tauste Campo, A.; Principe, A.; Calabria, M.; Costa, A.; Kringelbach, M. L.; Rocamora, R.
10.1101/089326 — neuroscience — Posted on 2016-11-23
142 Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders
Weiner, D. J.; Wigdor, E. M.; Ripke, S.; Walters, R. K.; Kosmicki, J. A.; Grove, J.; Samocha, K. E.; Goldstein, J.; Okbay, A.; Bybjerg-Gauholm, J.; Werge, T.; Hougaard, D. M.; Taylor, J.; Skuse, D.; Devlin, B.; Anney, R.; Sanders, S.; Bishop, S.; Bo Mortensen, P.; Borglum, A.; Davey Smith, G.; Daly, M. J.; Robinson, E. B.
10.1101/089342 — genetics — Posted on 2016-11-23
143 Homozygous c.259G>A variant in ISCA1 is associated with a new multiple mitochondrial dysfunctions syndrome
Shukla, A.; Hebbar, M.; Srivastava, A.; Kadavigere, R.; Upadhyai, P.; Kanthi, A.; Brandau, O.; Bielas, S.; Girisha, K.
10.1101/089292 — genetics — Posted on 2016-11-23
145 Ancient coding sequences underpin the spatial patterning of gene expression in C4 leaves
Reyna-Llorens, I.; Burgess, S. J.; Williams, B. P.; Stanley, S.; Boursnell, C.; Hibberd, J. M.
10.1101/085795 — plant biology — Posted on 2016-11-23
146 The type IVa pilus machinery is pre-installed during cell division
Carter, T.; Burensuceso, R. N. C.; Tammam, S.; Lamers, R. P.; Harvey, H.; Howell, P. L.; Burrows, L. L.
10.1101/087965 — microbiology — Posted on 2016-11-23
148 Transition into inflammatory cancer-associated adipocytes in breast cancer microenvironment requires microRNA regulatory mechanism
Lee, J.; Ryu, H. S.; Hong, B. S.; Lee, H.-B.; Lee, M.; Park, I. A.; Kim, J.; Han, W.; Noh, D.-Y.; Moon, H.-G.
10.1101/089243 — cancer biology — Posted on 2016-11-23
149 Super-resolution microscopy of the β-carboxysome reveals a homogenous matrix
Niederhuber, M. J.; Lambert, T. J.; Yapp, C.; Silver, P. A.; Polka, J. K.
10.1101/086090 — cell biology — Posted on 2016-11-23
150 Probing cytoskeletal modulation of passive and active intracellular dynamics using nanobody-functionalized quantum dots
Katrukha, E. A.; Mikhaylova, M.; van Brakel, H. X.; van Bergen en Henegouwen, P. M.; Akhmanova, A.; Hoogenraad, C. C.; Kapitein, L. C.
10.1101/089284 — biophysics — Posted on 2016-11-23
155 Phylodynamics on local sexual contact networks
Rasmussen, D. A.; Kouyos, R.; Gunthard, H. F.; Stadler, T.
10.1101/082966 — epidemiology — Posted on 2016-11-23
157 Unexpected diversity in socially synchronized rhythms of shorebirds
Bulla, M.; Valcu, M.; Dokter, A. M.; Dondua, A. A.; Kosztolanyi, A.; Rutten, A.; Helm, B.; Sandercock, B. K.; Casler, B.; Ens, B. J.; Spiegel, C. S.; Hassell, C. J.; Kupper, C.; Minton, C.; Burgas, D.; Lank, D. B.; Payer, D. C.; Loktionov, E. Y.; Nol, E.; Kwon, E.; Smith, F.; Gates, H. R.; Vitnerova, H.; Pruter, H.; Johnson, J. A.; St Clair, J. J. H.; Lamarre, J.-F.; Rausch, J.; Reneerkens, J.; Conklin, J. R.; Burger, J.; Liebezeit, J.; Bety, J.; Coleman, J. T.; Figuerola, J.; Hooijmeijer, J. C. E. W.; Alves, J. A.; Smith, J. A. M.; Weidinger, K.; Koivula, K.; Gosbell, K.; Niles, L.; Koloski,
10.1101/084806 — animal behavior and cognition — Posted on 2016-11-23
160 Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing
Mangul, S.; Mandric, I.; Yang, H. T.; Strauli, N.; Montoya, D.; Rotman, J.; Der Wey, W. V.; Ronas, J. R.; Statz, B.; Zelikovsky, A.; Spreafico, R.; Shifman, S.; Zaitlen, N.; Rossetti, M.; Ansel, K. M.; Eskin, E.
10.1101/089235 — immunology — Posted on 2016-11-22
163 The rate and effect of de novo mutations in a colonizing lineage of Arabidopsis thaliana
Exposito-Alonso, M.; Becker, C.; Schuenemann, V. J.; Reiter, E.; Setzer, C.; Slovak, R.; Brachi, B.; Hagmann, J.; Grimm, D. G.; Jiahui, C.; Busch, W.; Bergelson, J.; Ness, R. W.; Krause, J.; Burbano, H. A.; Weigel, D.
10.1101/050203 — genomics — Posted on 2016-11-22
165 A new coactivator complex required for retinoic acid-dependent regulation of embryonic symmetry
Vilhais-Neto, G. C.; Fournier, M.; Plassat, J.-L.; Sardiu, M. E.; Saraf, A.; Garnier, J.-M.; Maruhashi, M.; Florens, L.; Washburn, M. P.; Pourquie, O.
10.1101/089201 — developmental biology — Posted on 2016-11-22
168 Age and sex affect intersubject correlation of EEGthroughout development
Petroni, A.; Cohen, S.; Langer, N.; Henin, S.; Vanderwal, T.; Milham, M. P.; Parra, L. C.
10.1101/089060 — neuroscience — Posted on 2016-11-22
175 Ancient hybridization and strong adaptation to viruses across African vervet monkey populations
Svardal, H.; Jasinska, A.; Apetrei, C.; Coppola, G.; Huang, Y.; Schmitt, C.; Jacquelin, B.; Müller-Trutwin, M.; Weinstock, G.; Grobler, P.; Wilson, R.; Turner, T.; Warren, W.; Freimer, N.; Nordborg, M.
10.1101/088989 — evolutionary biology — Posted on 2016-11-22
177 In vivo imaging of coral tissue and skeleton with optical coherence tomography
Wangpraseurt, D.; Wentzel, C.; Jacques, S. L.; Wagner, M.; Kuhl, M.
10.1101/088682 — biophysics — Posted on 2016-11-22
180 Detecting hierarchical 3-D genome domain reconfiguration with network modularity
Norton, H. K.; Huang, H.; Emerson, D. J.; Kim, J.; Gu, S.; Bassett, D. S.; Phillips-Cremins, J. E.
10.1101/089011 — genomics — Posted on 2016-11-22
181 Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9
Montefiori, L.; Gonzales, L.; Zhang, Z.; Gilad, Y.; Ober, C.; Crawford, G.; Nobrega, M.; Sakabe, N. J.
10.1101/087890 — genomics — Posted on 2016-11-22
182 MYCOPLASMA FAUCIUM AND BREAST CANCER
Mitin, V.; Tumanova, L.; Botnariuc, N.
10.1101/089128 — cancer biology — Posted on 2016-11-22
185 Predicting gene expression level in E. coli from mRNA sequence information
Zhao, L.; Abedpour, N.; Blum, C.; Kolkhof, P.; Beller, M.; Kollmann, M.; Capriotti, E.
10.1101/089102 — bioinformatics — Posted on 2016-11-22
189 SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
Matsumoto, H.; Kiryu, H.; Furusawa, C.; Ko, M. S. H.; Ko, S. B. H.; Gouda, N.; Hayashi, T.; Nikaido, I.
10.1101/088856 — bioinformatics — Posted on 2016-11-22
191 Focused ultrasound enhances sensorimotor decision-making in monkeys
Downs, M.; Teichert, T.; Buch, A.; Karakatsani, M. E.; Sierra, C.; Chen, S.; Konofagou, E. E.; Ferrera, V. P.
10.1101/041152 — neuroscience — Posted on 2016-11-21
192 Mycobacterium ulcerans low infectious dose and atypical mechanical transmission support insect bites and puncturing injuries in the spread of Buruli ulcer.
Wallace, J. R.; Mangas, K. M.; Porter, J. L.; Marcsisin, R.; Pidot, S. J.; Howden, B. O.; Omansen, T. F.; Zeng, W.; Axford, J. K.; Johnson, P. D. R.; Stinear, T. P.
10.1101/071753 — microbiology — Posted on 2016-11-21
194 Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides: Understanding Randomness in Clinical Outcomes Following Stem Cell Transplantation
Koparde, V.; Abdul Razzaq, B.; Suntum, T.; Sabo, R.; Scalora, A.; Serrano, M.; Jameson-Lee, M.; Hall, C.; Kobulnicky, D.; Sheth, N.; Sampson, J.; Roberts, C.; Buck, G.; Neale, M.; Toor, A.
10.1101/088831 — immunology — Posted on 2016-11-21
195 New single nucleotide polymorphisms (SNPs) in homologous recombination repair genes detected by microarray analysis in Polish breast cancer patients
Romanowicz, H.; Strapagiel, D.; Slomka, M.; Sobalska-Kwapis, M.; Kepka, E.; Siewierska-Gorska, A.; Zadrozny, M.; Smolarz, B.
