bioRxiv directory

Baglietto, G.; Gigante, G.; Del Giudice, P.

10.1101/097592 — neuroscience — Posted on 2016-12-31

3 Joint genetic analysis using variant sets reveals polygenic gene-context interactions

Casale, F. P.; Horta, D.; Rakitsch, B.; Stegle, O.

10.1101/097477 — genetics — Posted on 2016-12-31

4 Arabidopsis HAP2/GCS1 is a gamete fusion protein homologous to somatic and viral fusogens

Valansi, C.; Moi, D.; Leikina, E.; Matveev, E.; Grana, M.; Chernomordik, L. V.; Romero, H.; Aguilar, P. S.; Podbilewicz, B.

10.1101/097568 — cell biology — Posted on 2016-12-31

5 Surveillance to Establish Elimination of Transmission and Freedom from Dog-mediated Rabies

Hampson, K.; Abela-Ridder, B.; Brunker, K.; Bucheli, S. T. M.; Carvalho, M.; Caldas, E.; Changalucha, J.; Cleaveland, S.; Dushoff, J.; Gutierrez, V.; Fooks, A. R.; Hotopp, K.; Haydon, D. T.; Lugelo, A.; Lushasi, K.; Mancy, R.; Marston, D.; Mtema, Z.; Rajeev, M.; Montebello P Dourado, L. R.; Gonzalez Roldan, J. F.; Rysava, K.; Rocha, S. M.; Sambo, M.; Sikana, L.; Vigilato, M.; Del Rio Vilas, V.

10.1101/096883 — epidemiology — Posted on 2016-12-31

6 Modeling HIV disease progression and transmission at population-level: The potential impact of modifying disease progression in HIV treatment programs

Ross, J. M.; Ying, R.; Celum, C. L.; Baeten, J. M.; Lingappa, J. R.; Thomas, K. K.; Murnane, P. M.; Krows, M.; van Rooyen, H.; Hughes, J. P.; Barnabas, R. V.

10.1101/097337 — epidemiology — Posted on 2016-12-31

7 Contributions of local speech encoding and functional connectivity to audio-visual speech integration

Giordano, B. L.; Ince, R. A. A.; Gross, J.; Panzeri, S.; Schyns, P. G.; Kayser, C.

10.1101/097493 — neuroscience — Posted on 2016-12-30

8 Generating in vivo somatic mouse mosaics with locus-specific, stably-integrated transgenic elements

Kim, G. B.; Dutra-Clarke, M.; Levy, R.; Park, H.; Sabet, S.; Molina, J.; Akhtar, A. A.; Bannykh, S.; Danielpour, M.; Breunig, J. J.

10.1101/097386 — neuroscience — Posted on 2016-12-30

9 Fusing tree-ring and forest inventory data to infer influences on tree growth

Evans, M. E. K.; Falk, D. A.; Arizpe, A.; Swetnam, T. L.; Babst, F.; Holsinger, K. E.

10.1101/097535 — ecology — Posted on 2016-12-30

10 grID: A CRISPR-Cas9 guide RNA Database and Resource for Genome-Editing

Jaskula-Ranga, V.; Zack, D. J.

10.1101/097352 — bioinformatics — Posted on 2016-12-30

11 Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome

Zhao, Z.; Xie, L.; Bourne, P. E.

10.1101/076711 — pharmacology and toxicology — Posted on 2016-12-30

12 Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona

Gandhi, S.; Haeussler, M.; Razy-Krajka, F.; Christiaen, L.; Stolfi, A.

10.1101/041632 — developmental biology — Posted on 2016-12-30

13 When Attended and Conscious Perception Deactivates Fronto-Parietal Regions

Farooqui, A. A.; Manly, T.

10.1101/097410 — neuroscience — Posted on 2016-12-30

14 Environment driven conformational changes modulate H-NS DNA bridging activity

van der Valk, R. A.; Vreede, J.; Moolenaar, G. F.; Hofmann, A.; Goosen, N.; Dame, R. T.

10.1101/097436 — biochemistry — Posted on 2016-12-30

15 A new improved and extended version of the multicell bacterial simulator gro

Gutierrez, M. E.; Gregorio-Godoy, P.; Perez del Pulgar, G.; Munoz, L. E.; Saez, S.; Rodriguez-Paton, A.

10.1101/097444 — synthetic biology — Posted on 2016-12-30

16 Parallel streams define the temporal dynamics of speech processing across human auditory cortex

Hamilton, L. S.; Edwards, E.; Chang, E. F.

10.1101/097485 — neuroscience — Posted on 2016-12-30

17 Comparison of linear spatial filters for identifying oscillatory activity in multichannel data

Cohen, M. X.

10.1101/097402 — neuroscience — Posted on 2016-12-30

18 Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer

Sallari, R. C.; Sinnott-Armstrong, N. A.; French, J. D.; Kron, K. J.; Ho, J.; Moore, J. H.; Stambolic, V.; Edwards, S. L.; Lupien, M.; Kellis, M.

10.1101/097451 — genomics — Posted on 2016-12-30

19 Interspecific plastome recombination reveals ancient reticulate evolution in Picea (Pinaceae)

Sullivan, A. R.; Schiffthaler, B.; Thompson, S. L.; Street, N. R.; Wang, X.-R.

10.1101/097519 — genomics — Posted on 2016-12-30

20 Tandem duplications lead to novel expression patterns through exon shuffling in D. yakuba

Rogers, R. L.; Shao, L.; Thornton, K. R.

10.1101/097501 — evolutionary biology — Posted on 2016-12-30

21 Training Genotype Callers with Neural Networks

Torracinta, R.; Campagne, F.

10.1101/097469 — bioinformatics — Posted on 2016-12-30

22 The replisomes remain spatially proximal throughout the cell cycle in bacteria

Mangiameli, S. M.; Veit, B. T.; Merrikh, H.; Wiggins, P. A.

10.1101/097303 — cell biology — Posted on 2016-12-30

23 Choreography of budding yeast chromosomes during the cell cycle

Lazar-Stefanita, L.; Scolari, V.; Mercy, G.; Thierry, A.; Muller, H.; Mozziconacci, J.; Koszul, R.

10.1101/096826 — genetics — Posted on 2016-12-30

24 Dopamine Negatively Regulates the NCA Ion Channels in C. elegans

Topalidou, I.; Cooper, K.; Ailion, M.

10.1101/097394 — genetics — Posted on 2016-12-30

25 FORENSIC POST-MORTEM INTERVAL (PMI) ESTIMATES: VARIATION IN FLY DEVELOPMENTAL TIMES OF INDIVIDUALS

Foldvari, M.

10.1101/064782 — developmental biology — Posted on 2016-12-30

26 Bioorthogonal pro-metabolites for profiling short chain fatty acylation

Sinclair, W. R.; Zengeya, T. T.; Garlick, J. M.; Worth, A. J.; Blair, I. A.; Snyder, N. W.; Meier, J. L.

10.1101/097360 — cell biology — Posted on 2016-12-30

27 MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

Yan, K.-K.; Gerstein, M.

10.1101/097345 — genomics — Posted on 2016-12-29

28 Microprocessor dynamics shows co- and post-transcriptional processingof pri-miRNAs

Louloupi, A.; Ntini, E.; Liz, J.; Orom, U. A.

10.1101/097311 — molecular biology — Posted on 2016-12-29

29 Tracking stem cell differentiation without biomarkers using pattern recognition and phase contrast imaging

Delaney, J. D.; Nakatake, Y.; Eckley, D. M.; Orlov, N. V.; Coletta, C. E.; Chen, C.; Ko, M. S.; Goldberg, I. G.

10.1101/097329 — cell biology — Posted on 2016-12-29

30 DeepScope: Nonintrusive Whole Slide Saliency Annotation and Prediction from Pathologists at the Microscope

Schaumberg, A. J.; Sirintrapun, S. J.; Al-Ahmadie, H. A.; Schueffler, P. J.; Fuchs, T. J.

10.1101/097246 — pathology — Posted on 2016-12-29

31 Electro-diffusion modulation of synaptic input in dendritic spines using deconvolved voltage sensor time series

Cartailler, J.; Kwon, T.; Yuste, R.; Holcman, D.

10.1101/097279 — neuroscience — Posted on 2016-12-29

32 Fast Assembling of Neuron Fragments in Serial 3D Sections

Chen, H.; Iascone, D. M.; da Costa, N. M.; Lein, E.; Liu, T.; Peng, H.

10.1101/097253 — neuroscience — Posted on 2016-12-29

33 A more accurate account of the effect of k-space sampling and signal decay on the effective spatial resolution in functional MRI

Chaimow, D.; Shmuel, A.

10.1101/097154 — neuroscience — Posted on 2016-12-29

34 Spatial specificity of the functional MRI blood oxygenation response relative to neuronal activity

Chaimow, D.; Yacoub, E.; Ugurbil, K.; Shmuel, A.

10.1101/097287 — neuroscience — Posted on 2016-12-29

35 Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies

Mukherjee, A.; Chettri, B.; Langpoklakpam, J. S.; Basak, P.; Prasad, A.; Mukherjee, A. K.; Bhattacharyya, M.; Singh, A. K.; Chattopadhyay, D.

10.1101/097063 — microbiology — Posted on 2016-12-29

36 An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

Skene, P. J.; Henikoff, S.

10.1101/097188 — genomics — Posted on 2016-12-29

37 Parallel adaptation to higher temperatures in divergent clades of the nematode Pristionchus pacificus

Leaver, M.; Kayhan, M.; McGaughran, A.; Roedelsperger, C.; Hyman, A. A.; Sommer, R.

10.1101/096727 — evolutionary biology — Posted on 2016-12-29

38 Integrated deep learned transcriptomic and structure-based predictor of clinical trials outcomes

Artemov, A. V.; Putin, E.; Vanhaelen, Q.; Aliper, A.; Ozerov, I. V.; Zhavoronkov, A.

10.1101/095653 — bioinformatics — Posted on 2016-12-29

39 tensorBF: an R package for Bayesian tensor factorization

Khan, S. A.; Ammad-ud-din, M.

10.1101/097048 — bioinformatics — Posted on 2016-12-29

40 The CARD-CC/Bcl10/paracaspase signaling complex is functionally conserved since the last common ancestor of planulozoa.

Staal, J.; Driege, Y.; Borghi, A.; Hulpiau, P.; Lievens, L.; Gul, I.; Sundararaman, S.; Goncalves, A.; Dhondt, I.; Braeckman, B.; Technau, U.; Saeys, Y.; Van Roy, F.; Beyaert, R.

10.1101/046789 — evolutionary biology — Posted on 2016-12-29

41 Head and gaze tracking of unrestrained marmosets.

Turesson, H. K.; Ribeiro Conceicao, T. B.; Ribeiro, S.

10.1101/079566 — animal behavior and cognition — Posted on 2016-12-29

42 Peripheral Htt silencing does not ameliorate central signs of disease in the B6.HttQ111/+ mouse model of Huntington’s Disease

Coffey, S.; Bragg, R. M.; Minnig, S.; Ament, S. A.; Glickenhaus, A.; Shelnut, D.; Carrillo, J.; Shuttleworth, D. D.; Rodier, J.-A.; Noguchi, K.; Bennet, C. F.; Price, N. D.; Kordasiewicz, H. B.; Carroll, J. B.

10.1101/096990 — neuroscience — Posted on 2016-12-29

43 Rab5-mediated Yolk Endocytosis modulates Zebrafish Epiboly Biomechanics and Tissue Movements

Marsal, M.; Hernandez-Vega, A.; Pouille, P.-A.; Martin-Blanco, E.

10.1101/097212 — developmental biology — Posted on 2016-12-29

44 Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation

Timmins-Schiffman, E. B.; Crandall, G. A.; Vadopalas, B.; Riffle, M. E.; Nunn, B. L.; Roberts, S. B.

10.1101/094615 — physiology — Posted on 2016-12-28

45 Optimal use of EEG recordings to target active brain areas with transcranial electrical stimulation

Dmochowski, J. P.; Koessler, L.; Norcia, A. M.; Bikson, M.; Parra, L. C.

10.1101/078758 — neuroscience — Posted on 2016-12-28

46 Detailed dendritic excitatory/inhibitory balance through heterosynaptic spike-timing-dependent plasticity

Hiratani, N.; Fukai, T.

10.1101/056093 — neuroscience — Posted on 2016-12-28

47 Analysis of copy number variants on chromosome 21 in Down syndrome-associated congenital heart defects

Rambo-Martin, B. L.; Mulle, J. G.; Cutler, D. J.; Bean, L. J. H.; Rosser, T. C.; Dooley, K. J.; Cua, C.; Capone, G.; Maslen, C. L.; Reeves, R. H.; Sherman, S. L.; Zwick, M. E.

10.1101/093583 — genomics — Posted on 2016-12-28

48 Highly-efficient Cpf1-mediated gene targeting in mice following high concentration pronuclear injection

Watkins-Chow, D. E.; Varshney, G. K. K.; Garrett, L.; Chen, Z.; Jimenez, E.; Rivas, C.; Bishop, K.; Sood, R.; Harper, U.; Pavan, W.; Burgess, S. M.

10.1101/097220 — genetics — Posted on 2016-12-28

49 DNA damage in 3D constricted migration or after lamin-A depletion in 2D: shared mechanisms of repair factor mis-localization under nuclear stress

Xia, Y.; Irianto, J.; Pfeifer, C.; Ji, J.; Ivanovska, I.; Tewari, M.; Bennett, R.; Harding, S.; Liu, A.; Greenberg, R.; Discher, D.

10.1101/097162 — cell biology — Posted on 2016-12-28

50 Phylo-Node: a molecular phylogenetic toolkit using Node.js

O'Halloran, D. M.

10.1101/075101 — bioinformatics — Posted on 2016-12-28

51 A Data Citation Roadmap for Scholarly Data Repositories

Fenner, M.; Crosas, M.; Grethe, J.; Kennedy, D.; Hermjakob, H.; Rocca-Serra, P.; Berjon, R.; Karcher, S.; Martone, M.; Clark, T.

10.1101/097196 — scientific communication and education — Posted on 2016-12-28

52 Identification of the maize Mediator CDK8 module, and Dissociation insertional mutagenesis of ZmMed12a

Nunez-Rios, T.; Ahern, K. R.; Alonso-Nieves, A. L.; Lepe-Soltero, D.; Martinez-Camacho, C.; Garcia-Aguilar, M.; Brutnell, T. P.; Gillmor, C. S.; Sawers, R. J. H.

10.1101/097204 — plant biology — Posted on 2016-12-28

53 The hippocampus as a predictive map

Stachenfeld, K. L.; Botvinick, M. M.; Gershman, S. J.

10.1101/097170 — neuroscience — Posted on 2016-12-28

54 Delivery of BACE1 siRNA mediated by TARBP-BTP fusion protein reduces β-amyloid deposits in a transgenic mouse model of Alzheimers disease

Haroon, M. M.; Saba, K.; Boddeda, V. H.; Kumar, J. M.; Patel, A. B.; Gopal, V.

10.1101/097121 — neuroscience — Posted on 2016-12-28

55 Bio.Ontology - Python tools for enrichment analysis and visualization of ontologies

Koziara, K.; Herman-Izycka, J.; Wilczynski, B.