10.1101/088948 — genetics — Posted on 2016-11-21
198 Estimating Drivers of Cell State Transitions Using Gene Regulatory Network Models
Schlauch, D.; Glass, K.; Hersh, C. P.; Silverman, E. K.; Quackenbush, J.
10.1101/089003 — systems biology — Posted on 2016-11-21
202 SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
Matsumoto, H.; Kiryu, H.; Furusawa, C.; Ko, M. S. H.; Ko, S. B. H.; Gouda, N.; Hayashi, T.; Nikaido, I.
10.1101/088856 — bioinformatics — Posted on 2016-11-21
206 An RNA binding polymer specifies nematode sperm fate
Aoki, S. T.; Porter, D. F.; Prasad, A.; Wickens, M.; Bingman, C. A.; Kimble, J.
10.1101/088914 — developmental biology — Posted on 2016-11-21
207 Tractography-based connectomes are dominated by false-positive connections
Maier-Hein, K.; Neher, P.; Houde, J.-C.; Cote, M.-A.; Garyfallidis, E.; Zhong, J.; Chamberland, M.; Yeh, F.-C.; Lin, Y. C.; Ji, Q.; Reddick, W. E.; Glass, J. O.; Chen, D. Q.; Feng, Y.; Gao, C.; Wu, Y.; Ma, J.; Renjie, H.; Li, Q.; Westin, C.-F.; Deslauriers-Gauthier, S.; Gonzalez, J. O. O.; Paquette, M.; St-Jean, S.; Girard, G.; Rheault, F.; Sidhu, J.; Tax, C. M. W.; Guo, F.; Mesri, H. Y.; David, S.; Froeling, M.; Heemskerk, A. M.; Leemans, A.; Bore, A.; Pinsard, B.; Bedetti, C.; Desrosiers, M.; Brambati, S.; Doyon, J.; Sarica, A.; Vasta, R.; Cerasa, A.; Quattrone, A.; Yeatman, J.; Khan, A. R.;
10.1101/084137 — neuroscience — Posted on 2016-11-21
209 High temporal resolution of gene expression dynamics in developing mouse embryonic stem cells
Gloss, B. S.; Signal, B.; Cheetham, S. W.; Gruhl, F.; Kaczorowski, D.; Perkins, A. C.; Dinger, M. E.
10.1101/084442 — systems biology — Posted on 2016-11-21
211 Cerebellar learning using perturbations
Bouvier, G.; Clopath, C.; Bimbard, C.; Nadal, J.-P.; Brunel, N.; Hakim, V.; Barbour, B.
10.1101/053785 — neuroscience — Posted on 2016-11-21
214 Extracellular peptidases in subsurface sediments of the White Oak River estuary, NC, suggest microbial community adaptation to oxidize degraded organic matter
Steen, A. D.; Kevorkian, R. T.; Bird, J. T.; Dombrowski, N.; Baker, B. J.; Hagen, S. M.; Mulligan, K. H.; Schmidt, J. M.; Webber, A. T.; Alperin, M. J.
10.1101/080671 — ecology — Posted on 2016-11-21
215 Size-Dependent Accumulation of the Mitotic Activator Cdc25 as a Mechanism of Size Control in Fission Yeast
Keifenheim, D.; Sun, X.-M.; D'Souza, E.; Ohira, M.; Magner, M.; Mayhew, M. B.; Marguerat, S.; Rhind, N.
10.1101/078592 — cell biology — Posted on 2016-11-21
217 Immunological Patterns from Four Melioidosis Cases: Constant and Variable Protein Antigens
Yi, J.; Herring, K.; Sanchez, T. C.; Iyer, S.; Stone, J. K.; Lee, J.; Mayo, M.; Currie, B. J.; Tuanyok, A.; Keim, P.
10.1101/082057 — immunology — Posted on 2016-11-20
218 Engineered tRNA suppression of a CFTR nonsense mutation
Lueck, J. D.; Infield, D. T.; Mackey, A. L.; Pope, M. R.; McCray, P. B.; Ahern, C. A.
10.1101/088690 — cell biology — Posted on 2016-11-20
219 E-scape: Interactive visualization of single cell phylogenetics and spatio-temporal evolution in cancer
Smith, M. A.; Nielsen, C.; Chan, F. C.; McPherson, A.; Roth, A.; Farahani, H.; Machev, D.; Steif, A.; Shah, S. P.
10.1101/080622 — cancer biology — Posted on 2016-11-20
220 Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments
Jones, D. C.; Kuppusamy, K. T.; Palpant, N. J.; Peng, X.; Murry, C. E.; Ruohola-Baker, H.; Ruzzo, W. L.
10.1101/088765 — bioinformatics — Posted on 2016-11-20
222 Optimizing complex phenotypes through model-guided multiplex genome engineering
Kuznetsov, G.; Goodman, D. B.; Filsinger, G. T.; Landon, M.; Rohland, N.; Aach, J.; Lajoie, M. J.; Church, G. M.
10.1101/086595 — synthetic biology — Posted on 2016-11-20
223 A SIMPLE pipeline for mapping point mutations
Wachsman, G.; Modliszewski, J. L.; Valdes, M.; Benfey, P. N.
10.1101/088591 — bioinformatics — Posted on 2016-11-20
226 Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
Daugherty, A. C.; Yeo, R.; Buenrostro, J. D.; Greenleaf, W. J.; Kundaje, A.; Brunet, A.
10.1101/088732 — genomics — Posted on 2016-11-19
228 Resting-state fMRI correlations: from link-wiseunreliability to whole brain stability
Pannunzi, M.; Hindriks, R.; Bettinardi, R.; Wenger, E.; Lisofsky, N.; Martensson, J.; Butler, O.; Filevich, E.; Becker, M.; Lochstet, M.; Lindenberger, U.; Kuehn, S.; Deco, G.
10.1101/081976 — neuroscience — Posted on 2016-11-19
230 Chromosome assembly of large and complex genomes using multiple references
Kolmogorov, M.; Armstrong, J.; Raney, B. J.; Streeter, I.; Dunn, M.; Yang, F.; Odom, D.; Flicek, P.; Keane, T.; Thybert, D.; Paten, B.; Pham, S.
10.1101/088435 — bioinformatics — Posted on 2016-11-19
233 Microtubules with a twist: a lumenal interrupted helix in human sperm tail microtubules
Heumann, J. M.; Schwartz, C. L.; Suzuki-Shinjo, A.; Morgan, G.; Widlund, P. O.; Hoog, J. L.
10.1101/088476 — cell biology — Posted on 2016-11-19
234 Host Vesicle Fusion Proteins VAPB, Rab11b and Rab18 Contribute to HSV-1 Infectivity by Facilitating Egress through the Nuclear Membrane
Saiz-Ros, N.; Czapiewski, R.; Stevenson, A.; Epifano, I.; Swanson, S. K.; McElwee, M.; Vijayakrishnan, S.; Richardson, C. A.; Dixon, C.; Pytowski, L.; Goldberg, M. W.; Florens, L.; Graham, S. V.; Schirmer, E. C.
10.1101/088633 — cell biology — Posted on 2016-11-19
237 Conformational landscape of the p28-bound human proteasome regulatory particle
Lu, Y.; Wu, J.; Chen, S.; Sun, S.; Ma, Y.-B.; Ouyang, Q.; Finley, D.; Kirschner, M. W.; Mao, Y.
10.1101/088492 — biochemistry — Posted on 2016-11-19
240 Floral Radiometry: A Biophysical Basis to Characterize Landscapes.
Raghunathan Nair, J.; P, S. N.; Pillai, S. M.; Kakkara, A.; Joseph, A.; Krishna, A.; I, I.; Vasundharan, S. K.
10.1101/088583 — ecology — Posted on 2016-11-18
241 Deterministic assembly processes govern seasonal and spatial variation in microbiomes across hydrologically-connected hyporheic zones
Graham, E. B.; Crump, A. R.; Resch, C. T.; Fansler, S.; Arntzen, E.; Kennedy, D. W.; Fredrickson, J. K.; Stegen, J. C.
10.1101/088518 — ecology — Posted on 2016-11-18
247 Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
Mele, M.; Mattioli, K.; Mallard, W.; Shechner, D. M.; Gerhardinger, C.; Rinn, J.
10.1101/088484 — genomics — Posted on 2016-11-17
249 GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data
Pal, K.; Bystry, V.; Reigl, T.; Demko, M.; Krejci, A.; Touloumenidou, T.; Stalika, E.; Tichy, B.; Ghia, P.; Stamatopoulos, K.; Pospisilova, S.; Malcikova, J.; Darzentas, N.; also on behalf of ERIC - TP53 Network,
10.1101/088401 — bioinformatics — Posted on 2016-11-17
252 What can genomics tell us about the success of enhancement programs in anadromous Chinook salmon? A comparative analysis across four generations
Waters, C. D.; Hard, J. J.; Brieuc, M. S. O.; Fast, D. E.; Warheit, K. I.; Waples, R. S.; Knudsen, C. M.; Bosch, W. J.; Naish, K. A.
10.1101/087973 — evolutionary biology — Posted on 2016-11-17
256 miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family
Wehrkamp, C. J.; Natarajan, S. K.; Mohr, A. M.; Phillippi, M. A.; Mott, J. L.
10.1101/088229 — molecular biology — Posted on 2016-11-17
257 High-throughput CRISPRi phenotyping in Streptococcus pneumoniae identifies new essential genes involved in cell wall synthesis and competence development
Liu, X.; Gallay, C.; Kjos, M.; Domenech, A.; Slager, J.; van Kessel, S. P.; Knoops, K.; Sorg, R. A.; Zhang, J.-R.; Veening, J.-W.
10.1101/088336 — microbiology — Posted on 2016-11-17
258 Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping
Schlautman, B.; Covarrubias-Pazaran, G.; Diaz-Garcia, L.; Iorizzo, M.; Polashock, J.; Grygleski, E.; Vorsa, N.; Zalapa, J.
10.1101/088419 — genomics — Posted on 2016-11-17
260 SOFIA: an R package for enhancing genetic visualization with Circos
Diaz-Garcia, L.; Covarrubias-Pazaran, G.; Schlautman, B.; Zalapa, J.
10.1101/088377 — genetics — Posted on 2016-11-17
261 Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment
Vysotskaia, V. S.; Hogan, G. J.; Gould, G. M.; Wang, X.; Robertson, A. D.; Haas, K. R.; Theilmann, M. R.; Spurka, L.; Grauman, P. V.; Lai, H. H.; Jeon, D.; Haliburton, G.; Leggett, M.; Chu, C. S.; Lori, K.; Maguire, J. R.; Ready, K.; Evans, E. A.; Kang, H. P.; Haque, I. S.
10.1101/088252 — genetics — Posted on 2016-11-17
264 Modeling of axonal endoplasmic reticulum network by spastic paraplegia proteins
Yalçın, B.;Zhao, Lu;Stofanko, M;O'Sullivan,N. C.;Kang, Z. H.; Annika Roost, Matthew R Thomas, Sophie Zaessinger, Olivier Blard, Alex L Patto, Valentina Baena, Mark Terasaki, View ORCID ProfileCahir J. O'Kane
10.1101/069005 — cell biology — Posted on 2016-11-17
265 Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade
Nathanson, T.; Ahuja, A.; Rubinsteyn, A.; Aksoy, B. A.; Hellmann, M. D.; Miao, D.; Van Allen, E.; Merghoub, T.; Wolchok, J.; Snyder, A.; Hammerbacher, J.
10.1101/088286 — cancer biology — Posted on 2016-11-17
266 A community-based collaboration to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer
Seyednasrollah, F.; Koestler, D. C.; Wang, T.; Piccolo, S. R.; Vega, R.; Greiner, R.; Fuchs, C.; Gofer, E.; Kumar, L.; Wolfinger, R. D.; Kanigel Winner, K.; Bare, C.; Neto, E. C.; Yu, T.; Shen, L.; Abdallah, K.; Norman, T.; Stolovitzky, G.; PCC-DREAM Community, ; Soule, H.; Sweeney, C. J.; Ryan, C. J.; Scher, H. I.; Sartor, O.; Elo, L. L.; Zhou, F. L.; Guinney, J.; Costello, J. C.
10.1101/087809 — bioinformatics — Posted on 2016-11-17
267 Investigating resting-state functional connectivity in the cervical spinal cord at 3T
Eippert, F.; Kong, Y.; Winkler, A. M.; Andersson, J. L.; Finsterbusch, J.; Buchel, C.; Brooks, J. C.; Tracey, I.
10.1101/073569 — neuroscience — Posted on 2016-11-17
268 “Gap hunting” to characterize clustered probe signals in Illumina methylation array data
Andrews, S. V.; Ladd-Acosta, C.; Feinberg, A. P.; Hansen, K. D.; Fallin, M. D.
10.1101/059659 — genomics — Posted on 2016-11-17
270 Shared characteristics underpinning C4 leaf maturation derived from analysis of multiple C3 and C4 species of Flaveria
Kumpers, B. M.; Burgess, S. J.; Reyna-Llorens, I.; Smith-Unna, R.; Boursnell, C.; Hibberd, J. M.
10.1101/088153 — plant biology — Posted on 2016-11-16
271 Activity of the C. elegans egg-laying behavior circuit is controlledby competing activation and feedback inhibition
Collins, K.; Bode, A.; Fernandez, R. W.; Tanis, J. E.; Brewer, J.; Creamer, M.; Koelle, M. R.
10.1101/073049 — neuroscience — Posted on 2016-11-16
273 An efficient extension of N-mixture models for multi-species abundance estimation
Gomez, J. P.; Robinson, S. K.; Blackburn, J. K.; Ponciano, J. M.
10.1101/073577 — ecology — Posted on 2016-11-16
277 Compensation masks trophic cascades in complex food webs
Fahimipour, A. K.; Anderson, K. E.; Williams, R. J.
10.1101/068569 — ecology — Posted on 2016-11-16
279 Optimization of lag phase shapes the evolution of a bacterial enzyme
Adkar, B. V.; Manhart, M.; Bhattacharyya, S.; Tian, J.; Musharbash, M.; Shakhnovich, E. I.
10.1101/088013 — evolutionary biology — Posted on 2016-11-16
283 Unstable inheritance of 45S rRNA genes in Arabidopsis thaliana
Rabanal, F. A.; Nizhynska, V.; Mandakova, T.; Novikova, P. Y.; Lysak, M.; Mott, R.; Nordborg, M.
10.1101/088088 — genetics — Posted on 2016-11-16
284 Chimeras Link to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish
Ye, L.; Tang, X.; Chen, Y.; Ye, X.; Ren, L.; Hu, F.; Wang, S.; Wen, M.; Zhang, C.; Tao, M.; Zhao, R.; Yao, Z.; Liu, S.
10.1101/088070 — genetics — Posted on 2016-11-16
285 What can genomics tell us about the success of enhancement programs in anadromous Chinook salmon? A comparative analysis across four generations
Waters, C. D.; Hard, J. J.; Brieuc, M. S. O.; Fast, D. E.; Warheit, K. I.; Waples, R. S.; Knudsen, C. M.; Bosch, W. J.; Naish, K. A.
10.1101/087973 — evolutionary biology — Posted on 2016-11-16
288 Eco-evolutionary theory and insect outbreaks
Paez, D.; Dukic, V.; Dushoff, J.; Fleming-Davies, A.; Dwyer, G.
10.1101/088047 — ecology — Posted on 2016-11-16
292 Neuroendocrine Modulation Sustains the C. elegans Forward Motor State
Lim, M. A.; Chitturi, J.; Laskova, V.; Meng, J.; Findeis, D.; Wiekenberg, A.; Mulcahy, B.; Luo, L.; Li, Y.; Lu, Y.; Hung, W.; Qu, Y.; Ho, C.-Y.; Holmyard, D.; Ji, N.; WcWhirter, R.; Samuel, A. D. T.; Miller, D.; Schnabel, R.; Calarco, J.; Zhen, M.
10.1101/065235 — neuroscience — Posted on 2016-11-16
300 The type IVa pilus machinery is pre-installed during cell division
Burrows, L. L.; Howell, P. L.; Buensuceso, R. N. C.; Tammam, S.; Carter, T.; Harvey, H.; Lamers, R. P.
10.1101/087965 — microbiology — Posted on 2016-11-15
301 Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations
Bray, M. S.; Wu, J.; Reed, B. C.; Kretz, C. B.; Simister, R. L.; Henny, C.; Stewart, F. J.; DiChristina, T. J.; Brandes, J. A.; Fowle, D. A.; Crowe, S. A.; Glass, J. B.
10.1101/087783 — microbiology — Posted on 2016-11-15
308 Microtubule organization within mitotic spindles revealed by serial block face scanning EM and image analysis
Nixon, F. M.; Honnor, T. R.; Starling, G. P.; Beckett, A. J.; Johansen, A. M.; Brettschneider, J. A.; Prior, I. A.; Royle, S. J.
10.1101/087866 — cell biology — Posted on 2016-11-15
314 Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria
Feldman, M. J.; Paul, R. E.; Banan, D.; Barrett, J. F.; Sebastian, J.; Yee, M.-C.; Jiang, H.; Lipka, A. E.; Brutnell, T. P.; Dinneny, J. R.; Leakey, A. D.; Baxter, I.
10.1101/083865 — plant biology — Posted on 2016-11-15
317 Determining causal genes from GWAS signals using topologically associating domains
Way, G. P.; Youngstrom, D. W.; Hankenson, K. D.; Greene, C. S.; Grant, S. F. A.
10.1101/087718 — bioinformatics — Posted on 2016-11-15
318 A community-based collaboration to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer patients
Seyednasrollah, F.; Koestler, D. C.; Wang, T.; Piccolo, S. R.; Vega, R.; Greiner, R.; Fuchs, C.; Gofer, E.; Kumar, L.; Wolfinger, R. D.; Kanigel Winner, K.; Bare, C.; Neto, E. C.; Yu, T.; Shen, L.; Abdallah, K.; Norman, T.; Stolovitzky, G.; PCC-DREAM Community, ; Soule, H.; Sweeney, C. J.; Ryan, C. J.; Scher, H. I.; Sartor, O.; Elo, L. L.; Zhou, F. L.; Guinney, J.; Costello, J. C.
10.1101/087809 — bioinformatics — Posted on 2016-11-15
323 Spike interval coding of translatory optic flow and depth from motion in the fly visual system
Longden, K. D.; Wicklein, M.; Hardcastle, B. J.; Huston, S. J.; Krapp, H. G.
10.1101/086934 — neuroscience — Posted on 2016-11-15
329 Automatic Tracing of Ultra-Volume of Neuronal Images
Peng, H.; Zhou, Z.; Meijering, E.; Zhao, T.; Ascoli, G.; Hawrylycz, M.