10.1101/097139 — bioinformatics — Posted on 2016-12-28

56 Dynamics of Cortical Dendritic Membrane Potential and Spikes in Freely Behaving Rats

Moore, J. J.; Ravassard, P.; Ho, D.; Acharya, L.; Kees, A.; Vuong, C.; Mehta, M. R.

10.1101/096941 — neuroscience — Posted on 2016-12-28

57 Hnf4a mediates microbial control of intestinal gene expression and inflammation

Davison, J. M.; Lickwar, C. R.; Song, L.; Breton, G.; Crawford, G. E.; Rawls, J. F.

10.1101/097055 — genomics — Posted on 2016-12-28

58 Ecological speciation within the Phytophthora group

Mideros, M. F.; Turissini, D. A.; Guayazan, N.; Danies, G.; Cardenas, M.; Myers, K.; Tabima, J.; Goss, E. M.; Bernal, A.; Lagos, L. E.; Grajales, A.; Gonzalez, L. N.; Cooke, D. E. L.; Fry, W. E.; Grunwald, N.; Matute, D. R.; Restrepo, S.

10.1101/096842 — evolutionary biology — Posted on 2016-12-28

59 Label-free high-resolution 3-D imaging of gold nanoparticles inside live cells using optical diffraction tomography

Kim, D.; Oh, N.; Kim, K.; Lee, S.; Park, J.; Park, Y.

10.1101/097113 — biophysics — Posted on 2016-12-28

60 ECL 2.0: Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity

Yu, F.; Li, N.; Yu, W.

10.1101/097089 — bioinformatics — Posted on 2016-12-28

61 CpG traffic lights are markers of regulatory regions in humans

Khamis, A. M.; Lioznova, A. V.; Artemov, A. V.; Ramensky, V.; Bajic, V. B.; Medvedeva, Y. A.

10.1101/095968 — bioinformatics — Posted on 2016-12-28

62 HILAQ: A Novel Strategy for Newly Synthesized Protein Quantification

Ma, Y.; McClatchy, D. B.; Barkallah, S.; Wood, W. W.; Yates, J. R.

10.1101/096925 — biochemistry — Posted on 2016-12-28

63 Quantum Theory on Genome Evolution

Luo, L.

10.1101/034710 — evolutionary biology — Posted on 2016-12-28

64 Community structure follows simple assembly rules in microbial microcosms

Friedman, J.; Higgins, L. M.; Gore, J.

10.1101/067926 — ecology — Posted on 2016-12-28

65 Criticality in Cell Differentiation

Bose, I.; Pal, M.

10.1101/096818 — cell biology — Posted on 2016-12-28

66 Super-resolution Imaging of Synaptic and Extra-synaptic Pools of AMPA Receptors with Different-sized Fluorescent Probes

Lee, S. H.; Jin, C.; Cai, E.; Ge, P.; Ishitsuka, Y.; Teng, K. W.; Thomaz, A. A. d.; Nall, D. L.; Baday, M.; Jeyifous, O.; Demonte, D.; Dundas, C. M.; Park, S.; Green, W. N.; Selvin, P. R.

10.1101/096966 — neuroscience — Posted on 2016-12-27

67 Canonical and cross-reactive binding of NK cell inhibitory receptors to HLA-C allotypes is dictated by peptides bound to HLA-C

Sim, M. J. W.; Malaker, S. A.; Khan, A.; Stowell, J. M.; Shabanowitz, J.; Peterson, M. E.; Rajagopalan, S.; Hunt, D. F.; Altmann, D. M.; Long, E. O.; Boyton, R. J.

10.1101/096958 — immunology — Posted on 2016-12-27

68 Network based conditional genome wide association analysis of human metabolomics

Tsepilov, Y. A.; Sharapov, S. Z.; Zaytseva, O. O.; Krumsiek, J.; Prehn, C.; Adamski, J.; Kastenmuller, G.; Wang-Sattler, R.; Strauch, K.; Gieger, C.; Aulchenko, Y. S.

10.1101/096982 — genomics — Posted on 2016-12-27

69 Environment determines evolutionary trajectory in a constrained phenotypic space

Fraebel, D. T.; Mickalide, H.; Schnitkey, D.; Merritt, J.; Kuhlman, T. E.; Kuehn, S.

10.1101/096909 — evolutionary biology — Posted on 2016-12-27

70 NATURAL SELECTION ON MHC IIB IN PARAPATRIC LAKE AND STREAM STICKLEBACK: BALANCING, DIVERGENT, BOTH, OR NEITHER?

Stutz, W.; Bolnick, D.

10.1101/096917 — evolutionary biology — Posted on 2016-12-27

71 Dealing with many correlated covariates in capture-recapture models

Gimenez, O.; Barbraud, C.

10.1101/097006 — ecology — Posted on 2016-12-27

72 The food web of Potter Cove (Antarctica): complexity, structure and function

Marina, T. I.; Salinas, V.; Cordone, G.; Campana, G.; Moreira, M. E.; Deregibus, D.; Torre, L.; Sahade, R.; Tatian, M.; Barrera Oro, E.; De Troch, M.; Doyle, S.; Quartino, M. L.; Saravia, L.; Momo, F. R.

10.1101/094557 — ecology — Posted on 2016-12-27

73 DNAlogo: a smart mini application for generating DNA sequence logos

GUO, Y.

10.1101/096933 — bioinformatics — Posted on 2016-12-27

74 tensorBF: an R package for Bayesian tensor factorization

Khan, S. A.; Ammad-ud-din, M.

10.1101/097048 — bioinformatics — Posted on 2016-12-27

75 Fenton-type chemistry by a copper enzyme: molecular mechanism of polysaccharide oxidative cleavage

Bissaro, B.; Rohr, A. K.; Skaugen, M.; Forsberg, Z.; Horn, S. J.; Vaaje-Kolstad, G.; Eijsink, V.

10.1101/097022 — biochemistry — Posted on 2016-12-27

76 A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing

Hosoya, H.; Hyvarinen, A.

10.1101/086637 — neuroscience — Posted on 2016-12-27

77 AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment

Pjevac, P.; Schauberger, C.; Poghosyan, L.; Herbold, C. W.; van Kessel, M. A.; Daebeler, A.; Steinberger, M.; Jetten, M. S.; Lucker, S.; Wagner, M.; Daims, H.

10.1101/096891 — microbiology — Posted on 2016-12-27

78 Creating a National Vector Surveillance System: Integrated mosquito trap data and digital epidemiology

Rund, S. S. C.; Martinez, M. E.

10.1101/096875 — ecology — Posted on 2016-12-27

79 Opportune cell culture conditions permit transfer of the neurosphere paradigm to cells of the cerebellar granule cell lineage by being permissive to sonic hedgehog signaling

Heil, C.

10.1101/096859 — cell biology — Posted on 2016-12-27

80 Cell-free translation is more variable than transcription

Chizzolini, F.; Forlin, M.; Yeh Martin, N.; Berloffa, G.; Cecchi, D.; Mansy, S. S.

10.1101/073841 — synthetic biology — Posted on 2016-12-26

81 Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9

Montefiori, L.; Hernandez, L.; Zhang, Z.; Gilad, Y.; Ober, C.; Crawford, G.; Nobrega, M.; Sakabe, N. J.

10.1101/087890 — genomics — Posted on 2016-12-26

82 Evolutionary history of the brown rat: out of southern East Asia and selection

Zeng, L.; Ming, C.; Li, Y.; Su, L.-Y.; Su, Y.-H.; Otecko, N. O.; Dalecky, A.; Donnellan, S.; Aplin, K.; Liu, X.-H.; Song, Y.; Zhang, Z.-B.; Esmailizadeh, A.; Sohrabi, S. S.; Nanaei, H. A.; Liu, H.-Q.; Wang, M.-S.; Atteynine, S. A.; Rocamora, G.; Brescia, F.; Morand, S.; Irwin, D. M.; Peng, M.-s.; Yao, Y.-G.; Li, H.-P.; Wu, D.-D.; Zhang, Y.-P.

10.1101/096800 — evolutionary biology — Posted on 2016-12-26

83 Viral Quasispecies Reconstruction via Correlation Clustering

Barik, S.; Das, S.; Vikalo, H.

10.1101/096768 — bioinformatics — Posted on 2016-12-26

84 Quantifying variation by the ratio of CSS to UCSS

Pahlevani, M.

10.1101/096784 — bioinformatics — Posted on 2016-12-26

85 A highly parallel strategy for storage of digital information in living cells

Akhmetov, A.; Ellington, A.; Marcotte, E.

10.1101/096792 — synthetic biology — Posted on 2016-12-26

86 CART neuropeptide modulates the extended amygdalar CeA-vBNST circuit to gate expression of innate fear

Rale, A.; Shendye, N.; Subhedar, N.; Ghose, A.

10.1101/096610 — neuroscience — Posted on 2016-12-26

87 Genome-wide association study in Collaborative Cross mice reveal a skeletal role for Rhbdf2

Levy, R.; Levet, C.; Cohen, K.; Freeman, M.; Mott, R.; Iraqi, F.; Gabet, Y.

10.1101/094698 — genetics — Posted on 2016-12-25

88 Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Osmanovic, D.; Kessler, D. A.; Rabin, Y.; Soen, Y.

10.1101/093120 — evolutionary biology — Posted on 2016-12-25

89 K-mer Motif Multinomial Mixtures

Trippe, B. L.; Prabhakaran, S.; Bussemaker, H.

10.1101/096735 — bioinformatics — Posted on 2016-12-24

90 A network theory of the origin of life

Hoffmann, G. W.

10.1101/096701 — systems biology — Posted on 2016-12-24

91 RealTime Heart Rate Monitoring Using Photoplethysmographic (PPG) Signals During Intensive Physical Exercises

Farhadi, M.; Boloursaz Mashhadi, M.; Essalat, M.; Marvasti, F.

10.1101/092627 — bioinformatics — Posted on 2016-12-24

92 rAmpSeq: Using repetitive sequences for robust genotyping

Buckler, E. S.; Ilut, D. C.; Wang, X.; Kretzschmar, T.; Gore, M. A.; Mitchell, S. E.

10.1101/096628 — genomics — Posted on 2016-12-24

93 Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

Urbut, S. M.; Wang, G.; Stephens, M.

10.1101/096552 — genomics — Posted on 2016-12-24

94 diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data

Lareau, C.; Aryee, M.

10.1101/087338 — bioinformatics — Posted on 2016-12-24

95 Metagenomic Binning through Multi-resolution Genomic Binary Patterns

Kouchaki, S.; Tapinos, A.; Robertson, D. L.

10.1101/096719 — bioinformatics — Posted on 2016-12-24

96 Two loci contribute epistastically to heterospecific pollen rejection, a postmating isolating barrier between species

Hamlin, J.; Sherman, N.; Moyle, L. C.

10.1101/094912 — evolutionary biology — Posted on 2016-12-24

97 Incorporating the Rate of Transcriptional Change Improves Construction of Transcription Factor Regulatory Networks

Desai, J.; Sartor, R. C.; Lawas, L. M.; Jagadish SV, K.; Doherty, C. J.

10.1101/093807 — bioinformatics — Posted on 2016-12-24

98 Dorsal hippocampus plays a causal role in model-based planning

Miller, K. J.; Botvinick, M. M.; Brody, C. D.

10.1101/096594 — neuroscience — Posted on 2016-12-24

99 Assembly of photoactive Orange Carotenoid Protein from its domains unravels a carotenoid shuttle mechanism

Moldenhauer, M.; Sluchanko, N. N.; Buhrke, D.; Zlenko, D. V.; Tavraz, N. N.; Schmitt, F.-J.; Hildebrandt, P.; Maksimov, E. G.; Friedrich, T.

10.1101/096651 — biophysics — Posted on 2016-12-24

100 Inferring Weighted Gene Annotations from Expression Dat

Cary, M. P.; Kenyon, C.

10.1101/096677 — bioinformatics — Posted on 2016-12-24

101 Identifying Model-Based and Model-Free Patterns in Behavior on Multi-Step Tasks

Miller, K. J.; Brody, C. D.; Botvinick, M. M.

10.1101/096339 — neuroscience — Posted on 2016-12-24

102 From static to temporal network theory - applications to functional brain connectivity

Thompson, W. H.; Brantefors, P.; Fransson, P.

10.1101/096461 — neuroscience — Posted on 2016-12-24

103 Quantification of subclonal selection in cancer from bulk sequencing data

Williams, M. J.; Werner, B.; Curtis, C.; Barnes, C.; Sottoriva, A.; Graham, T. A.

10.1101/096305 — cancer biology — Posted on 2016-12-24

104 Neuronal gain modulability is determined by dendritic morphology: a computational optogenetic study

Jarvis, S.; Nikolic, K.; Schultz, S.

10.1101/096586 — neuroscience — Posted on 2016-12-23

105 Genetic and transgenic reagents for Drosophila simulans, D.mauritiana, D. yakuba, D. santomea and D. virilis

Stern, D.; Crocker, J.; Ding, Y.; Frankel, N.; Kappes, G.; Kim, E.; Kuzmickas, R.; Lemire, A.; Picard, S.

10.1101/096644 — genetics — Posted on 2016-12-23

106 Feedback Determines the Structure of Correlated Variability in Visual Cortex

Bondy, A. G.; Cumming, B. G.

10.1101/086256 — neuroscience — Posted on 2016-12-23

107 An approximation of the error back-propagation algorithm in a predictive coding network with local Hebbian synaptic plasticity

Whittington, J.; Bogacz, R.

10.1101/035451 — neuroscience — Posted on 2016-12-23

108 Spiraling complexity: a test of the snowball effect in a computational model of RNA folding

Kalirad, A.; Azevedo, R. B. R.

10.1101/076232 — evolutionary biology — Posted on 2016-12-23

109 Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Tumor Subpopulations and Genotype-phenotype Linkage

Poirion, O. B.; Zhu, X.; Ching, T.; Garmire, L. X.

10.1101/095810 — bioinformatics — Posted on 2016-12-23

110 Aggregation of biological particles under radial directional guidance.

Bica, I.; Hillen, T.; Painter, K. J.

10.1101/096602 — systems biology — Posted on 2016-12-23

111 Gene expression patterns associated with neurological disease in HIV infection

Sanna, P. P.; Repunte-Canonigo, V.; Masliah, E.; Lefebvre, C.

10.1101/096172 — neuroscience — Posted on 2016-12-23

112 Brain connectivity dynamics during social interaction reflect social network structure

Schmaelzle, R.; Brook O'Donnell, M.; Garcia, J. O.; Cascio, C. N. C.; Bayer, J.; Vettel, J.; Falk, E. B.

10.1101/096420 — neuroscience — Posted on 2016-12-23

113 Histone H3K4 and H3K36 methylation promotes recruitment, but not activity, of the NuA3 histone acetyltransferase complex in S. cerevisiae

Martin, B. J.; McBurney, K. L.; Maltby, V. E.; Jensen, K. N.; Brind Amour, J.; Howe, L. J.

10.1101/096511 — molecular biology — Posted on 2016-12-23

114 Generation of heritable germline mutations in the jewel wasp Nasonia vitri pennis using CRISPR/Cas9

Li, M.; Cook, L. Y.; Douglah, D.; Chong, A.; White, B. J.; Ferree, P.; Akbari, O. S.

10.1101/096578 — molecular biology — Posted on 2016-12-23

115 OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units

Westcott, S. L.; Schloss, P. D.

10.1101/096537 — microbiology — Posted on 2016-12-23

116 THE GENOMIC CODE: ISOCHORES ENCODE AND MOLD CHROMATIN DOMAINS

Bernardi, G.

10.1101/096487 — genomics — Posted on 2016-12-23

117 Human pancreatic β cell lncRNAs control cell-specific regulatory networks

Akerman, I.; Tu, Z.; Beucher, A.; Rolando, D.; Sauty-Colace, C.; Benazra, M.; Nakic, N.; Yang, J.; Wang, H.; Pasquali, L.; Moran, I.; Garcia-Hurtado, J.; Castro, N.; Gonzalez-Franco, R.; Stewart, A. F.; Bonner, C.; Piemonti, L.; Berney, T.; Groop, L.; Kerr-Conte, J.; Pattou, F.; Argmann, C.; Schadt, E.; Ravassard, P.; Ferrer, J.

10.1101/096230 — genomics — Posted on 2016-12-23

118 No evidence for a bovine mastitis Escherichia coli pathotype

Leimbach, A.; Poehlein, A.; Vollmers, J.; Daniel, R.; Dobrindt, U.

10.1101/096479 — genomics — Posted on 2016-12-23

119 When GWAS meets the Connectivity Map: drug repositioning for seven psychiatric disorders

So, H.-C.; Chau, C. K. L.; Chiu, W.-T.; Ho, K.-S.; Lo, C.-P.; Yim, S. H.-Y.; Sham, P. C.

10.1101/096503 — genomics — Posted on 2016-12-23

120 Cell reprogramming modelled as transitions in a hierarchy of cell cycles

Hannam, R.; Annibale, A.; Kuehn, R.

10.1101/096636 — genetics — Posted on 2016-12-23

121 Tradeoffs between microbial growth phases lead to frequency-dependent and non-transitive selection

Manhart, M.; Adkar, B. V.; Shakhnovich, E. I.

10.1101/096453 — evolutionary biology — Posted on 2016-12-23

122 Genotypic complexity of Fisher’s geometric model

Hwang, S.; Park, S.-C.; Krug, J.

10.1101/096438 — evolutionary biology — Posted on 2016-12-23

123 From static to temporal network theory - applications to functional brain connectivity

Thompson, W. H. H.; Brantefors, P.; Fransson, P.

10.1101/096461 — neuroscience — Posted on 2016-12-23

124 The primary motor cortex is critical for the retention of implicit sensorimotor adaptation

Leow, L.-A.; Marinovic, W.; Chye, L.; Carroll, T. J.; Riek, S.

10.1101/096404 — neuroscience — Posted on 2016-12-23

125 Gastrointestinal carriage is a major reservoir of K. pneumoniae infection in intensive care patients

Gorrie, C. L.; Mirceta, M.; Wick, R. R.; Edwards, D. J.; Strugnell, R. A.; Pratt, N.; Garlick, J.; Watson, K.; Pilcher, D.; McGloughlin, S.; Spelman, D. W.; Jenney, A. W. J.; Holt, K. E.

10.1101/096446 — microbiology — Posted on 2016-12-23

126 Inference of Multiple-wave Admixtures by Length Distribution of Ancestral Tracks

Ni, X.; Yang, X.; Yuan, K.; Feng, Q.; Guo, W.; Ma, Z.; Xu, S.

10.1101/096560 — genetics — Posted on 2016-12-23

127 GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

Thanki, A. S.; Soranzo, N.; Haerty, W.; Muffato, M.; Davey, R. P.

10.1101/096529 — bioinformatics — Posted on 2016-12-23

128 Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo

Smith, R. A.; Ionides, E. L.; King, A. A.

10.1101/096396 — epidemiology — Posted on 2016-12-23

129 Dynamic compensation, parameter identifiability, and equivariances

Sontag, E.

10.1101/095828 — systems biology — Posted on 2016-12-23

130 Inferring the brain’s internal model from sensory responses in a probabilistic inference framework

Lange, R. D.; Haefner, R. M.

10.1101/081661 — neuroscience — Posted on 2016-12-23

131 Cassava HapMap: Masking deleterious mutations in a clonal crop species

Ramu, P.; Esuma, W.; Kawuki, R.; Rabbi, I. Y.; Egesi, C.; Bredeson, J. V.; Bart, R. S.; Verma, J.; Buckler, E. S.; Lu, F.

10.1101/077123 — genetics — Posted on 2016-12-23

132 DeepAD: Alzheimer’s Disease Classification via Deep Convolutional Neural Networks using MRI and fMRI

Sarraf, S.; Anderson, J.; Tofighi, G.; for the Alzheimer's Disease Neuroimaging Initiativ,

10.1101/070441 — bioinformatics — Posted on 2016-12-23

133 Identifying Model-Based and Model-Free Patterns in Behavior on Multi-Step Tasks

Miller, K. J.; Botvinick, M.; Brody, C. D.

10.1101/096339 — neuroscience — Posted on 2016-12-23

134 Spatiotemporal Dynamics of the Bacterial Microbiota and Methanotrophic Bacteria on Lotic Cladophora glomerata (Chlorophyta)

Braus, M. J.; Whitman, T.; Graham, L.

10.1101/096347 — microbiology — Posted on 2016-12-23

135 Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks

Lages, J.; Shepelyansky, D.; Zinovyev, A.

10.1101/096362 — systems biology — Posted on 2016-12-22

136 Quantitative mRNA Imaging Throughout the Entire Drosophila Brain

Long, X.; Colonell, J.; Wong, A. M.; Singer, R. H.; Lionnet, T.

10.1101/096388 — neuroscience — Posted on 2016-12-22

137 ASAP: a Web-based platform for the analysis and inter-active visualization of single-cell RNA-seq data

Gardeux, V.; David, F.; Shajkofci, A.; Schwalie, P. C.; Deplancke, B.

10.1101/096222 — bioinformatics — Posted on 2016-12-22

138 Unicycler: resolving bacterial genome assemblies from short and long sequencing reads

Wick, R. R.; Judd, L. M.; Gorrie, C. L.; Holt, K. E.

10.1101/096412 — bioinformatics — Posted on 2016-12-22

139 High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula

Sundell, D.; Street, N. R.; Kumar, M.; Mellerowicz, E. J.; Kucukoglu, M.; Johnsson, C.; Kumar, V.; Mannapperuma, C.; Nilsson, O.; Tuominen, H.; Pesquet, E.; Fischer, U.; Niittyla, T.; Sundberg, B.; Hvidsten, T. R.

10.1101/094060 — plant biology — Posted on 2016-12-22

140 The correlation between central and peripheral oxytocin concentrations: a systematic review and meta-analysis

Valstad, M.; Alvares, G. A.; Egknud, M.; Matziorinis, A. M.; Andreassen, O. A.; Westlye, L. T.; Quintana, D. S.

10.1101/096263 — physiology — Posted on 2016-12-22

141 Drug repurposing for ageing research using model organisms

Ziehm, M.; Kaur, S.; Ivanov, D. K.; Ballester, P. J.; Marcus, D.; Partridge, L.; Thornton, J. M.

10.1101/095380 — pharmacology and toxicology — Posted on 2016-12-22

142 Closed-loop estimation of retinal network sensitivity reveals signature of efficient coding

Ferrari, U.; Gardella, C.; Marre, O.; Mora, T.

10.1101/096313 — neuroscience — Posted on 2016-12-22

143 Trial-by-trial neural variability is a stable individual trait of adult humans

Arazi, A.; Gonen-Yaacovi, G.; Dinstein, I.

10.1101/096198 — neuroscience — Posted on 2016-12-22

144 Inter-Subject Alignment of MEG Datasets at the Neural Representational Space

Zhang, Q.; Borst, J.; Kass, R. E.; Anderson, J. R.

10.1101/096040 — neuroscience — Posted on 2016-12-22

145 Diatom Centromeres Suggest a Novel Mechanism for Nuclear Gene Acquisition

Diner, R. E.; Noddings, C. M.; Lian, N. C.; Kang, A. K.; McQuaid, J. B.; Jablanovic, J.; Espinoza, J. L.; Nguyen, N. A.; Anzelmatti, M. A.; Jansson, J.; Bielinski, V. A.; Karas, B. J.; Dupont, C. L.; Allen, A. E.; Weyman, P. D.

10.1101/096016 — molecular biology — Posted on 2016-12-22

146 Histone gene expression is regulated by histone H2B ubiquitylation in fission yeast

Page, V.; Grabowski, D.; Allis, C. D.; Tanny, J.

10.1101/094565 — molecular biology — Posted on 2016-12-22

147 Natural diversity of the malaria vector Anopheles gambiae

Miles, A.; Harding, N. J.; Botta, G.; Clarkson, C.; Antao, T.; Kozak, K.; Schrider, D.; Kern, A.; Redmond, S.; Sharakhov, I.; Pearson, R.; Bergey, C.; Fontaine, M.; Troco, A.; Diabate, A.; Costantini, C.; Rohatgi, K.; Elissa, N.; Coulibaly, B.; Dinis, J.; Midega, J.; Mbogo, C.; Mawejje, H.; Stalker, J.; Rockett, K.; Drury, E.; Mead, D.; Jeffreys, A.; Hubbart, C.; Rowlands, K.; Isaacs, A.; Jyothi, D.; Malangone, C.; Vauterin, P.; Jeffrey, B.; Wright, I.; Hart, L.; Kluczynski, K.; Cornelius, V.; MacInnis, B.; Henrichs, C.; Giacomantonio, R.; Ayala, D.; Bejon, P.; Besansky, N.; Burt, A.; Caputo,

10.1101/096289 — genomics — Posted on 2016-12-22

148 Associations of coffee genetic risk scores with coffee, tea and other beverages in the UK Biobank

Taylor, A. E.; Munafo, M. R.

10.1101/096214 — genetics — Posted on 2016-12-22

149 Sequence and structural diversity of mouse Y chromosomes

Morgan, A. P.; Pardo Manuel de Villena, F.

10.1101/096297 — genetics — Posted on 2016-12-22

150 Rampant Reverse Evolution towards Specialization in Commensal Bacteria Colonizing the Gut

Sousa, A.; Ramiro, R.; Batista, J.; Guleresi, D.; Lourenco, M.; Gordo, I.

10.1101/096206 — evolutionary biology — Posted on 2016-12-22

151 The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia formation via ubiquitylation of CSPP-L.

Shearer, R. F.; Frikstad, K.-A. M.; McKenna, J.; McCloy, R.; Deng, N.; Burgess, A.; Stokke, T.; Patzke, S.; Saunders, D. N.

10.1101/090100 — cell biology — Posted on 2016-12-22

152 The DOE Systems Biology Knowledgebase (KBase)

Arkin, A. P.; Stevens, R. L.; Cottingham, R. W.; Maslov, S.; Henry, C. S.; Dehal, P.; Ware, D.; Perez, F.; Harris, N. L.; Canon, S.; Sneddon, M. W.; Henderson, M. L.; Riehl, W. J.; Gunter, D.; Murphy-Olson, D.; Chan, S.; Kamimura, R. T.; Brettin, T. S.; Meyer, F.; Chivian, D.; Weston, D. J.; Glass, E. M.; Davison, B. H.; Kumari, S.; Allen, B. H.; Baumohl, J.; Best, A. A.; Bowen, B.; Brenner, S. E.; Bun, C. C.; Chandonia, J.-M.; Chia, J.-M.; Colasanti, R.; Conrad, N.; Davis, J. J.; DeJongh, M.; Devoid, S.; Dietrich, E.; Drake, M. M.; Dubchak, I.; Edirisinghe, J. N.; Fang, G.; Faria, J. P.; Fryb

10.1101/096354 — bioinformatics — Posted on 2016-12-22

153 Regulation of eIF4F complex by the peptidyl prolyl isomerase FKBP7 in taxane-resistant prostate cancer

GARRIDO, M. F.; MARTIN, N. J.; GAUDIN, C.; Commo, F.; AL NAKOUZI, N.; FAZLI, L.; DEL NERY, E.; Camonis, J.; Perez, F.; LERONDEL, S.; LE PAPE, A.; ABOU-HAMDAN, H.; Gleave, M.; Loriot, Y.; DESAUBRY, L.; VAGNER, s.; FIZAZI, K.; CHAUCHEREAU, A.

10.1101/096271 — cancer biology — Posted on 2016-12-22

154 Quantification of subclonal selection in cancer from bulk sequencing data

Williams, M. J.; Werner, B.; Curtis, C.; Barnes, C.; Sottoriva, A.; Graham, T. A.

10.1101/096305 — cancer biology — Posted on 2016-12-22

155 Using a structural root system model to evaluate and improve the accuracy of root image analysis pipelines.

Lobet, G.; Koevoets, I.; Noll, M.; Meyer, P. E.; Tocquin, P.; Pages, L.; Perilleux, C.

10.1101/074922 — plant biology — Posted on 2016-12-22

156 Statistical testing and power analysis for brain-wide association study

Gong, W.; Wan, L.; Lu, W.; Ma, L.; Cheng, F.; Cheng, W.; Gruenewald, S.; Feng, J.

10.1101/089870 — neuroscience — Posted on 2016-12-22

157 MODELING THE MULTIPLE FACETS OF SPECIATION-WITH-GENE-FLOW TOWARDS INFERRING THE DIVERGENCE HISTORY OF LAKE WHITEFISH SPECIES PAIRS (COREGONUS CLUPEAFORMIS).

Rougeux, C.; Bernatchez, L.; Gagnaire, P.-A.

10.1101/068932 — evolutionary biology — Posted on 2016-12-22

158 Containing Emerging Epidemics: a Quantitative Comparison of Quarantine and Symptom Monitoring

Peak, C. M.; Childs, L. M.; Grad, Y. H.; Buckee, C. O.

10.1101/072652 — epidemiology — Posted on 2016-12-22

159 A Unique Ribosome Signature Reveals Bacterial Translation Initiation Sites

Giess, A.; Ndah, E.; Jonckheere, V.; Van Damme, P.; Valen, E.

10.1101/095893 — bioinformatics — Posted on 2016-12-22

160 Control of Lipid Domain Organization by a Biomimetic Contractile Actomyosin Cortex

Vogel, S. K.; Greiss, F.; Khmelinskaia, A.; Schwille, P.

10.1101/096248 — synthetic biology — Posted on 2016-12-22

161 The Effects of Personal Pharmacogenetic Testing on the Effects of Pharmacy Student Perceptions of Knowledge and Attitudes Towards Precision Medicine

Surofchy, D.; Oh, S.; Galanter, J.; Xiang, P.; Li, M.; Guo, S.; Desai, T.; Guglielmo, B. J.; Giacomini, K.; Long-Boyle, J.; Wu, A. H.; Burchard, E. G.