10.1101/087726 — bioinformatics — Posted on 2016-11-14
336 Cobalt enrichment in anaerobic microbial cocultures revealed by synchrotron X-ray fluorescence imaging
Glass, J. B.; Chen, S.; Dawson, K. S.; Horton, D. R.; Vogt, S.; Ingall, E. D.; Twining, B. S.; Orphan, V. J.
10.1101/087585 — microbiology — Posted on 2016-11-14
343 Microbiome engineers: Grazers, browsers, and the phytobiome stampede
Garrett, K. A.; Frank, E. E.; Dendy, S. P.; Leslie, J. F.; Saleh, A.
10.1101/087494 — ecology — Posted on 2016-11-14
344 Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Himmelstein, D. S.; Lizee, A.; Hessler, C.; Brueggeman, L.; Chen, S. L.; Hadley, D.; Green, A.; Khankhanian, P.; Baranzini, S. E.
10.1101/087619 — bioinformatics — Posted on 2016-11-14
345 Efficient repositioning of approved drugs as anti-HIV agents using Anti-HIV-Predictor
Dai, S.-X.; Chen, H.; Li, W.-X.; Guo, Y.-C.; Liu, J.-Q.; Zheng, J.-J.; Wang, Q.; Li, H.-J.; Chen, B.-W.; Gao, Y.-D.; Li, G.-H.; Zheng, Y.-T.; Huang, J.-F.
10.1101/087445 — bioinformatics — Posted on 2016-11-14
347 WhatsHap: fast and accurate read-based phasing
Martin, M.; Patterson, M.; Garg, S.; Fischer, S. O.; Pisanti, N.; Klau, G. W.; Schoenhuth, A.; Marschall, T.
10.1101/085050 — bioinformatics — Posted on 2016-11-14
352 Nitrogen cost minimization is promoted by structural changes in the transcriptome of N deprived Prochlorococcus cells
Read, R. W.; Berube, P. M.; Biller, S. J.; Neveux, I.; Cubillos-Ruiz, A.; Chisholm, S. W.; Grzymski, J. J.
10.1101/087643 — genomics — Posted on 2016-11-14
355 Domains of methylated CAC and CG target MeCP2 to tune transcription in the brain
Lagger, S.; Connelly, J. C.; Schweikert, G.; Webb, S.; Selfridge, J.; Ramsahoye, B. H.; Yu, M.; DeSousa, D.; Seiser, C.; He, C.; Sanguinetti, G.; Sowers, L. C.; Walkinshaw, M. D.; Bird, A. P.
10.1101/087577 — molecular biology — Posted on 2016-11-14
358 Evaluation of the accuracy of imputed sequence variants and their utility for causal variant detection in cattle
Pausch, H.; MacLeod, I. M.; Fries, R.; Emmerling, R.; Bowman, P. J.; Daetwyler, H. D.; Goddard, M. E.
10.1101/085399 — genomics — Posted on 2016-11-14
359 Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria
Feldman, M. J.; Paul, R. E.; Banan, D.; Barrett, J. F.; Sebastian, J.; Yee, M.-C.; Jiang, H.; Lipka, A. E.; Brutnell, T. P.; Dinneny, J. R.; Leakey, A. D.; Baxter, I.
10.1101/083865 — plant biology — Posted on 2016-11-14
362 Time-resolved proteomics vs. ribosome profiling reveals translation dynamics under stress
Liu, T.-Y.; Huang, H. H.; Wheeler, D.; Wells, J. A.; Song, Y. S.; Wiita, A. P.
10.1101/087486 — cancer biology — Posted on 2016-11-14
366 Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells
Danko, C. G.; Wang, Z.; Rice, E. J.; Chu, T.; Martins, A. L.; Tait Wojno, E.; Lis, J. T.; Kraus, L. W.; Siepel, A.
10.1101/083212 — genomics — Posted on 2016-11-12
369 Climatic warming strengthens a positive feedback between alpine shrubs and fire
Camac, J. S.; Williams, R. J.; Wahren, C.-H.; Hoffmann, A. A.; Vesk, P. A.
10.1101/043919 — ecology — Posted on 2016-11-12
372 Genomic Rearrangements Considered as Quantitative Traits
Imprialou, M.; Kahles, A.; Steffen, J. B.; Osborne, E. J.; Gan, X.; Lempe, J.; Bhomra, A.; Belfield, E. J.; Visscher, A.; Greenhalgh, R.; Harberd, N. P.; Goram, R.; Hein, J. J.; Robert-Seilaniantz, A.; Jones, J. J.; Stegle, O.; Kover, P. X.; Tsiantis, M.; Nordborg, M.; Ratsch, G.; Clark, R.; Mott, R.
10.1101/087387 — genetics — Posted on 2016-11-12
375 Association of five SNPs with human hair colour in the Polish population
Siewierska-Gorska, A.; Sitek, A.; Zadzinska, E.; Bartosz, G.; Strapagiel, D.
10.1101/087429 — genetics — Posted on 2016-11-12
381 Astrocytes locally translate transcripts in their peripheral processes
Sakers, K.; Lake, A. M.; Khazanchi, R.; Ouwenga, R.; Vasek, M. J.; Dani, A.; Dougherty, J. D.
10.1101/071795 — neuroscience — Posted on 2016-11-11
382 Genetic overlap between in-scanner head motion and the default network connectivity
Zhou, Y.; Chen, J.; Luo, Y.; Zheng, D.; Rao, L.-L.; Li, X.; Zhang, J.; Li, S.; Friston, K.; Zuo, X.-N.
10.1101/087023 — neuroscience — Posted on 2016-11-11
384 Proteotype profiling unmasks a viral signaling network essential for poxvirus assembly and transcriptional competence
Novy, K.; Kilcher, S.; Omasits, U.; Bleck, C. K. E.; Beerli, C.; Syedbasha, M.; Maiolica, A.; Mercer, J.; Wollscheid, B.
10.1101/087270 — microbiology — Posted on 2016-11-11
385 An annotated draft genome for Radix auricularia(Gastropoda, Mollusca)
Schell, T.; Feldmeyer, B.; Schmidt, H.; Greshake, B.; Tills, O.; Truebano, M.; Rundle, S. D.; Paule, J.; Ebersberger, I.; Pfenninger, M.
10.1101/087254 — genomics — Posted on 2016-11-11
389 Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast
Wang, Z.; Danziger, S. A.; Heavner, B. D.; Ma, S.; Smith, J. J.; Li, S.; Herricks, T.; Simeonidis, E.; Baliga, N. S.; Aitchison, J. D.; Price, N. D.
10.1101/087148 — systems biology — Posted on 2016-11-11
390 Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation
Ruffier, M.; Kahari, A.; Komorowska, M.; Keenan, S.; Laird, M. R.; Longden, I.; Proctor, G.; Searle, S.; Staines, D.; Taylor, K.; Vullo, A.; Yates, A.; Zerbino, D.; Flicek, P.
10.1101/087239 — bioinformatics — Posted on 2016-11-11
395 Systematic Design and Comparison of Expanded Carrier Screening Panels
Beauchamp, K. A.; Muzzey, D.; Wong, K. K.; Hogan, G. J.; Karimi, K.; Candille, S. I.; Mehta, N.; Kaseniit, K. E.; Mar-Heyming, R.; Kang, H. P.; Evans, E. A.; Goldberg, J. D.; Lazarin, G. A.; Haque, I. S.
10.1101/080713 — genetics — Posted on 2016-11-11
397 Resilience, invariability, and ecological stability across levels of organization
Haegeman, B.; Arnoldi, J.-F.; Wang, S.; de Mazancourt, C.; Montoya, J. M.; Loreau, M.
10.1101/085852 — ecology — Posted on 2016-11-11
398 Genome-scale transcriptional regulatory network models for the mouse and human striatum predict roles for SMAD3 and other transcription factors in Huntington’s disease
Ament, S. A.; Pearl, J. R.; Bragg, R.; Skene, P. J.; Coffey, S.; Bergey, D. E.; Plaisier, C.; Wheeler, V.; MacDonald, M.; Baliga, N. S.; Rosinski, J.; Hood, L. E.; Carroll, J. B.; Price, N. D.
10.1101/087114 — systems biology — Posted on 2016-11-10
400 Influenza C incidence and herd immunity in Lancaster, UK, in the winter of 2014-2015
Atkinson, K. V.; Bishop, L. A.; Rhodes, G.; Salez, N.; McEwan, N. R.; Hegarty, M. J.; Robey, J.; Harding, N.; Wetherell, S.; Lauder, R. M. M.; Pickup, R. W. W.; Wilkinson, M.; Gatherer, D.
10.1101/061705 — microbiology — Posted on 2016-11-10
401 Y-RNA and tRNA Cleavage by RNase L Mediates Terminal dsRNA Response
Donovan, J.; Rath, S.; Kolet-Mandrikov, D.; Korennykh, A.
10.1101/087106 — immunology — Posted on 2016-11-10
405 Fast and accurate differential splicing analysis across multiple conditions with replicates
Entizne, J. C.; Trincado, J. L.; Hysenaj, G.; Singh, B.; Skalic, M.; Elliott, D. J.; Eyras, E.
10.1101/086876 — bioinformatics — Posted on 2016-11-10
412 Spike interval coding of translatory optic flow and depth from motion in the fly visual system
Longden, K. D.; Wicklein, M.; Hardcastle, B. J.; Huston, S. J.; Krapp, H. G.
10.1101/086934 — neuroscience — Posted on 2016-11-10
413 Mouse T cell repertoires as statistical ensembles: overall characterization and age dependence
Sethna, Z.; Elhanati, Y.; Dudgeon, C. S.; Callan, C. G.; Levine, A.; Mora, T.; Walczak, A.
10.1101/086884 — immunology — Posted on 2016-11-10
414 The NDE1 Genomic Locus Affects Treatment of Psychiatric Illness through Gene Expression Changes Related to MicroRNA-484
Bradshaw, N. J.; Pankakoski, M.; Ukkola-Vuoti, L.; Zheutlin, A. B.; Ortega-Alonso, A.; Torniainen-Holm, M.; Sinha, V.; Therman, S.; Paunio, T.; Suvisaari, J.; Lonnqvist, J.; Cannon, T. D.; Haukka, J.; Hennah, W.
10.1101/087007 — genetics — Posted on 2016-11-10
416 Millstone: Software for Multiplex Microbial Genome Analysis and Engineering
Goodman, D. B.; Kuznetsov, G.; Lajoie, M. J.; Ahern, B. W.; Napolitano, M. G.; Chen, K. Y.; Chen, C.; Church, G. M.
10.1101/086868 — synthetic biology — Posted on 2016-11-10
417 Multi-omic analysis of urothelial cancer patients treated with PD-L1 blockade demonstrates the contribution of both systemic and somatic factors to the biology of response and resistance
Snyder, A.; Nathanson, T.; Funt, S.; Ahuja, A.; Buros Novik, J.; Hellmann, M. D.; Chang, E.; Aksoy, B. A.; Al-Ahmadie, H.; Yusko, E.; Vignali, M.; Benzeno, S.; Boyd, M.; Moran, M.; Iyer, G.; Robins, H. S.; Mardis, E. R.; Merghoub, T.; Hammerbacher, J.; Rosenberg, J.; Bajorin, D.
10.1101/086843 — cancer biology — Posted on 2016-11-10
422 Optimizing complex phenotypes through model-guided multiplex genome engineering
Kuznetsov, G.; Goodman, D. B.; Filsinger, G. T.; Landon, M.; Rohland, N.; Aach, J.; Lajoie, M. J.; Church, G. M.
10.1101/086595 — synthetic biology — Posted on 2016-11-09
425 Connecting genetic risk to disease endpoints through the human blood plasma proteome
Suhre, K.; Arnold, M.; Bhagwat, A.; Cotton, R. J.; Engelke, R.; Laser, A.; Raffler, J.; Sarwath, H.; Thareja, G.; DeLisle, R. K.; Gold, L.; Pezer, M.; Lauc, G.; Selim, M. A. E.-D.; Mook-Kanamori, D. O.; Al-Dous, E. K.; Mohamoud, Y. A.; Malek, J.; Strauch, K.; Grallert, H.; Peters, A.; Kastenmuller, G.; Gieger, C.; Graumann, J.
10.1101/086793 — genetics — Posted on 2016-11-09
426 Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades
Gaudry, M.; Jastroch, M.; Treberg, J.; Hofreiter, M.; Paijmans, J.; Starett, J.; Wales, N.; Signore, A.; Springer, M.; Campbell, K. L.
10.1101/086819 — evolutionary biology — Posted on 2016-11-09
431 A network-based approach to eQTL interpretation and SNP functional characterization
Fagny, M.; Paulson, J. N.; Kuijjer, M. L.; Sonawane, A. R.; Chen, C.-Y.; Lopes-Ramos, C. M.; Glass, K.; Quackenbush, J.; Platig, J.
10.1101/086587 — genomics — Posted on 2016-11-09
432 Complete avian malaria parasite genomes reveal host-specific parasite evolution in birds and mammals
Boehme, U.; Otto, T. D.; Cotton, J.; Steinbiss, S.; Sanders, M.; Oyola, S. O.; Nicot, A.; Gandon, S.; Patra, K. P.; Herd, C.; Bushell, E.; Modrzynska, K. K.; Billker, O.; Vinetz, J. M.; Rivero, A.; Newbold, C. I.; Berriman, M.
10.1101/086504 — genomics — Posted on 2016-11-09
436 Differential protein expression marks the transition from infection with Opisthorchis viverrini to cholangiocarcinoma
Khoontawad, J.; Pairojkul, C.; Rucksaken, R.; Pinlaor, P.; Wongkham, C.; Yongvanit, P.; Pugkhem, A.; Jones, A.; Plieskatt, J.; Potriquet, J.; Bethony, J.; Pinlaor, S.; Mulvenna, J.
10.1101/086645 — cancer biology — Posted on 2016-11-09
438 T cell co-stimulatory receptor CD28 is a primary target for PD-1-mediated inhibition
Hui, E.; Cheung, J.; Zhu, J.; Su, X.; Taylor, M. J.; Wallweber, H. A.; Sasmal, D. K.; Huang, J.; Kim, J. M.; Mellman, I.; Vale, R. D.
10.1101/086652 — biochemistry — Posted on 2016-11-09
441 Impact of Zygosity in Bimodal Phenotype Distributions
Holst-Hansen, T.; Abad, E.; Muntasell, A.; Lopez-Botet, M.; Jensen, M. H.; Trusina, A.; Garcia-Ojalvo, J.
10.1101/086215 — systems biology — Posted on 2016-11-09
442 Inducible nitric oxide synthase (NOS2) knockout mice as a model of trichotillomania
Casarotto, P. C.; Biojone, C.; Montezuma, K.; Cunha, F. Q.; Joca, S. R. L.; Castren, E.; Guimaraes, F. S.
10.1101/086173 — animal behavior and cognition — Posted on 2016-11-09
444 Complete avian malaria parasite genomes reveal host-specific parasite evolution in birds and mammals
Boehme, U.; Otto, T. D.; Cotton, J.; Steinbiss, S.; Sanders, M.; Oyola, S. O.; Nicot, A.; Gandon, S.; Patra, K. P.; Herd, C.; Bushell, E.; Modrzynska, K. K.; Billker, O.; Vinetz, J. M.; Rivero, A.; Newbold, C. I.; Berriman, M.
10.1101/086504 — genomics — Posted on 2016-11-08
446 Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution
Jonsson, V. D.; Blakely, C. M.; Lin, L.; Asthana, S.; Olivas, V.; Gubens, M. A.; Matni, N.; Bastian, B. C.; Taylor, B. S.; Doyle, J. C.; Bivona, T. G.
10.1101/086553 — cancer biology — Posted on 2016-11-08
448 Neuromodulatory circuit effects on Drosophila feeding behaviour and metabolism
Eriksson, A.; Raczkowska, M.; Navawongse, R.; Choudhury, D.; Stewart, J.; Tang, Y. L.; Wang, Z.; Claridge-Chang, A.
10.1101/086413 — animal behavior and cognition — Posted on 2016-11-08
453 Selection on the FADS region in Europeans
Buckley, M. T.; Racimo, F.; Allentoft, M. E.; Karoline, M. K.; Jonsson, A.; Huang, H.; Hormozdiari, F.; Sikora, M.; Marnetto, D.; Eskin, E.; Jorgensen, M. E.; Grarup, N.; Pedersen, O.; Hansen, T.; Kraft, P.; Willerslev, E.; Nielsen, R.
10.1101/086439 — genetics — Posted on 2016-11-08
456 Rotamer libraries for the high-resolution design of beta-amino acid foldamers
Watkins, A. W.; Renfrew, P. D.; Craven, T. W.; Arora, P. S.; Bonneau, R.
10.1101/086389 — bioinformatics — Posted on 2016-11-08
461 Ribo-attenuators: novel elements for reliable and modular riboswitch engineering
Folliard, T.; Prescott, T. P.; Jones, C. W.; Bayer, T.; Armitage, J. P.; Papachristodoulou, A.; Rothschild, L. J.
10.1101/086199 — synthetic biology — Posted on 2016-11-08
462 Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates
Budenhagen, C.; Lemmon, A. R.; Lemmon, E. M.; Bruhl, J.; Cappa, J.; Clement, W. L.; Donoghue, M.; Edwards, E. J.; Hipp, A. L.; Kortyna, M.; Mitchell, N.; Moore, A.; Prychid, C. J.; Segovia-Salcedo, M. C.; Simmons, M. P.; Soltis, P. S.; Wanke, S.; Mast, A.
10.1101/086298 — evolutionary biology — Posted on 2016-11-08
465 Rapid shift in substrate utilization driven by hypothalamic Agrp neurons
Cavalcanti-de-Albuquerque, J. P.; Zimmer, M. R.; Bober, J.; Dietrich, M. O.
10.1101/086348 — physiology — Posted on 2016-11-07
466 Multidimensional imbalances in cortical circuit activity in Fragile-X Syndrome mice
O'Donnell, C.; Goncalves, J. T.; Portera-Cailliau, C.; Sejnowski, T. J.
10.1101/086363 — neuroscience — Posted on 2016-11-07
467 PRDX6 inhibits neurogenesis of neural precursor cells through downregulation of wdfy1 mediated TLR4 signal
Park, M. H.; Son, D. J.; Nam, K. T.; Kim, S. Y.; Oh, S. Y.; Song, M. J.; Chun, H. O.; Lee, T. H.; Hong, J. T.