10.1101/052043 — scientific communication and education — Posted on 2016-12-22

162 Variable penetrance of the 15q11.2 BP1-BP2 microduplication in a family with cognitive and language impairment

Benitez-Burraco, A.; Barcos-Martinez, M.; Espejo-Portero, I.; Jimenez-Romero, M. S.

10.1101/095919 — neuroscience — Posted on 2016-12-22

163 Sex matters in Massive Parallel Sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

Benestan, L.; Moore, J.-S.; Sutherland, B. J. G.; Le Luyer, J.; Maaroufi, H.; Rougeux, C.; Normandeau, E.; Rycroft, N.; Atema, J.; Harris, L. N.; Tallman, R. F.; Greenwood, S. J.; Clark, K. F.; Bernatchez, L.

10.1101/096065 — genomics — Posted on 2016-12-22

164 Detecting the impact of temperature on transmission of Zika, dengue and chikungunya using mechanistic models

Mordecai, E.; Cohen, J.; Evans, M. V.; Gudapati, P.; Johnson, L. R.; Lippi, C. A.; Miazgowicz, K.; Murdock, C. C.; Rohr, J. R.; Ryan, S. J.; Savage, V.; Shocket, M.; Stewart Ibarra, A.; Thomas, M. B.; Weikel, D. P.

10.1101/063735 — ecology — Posted on 2016-12-22

165 Looking at my own Face: Visual Processing Strategies in Physical Self-representation

Chakraborty, A.; Chakrabarti, B.

10.1101/096073 — animal behavior and cognition — Posted on 2016-12-22

166 Design principles for robust vesiculation in clathrin-mediated endocytosis

Hassinger, J. E.; Oster, G.; Drubin, D. G.; Rangamani, P.

10.1101/050484 — biophysics — Posted on 2016-12-22

167 Critical transitions and the fragmenting of global forests

Saravia, L. A.; Doyle, S. R.; Bond-Lamberty, B.

10.1101/091751 — ecology — Posted on 2016-12-22

168 Dynamic compensation, parameter identifiability, and equivariances

Sontag, E.

10.1101/095828 — systems biology — Posted on 2016-12-21

169 Adaptation-induced blindness is orientation-tuned and monocular

Apthorp, D.; Griffiths, S.; Alais, D.; Cass, J.

10.1101/048918 — neuroscience — Posted on 2016-12-21

170 Flagellar synchronization is a simple alternative to cell cycle synchronization for ciliary and flagellar studies

Dutta, S.; Avasthi, P.

10.1101/089185 — cell biology — Posted on 2016-12-21

171 RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

Castro-Mondragon, J.; Jaeger, S.; Thieffry, D.; Thomas-Chollier, M.; van Helden, J.

10.1101/065565 — bioinformatics — Posted on 2016-12-21

172 BAYESIAN NON-CENTRAL CHI REGRESSION FOR NEUROIMAGING

Wegmann, B.; Eklund, A.; Villani, M.

10.1101/095844 — neuroscience — Posted on 2016-12-21

173 Online control of prehension predicts performance on a standardised motor assessment test in 8-12 year-old children

Blanchard, C. C. V.; McGlashan, H. L.; French, B.; Sperring, R. J.; Petrocochino, B.; Holmes, N. P.

10.1101/095703 — neuroscience — Posted on 2016-12-21

174 The Constancy of Colored After-Images

Zeki, S.; Cheadle, S.; Pepper, J.; Mylonas, D.

10.1101/095935 — neuroscience — Posted on 2016-12-21

175 Transcranial stimulation enhances memory-relevant sleep oscillations and their functional coupling in mild cognitive impairment

Ladenbauer, J.; Ladenbauer, J.; Kulzow, N.; de Boor, R.; Avramova, E.; Grittner, U.; Floel, A.

10.1101/095588 — neuroscience — Posted on 2016-12-21

176 Activity-dependent expression of reporter proteins at dendritic spines for synaptic activity mapping and optogenetic stimulation

Gobbo, F.; Marchetti, L.; Alia, C.; Luin, S.; Cattaneo, A.

10.1101/095984 — neuroscience — Posted on 2016-12-21

177 Acidic pH-dependent depletion of Mycobacterium tuberculosis thiol pools potentiates antibiotics and oxidizing agents

Coulson, G. B.; Johnson, B. K.; Colvin, C. J.; Fillinger, R. J.; Zheng, H.; Haiderer, E. R.; Hammer, N. D.; Abramovitch, R. B.

10.1101/095448 — microbiology — Posted on 2016-12-21

178 Transcriptional study of the ABC transporter-encoding genes in response to fungicide treatment and during plant infection in the phytopathogenic fungus Botrytis cinerea

LOISEL, E.; GONCALVES, I. R.; POUSSEREAU, N.; GROSJEAN-COURNOYER, M.-C.; VILLALBA, F.; BRUEL, C.

10.1101/095869 — microbiology — Posted on 2016-12-21

179 Coefficient of determination R2 and intra-class correlation coefficient ICC from generalized linear mixed-effects models revisited and expanded

Nakagawa, S.; Schielzeth, H.

10.1101/095851 — ecology — Posted on 2016-12-21

180 Behavioural, modeling, and electrophysiological evidence for domain-generality in human metacognition

Faivre, N.; Filevich, E.; Solovey, G.; Kuhn, S.; Blanke, O.

10.1101/095950 — neuroscience — Posted on 2016-12-21

181 Speciation trajectories in recombining bacterial species

Marttinen, P.; Hanage, B.

10.1101/095885 — microbiology — Posted on 2016-12-21

182 Noninvasive Prenatal Screening at Low Fetal Fraction: Comparing Whole- Genome Sequencing and Single-Nucleotide Polymorphism Methods

Artieri, C. G.; Haverty, C.; Evans, E. A.; Goldberg, J. D.; Haque, I. S.; Yaron, Y.; Muzzey, D.

10.1101/096024 — genomics — Posted on 2016-12-21

183 A SUMO-Ubiquitin Relay Recruits Proteasomes to Chromosome Axes to Regulate Meiotic Recombination

Rao, H. B. D. P.; Qiao, H.; Bhatt, S. K.; Bailey, L. R. J.; Tran, H. D.; Bourne, S. L.; Qiu, W.; Deshpande, A.; Sharma, A. N.; Beebout, C. J.; Pezza, R. J.; Hunter, N.

10.1101/095711 — genetics — Posted on 2016-12-21

184 Non-random mating and information theory

Carvajal-Rodriguez, A.

10.1101/095901 — evolutionary biology — Posted on 2016-12-21

185 Isolation and Gene Flow in a Speciation Continuum in Newts

Pabijan, M.; Zielinski, P.; Dudek, K.; Stuglik, M.; Babik, W.

10.1101/095877 — evolutionary biology — Posted on 2016-12-21

186 Transcriptomic Evidence for Reproductive Suppression in Male Peromyscus eremicus (Cactus Mouse) Subjected to Acute Dehydration

Kordonowy, L.; MacManes, M.

10.1101/096057 — evolutionary biology — Posted on 2016-12-21

187 The Liquid Structure of Elastin

Rauscher, S.; Pomes, R.

10.1101/095927 — biophysics — Posted on 2016-12-21

188 A Unique Ribosome Signature Reveals Bacterial Translation Initiation Sites

Giess, A.; Ndah, E.; Jonckheere, V.; Van Damme, P.; Valen, E.

10.1101/095893 — bioinformatics — Posted on 2016-12-21

189 Cultured Ostreococcus is cobalamin-independent

Pasek, M.

10.1101/065771 — genomics — Posted on 2016-12-21

190 Chlamydomonas reinhardtii formin and profilin are optimized for acute rapid actin filament assembly

Christensen, J. R.; Glista, M. J.; Mueller, D. M.; Li, Y.; Sees, J. A.; Skau, C. T.; Mets, L. J.; Avasthi, P.; Kovar, D. R.

10.1101/096008 — cell biology — Posted on 2016-12-21

191 Cell Mechanosensing and Avoidance of Strain Gradients

Chagnon-Lessard, S.; Jean-Ruel, H.; Godin, M.; Pelling, A. E.

10.1101/095976 — biophysics — Posted on 2016-12-21

192 Non-equilibrium chromosome looping via molecular slip-links

Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

10.1101/095992 — biophysics — Posted on 2016-12-21

193 Statistical testing and power analysis for brain-wide association study

Gong, W.; Wan, L.; Lu, W.; Ma, L.; Cheng, F.; Cheng, W.; Gruenewald, S.; Feng, J.

10.1101/089870 — neuroscience — Posted on 2016-12-21

194 Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization

Nora, E. P.; Goloborodko, A.; Valton, A.-L.; Gibcus, J.; Uebsersohn, A.; Abdennur, N.; Dekker, J.; Mirny, L.; Bruneau, B.

10.1101/095802 — genomics — Posted on 2016-12-21

195 Using Single Nucleotide Variations in Cancer Single-Cell RNA-Seq Data for Subpopulation Identification and Genotype-phenotype Linkage Analysis

Poirion, O. B.; Zhu, X.; Ching, T.; Garmire, L. X.

10.1101/095810 — bioinformatics — Posted on 2016-12-21

196 Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Osmanovic, D.; Kessler, D. A.; Rabin, Y.; Soen, Y.

10.1101/093120 — evolutionary biology — Posted on 2016-12-21

197 iSUMO - integrative prediction of functionally relevant SUMOylated proteins

Yao, X.; Gandhi, S.; Bish, R.; Vogel, C.

10.1101/056564 — systems biology — Posted on 2016-12-21

198 The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core

Deco, G.; Kringelbach, M. L.; Jirsa, V.; Ritter, P.

10.1101/065284 — neuroscience — Posted on 2016-12-21

199 Revealing neuro-computational mechanisms of reinforcement learning and decision-making with the hBayesDM package

Ahn, W.-Y.; Haines, N.; Zhang, L.

10.1101/064287 — neuroscience — Posted on 2016-12-21

200 Creating a universal SNP and small indel variant caller with deep neural networks

Poplin, R.; Newburger, D.; Dijamco, J.; Nguyen, N.; Loy, D.; Gross, S. S.; McLean, C. Y.; DePristo, M. A.

10.1101/092890 — genomics — Posted on 2016-12-21

201 SuperTranscript: a data driven reference for analysis and visualisation of transcriptomes

Hawkins, A. D.; Oshlack, A.; Davidson, N. M.

10.1101/077750 — bioinformatics — Posted on 2016-12-21

202 The thalamus drives light-evoked activity in the habenula of larval zebrafish

Cheng, R. K.; Krishnan, S.; Lin, Q.; Hildebrand, D. G. C.; Bianco, I. H.; Kibat, C.; Jesuthasan, S.

10.1101/047936 — neuroscience — Posted on 2016-12-21

203 How to improve parameter estimates in GLM-based fMRI data analysis: cross-validated Bayesian model averaging

Soch, J.; Meyer, A. P.; Haynes, J.-D.; Allefeld, C.

10.1101/095778 — neuroscience — Posted on 2016-12-20

204 Cleanliness in context: reconciling hygiene with a modern microbial perspective

Vandegrift, R.; Bateman, A. C.; Siemens, K. N.; Nguyen, M.; Green, J. L.; Van Den Wymelenberg, K. G.; Hickey, R. J.

10.1101/095745 — microbiology — Posted on 2016-12-20

205 Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Macqueen, D. J.; Primmer, C. R.; Houston, R. D.; Nowak, B. F.; Bernatchez, L.; Bergseth, S.; Davidson, W. S.; Gallardo-Escarate, C.; Goldammer, T.; Guiguen, Y.; Iturra, P.; Kijas, J. W.; Koop, B. F.; Lien, S.; Maass, A.; Martin, S. A. M.; McGinnity, P.; Montecino, M.; Naish, K. A.; Nichols, K. M.; Olafsson, K.; Omholt, S. W.; Palti, Y.; Plastow, G. S.; Rexroa, C. E.; Rise, M. L.; Ritchie, R. J.; Sandve, S. R.; Schulte, P. M.; Tello, A.; Vidal, R.; Vik, J. O.; Wargelius, A.; Yanez, J. M.

10.1101/095737 — genomics — Posted on 2016-12-20

206 The interplay of stiffness and force anisotropies drive embryo elongation

Vuong-Brender, T. T. K.; Ben Amar, M.; Pontabry, J.; Labouesse, M.

10.1101/095752 — developmental biology — Posted on 2016-12-20

207 Mechanism of Nuclear Movements in a Multinucleated Cell

Gibeaux, R.; Politi, A.; Philippsen, P.; Nedelec, F.

10.1101/095695 — cell biology — Posted on 2016-12-20

208 Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification

Zhu, W.; Lou, Q.; Vang, Y. S.; Xie, X.

10.1101/095794 — bioinformatics — Posted on 2016-12-20

209 Adversarial Deep Structural Networks for Mammographic Mass Segmentation

Zhu, W.; Xie, X.

10.1101/095786 — bioinformatics — Posted on 2016-12-20

210 Structural and Functional Characterization of the Alanine Racemase from Streptomyces coelicolor A3(2)

Tassoni, R.; van der Aart, L.; Ubbink, M.; van Wezel, G. P.; Pannu, N.

10.1101/089938 — molecular biology — Posted on 2016-12-20

211 Evolutionary thrift: mycobacteria repurpose plasmid diversity during adaptation of type VII secretion systems

Mortimer, T. D.; Weber, A. M.; Pepperell, C. S.

10.1101/067207 — evolutionary biology — Posted on 2016-12-20

212 Population dynamics of synthetic Terraformation motifs

Sole, R.; Montanez, R.; Duran-Nebreda, S.; Amor, D. R.; Vidiella, B.; Sardanyes, J.

10.1101/095687 — synthetic biology — Posted on 2016-12-20

213 Multivariate pattern analysis of MEG and EEG: a comparison of representational structure in time and space

Cichy, R. M.; Pantazis, D.

10.1101/095620 — neuroscience — Posted on 2016-12-20

214 When null hypothesis significance testing is unsuitable for research: a reassessment

Szucs, D.; Ioannidis, J. P.

10.1101/095570 — neuroscience — Posted on 2016-12-20

215 Decoding bacterioplankton metabolism in the northern Gulf of Mexico Dead Zone

Thrash, J. C.; Seitz, K. W.; Baker, B. J.; Temperton, B.; Gillies, L. E.; Rabalais, N. N.; Henrissat, B.; Mason, O. U.

10.1101/095471 — microbiology — Posted on 2016-12-20

216 Two-zone tumor tolerance can arise from a simple immunological feedforward motif that estimates tumor growth rates

Sontag, E.

10.1101/095455 — immunology — Posted on 2016-12-20

217 Umap and Bismap: quantifying genome and methylome mappability

Karimzadeh, M.; Ernst, C.; Kundaje, A.; Hoffman, M. M.

10.1101/095463 — genomics — Posted on 2016-12-20

218 Loss of the homologous recombination gene rad51 leads to Fanconi anemia-like symptoms in zebrafish

Botthof, J. G.; Bielczyk-Maczyłska, E.; Ferreira, L.; Cvejic, A.

10.1101/095646 — genetics — Posted on 2016-12-20

219 Biased phylodynamic inferences from analysing clusters of viral sequences

Dearlove, B.; Xiang, F.; Frost, S.