10.1101/086371 — developmental biology — Posted on 2016-11-07
469 Modeling trophic dependencies and exchanges among insects’ bacterial symbionts in a host-simulated environment
Opatovsky, I.; Santos-Garcia, D.; Lahav, T.; Ofaim, S.; Mouton, L.; Barbe, V.; Zchori-Fein, E.; Freilich, S.
10.1101/086165 — systems biology — Posted on 2016-11-07
470 L-DOPA reduces model-free control of behavior by attenuating the transfer of value to action
Kroemer, N. B.; Lee, Y.; Pooseh, S.; Eppinger, B.; Goschke, T.; Smolka, M. N.
10.1101/086116 — neuroscience — Posted on 2016-11-07
472 Tractography-based connectomes are dominated by false-positive connections
Maier-Hein, K.; Neher, P.; Houde, J.-C.; Cote, M.-A.; Garyfallidis, E.; Zhong, J.; Chamberland, M.; Yeh, F.-C.; Lin, Y. C.; Ji, Q.; Reddick, W. E.; Glass, J. O.; Chen, D. Q.; Feng, Y.; Gao, C.; Wu, Y.; Ma, J.; Renjie, H.; Li, Q.; Westin, C.-F.; Deslauriers-Gauthier, S.; Gonzalez, J. O. O.; Paquette, M.; St-Jean, S.; Girard, G.; Rheault, F.; Sidhu, J.; Tax, C. M. W.; Guo, F.; Mesri, H. Y.; David, S.; Froeling, M.; Heemskerk, A. M.; Leemans, A.; Bore, A.; Pinsard, B.; Bedetti, C.; Desrosiers, M.; Brambati, S.; Doyon, J.; Sarica, A.; Vasta, R.; Cerasa, A.; Quattrone, A.; Yeatman, J.; Khan, A. R.;
10.1101/084137 — neuroscience — Posted on 2016-11-07
474 A Canonical Neural Mechanism for Behavioral Variability
Darshan, R.; Wood, W. E.; Peters, S.; Leblois, A.; Hansel, D.
10.1101/086074 — neuroscience — Posted on 2016-11-07
475 Predicting brain-age from multimodal imaging data captures cognitive impairment
Liem, F.; Varoquaux, G.; Kynast, J.; Beyer, F.; Kharabian Masouleh, S.; Huntenburg, J. M.; Lampe, L.; Rahim, M.; Abraham, A.; Craddock, R. C.; Riedel-Heller, S.; Luck, T.; Loeffler, M.; Schroeter, M. L.; Witte, A. V.; Villringer, A.; Margulies, D. S.
10.1101/085506 — neuroscience — Posted on 2016-11-07
479 Incomplete dominance of deleterious alleles contribute substantially to trait variation and heterosis in maize
Yang, J.; Mezmouk, S.; Baumgarten, A.; Buckler, E. S.; Guill, K. E.; McMullen, M. D.; Mumm, R. H.; Ross-Ibarra, J.
10.1101/086132 — genetics — Posted on 2016-11-07
480 A large scale joint analysis of flowering time reveals independent temperate adaptations in maize
Swarts, K.; Bauer, E.; Glaubitz, J. C.; Ho, T.; Johnson, L.; Li, Y.; Li, Y.; Miller, Z.; Romay, C.; Schoen, C.-C.; Wang, T.; Zhang, Z.; Buckler, E. S.; Bradbury, P. J.
10.1101/086082 — genetics — Posted on 2016-11-07
483 Evolutionary forces affecting synonymous variations in plant genomes
Clement, Y.; Sarah, G.; Holtz, Y.; Homa, F.; Pointet, S.; Contreras, S.; Nabholz, B.; Sabot, F.; Saune, L.; Ardisson, M.; Bacilieri, R.; Besnard, G.; Berger, A.; Cardi, C.; De Bellis, F.; Fouet, O.; Jourda, C.; Khadari, B.; Lanaud, C.; Leroy, T.; Pot, D.; Sauvage, C.; Sarcelli, N.; Tregear, J.; Vigouroux, Y.; Yahiaoui, N.; Ruiz, M.; Santoni, S.; Labouisse, J.-P.; Pham, J.-L.; David, J.; Glemin, S.
10.1101/086231 — evolutionary biology — Posted on 2016-11-07
485 Hosts, parasites, and their interactions respond to different climatic variables
Poisot, T.; Gueveneux-Julien, C.; Fortin, M.-J.; Gravel, D.; Legendre, P.
10.1101/079780 — ecology — Posted on 2016-11-07
493 Origin and evolution of a pandemic lineage of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae
McCann, H. C.; Li, L.; Liu, Y.; Li, D.; Hui, P.; Zhong, C.; Rikkerink, E.; Templeton, M.; Straub, C.; Colombi, E.; Rainey, P. B.; Huang, H.
10.1101/085613 — epidemiology — Posted on 2016-11-07
497 Cassava brown streak virus has a rapidly evolving genome: implications for virus speciation, variability, diagnosis and host resistance
Alicai, T.; Ndunguru, J.; Sseruwagi, P.; Tairo, F.; Okao-Okuja, G.; Nanvubya, R.; Kiiza, L.; Kubatko, L.; Kehoe, M. A.; Boykin, L. M.
10.1101/053546 — evolutionary biology — Posted on 2016-11-07
502 Short CT-rich motifs can trigger context-specific silencing of gene expression in bacteria
Levy, L.; Anavy, L.; Solomon, O.; Cohen, R.; Ohayon, S.; Atar, O.; Goldberg, S.; Yakhini, Z.; Amit, R.
10.1101/086108 — systems biology — Posted on 2016-11-07
504 Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
Debbink, K.; McCrone, J. T.; Petrie, J. G.; Truscon, R.; Johnson, E.; Mantlo, E. K.; Monto, A. S.; Lauring, A. S.
10.1101/085985 — microbiology — Posted on 2016-11-07
505 GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Iotchkova, V.; Ritchie, G. R. S.; Geihs, M.; Morganella, S.; Min, J. L.; Walter, K.; Timpson, N. J.; UK10K Consortium, ; Dunham, I.; Birney, E.; Soranzo, N.
10.1101/085738 — genomics — Posted on 2016-11-07
511 Origin and evolution of a pandemic lineage of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae
McCann, H. C.; Li, L.; Liu, Y.; Li, D.; Hui, P.; Zhong, C.; Rikkerink, E.; Templeton, M.; Straub, C.; Colombi, E.; Rainey, P. B.; Huang, H.
10.1101/085613 — epidemiology — Posted on 2016-11-06
517 Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts
Kombrink, A.; Rovenich, H.; Shi-Kunne, X.; Rojas-Padilla, E.; van den Berg, G.; Domazakis, E.; de Jonge, R.; Valkenburg, D.-J.; Sanchez-Vallet, A.; Seidl, M.; Thomma, B.
10.1101/085894 — plant biology — Posted on 2016-11-05
518 Harnessing the lymphocyte meta-phenotype to optimize adoptive cell therapy
Buttenschoen, A.; Elkenawi, A.; El Moustaid, F.; Fletcher, A.; Grassberger, C.; Kim, E.; Marusyk, A.; McClelland, H.-L.; Miroshnychenko, D.; Nichol, D.; Mullinax, J.; O'Farrely, C.; Scott, J.
10.1101/085910 — cancer biology — Posted on 2016-11-05
522 Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape
Trizzino, M.; Park, Y.; Holsbach-Beltrame, M.; Aracena, K.; Mika, K.; Caliskan, M.; Perry, G. H.; Lynch, V. J.; Brown, C. D.
10.1101/083980 — genomics — Posted on 2016-11-05
524 The origin and evolution of a pandemic lineage of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae
McCann, H. C.; Li, L.; Liu, Y.; Li, D.; Hui, P.; Zhong, C.; Rikkerink, E.; Templeton, M.; Straub, C.; Colombi, E.; Rainey, P. B.; Huang, H.
10.1101/085613 — epidemiology — Posted on 2016-11-05
525 Thermally moderated firefly activity is delayed by precipitation extremes
Hermann, S. L.; Xue, S.; Rowe, L.; Davidson-Lowe, E.; Myers, A.; Eshchanov, B.; Bahlai, C. A.
10.1101/074633 — ecology — Posted on 2016-11-05
528 Genome-Wide Fitness Analyses of the Foodborne Pathogen Campylobacter jejuni in In Vitro and In Vivo Models
de Vries, S.; Gupta, S.; Baig, A.; Wright, E.; Wedley, A.; Nygaard Jensen, A.; LaCharme Lora, L.; Humphrey, S.; Skovgard, H.; Macleod, K.; Pont, E.; Wolanska, D.; L'Heureux, J.; Mobegi, F.; Smith, D.; Everest, P.; Zomer, A.; Williams, N.; Wigley, P.; Humphrey, T.; Maskell, D.; Grant, A.
10.1101/085720 — microbiology — Posted on 2016-11-05
534 Gentle, fast and effective crystal soaking by acoustic dispensing
Collins, P. M.; Ng, J. T.; Talon, R.; Nekrosiute, K.; Krojer, T.; Douangamath, A.; Brandao-Neto, J.; Wright, N.; Pearce, N. M.; von Delft, F.