10.1101/095661 — genetics — Posted on 2016-12-20

220 Whole genome sequence accuracy is improved by replication in a population of mutagenized sorghum.

Addo-Quaye, C.; Tuinstra, M.; Carraro, N.; Weil, C.; Dilkes, B. P.

10.1101/095513 — genetics — Posted on 2016-12-20

221 Mitochondrial-nuclear interactions maintain a deep mitochondrial split in the face of nuclear gene flow

Morales, H. E.; Pavlova, A.; Amos, N.; Major, R.; Bragg, J.; Kilian, A.; Greening, C.; Sunnucks, P.

10.1101/095596 — evolutionary biology — Posted on 2016-12-20

222 Genomes of an entire Plasmodium subgenus reveal paths to virulent human malaria

Otto, T. D.; Gilabert, A.; Crellen, T.; Bohme, U.; Arnathau, C.; Sanders, M.; Oyola, S.; Okauga, A. P.; Boundenga, L.; Wuillaume, E.; Ngoubangoye, B.; Moukodoum, N.; Paupy, C.; Durand, P.; Rougeron, V.; Ollomo, B.; Renaud, F.; Newbold, C.; Berriman, M.; Prugnolle, F.

10.1101/095679 — evolutionary biology — Posted on 2016-12-20

223 Single-enzyme approach predicts natural emergence of inhibitor-activator duality

Rotbart, T.; Reuveni, S.; Urbakh, M.

10.1101/095562 — biophysics — Posted on 2016-12-20

224 Integrated deep learned transcriptomic and structure-based predictor of clinical trials outcomes

Artemov, A. V.; Putin, E.; Vanhaelen, Q.; Aliper, A.; Ozerov, I. V.; Zhavoronkov, A.

10.1101/095653 — bioinformatics — Posted on 2016-12-20

225 Partitioned learning of deep Boltzmann machines for SNP data

Hess, M.; Lenz, S.; Blaette, T.; Bullinger, L.; Binder, H.

10.1101/095638 — bioinformatics — Posted on 2016-12-20

226 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 2016-12-20

227 Gene fractionation and function in the ancient subgenomes of maize

Renny-Byfield, S.; Rodgers-Melnick, E.; Ross-Ibarra, J.

10.1101/095547 — genomics — Posted on 2016-12-20

228 Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments

Jenior, M. L.; Leslie, J. L.; Young, V. B.; Schloss, P. D.

10.1101/092304 — microbiology — Posted on 2016-12-20

229 Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

Baillie, J. K.; Bretherick, A.; Haley, C.; Clohisey, S.; Gray, A.; Barret, J.; Stahl, E.; Tenesa, A.; Andersson, R.; Brown, J. B.; Faulkner, G.; Lizio, M.; Schaefer, U.; Daub, C.; Itoh, M.; Kondo, N.; Lassmann, T.; Kawai, J.; IIBDGC Consortium, ; FANTOM5 Consortium, ; Bajic, V. B.; Heutink, P.; Rehli, M.; Kawaji, H.; Sandelin, A.; Suzuki, H.; Satsangi, J.; Wells, C.; Nir, H.; Freeman, T.; Hayashizaki, Y.; Carninci, P.; Forrest, A. R.; Hume, D. A.

10.1101/095349 — genomics — Posted on 2016-12-20

230 Eph/ephrin signaling controls progenitor identities in the ventral spinal cord

Laussu, J.; Audouard, C.; Kischel, A.; Assis-Nascimento, P.; Escalas, N.; Liebl, D.; Soula, C.; Davy, A.

10.1101/070227 — developmental biology — Posted on 2016-12-20

231 Negative regulation of uPAR activity by a GPI-specific phospholipase C

van Veen, M.; Matas-Rico, E.; van de Wetering, K.; Leyton-Puig, D.; Kedziora, K. M.; Sidenius, N.; Jalink, K.; Perrakis, A.; Moolenaar, W. H.

10.1101/091272 — cell biology — Posted on 2016-12-20

232 Myotome adaptability confers developmental robustness to somitic myogenesis in response to fibre number alteration.

duttaroy, S. D.; Williams-Ward, V. C.; Pipalia, T. G.; Hammond, C. L.; Knappe, S.; Knight, R. D.; Hughes, S. M.; Li, K.

10.1101/095554 — developmental biology — Posted on 2016-12-20

233 Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations

Assaf, Z. J.; Tilk, S.; Park, J.; Siegal, M. L.; Petrov, D.

10.1101/095182 — evolutionary biology — Posted on 2016-12-19

234 MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Bernstein, M. N.; Doan, A.; Dewey, C. N.

10.1101/090506 — bioinformatics — Posted on 2016-12-19

235 Optimal use of EEG recordings to target active brain areas with transcranial electrical stimulation

Dmochowski, J. P.; Koessler, L.; Norcia, A. M.; Bikson, M.; Parra, L. C.

10.1101/078758 — neuroscience — Posted on 2016-12-19

236 StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates

Ogilvie, H. A.; Bouckaert, R.; Drummond, A. J.

10.1101/070169 — bioinformatics — Posted on 2016-12-19

237 Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate

Mora-Macias, J.; Ojeda-Rivera, J. O.; Gutierrez-Alanis, D.; Yong-Villalobos, L.; Oropeza-Aburto, A.; Raya-Gonzalez, J.; Jimenez-Dominguez, G.; Chavez-Calvillo, G.; Rellan-Alvarez, R.; Herrera-Estrella, L. R.

10.1101/095497 — plant biology — Posted on 2016-12-19

238 Co-estimating Reticulate Phylogenies and Gene Trees from Multi-locus Sequence Data

Wen, D.; Nakhleh, L.

10.1101/095539 — evolutionary biology — Posted on 2016-12-19

239 Hardy Weinberg Exact Test In Large Scale Variant Calling Quality Control

Huang, Z.; Rustagi, N.; Zhi, D.; Cupples, A.; Gibbs, R.; Boerwinkle, E.; Yu, F.

10.1101/095521 — bioinformatics — Posted on 2016-12-19

240 In silico epitope prediction and 3D model analysis of Peste des petits ruminants virus nucleoprotein (PPRV N)

Baloi, B.

10.1101/095505 — bioinformatics — Posted on 2016-12-19

241 Mortality prediction in sepsis via gene expression analysis: a community approach

Sweeney, T. E.; Perumal, T. M.; Henao, R.; Nichols, M.; Howrylak, J. A.; Choi, A. M.; Bermejo-Martin, J. F.; Almansa, R.; Tamayo, E.; Davenport, E. E.; Burnham, K. L.; Hinds, C. J.; Knight, J. C.; Kingsmore, S. F.; Woods, C. W.; Ginsburg, G. S.; Wong, H. R.; Parnell, G. P.; Tang, B.; Moldawer, L. L.; Moore, F. E.; Omberg, L.; Khatri, P.; Tsalik, E. L.; Mangravite, L. M.; Langley, R. J.

10.1101/095489 — bioinformatics — Posted on 2016-12-19

242 Neuronal synchrony and the relation between the BOLD response and the local field potential.

Hermes, D.; Nguyen, M.; Winawer, J.

10.1101/083840 — neuroscience — Posted on 2016-12-19

243 Blood flow directs arterial-venous remodeling through Notch activation and endothelial cell migration

Weijts, B.; Gutierrez, E.; Saikin, S. K.; Ablooglu, A. J.; Traver, D.; Groisman, A.; Tkachenko, E.

10.1101/095307 — developmental biology — Posted on 2016-12-19

244 The Bayesian-Laplacian Brain

Zeki, S.; Chen, O. Y.

10.1101/094516 — neuroscience — Posted on 2016-12-19

245 Large-scale network dynamics of beta-band oscillations underlie auditory perceptual decision making

Alavash, M.; Daube, C.; Woestmann, M.; Brandmeyer, A.; Obleser, J.

10.1101/095356 — neuroscience — Posted on 2016-12-19

246 Second Generation Drosophila Chemical Tags: Sensitivity, Versatility and Speed

Sutcliffe, B.; Ng, J.; Auer, T. O.; Pasche, M.; Benton, R.; Jefferis, G. S. X. E.; Cachero, S.

10.1101/095398 — neuroscience — Posted on 2016-12-19

247 The social evolution of siderophore production in Pseudomonas aeruginosa is environmentally determined.

Harrison, F.; McNally, A.; da Silva, A. C.; Diggle, S. P.

10.1101/095323 — microbiology — Posted on 2016-12-19

248 In situ estimates of iron-oxidation and accretion rates for iron-oxidizing bacterial mats at Loihi Seamount.

Emerson, D.; Scott, J. J.; Leavitt, A. H.; Fleming, E.; Moyer, C. L.

10.1101/095414 — microbiology — Posted on 2016-12-19

249 Habitat predicts levels of genetic admixture in Saccharomyces cerevisiae

Tilakaratna, V.; Bensasson, D.

10.1101/095265 — evolutionary biology — Posted on 2016-12-19

250 Detection of long repeat expansions from PCR-free whole-genome sequence data

Dolzhenko, E.; van Vugt, J. J. F. A.; Shaw, R. J.; Bekritsky, M. A.; van Blitterswijk, M.; Kingsbury, Z.; Humphray, S. J.; Schellevis, R. D.; Brands, W. J.; Baker, M.; Rademakers, R.; Kooyman, M.; Tazelaar, G. H. P.; van Es, M. A.; McLaughlin, R.; Sproviero, W.; Shatunov, A.; Jones, A.; Al Khleifat, A.; Pittman, A.; Morgan, S.; Hardiman, O.; Al-Chalabi, A.; van den Berg, L. H.; Bentley, D. R.; Eberle, M. A.; Veldink, J. H.

10.1101/093831 — bioinformatics — Posted on 2016-12-19

251 Distributed alpha networks underlie individual differences in memory performance

Cox, R.; Schapiro, A. C.; Stickgold, R.

10.1101/095430 — neuroscience — Posted on 2016-12-19

252 The complex sequence landscape of maize revealed by single molecule technologies

Jiao, Y.; Peluso, P.; Shi, J.; Liang, T.; Stitzer, M. C.; Wang, B.; Campbell, M.; Stein, J. C.; Wei, X.; Chin, C.-S.; Guill, K.; Regulski, M.; Kumari, S.; Olson, A.; Gent, J.; Schneider, K. L.; Wolfgruber, T. K.; May, M.; Springer, N.; Antoniou, E.; McCombie, R.; Presting, G. G.; McMullen, M.; Ross-Ibarra, J.; Dawe, R. K.; Hastie, A.; Rank, D. R.; Ware, D.

10.1101/079004 — genomics — Posted on 2016-12-19

253 Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

10.1101/095349 — genomics — Posted on 2016-12-19

254 Environmental exposure does not explain putative maladaptation in road-adjacent populations

Brady, S. P.

10.1101/095273 — evolutionary biology — Posted on 2016-12-19

255 Fetal therapy model of myelomeningocele with three-dimensional skin using amniotic fluid cell-derived induced pluripotent stem cells

Kajiwara, K.; Tanemoto, T.; Wada, S.; Karibe, J.; Ihara, N.; Ikemoto, Y.; Kawasaki, T.; Ohishi, Y.; Samura, O.; Okamura, K.; Takada, S.; Akutsu, H.; Sago, H.; Okamoto, A.; UMEZAWA, A.

10.1101/095281 — cell biology — Posted on 2016-12-19

256 Incidental identification of maternal malignancies in two Asian women underwent noninvasive prenatal test

Ji, X.; Chen, F.; Zhou, Y.; LI, J.; Yuan, Y.; Mo, Y.; Liu, Q.; Tseng, J.-Y.; Lin, D. S.-C.; Shen, S.-H.; Liu, Y.; Ye, W.; Zhang, H.; Liu, N.; Shen, L.; Jin, X.; Sung, P.-L.; Mao, M.

10.1101/095364 — cancer biology — Posted on 2016-12-19

257 McClintock: An integrated pipeline for detecting transposable element insertions in whole genome shotgun sequencing data.

Nelson, M. G.; Linheiro, R. S.; Bergman, C. M.

10.1101/095372 — bioinformatics — Posted on 2016-12-19

258 RNAtor: an Android-based application for biologists to plan RNA sequencing experiments.

Kane, S.; Garg, H.; Krishnan, N. M.; Singh, A.; Panda, B.

10.1101/095315 — bioinformatics — Posted on 2016-12-19

259 poRe GUIs for parallel and real-time processing of MinION sequence data

Stewart, R.; Watson, M.

10.1101/094979 — bioinformatics — Posted on 2016-12-19

260 Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower.

Edger, P. P.; Smith, R. D.; McKain, M. R.; Cooley, A. M.; Vallejo-Marin, M.; Yuan, Y.; Bewick, A. J.; Ji, L.; Platts, A. E.; Bowman, M. J.; Childs, K. L.; Schmitz, R. J.; Smith, G. D.; Pires, J. C.; Puzey, J. R.

10.1101/094797 — genomics — Posted on 2016-12-19

261 Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

Doyle, S. R.; Bourguinat, C.; Nana-Djeunga, H. C.; Kengne-Ouafo, J. A.; Pion, S. D. S.; Bopda, J.; Kamgno, J.; Wanji, S.; Che, H.; Kuesel, A. C.; Walker, M.; Basanez, M.-G.; Boakye, D.; Osei-Atweneboana, M. Y.; Boussinesq, M.; Prichard, R. K.; Grant, W. N.

10.1101/094540 — genomics — Posted on 2016-12-19

262 Silversword and lobeliad reintroduction linked to landscape restoration on Mauna Loa and Kilauea, and its implications for plant adaptive radiation in Hawaii

Robichaux, R. H.; Moriyasu, P. Y.; Enoka, J. H.; McDaniel, S.; Loh, R. K.; Bio, K. F.; Bakutis, A.; Tunison, J. T.; Bergfeld, S. T.; Perry, J. L.; Warshauer, F. R.; Wasser, M.; Cole, T. C.; Agorastos, N. R.; Cole, I. W.; Camara, J. K.; Rubenstein, T.; Whitehead, A. N.; VanDeMark, J. R.; Loo, R.; Bruegmann, M. M.

10.1101/095216 — evolutionary biology — Posted on 2016-12-19

263 Genome Wide Computational Prediction of miRNAs in Kyasanur Forest Disease Virus and their Targeted Genes in Human

Saini, S.; Thakur, C. J.; Kumar, V.

10.1101/095083 — bioinformatics — Posted on 2016-12-19

264 Insights into grapevine defense response against drought as revealed by biochemical, physiological and RNA-Seq analysis

Muhammad Salman, H.; Zhang, C.; Kurjogi, M.; Pervaiz, T.; Zheng, T.; Zhang, C. b.; Lide, C.; Shangguan, L.; Fang, J.

10.1101/065136 — molecular biology — Posted on 2016-12-19

265 Resurrected protein interaction networks reveal the innovation potential of ancient whole genome duplication

Zhang, Z.; Coenen, H.; Ruelens, P.; Hazarika, R.; Al Hindi, T.; Oguis, G.; Van Noort, V.; Geuten, K.

10.1101/074989 — evolutionary biology — Posted on 2016-12-19

266 The Stone Age Plague: 1000 years of Persistence in Eurasia

Andrades Valtuena, A.; Mittnik, A.; Massy, K.; Allmae, R.; Daubaras, M.; Jankauskas, R.; Torv, M.; Pfrengle, S.; Spyrou, M. A.; Feldman, M.; Haak, W.; Bos, K. I.; Stockhammer, P. W.; Herbig, A.; Krause, J.

10.1101/094243 — evolutionary biology — Posted on 2016-12-19

267 Modelling the impact of curtailing antibiotic usage in food animals on antibiotic resistance in humans

van Bunnik, B.; Woolhouse, M.

10.1101/077776 — epidemiology — Posted on 2016-12-19

268 A tutorial on Gaussian process regression with a focus on exploration-exploitation scenarios

Schulz, E.; Speekenbrink, M.; Krause, A.

10.1101/095190 — animal behavior and cognition — Posted on 2016-12-19

269 Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

Votintseva, A. A.; Bradley, P.; Pankhurst, L.; del Ojo Elias, C.; Loose, M.; Nilgiriwala, K.; Chatterjee, A.; Smith, E. G.; Sanderson, N.; Walker, T. M.; Morgan, M. R.; Wyllie, D. H.; Walker, A. S.; Peto, T. E.; Crook, D. W.; Iqbal, Z.

10.1101/094789 — microbiology — Posted on 2016-12-19

270 Creating a universal SNP and small indel variant caller with deep neural networks

Poplin, R.; Newburger, D.; Dijamco, J.; Nguyen, N.; Loy, D.; Gross, S. S.; McLean, C. Y.; DePristo, M. A.

10.1101/092890 — genomics — Posted on 2016-12-19

271 An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

Torresen, O. K.; Star, B.; Jentoft, S.; Reinar, W. B.; Grove, H.; Miller, J. R.; Walenz, B. P.; Knight, J.; Ekholm, J. M.; Peluso, P.; Edvardsen, R. B.; Tooming-Klunderud, A.; Skage, M.; Lien, S.; Jakobsen, K. S.; Nederbragt, A. J.

10.1101/060921 — genomics — Posted on 2016-12-19

272 Universal expressions of population change by the Price equation: natural selection, information, and maximum entropy production

Frank, S. A.

10.1101/093757 — evolutionary biology — Posted on 2016-12-19

273 FerriTag: A Genetically-Encoded Inducible Tag for Correlative Light-Electron Microscopy

Clarke, N. I.; Royle, S. J.

10.1101/095208 — cell biology — Posted on 2016-12-18

274 Structurally distinct oligomers of islet amyloid polypeptide mediate toxic and non-toxic membrane poration

Birol, M.; Kumar, S.; Rhoades, E.; Miranker, A. D.

10.1101/095158 — cell biology — Posted on 2016-12-18

275 GeNNet: An Integrated Platform for Unifying Scientific Workflow Management and Graph Databases for Transcriptome Data Analysis

L. Costa, R.; Gadelha, L.; Ribeiro-Alves, M.; Porto, F.

10.1101/095257 — bioinformatics — Posted on 2016-12-18

276 Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations

Assaf, Z. J.; Tilk, S.; Park, J.; Siegal, M. L.; Petrov, D.

10.1101/095182 — evolutionary biology — Posted on 2016-12-18

277 Systematic assessment of multi-gene predictors of pan-cancer cell line sensitivity to drugs exploiting gene expression data

Nguyen, L.; Dang, C.; Ballester, P.

10.1101/095224 — bioinformatics — Posted on 2016-12-18

278 Serum extracellular vesicle depletion processes affect release and infectivity of HIV-1 in culture

Liao, Z.; Muth, D. C.; Eitan, E.; Travers, M.; Lehrmann, E.; Witwer, K. W.

10.1101/081687 — molecular biology — Posted on 2016-12-18

279 How Cancer Genomics Drives Cancer Biology: Does Synthetic Lethality Explain Mutually Exclusive Oncogenic Mutations?

Varmus, H.; Unni, A. M.; Lockwood, W. W.

10.1101/091173 — cancer biology — Posted on 2016-12-18

280 Microbes use encapsulin protein organelles to sequester toxic reactions

Giessen, T. W.; Silver, P. A.

10.1101/085266 — biochemistry — Posted on 2016-12-18

281 Unearthing new genomic markers of drug response by improved measurement of discriminative power

Dang, C.; Peon, A.; Ballester, P.

10.1101/033092 — bioinformatics — Posted on 2016-12-18

282 DNA damage response decreases during induced pluripotent and embryonic stem cell differentiation

Mujoo, K.; Pandita, R. K.; Tiwari, A.; Charaka, V.; Chakraborti, S.; Hittelman, W.; Horikoshi, N.; Hunt, C.; Khanna, K.; Kots, A.; Butler, B.; Murad, F.; Pandita, T. K.

10.1101/094938 — cell biology — Posted on 2016-12-18

283 New Insights into the Dynamics of Swarming Bacteria: A Theoretical Study

Hansmann, D.; Fier, G.; Buceta, R. C.

10.1101/095141 — biophysics — Posted on 2016-12-18

284 Active Vertex Model for Cell-Resolution Description of Epithelial Tissue Mechanics

Barton, D. L.; Henkes, S.; Weijer, C. J.; Sknepnek, R.

10.1101/095133 — biophysics — Posted on 2016-12-18

285 Retroviral origins of the Caenorhabditis elegans orphan gene F58H7.5.

Kapulkin, W. J.

10.1101/073510 — genomics — Posted on 2016-12-17

286 Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data

Shan, G.; Tian, X.; Sun, Y.; Wu, Z.; Cheng, Z.; Dong, P.; Zhao, Q.; He, B.; Ruan, J.; Bu, W.

10.1101/079517 — genomics — Posted on 2016-12-17

287 EM and component-wise boosting for Hidden Markov Models: a machine-learning approach to capture-recapture

Rankin, R. W.

10.1101/052266 — ecology — Posted on 2016-12-17

288 Bridging microscopic and macroscopic mechanisms of p53-MDM2 binding using molecular simulations and kinetic network models

Zhou, G.; Pantelopulos, G. A.; Mukherjee, S.; Voelz, V. A.

10.1101/086272 — biophysics — Posted on 2016-12-17

289 Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease

Patrick, E.; Rajagopal, S.; Wong, H.-K. A.; McCabe, C.; Xu, J.; Tang, A.; Imboywa, S. H.; Schneider, J. A.; Pochet, N.; Krichevsky, A. M.; Chibnik, L. B.; Bennett, D. A.; De Jager, P. L.

10.1101/095067 — neuroscience — Posted on 2016-12-17

290 Helical reconstruction in RELION

He, S.; Scheres, S.

10.1101/095034 — molecular biology — Posted on 2016-12-17

291 Bacterial communities affected by experimental disturbances to canopy soils of a temperate rainforest

Dangerfield, C. R.; Nadkarni, N. M.; Brazelton, W. J.

10.1101/094987 — microbiology — Posted on 2016-12-17

292 Recombinant DNA resources for the comparative genomics of Ancylostoma ceylanicum.

Kapulkin, W. J.; Magalska, A.; Janecka, E.; Ciesielski, A.; Lobocka, M.; Behnke, J.; Wedrychowicz, H.

10.1101/092494 — genomics — Posted on 2016-12-17

293 Evaluation on Detection of Structural Variants by Low-Coverage Long-Read Sequencing

Fang, L.; Hu, J.; Wang, D.; Wang, K.

10.1101/092544 — genomics — Posted on 2016-12-17

294 Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean

Chen, M.; Fontaine, M. C.; Ben Chehida, Y.; Zheng, J.; Mei, Z.; Hao, Y.; Wang, K.; Wu, M.; Zhao, Q.; Wang, D.

10.1101/094995 — evolutionary biology — Posted on 2016-12-17

295 Quantifying the Heat Dissipation from Molecular Motor’s Transport Properties in Nonequilibrium Steady States

Hwang, W.; Hyeon, C.

10.1101/095042 — biophysics — Posted on 2016-12-17

296 Benchmarking BarraCUDA on Epigenetic DNA and nVidia Pascal GPUs

Langdon, W.

10.1101/095075 — bioinformatics — Posted on 2016-12-17

297 In culture cross-linking of bacterial cells reveals proteome scale dynamic protein-protein interactions at peptide level

de Jong, L.; de Koning, E. A.; Roseboom, W.; Buncherd, H.; Wanner, M. J.; Jansen, P. J.; Dapic, I.; van Maarseveen, J. H.; Corthals, G. L.; Lewis, P. J.; Hamoen, L. W.; de Koster, C. G.

10.1101/094961 — biochemistry — Posted on 2016-12-17

298 Universal scaling of maximum speed with body mass - Why the largest animals are not the fastest

Hirt, M.; Jetz, W.; Rall, B. C.; Brose, U.

10.1101/095018 — ecology — Posted on 2016-12-17

299 poRe GUIs for parallel and real-time processing of MinION sequence data

Stewart, R.; Watson, M.

10.1101/094979 — bioinformatics — Posted on 2016-12-17

300 Computational studies of P-glycoprotein polymorphisms in antiepileptic drug resistance mechanisms

Varghese, S.; Palaniappan, A.

10.1101/095059 — bioinformatics — Posted on 2016-12-17

301 Ten simple rules for structuring papers

Kording, K. P.; Mensh, B.

10.1101/088278 — scientific communication and education — Posted on 2016-12-17

302 The thalamus drives light-evoked activity in the habenula of larval zebrafish

Cheng, R. K.; Krishnan, S.; Lin, Q.; Hildebrand, D. G. C.; Bianco, I. H.; Jesuthasan, S.

10.1101/047936 — neuroscience — Posted on 2016-12-17

303 Genome sequence of a diabetes-prone desert rodent reveals a mutation hotspot around the ParaHox gene cluster

Hargreaves, A. D.; Zhou, L.; Christensen, J.; Marletaz, F.; Liu, S.; Li, F.; Jansen, P. G.; Spiga, E.; Hansen, M. T.; Horn Pedersen, S. V.; Biswas, S.; Serikawa, K.; Fox, B. A.; Taylor, W. R.; Mulley, J. F.; Zhang, G.; Heller, R. S.; Holland, P. W. H.

10.1101/093401 — evolutionary biology — Posted on 2016-12-17

304 YeATSAM analysis of the chloroplast genome of walnut reveals several putative un-annotated genes and mis-annotation of the trans-spliced rps12 gene in other organisms

Chakraborty, S.

10.1101/094441 — genomics — Posted on 2016-12-17

305 Cohesin dependent compaction of mitotic chromosomes

Schalbetter, S. A.; Goloborodko, A.; Fudenberg, G.; Belton, J. M.; Miles, C.; Yu, M.; Dekker, J.; Mirny, L.; Baxter, J.

10.1101/094946 — genomics — Posted on 2016-12-17

306 DataMed: Finding useful data across multiple biomedical data repositories

Ohno-Machado, L.; Sansone, S.-A.; Alter, G.; Fore, I.; Grethe, J.; Xu, H.; Gonzalez-Beltran, A.; Rocca-Serra, P.; Soysal, E.; Zong, N.; Kim, H.-e.; bioCADDIE Consortium,

10.1101/094888 — bioinformatics — Posted on 2016-12-17

307 An Integrated Risk Predictor for Pulmonary Nodules

Kearney, P.; Li, X.-J.; Porter, A.; Springmeyer, S.; Mazzone, P.

10.1101/094920 — bioinformatics — Posted on 2016-12-17

308 Accuracy in wrist-worn, sensor-based measurements of heart rate and energy expenditure in a diverse cohort

Shcherbina, A.; Mattsson, C. M.; Waggott, D.; Salisbury, H.; Christle, J. W.; Hastie, T. J.; Wheeler, M. T.; Ashley, E. A.

10.1101/094862 — bioinformatics — Posted on 2016-12-17

309 Familial Mutations and Post-translational Modifications of UCH-L1 in Parkinson’s Disease and Neurodegenerative Disorders

Lee, Y.-T. C.; Hsu, S.-T. D.

10.1101/094953 — biochemistry — Posted on 2016-12-17

310 Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks

Baryshnikova, A.

10.1101/094904 — systems biology — Posted on 2016-12-17

311 A dense brown trout (Salmo trutta) linkage map reveals recent chromosomal rearrangements in the Salmo genus and the impact of selection on linked neutral diversity

Leitwein, M.; Guinand, B.; Pouzadoux, J.; Desmarais, E.; Berrebi, P.; Gagnaire, P.-A.

10.1101/094763 — genomics — Posted on 2016-12-17

312 FlashPCA2: principal component analysis of biobank-scale genotype datasets

Abraham, G.; Qiu, Y.; Inouye, M.

10.1101/094714 — genomics — Posted on 2016-12-17

313 Quantifying the relationship between pollinator behavior and plant reproductive isolation

Hopkins, R.

10.1101/094896 — evolutionary biology — Posted on 2016-12-17

314 Intensity-based axial localization approaches for multifocal plane microscopy

Velmurugan, R.; Chao, J.; Ram, S.; Ward, E. S.; Ober, R. J.

10.1101/093013 — biophysics — Posted on 2016-12-17

315 Ghrelin-Reactive Autoantibodies are elevated in Children with Prader-Willi Syndrome

Crisp, G.; Nyunt, O.; Chopin, L.; Seim, I.; Harris, M.; Jeffery, P.

10.1101/093930 — physiology — Posted on 2016-12-16

316 Opposing transcriptional mechanisms regulate Toxoplasma development.

Hong, D.-P.; Radke, J. B.; White, M. W.

10.1101/094847 — microbiology — Posted on 2016-12-16

317 Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower.

Edgar, P. P.; Smith, R. D.; McKain, M. R.; Cooley, A. M.; Vallejo-Marin, M.; Yuan, Y.; Bewick, A. J.; Ji, L.; Platts, A. E.; Bowman, M. J.; Childs, K. L.; Schmitz, R. J.; Smith, G. D.; Pires, J. C.; Puzey, J. R.

10.1101/094797 — genomics — Posted on 2016-12-16

318 Screening for the ancient polar bear mitochondrial genome reveals low integration of mitochondrial pseudogenes (numts) in bears

Lammers, F.; Janke, A.; Rueckle, C.; Zizka, V.; Nilsson, M. A.

10.1101/094771 — evolutionary biology — Posted on 2016-12-16

319 MR-Base: a platform for systematic causal inference across the phenome using billions of genetic associations

Hemani, G.; Zheng, J.; Wade, K. H.; Laurin, C.; Elsworth, B.; Burgess, S.; Bowden, J.; Langdon, R.; Tan, V.; Yarmolinsky, J.; Shihab, H. A.; Timpson, N.; Evans, D. M.; Relton, C.; Martin, R. M.; Davey Smith, G.; Gaunt, T. R.; Haycock, P. C.; The MR-Base Collaboration,

10.1101/078972 — epidemiology — Posted on 2016-12-16

320 Resolving Biology Beyond the Diffraction Limit with Single-Molecule Localization Microscopy

Rafiei, N.; Nino, D.; Milstein, J. N.