10.1101/085712 — biophysics — Posted on 2016-11-04
537 An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.
Clavijo, B. J.; Venturini, L.; Schudoma, C.; Garcia Accinelli, G.; Kaithakottil, G.; Wright, J.; Borrill, P.; Kettleborough, G.; Heavens, D.; Chapman, H.; Lipscombe, J.; Barker, T.; Lu, F.-H.; McKenzie, N.; Raats, D.; Ramirez-Gonzalez, R. H.; Coince, A.; Peel, N.; Percival-Alwyn, L.; Duncan, O.; Trosch, J.; Yu, G.; Bolser, D.; Naamati, G.; Kerhornou, A.; Spannagl, M.; Gundlach, H.; Haberer, G.; Davey, R. P.; Fosker, C.; Di Palma, F.; Phillips, A.; Millar, A. H.; Kersey, P. J.; Uauy, C.; Krasileva, K. V.; Swarbreck, D.; Bevan, M. W.; Clark, M. D.
10.1101/080796 — genomics — Posted on 2016-11-04
538 Prioritisation of Structural Variant Calls in Cancer Genomes
Ahdesmaki, M. J.; Chapman, B.; Cingolani, P. E.; Hofmann, O.; Sidoruk, A.; Lai, Z.; Zakharov, G.; Rodichenko, M.; Alperovich, M.; Jenkins, D.; Carr, T. H.; Stetson, D.; Dougherty, B.; Barrett, J. C.; Johnson, J.
10.1101/084640 — genomics — Posted on 2016-11-04
539 Exonic somatic mutations contribute risk for autism spectrum disorder
Krupp, D. R.; Barnard, R. A.; Duffourd, Y.; Evans, S.; Bernier, R.; Riviere, J.-B.; Fombonne, E.; O'Roak, B. J.
10.1101/083428 — genetics — Posted on 2016-11-04
541 Regulatory architecture of gene expression variation in the threespine stickleback, Gasterosteus aculeatus.
Pritchard, V. L.; Viitaniemi, H. M.; McCairns, R. J. S.; Merila, J.; Nikinmaa, M.; Primmer, C. R.; Leder, E. H.
10.1101/055061 — genomics — Posted on 2016-11-04
543 Interrogating the Topological Robustness of Gene Regulatory Circuits
Huang, B.; Lu, M.; Jia, D.; Ben-Jacob, E.; Levine, H.; Onuchic, J.
10.1101/084962 — systems biology — Posted on 2016-11-04
545 Exonic somatic mutations contribute risk for autism spectrum disorder
Krupp, D. R.; Barnard, R. A.; Duffourd, Y.; Evans, S.; Bernier, R.; Riviere, J.-B.; Fombonne, E.; O'Roak, B. J.
10.1101/083428 — genetics — Posted on 2016-11-04
546 Multispot single-molecule FRET: high-throughput analysis of freely diffusing molecules
Ingargiola, A.; Lerner, E.; Chung, S.; Panzeri, F.; Gulinatti, A.; Rech, I.; Ghioni, M.; Weiss, S.; Michalet, X.
10.1101/085027 — biophysics — Posted on 2016-11-04
553 Interrogating the Topological Robustness of Gene Regulatory Circuits
Huang, B.; Lu, M.; Jia, D.; Ben-Jacob, E.; Levine, H.; Onuchic, J.
10.1101/084962 — systems biology — Posted on 2016-11-03
555 Bridging multiple scales in the human brain using computational modelling
Schirner, M.; McIntosh, A. R.; Jirsa, V.; Deco, G.; Ritter, P.
10.1101/085548 — neuroscience — Posted on 2016-11-03
558 Genomic diagnosis for children with intellectual disability and/or developmental delay
Bowling, K. M.; Thompson, M. L.; Amaral, M. D.; Finnila, C. R.; Hiatt, S. M.; Engel, K. L.; Cochran, J. N.; Brothers, K. B.; East, K. M.; Gray, D. E.; Kelley, W. V.; Lamb, N. E.; Lose, E. J.; Rich, C. A.; Simmons, S.; Whittle, J. S.; Weaver, B. T.; Nesmith, A. S.; Myers, R. M.; Barsh, G. S.; Bebin, E. M.; Cooper, G. M.
10.1101/084251 — genomics — Posted on 2016-11-03
562 Assessment of Antibody Library Diversity through Next Generation Sequencing and Technical Error Compensation.
Fantini, M.; Pandolfini, L.; Lisi, S.; Chirichella, M.; Arisi, I.; Terrigno, M.; Goracci, M.; Cremisi, F.; Cattaneo, A.
10.1101/085498 — bioinformatics — Posted on 2016-11-03
565 Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites
Mahe, F.; de Vargas, C.; Bass, D.; Czech, L.; Stamatakis, A.; Lara, E.; Singer, D.; Mayor, J.; Bunge, J.; Sernaker, S.; Siemensmeyer, T.; Trautmann, I.; Romac, S.; Berney, C.; Kozlov, A.; Mitchell, E.; Seppey, C.; Egge, E.; Lentendu, G.; Wirth, R.; Trueba, G.; Dunthorn, M.
10.1101/050997 — microbiology — Posted on 2016-11-03
566 Smooth Quantile Normalization
Hicks, S. C.; Okrah, K.; Paulson, J. N.; Quackenbush, J.; Irizarry, R. A.; Corrada Bravo, H.
10.1101/085175 — genomics — Posted on 2016-11-03
574 Evaluation of the accuracy of imputed sequence variants and their utility for causal variant detection in cattle
Pausch, H.; MacLeod, I. M.; Fries, R.; Emmerling, R.; Bowman, P. J.; Daetwyler, H. D.; Goddard, M. E.
10.1101/085399 — genomics — Posted on 2016-11-03
577 Identifying Migrant Origins Using Genetics, Isotopes, and Habitat Suitability
Ruegg, K. C.; Anderson, E.; Harrigan, R. J.; Paxton, K. L.; Kelly, J.; Moore, F.; Smith, T. B.
10.1101/085456 — ecology — Posted on 2016-11-03
578 PBrowse: A web-based platform for real-time collaborative exploration of genomic data
Szot, P. S.; Yang, A.; Wang, X.; Parsania, C.; Rohm, U.; Wong, K. H.; Ho, J. W. K.
10.1101/068049 — bioinformatics — Posted on 2016-11-03
582 Sacral agenesis: A pilot whole exome sequencing and copy number study
Porsch, R. M.; Merello, E.; De Marco, P.; Cheng, G.; Rodriguez, L.; So, M.; Sham, P.; Tam, P.; Carpa, V.; Cherny, S.; Garcia-Barcelo, M.-M.; Campbell, D.
10.1101/058578 — pathology — Posted on 2016-11-03
587 The Monarch Initiative: Insights across species reveal human disease mechanisms
Mungall, C.; McMurry, J.; Koehler, S.; Balhoff, J.; Borromeo, C.; Brush, M.; Carbon, S.; CONLIN, T.; Dunn, N.; Engelstad, M.; Foster, E.; Gourdine, J.-P.; Jacobsen, J.; Keith, D.; Laraway, B.; Lewis, S.; Nguyen Xuan, J.; Shefchek, K.; Vasilevsky, N.; Yuan, Z.; Washington, N.; Hochheiser, H.; Groza, T.; Smedley, D.; Robinson, P.; Haendel, M.
10.1101/055756 — evolutionary biology — Posted on 2016-11-03
589 An evolving cancer instigates clonally unrelated neighboring cells to form distant metastases.
Dong, J.; Darini, C.; Kabeer, F.; Dendievel, S.; Min, J.; Hambardzumyan, D.; Gaboury, L.; Lenaerts, T.; Darrasse-Jeze, G.; Li, Y.; Podsypanina, K.
10.1101/085423 — cancer biology — Posted on 2016-11-03
591 Tissue specificity of in vitro drug sensitivity
Yao, F.; Tonekaboni, S. A. M.; Safikhani, Z.; Smirnov, P.; El-Hachem, N.; Freeman, M.; Manem, V. S. K.; Haibe-Kains, B.
10.1101/085357 — bioinformatics — Posted on 2016-11-03
592 Exploring Anti-correlated Resting State BOLD Signals Through Dynamic Functional Connectivity and Whole-brain Computational Modeling
Demirtas, M.; Gilson, M.; Murray, J. D.; Popovic, D.; Vieta, E.; Pintor, L.; Prčkovska, V.; Villoslada, P.; Deco, G.
10.1101/085274 — neuroscience — Posted on 2016-11-02
594 Automating Morphological Profiling with Generic Deep Convolutional Networks
Pawlowski, N.; Caicedo, J. C.; Singh, S.; Carpenter, A. E.; Storkey, A.
10.1101/085118 — bioinformatics — Posted on 2016-11-02
597 Simulations of biomass dynamics in community food webs
DELMAS, E.; Brose, U.; Gravel, D.; Stouffer, D.; Poisot, T.
10.1101/070946 — ecology — Posted on 2016-11-02
599 Unexpected diversity in socially synchronized rhythms of shorebirds
Bulla, M.; Valcu, M.; Dokter, A. M.; Dondua, A. A.; Kosztolanyi, A.; Rutten, A.; Helm, B.; Sandercock, B. K.; Casler, B.; Ens, B. J.; Spiegel, C. S.; Hassell, C. J.; Kupper, C.; Minton, C.; Burgas, D.; Lank, D. B.; Payer, D. C.; Loktionov, E. Y.; Nol, E.; Kwon, E.; Smith, F.; Gates, H. R.; Vitnerova, H.; Pruter, H.; Johnson, J. A.; St Clair, J. J. H.; Lamarre, J.-F.; Rausch, J.; Reneerkens, J.; Conklin, J. R.; Burger, J.; Liebezeit, J.; Bety, J.; Coleman, J. T.; Figuerola, J.; Hooijmeijer, J. C. E. W.; Alves, J. A.; Smith, J. A. M.; Weidinger, K.; Koivula, K.; Gosbell, K.; Niles, L.; Koloski,
10.1101/084806 — animal behavior and cognition — Posted on 2016-11-02
600 Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution
Liu, X. L.; Lopez, P. A.; Giessen, T. W.; Giles, M.; Way, J. C.; Silver, P. A.