10.1101/094839 — biophysics — Posted on 2016-12-16

321 CORTICO-CORTICAL FEEDBACK CONTROLS SPATIAL SUMMATION IN PRIMATE VISUAL CORTEX

Nurminen, L.; Merlin, S.; Bijanzadeh, M.; Federer, F.; Angelucci, A.

10.1101/094680 — neuroscience — Posted on 2016-12-16

322 Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

10.1101/094540 — genomics — Posted on 2016-12-16

323 Genome-wide association study in Collaborative Cross mice revealed a skeletal role for Rhbdf2

Levy, R.; Levet, C.; Cohen, K.; Freeman, M.; Mott, R.; Iraqi, F.; Gabet, Y.

10.1101/094698 — genetics — Posted on 2016-12-16

324 Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish

Fumey, J.; Hinaux, H.; Noirot, C.; Retaux, S.; Casane, D.

10.1101/094748 — evolutionary biology — Posted on 2016-12-16

325 A statistical test on single-cell data reveals widespread recurrent mutations in tumor evolution

Kuipers, J.; Jahn, K.; Raphael, B. J.; Beerenwinkel, N.

10.1101/094722 — cancer biology — Posted on 2016-12-16

326 Dissecting cancer resistance to therapies with cell-type-specific dynamic logic models

Eduati, F.; Doldan-Martelli, V.; Klinger, B.; Cokelaer, T.; Sieber, A.; Kogera, F.; Dorel, M.; Garnett, M. J.; Bluthgen, N.; Saez-Rodriguez, J.

10.1101/094755 — cancer biology — Posted on 2016-12-16

327 Rigid geometry solves "curse of dimensionality" effects: an application to proteomics

Adachi, S.

10.1101/094391 — bioinformatics — Posted on 2016-12-16

328 Cryo-EM structure of the ATP-sensitive potassium channel illuminates mechanisms of assembly and gating

Martin, G. M.; Yoshioka, C.; Rex, E. A.; Fay, J. F.; Xie, Q.; Whorton, M. R.; Chen, J. Z.; Shyng, S.-L.

10.1101/094649 — biochemistry — Posted on 2016-12-16

329 10 Simple Rules for Sharing Human Genomic Data

Corpas, M.; Whicher, C.; Kovalevskaya, N. V.; Byers, T.; McMurray, A. A.; Nielsen, F. G.; Khodiyar, V. K.

10.1101/094110 — genomics — Posted on 2016-12-15

330 Co-occurring eQTLs and mQTLs: detecting shared causal variants and shared biological mechanisms

Pierce, B.; Tong, L.; Argos, M.; Jasmine, F.; Rakibuz-Zaman, M.; Sarwar, G.; Islam, M. T.; Shahriar, H.; Islam, T.; Rahman, M.; Yunus, M.; Kibriya, M. G.; Chen, L. S.; Ahsan, H.

10.1101/094656 — genomics — Posted on 2016-12-15

331 De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

Stoiber, M. H.; Quick, J.; Egan, R.; Lee, J. E.; Celniker, S. E.; Neely, R.; Loman, N.; Pennacchio, L.; Brown, J. B.

10.1101/094672 — bioinformatics — Posted on 2016-12-15

332 Cross-species functional diversity within the PIN auxin efflux protein family

O'Connor, D. L.; Hsia, M. M.; Vogel, J.; Leyser, O.

10.1101/089854 — plant biology — Posted on 2016-12-15

333 The Bayesian-Laplacian Brain

Zeki, S.; Chen, O. Y.

10.1101/094516 — neuroscience — Posted on 2016-12-15

334 Dynamically controlled light delivery over large brain volumes through tapered optical fibers

Pisanello, F.; Mandelbaum, G.; Pisanello, M.; Oldenburg, I.; Sileo, L.; Markowitz, J.; Peterson, R.; Della Patria, A.; Haynes, T.; Emara, M.; Spagnolo, B.; Datta, S. R.; Sabatini, B.; De Vittorio, M.

10.1101/094524 — neuroscience — Posted on 2016-12-15

335 Two independent modes of chromosome organization are revealed by cohesin removal

Schwarzer, W.; Abdennur, N.; Goloborodko, A.; Pekowska, A.; Fudenberg, G.; Loe-Mie, Y.; Fonseca, N. A.; Huber, W.; Haering, C.; Mirny, L.; Spitz, F.

10.1101/094185 — genomics — Posted on 2016-12-15

336 A magnetic protein compass ?

Winklhofer, M.; Mouritsen, H.

10.1101/094607 — biophysics — Posted on 2016-12-15

337 ISCA1 and CRY4: An improbable proposition

Hochstoeger, T.; Nimpf, S.; Keays, D.

10.1101/094458 — animal behavior and cognition — Posted on 2016-12-15

338 Integrating proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation

Timmins-Schiffman, E. B.; Crandall, G. A.; Vadopalas, B.; Riffle, M. E.; Nunn, B. L.; Roberts, S. B.

10.1101/094615 — physiology — Posted on 2016-12-15

339 Development of Narrow Spectrum ATP-competitive Kinase Inhibitors as Probes for BIKE and AAK1

Counago, R. M.; Axtman, A. D.; Azevedo, H.; Drewry, D. H.; Elkins, J. M.; Gileadi, O.; Guimaraes, C. R. W.; Mascarello, A.; Wells, C. I.; Willson, T. M.; Zuercher, W. J.

10.1101/094631 — pharmacology and toxicology — Posted on 2016-12-15

340 Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells

Bottcher, M.; Kouno, T.; Madissoon, E.; Motakis, E.; Abugessaisa, I.; Kato, S.; Suzuki, H.; Hayashizaki, Y.; Kasukawa, T.; Carninci, P.; Lassmann, T.; Shin, J.; Plessy, C.

10.1101/088500 — genomics — Posted on 2016-12-15

341 Diversity patterns across 1,800 chloroplast genomes of wild (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.)

Civan, P.; Brown, T. A.

10.1101/094482 — genomics — Posted on 2016-12-15

342 Cell cycle dynamics of chromosomal organisation at single-cell resolution

Nagano, T.; Lubling, Y.; Varnai, C.; Dudley, C.; Leung, W.; Baran, Y.; Mandelson Cohen, N.; Wingett, S.; Fraser, P.; Tanay, A.

10.1101/094466 — genomics — Posted on 2016-12-15

343 Mathematical constraints on FST: biallelic markers in arbitrarily many populations

Alcala, N.; Rosenberg, N. A.

10.1101/094433 — genetics — Posted on 2016-12-15

344 The Stone Age Plague: 1000 years of Persistence in Eurasia

10.1101/094243 — evolutionary biology — Posted on 2016-12-15

345 Patterns of temporal and enemy niche use by a community of leaf cone moths (Caloptilia) coexisting on maples (Acer) as revealed by metabarcoding

Nakadai, R.; Kawakita, A.

10.1101/094417 — ecology — Posted on 2016-12-15

346 Biodiversity of Tropical Forests

Tovo, A.; Suweis, S.; Formentin, M.; Favretti, M.; Banavar, J. R.; Azaele, S.; Maritan, A.

10.1101/088534 — ecology — Posted on 2016-12-15

347 Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence factors

Zanzoni, A.; Braham, S.; Spinelli, L.; Brun, C.

10.1101/094136 — bioinformatics — Posted on 2016-12-15

348 MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

Xiao, C.-L.; Chen, Y.; Xie, S.-Q.; Chen, K.-N.; Wang, Y.; Luo, F.; Xie, Z.

10.1101/089250 — bioinformatics — Posted on 2016-12-15

349 A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent recombination

Pang, T. Y.

10.1101/094599 — bioinformatics — Posted on 2016-12-15

350 A computational method for detection of structural variants using Deviant Reads and read pair Orientation: DevRO

Sayyab, S.; Rafati, N.; Carneiro, M.; Garreau, H.; Andersson, G.; Andersson, L.; Johan Rubin, C.

10.1101/094474 — bioinformatics — Posted on 2016-12-15

351 Model-based branching point detection in single-cell data by K-Branches clustering

Chlis, N. K.; Wolf, F. A.; Theis, F. J.

10.1101/094532 — bioinformatics — Posted on 2016-12-15

352 Single-channel in-Ear-EEG predicts the focus of auditory attention to concurrent tone streams and mixed speech

Fiedler, L.; Woestmann, M.; Graversen, C.; Brandmeyer, A.; Lunner, T.; Obleser, J.

10.1101/094490 — bioengineering — Posted on 2016-12-15

353 Vitrification after multiple rounds of sample application and blotting improves particle density on cryo-electron microscopy grids.

Snijder, J.; Borst, A. J.; Dosey, A.; Walls, A. C.; Burrell, A.; Reddy, V. S.; Kollman, J. M.; Veesler, D.

10.1101/094623 — biochemistry — Posted on 2016-12-15

354 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 2016-12-15

355 BuddySuite: Command-line toolkits for manipulating sequences, alignments, and phylogenetic trees

Bond, S. R.; Keat, K. E.; Barreira, S.; Baxevanis, A. D.

10.1101/040675 — bioinformatics — Posted on 2016-12-15

356 The value of prior knowledge in machine learning of complex network systems

Craft, D.; Ferranti, D.; Krane, D.

10.1101/094151 — bioinformatics — Posted on 2016-12-15

357 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 2016-12-15

358 Ten simple rules for structuring papers

Kording, K. P.; Mensh, B.

10.1101/088278 — scientific communication and education — Posted on 2016-12-15

359 Dynamic flexibility in striatal-cortical circuits supports reinforcement learning

Gerraty, R. T.; Davidow, J. Y.; Foerde, K.; Galvan, A.; Bassett, D. S.; Shohamy, D.

10.1101/094383 — neuroscience — Posted on 2016-12-15

360 Functional connectivity models for decoding of spatial representations from hippocampal CA1 recordings

Posani, L.; Cocco, S.; Jezek, K.; Monasson, R.

10.1101/073759 — neuroscience — Posted on 2016-12-15

361 Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

Lindo, J.; Achilli, A.; Perego, U.; Archer, D.; Valdiosera, C.; Petzelt, B.; Mitchell, J.; Worl, R.; Dixon, E. J.; Fifield, T.; Rasmussen, M.; Willerslev, E.; Cybulski, J.; Kemp, B.; DeGiorgio, M.; Malhi, R. S.

10.1101/093468 — genomics — Posted on 2016-12-15

362 Predicting the impact of non-coding variants on DNA methylation

Zeng, H.; Gifford, D. K.

10.1101/073809 — genomics — Posted on 2016-12-15

363 Whole genome sequence analysis of Salmonella Typhi isolated in Thailand before and after the introduction of a national immunization program

Dyson, Z. A.; Thanh, D. P.; Bodhidatta, L.; Mason, C. J.; Srijan, A.; Rabaa, M. A.; Vinh, P. V.; Thanh, T. H.; Thwaites, G. E.; Baker, S.; Holt, K.

10.1101/076422 — genomics — Posted on 2016-12-15

364 A simulation-based evaluation of STRUCTURE software for exploring the introduction routes of invasive species

Lombaert, E.; Guillemaud, T.; Deleury, E.

10.1101/094029 — evolutionary biology — Posted on 2016-12-15

365 A Reaction-Diffusion Model for Radiation-InducedBystander Effects

Olobatuyi, O.; Hillen, T.; de Vries, G.

10.1101/094375 — cancer biology — Posted on 2016-12-15

366 Rigid geometry solves "curse of dimensionality" effects: an application to proteomics

Adachi, S.

10.1101/094391 — bioinformatics — Posted on 2016-12-15

367 Shared Nearest Neighbor clustering in a Locality Sensitive Hashing framework

Kanj, S.; Bruls, T.; Gazut, S.

10.1101/093898 — bioinformatics — Posted on 2016-12-15

368 Strong and Fluctuating Sequence Constraints Drive Alu Evolution

Wacholder, A. C.; Pollock, D.

10.1101/094326 — genomics — Posted on 2016-12-14

369 The contribution of area MT to visual motion perception depends on training

Liu, L.; Pack, C.

10.1101/094128 — neuroscience — Posted on 2016-12-14

370 A theory of working memory without consciousness or sustained activity

Trubutschek, D.; Marti, S.; Ojeda, A.; King, J.-R.; Mi, Y.; Tsodyks, M.; Dehaene, S.

10.1101/093815 — neuroscience — Posted on 2016-12-14

371 Stabilized supralinear network dynamics account for stimulus-induced changes of noise variability in the cortex

Hennequin, G.; Ahmadian, Y.; Rubin, D. B.; Lengyel, M.; Miller, K. D.

10.1101/094334 — neuroscience — Posted on 2016-12-14

372 Reversible metamorphosis in a bacterium

Ramijan, K.; Willemse, J.; Ultee, E.; Wondergem, J.; van der Meij, A.; Briegel, A.; Heinrich, D.; van Wezel, G.; Claessen, D.

10.1101/094037 — microbiology — Posted on 2016-12-14

373 Ancient recombination events between human herpes simplex viruses

Burrel, S.; Boutolleau, D.; Ryu, D.; Agut, H.; Merkel, K.; Leendertz, F.; Calvignac-Spencer, S.

10.1101/093641 — microbiology — Posted on 2016-12-14

374 Magnitude and mechanism of siderophore-mediated competition in bacterial interactions

Schiessl, K.; Janssen, E. M.- L.; Kraemer, S. M.; McNeill, K.; Ackermann, M.

10.1101/094094 — microbiology — Posted on 2016-12-14

375 A systematic cell size screen uncovers coupling of growth to division by the p38/HOG network in Candida albicans

Sellam, A.; Chaillot, J.; Mallick, J.; Tebbji, F.; Richard Albert, J.; Cook, M. A.; Tyers, M.

10.1101/094144 — cell biology — Posted on 2016-12-14

376 Domain prediction with probabilistic directional context

Ochoa, A.; Singh, M.

10.1101/094284 — bioinformatics — Posted on 2016-12-14

377 The sharing of open data: a game-theoretic approach

Alicea, B.

10.1101/093518 — scientific communication and education — Posted on 2016-12-14

378 Searching for Principles of Brain Computation

Maass, W.

10.1101/094102 — neuroscience — Posted on 2016-12-14

379 Fractone bulbs derive from ependymal cells and their laminin composition affects cell proliferation in the subventricular zone

Nascimento, M. A.; Coelho-Sampaio, T.; Sorokin, L.

10.1101/093351 — neuroscience — Posted on 2016-12-14

380 Impact of gray matter signal regression in resting state and language task functional networks

Herrera, L. C. T.; Coan, A.; Marenco, L.; Cesar, C. L.; Castellano, G.

10.1101/094078 — neuroscience — Posted on 2016-12-14

381 Benefits of siderophore release lie in mediating diffusion limitation at low iron solubility

Leventhal, G.; Ackermann, M.; Schiessl, K.

10.1101/093948 — microbiology — Posted on 2016-12-14

382 Novel chromosome organization pattern in actinomycetales-overlapping replication cycles combined with diploidy

Boehm, K.; Meyer, F.; Rhomberg, A.; Kalinowski, J.; Donovan, C.; Bramkamp, M.

10.1101/094169 — microbiology — Posted on 2016-12-14

383 Creating a universal SNP and small indel variant caller with deep neural networks

Poplin, R.; Newburger, D.; Dijamco, J.; Nguyen, N.; Loy, D.; Gross, S.; McLean, C. Y.; DePristo, M.