10.1101/085233 — synthetic biology — Posted on 2016-11-02
601 Industry-wide surveillance of Marek’s disease virus on commercial poultry farms
Kennedy, D. A.; Cairns, C.; Jones, M. J.; Bell, A. S.; Salathe, R. M.; Baigent, S. J.; Nair, V. K.; Dunn, P. A.; Read, A. F.
10.1101/075192 — epidemiology — Posted on 2016-11-02
604 Smooth Quantile Normalization
Hicks, S. C.; Okrah, K.; Paulson, J. N.; Quackenbush, J.; Irizarry, R. A.; Corrada Bravo, H.
10.1101/085175 — genomics — Posted on 2016-11-02
605 A positive association between population genetic differentiation and speciation rates in New World birds
Harvey, M.; Seeholzer, G. F.; Smith, B. T.; Rabosky, D. L.; Cuervo, A. M.; Klicka, J. T.; Brumfield, R. T.
10.1101/085134 — evolutionary biology — Posted on 2016-11-02
610 Individual differences in functional connectivity during naturalistic viewing conditions
Vanderwal, T.; Eilbott, J.; Finn, E. S.; Craddock, R. C.; Turnbull, A. G.; Castellanos, F. X.
10.1101/084665 — neuroscience — Posted on 2016-11-02
611 TrkB signaling underlies the rapid antidepressant effects of isoflurane
Antila, H.; Casarotto, P.; Popova, D.; Sipila, P.; Guirado, R.; Kohtala, S.; Ryazantseva, M.; Vesa, L.; Lindholm, J.; Yalcin, I.; Sato, V.; Goos, H.; Lempriere, S.; Cordeira, J.; Autio, H.; Kislin, M.; Rios, M.; Joca, S.; Khiroug, L.; Lauri, S.; Varjosalo, M.; Grant, S. G. N.; Taira, T.; Castren, E.; Rantamaki, T.
10.1101/084525 — neuroscience — Posted on 2016-11-02
613 Using high-resolution variant frequencies to empower clinical genome interpretation
Whiffin, N.; Minikel, E.; Walsh, R.; O'Donnell-Luria, A.; Karczewski, K.; Ing, A. Y.; Barton, P. J. R.; Funke, B.; Cook, S. A.; MacArthur, D. G.; Ware, J. S.
10.1101/073114 — genomics — Posted on 2016-11-02
614 Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance in western Thailand
Cerqueira, G. C.; Cheeseman, I. H.; Schaffner, S. F.; Nair, S.; McDew-White, M.; Phyo, A. P.; Ashley, E. A.; Melnikov, A.; Rogov, P.; Birren, B. W.; Nosten, F.; Anderson, T. J. C.; Neafsey, D. E.
10.1101/084897 — genomics — Posted on 2016-11-02
615 Prioritisation of Structural Variant Calls in Cancer Genomes
Ahdesmaki, M. J.; Chapman, B.; Cingolani, P. E.; Hofmann, O.; Sidoruk, A.; Lai, Z.; Zakharov, G.; Rodichenko, M.; Alperovich, M.; Jenkins, D.; Carr, T. H.; Stetson, D.; Dougherty, B.; Barrett, J. C.; Johnson, J. J.
10.1101/084640 — genomics — Posted on 2016-11-02
619 WhatsHap: fast and accurate read-based phasing
Martin, M.; Patterson, M.; Garg, S.; Fischer, S.; Pisanti, N.; Klau, G. W.; Schoenhuth, A.; Marschall, T.
10.1101/085050 — bioinformatics — Posted on 2016-11-02
620 PopPAnTe: population and pedigree association testing for quantitative data
Visconti, A.; Al-Shafai, M.; Al Muftah, W. A.; Zaghlool, S. B.; Mangino, M.; Suhre, K.; Falchi, M.
10.1101/084871 — bioinformatics — Posted on 2016-11-02
621 Dynamic Modeling, Parameter Estimation and Uncertainty Analysis in R
Kaschek, D.; Mader, W.; Fehling-Kaschek, M.; Rosenblatt, M.; Timmer, J.
10.1101/085001 — bioinformatics — Posted on 2016-11-02
623 Linked Data in Neuroscience: Applications, Benefits, and Challenges
Nichols, B. N.; Ghosh, S. S.; Auer, T.; Grabowskith, T. J.; Maumet, C.; Keator, D.; Pohl, K.; Poline, J.-B.
10.1101/053934 — scientific communication and education — Posted on 2016-11-02
626 Local field potentials primarily reflect inhibitory neuron activity in human and monkey cortex
Telenczuk, B.; Dehghani, N.; Le Van Quyen, M.; Cash, S. S.; Halgren, E.; Hatsopoulos, N. G.; Destexhe, A.
10.1101/052282 — neuroscience — Posted on 2016-11-02
627 Capture of Vibrio cholerae by charged polymers inhibits pathogenicity by inducing a sessile lifestyle
Perez-Soto, N.; Moule, L.; Crisan, D. N.; Insua, I.; Taylor-Smith, L. M.; Voelz, K.; Fernandez-Trillo, F.; Krachler, A.
10.1101/066563 — microbiology — Posted on 2016-11-02
629 Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities
Karl, J. A.; Graham, M. E.; Wiseman, R. W.; Heimbruch, K. E.; Gieger, S. M.; Doxiadis, G. G.; Bontrop, R. E.; O'Connor, D. H.
10.1101/084947 — genetics — Posted on 2016-11-02
632 A mouse model of hereditary hemorrhagic telangiectasia generated by transmammary-delivered immunoblocking of BMP9 and BMP10
Ruiz, S.; Zhao, H.; Chandakkar, P.; Chatterjee, P.; Blanc, L.; Metz, C.; Campagne, F.; Marambaud, P.
10.1101/084889 — cell biology — Posted on 2016-11-02
633 Multispot single-molecule FRET: high-throughput analysis of freely diffusing molecules
Ingargiola, A.; Lerner, E.; Chung, S.; Panzeri, F.; Gulinatti, A.; Rech, I.; Ghioni, M.; Weiss, S.; Michalet, X.
10.1101/085027 — biophysics — Posted on 2016-11-02
635 Palmitoylation of the oncogenic RhoGEF TGAT is dispensable for membrane localization and consequent activation of RhoA
van Unen, J.; Botman, D.; Yin, T.; Wu, Y. I.; Hink, M. A.; Gadella, T. W. J.; Postma, M.; Goedhart, J.
10.1101/062729 — cell biology — Posted on 2016-11-01
638 Sleep regulation of the distribution of cortical firing rates
Levenstein, D.; Watson, B. O.; Rinzel, J.; Buzsaki, G.
10.1101/084731 — neuroscience — Posted on 2016-11-01
640 The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only.
Datema, E.; Hulzink, R. J. M.; Blommers, L.; Espejo Valle-Inclan, J.; Van Orsouw, N.; Wittenberg, A. H. J.; De Vos, M.
10.1101/084772 — genomics — Posted on 2016-11-01
646 PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool
Tocquin, P.; Naome, A.; Jourdan, S.; Anderssen, S.; Hiard, S.; van Wezel, G. P.; Hanikenne, M.; Baurain, D.; Rigali, S.
10.1101/084780 — bioinformatics — Posted on 2016-11-01
647 Unexpected diversity in socially synchronized rhythms of shorebirds
Bulla, M.; Valcu, M.; Dokter, A. A.; Dondua, A. A.; Kosztolanyi, A.; Rutten, A.; Helm, B.; Sandercock, B. K.; Casler, B.; Ens, B. J.; Spiegel, C. S.; Hassell, C. J.; Kupper, C.; Minton, C.; Burgas, D.; Lank, D. B.; Payer, D. C.; Loktinov, E. E.; Nol, E.; Kwon, E.; Smith, F.; Gates, H. R.; Vitnerova, H.; Pruter, H.; Johnson, J. A.; St Clair, J. J. H.; Lamarre, J.-F.; Rausch, J.; Reneerkens, J.; Conklin, J. R.; Burger, J.; Liebezeit, J.; Bety, J.; Coleman, J. T.; Figuerola, J.; Hooijmeijer, J. C. E. W.; Alves, J. A.; Smith, J. A. M.; Weidinger, K.; Koivula, K.; Gosbell, K.; Niles, L.; Koloski, L
10.1101/084806 — animal behavior and cognition — Posted on 2016-11-01
648 Lower brain pH as a shared endophenotype of psychotic disorders
Hagihara, H.; Catts, V. S.; Katayama, Y.; Takagi, T.; Huang, F. L.; Huang, K.-P.; Ishii, S.; Graef, I. A.; Crabtree, G. R.; Nakayama, K. I.; Weickert, C. S.; Miyakawa, T.
10.1101/083550 — neuroscience — Posted on 2016-11-01
651 Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade
Charoentong, P.; Finotello, F.; Angelova, M.; Mayer, C.; Efremova, M.; Rieder, D.; Hackl, H.; Trajanoski, Z.
10.1101/056101 — genomics — Posted on 2016-11-01