10.1101/092890 — genomics — Posted on 2016-12-14

384 Individual- versus group-optimality in the production of secreted bacterial compounds

Schiessl, K.; Ross-Gillespie, A.; Cornforth, D. M.; Weigert, M.; Bigosch, C.; Brown, S. P.; Ackermann, M.; Kümmerli, R.

10.1101/094086 — evolutionary biology — Posted on 2016-12-14

385 First record of double-edged sword effect of caterpillar-induced plant volatiles in nature

El Sayed, A.; Suckling, D. M.

10.1101/093963 — ecology — Posted on 2016-12-14

386 Exosomes purified from a single cell type have diverse morphology and composition

Zabeo, D.; Cvjetkovic, A.; Lasser, C.; Schorb, M.; Lotvall, J.; Hoog, J. L.

10.1101/094045 — cell biology — Posted on 2016-12-14

387 BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

de Santiago, I.; Liu, W.; Yuan, K.; O'Reilly, M.; Chilamakuri, C. S.; Ponder, B. A.; Meyer, K. B.; Markowetz, F.

10.1101/093393 — cancer biology — Posted on 2016-12-14

388 Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics

Eduati, F.; Utharala, R.; Madhavan, D.; Neumann, U. P.; Cramer, T.; Saez-Rodriguez, J.; Merten, C. A.

10.1101/093906 — cancer biology — Posted on 2016-12-14

389 Diffusion or advection? Mass transfer and diffusive boundary layer landscapes of the brown alga Fucus vesiculosus

Lichtenberg, M.; Noerregaard, R. D.; Kuhl, M.

10.1101/094052 — biophysics — Posted on 2016-12-14

390 HICL table can manipulate all proteins in human complete proteome

Xie, Z.

10.1101/093971 — bioinformatics — Posted on 2016-12-14

391 Disentangled Long-Read De Bruijn Graphs via Optical Maps

Alipanahi, B.; Salmela, L.; Puglisi, S.; Muggli, M.; Boucher, C.

10.1101/094235 — bioinformatics — Posted on 2016-12-14

392 The value of prior knowledge in machine learning of complex network systems

Craft, D.; Ferranti, D.; Krane, D.

10.1101/094151 — bioinformatics — Posted on 2016-12-14

393 Repliscan: a tool for classifying replication timing regions

Zynda, G. J.; Song, J.; Concia, L.; Wear, E. E.; Hanley-Bowdoin, L.; Thompson, W. F.; Vaughn, M. W.

10.1101/094177 — bioinformatics — Posted on 2016-12-14

394 On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

Poux, S.; Arighi, C. N.; Magrane, M.; Bateman, A.; Wei, C.-H.; Lu, Z.; Boutet, E.; Bye-A-Jee, H.; Famiglietti, M. L.; Roechert, B.

10.1101/094011 — bioinformatics — Posted on 2016-12-14

395 Machine-learning annotation of human splicing branchpoints

Signal, B.; Gloss, B. S.; Dinger, M. E.; Mercer, T. R.

10.1101/094003 — bioinformatics — Posted on 2016-12-14

396 Deep learning is effective for the classification of OCT images of normal versus Age-related Macular Degeneration

Lee, C. S.; Baughman, D. M.; Lee, A. Y.

10.1101/094276 — bioinformatics — Posted on 2016-12-14

397 Localizing hidden regularities with known temporal structure in the EEG evoked response data

Kuznetsova, A.; Krugliakova, E.; Ossadtchi, A.

10.1101/093922 — animal behavior and cognition — Posted on 2016-12-14

398 Deconstructing isolation-by-distance: the genomic consequences of limited dispersal

Aguillon, S.; Fitzpatrick, J. W.; Bowman, R.; Schoech, S. J.; Clark, A. G.; Coop, G.; Chen, N.

10.1101/093989 — evolutionary biology — Posted on 2016-12-14

399 A simulation-based evaluation of STRUCTURE software for exploring the introduction routes of invasive species

Lombaert, E.; Guillemaud, T.; Deleury, E.

10.1101/094029 — evolutionary biology — Posted on 2016-12-14

400 Adaptive and Non-adaptive Responses of Populations to Environmental Change

Coulson, T.; Kendall, B. E.; Barthold, J.; Plard, F.; Schindler, S.; Ozgul, A.; Gaillard, J.-M.

10.1101/090894 — evolutionary biology — Posted on 2016-12-14

401 Pharmacogenetics of antidepressant response: a polygenic approach

García-González, J; Tansey, K; Hauser, J; Henigsberg, N; Maier, W; Mors, O; Placentino, A; Rietschel, M; Souery, D; Žagar, T; Czerski, P; Jerman, B; Buttenschøn, H; Schulze, T; Zobel, A; Farmer, A; Aitchison, K; Craig, I; McGuffin, P; Giupponi, M; Perroud, N; Bondolfi, G; Evans, D; O'Donovan, M; Peters, T; Wendland, J; Lewis, G; Kapur, S; Perlis, R; Arolt, V; Domschke, K; Breen, G; Curtis, C; Sang-Hyuk, L; Kan, C; Newhouse, S; Patel, H; Baune, B; Uher, R; Lewis, C; Fabbri, C

10.1101/093799 — genetics — Posted on 2016-12-14

402 Universal expressions of population change by the Price equation: natural selection, information, and maximum entropy production

Frank, S. A.

10.1101/093757 — evolutionary biology — Posted on 2016-12-14

403 A global co-expression network approach for connecting genes to specialized metabolic pathways in plants

Wisecaver, J. H.; Borowsky, A. T.; Tzin, V.; Jander, G.; Kliebenstein, D.; Rokas, A.

10.1101/093914 — plant biology — Posted on 2016-12-14

404 Cortical excitability controls the strength of mental imagery

Keogh, R.; Bergmann, J.; Pearson, J.

10.1101/093690 — neuroscience — Posted on 2016-12-14

405 Development of 2-phenylethanol plus acetic acid lures to monitor obliquebanded leafroller (Lepidoptera: Tortricidae) under mating disruption

El Sayed, A.

10.1101/093955 — ecology — Posted on 2016-12-14

406 Ten simple rules for structuring papers

Kording, K. P.; Mensh, B.

10.1101/088278 — scientific communication and education — Posted on 2016-12-14

407 Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

Vandenbon, A.; Kumagai, Y.; Lin, M.; Suzuki, Y.; Nakai, K.

10.1101/066472 — genomics — Posted on 2016-12-14

408 Deleterious variants in Asian rice and the potential cost of domestication

Liu, Q.; Zhou, Y.; Morrell, P. L.; Gaut, B. S.

10.1101/057224 — evolutionary biology — Posted on 2016-12-14

409 EM and component-wise boosting for Hidden Markov Models: a machine-learning approach to capture-recapture

Rankin, R. W.

10.1101/052266 — ecology — Posted on 2016-12-14

410 Hot-wiring clathrin-mediated endocytosis in human cells

Wood, L. A.; Clarke, N. I.; Sarkar, S.; Royle, S. J.

10.1101/061986 — cell biology — Posted on 2016-12-14

411 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 2016-12-14

412 NeuroGFX: a graphical functional explorer for fruit fly brain circuits

Yeh, C.-H.; Zhou, Y.; Ukani, N. H.; Lazar, A. A.

10.1101/092437 — neuroscience — Posted on 2016-12-14

413 The Fruit Fly Brain Observatory: from structure to function

Ukani, N. H.; Yeh, C.-H.; Tomkins, A.; Zhou, Y.; Florescu, D.; Ortiz, C. L.; Huang, Y.-C.; Wang, C.-T.; Richmond, P.; Lo, C.-C.; Coca, D.; Chiang, A.-S.; Lazar, A. A.

10.1101/092288 — neuroscience — Posted on 2016-12-14

414 NeuroNLP: a natural language portal for aggregated fruit fly brain data

Ukani, N. H.; Tomkins, A.; Yeh, C.-H.; Bruning, W.; Fenichel, A. L.; Zhou, Y.; Huang, Y.-C.; Florescu, D.; Ortiz, C. L.; Richmond, P.; Lo, C.-C.; Coca, D.; Chiang, A.-S.; Lazar, A. A.

10.1101/092429 — neuroscience — Posted on 2016-12-14

415 Defining the genetic architecture of stripe rust resistance in the barley accession HOR1428

Clare, S.; Kitcher, W.; Gardiner, M.; Green, P.; Hubbard, A.; Moscou, M. J.

10.1101/093773 — plant biology — Posted on 2016-12-13

416 Openspritzer: an open hardware pressure ejection system for reliably delivering picolitre volumes.

Forman, C. J.; Tomes, H.; Mbobo, B.; Baden, T.; Raimondo, J. V.

10.1101/093633 — neuroscience — Posted on 2016-12-13

417 Quantitative Analysis of Dopamine Neuron Subtypes Generated from Mouse Embryonic Stem Cells

Dingle, Y.-T. L.; Xiong, K.; Machan, J. T.; Seymour, K. A.; Ellisor, D.; Hoffman-Kim, D.; Zervas, M.

10.1101/093419 — neuroscience — Posted on 2016-12-13

418 VIRUS-HOST INFECTION DYNAMICS OF MARINE SINGLE-CELLED EUKARYOTES RESOLVED FROM METATRANSCRIPTOMICS

Moniruzzaman, M.; Wurch, L. L.; Alexander, H.; Dyhrman, S. T.; Gobler, C. J.; Wilhelm, S. W.

10.1101/093716 — microbiology — Posted on 2016-12-13

419 Accumulation of deleterious mutations during bacterial range expansions

Bosshard, L.; Dupanloup, I.; Tenaillon, O.; Bruggmann, R.; Ackermann, M.; Peischl, S.; Excoffier, L.

10.1101/093658 — evolutionary biology — Posted on 2016-12-13

420 Nodal secures pluripotency upon embryonic stem cell progression from the ground state

Mulas, C.; Kalkan, T.; Smith, A.

10.1101/093880 — developmental biology — Posted on 2016-12-13

421 The sek-1 p38 MAP kinase pathway regulates Gq signaling in C. elegans

Hoyt, J. M.; Wilson, S. K.; Kasa, M.; Rise, J. S.; Topalidou, I.; Ailion, M.

10.1101/093252 — genetics — Posted on 2016-12-13

422 Easy and Accurate Reconstruction of Whole HIV Genomes from Short-Read Sequence Data

Wymant, C.; Blanquart, F.; Gall, A.; Bakker, M.; Bezemer, D.; Croucher, N. J.; Golubchik, T.; Hall, M.; Hillebregt, M.; Ong, S. H.; Albert, J.; Bannert, N.; Fellay, J.; Fransen, K.; Gourlay, A.; Grabowski, M. K.; Gunsenheimer-Bartmeyer, B.; Gunthard, H. F.; Kivela, P.; Kouyos, R.; Laeyendecker, O.; Liitsola, K.; Meyer, L.; Porter, K.; Ristola, M.; van Sighem, A.; Vanham, G.; Berkhout, B.; Cornelissen, M.; Kellam, P.; Reiss, P.; Fraser, C.

10.1101/092916 — bioinformatics — Posted on 2016-12-13

423 A space-jump derivation for non-local models of cell-cell adhesion and non-local chemotaxis

Buttenschoen, A.; Hillen, T.; Gerisch, A.; Painter, K.

10.1101/093617 — systems biology — Posted on 2016-12-13

424 Architecture and dynamics of the jasmonic acid gene regulatory network

Hickman, R. J.; Van Verk, M. C.; Van Dijken, A. J. H.; Pereira Mendes, M.; Vos, I. A.; Caarls, L.; Steenbergen, M.; Van Der Nagel, I.; Wesselink, G. J.; Jironkin, A.; Talbot, A.; Rhodes, J.; De Vries, M.; Schuurink, R. C.; Denby, K. J.; Pieterse, C. M. J.; Van Wees, S.

10.1101/093682 — plant biology — Posted on 2016-12-13

425 Slice-sampled Bayesian PRF mapping

Quax, S. C.; van Koppen, T. C.; Jylanki, P.; Dumoulin, S. O.; van Gerven, M. A. J.

10.1101/093724 — neuroscience — Posted on 2016-12-13

426 The triple-flash illusion reveals a driving role of alpha-band reverberations in visual perception

Gulbinaite, R.; Ilhan, B.; VanRullen, R.

10.1101/093500 — neuroscience — Posted on 2016-12-13

427 Genome-wide analysis of phased nucleosomal arrays reveals the functional characteristic of the nucleosome remodeler ACF

Jain, D. S.; Baldi, S.; Zabel, A.; Straub, T.; Becker, P. B.

10.1101/093666 — molecular biology — Posted on 2016-12-13

428 A polymerisation-associated conformational switch in FtsZ that enables treadmilling

Wagstaff, J. M.; Tsim, M.; Oliva, M. A.; Garcia-Sanchez, A.; Kureisaite-Ciziene, D.; Andreu, J. M.; Lowe, J.

10.1101/093708 — microbiology — Posted on 2016-12-13

429 Identifying the diamond in the rough: a study of allelic diversity underlying flowering time adaptation in maize landraces

Romero Navarro, J. A.; Wilcox, M.; Burgueno, J.; Romay, C.; Swarts, K.; Trachsel, S.; Preciado, E.; Terron, A.; Vallejo Delgado, H.; Vidal, V.; Ortega, A.; Espinoza Banda, A.; Gomez Montiel, N. O.; Ortiz-Monasterio, I.; San Vicente, F.; Guadarrama Espinoza, A.; Atlin, G.; Wenzl, P.; Hearne, S.; Buckler, E. S.

10.1101/092528 — genetics — Posted on 2016-12-13

430 Comparative genomics of beetle-vectored fungal pathogens reveals a reduction in genome size and independent evolution of pathogenicity of two tree pathogens

Schuelke, T. A.; Westbrook, A.; Woeste, K.; Plachetzki, D.; Broders, K.; MacManes, M.

10.1101/093856 — evolutionary biology — Posted on 2016-12-13

431 Critical minimum temperature limits xylogenesis and maintains treelines on the Tibetan Plateau

Li, X.; Liang, E.; Gricar, J.; Rossi, S.; Cufar, K.; Ellison, A.

10.1101/093781 — ecology — Posted on 2016-12-13

432 Trade-offs in the use of multiple survey methods for spiders and harvestmen assemblages in an Amazonian upland forest

Tourinho, A. L.; Dias, S. C.; Lo Man Hung, N.; Pinto-da-Rocha, R.; Baccaro, F. B.; Bonaldo, A. B.

10.1101/093740 — ecology — Posted on 2016-12-13

433 DiffTAD: Detecting Differential contact frequency in Topologically Associating Domains Hi-C experiments between conditions

Zaborowski, R.; Wilczynski, B.

10.1101/093625 — bioinformatics — Posted on 2016-12-13

434 Origins of pandemic clones from environmental gene pools

Shapiro, B. J.; Levade, I.; Kovacikova, G.; Taylor, R. K.; Almagro-Moreno, S.

10.1101/063115 — microbiology — Posted on 2016-12-13

435 VarMatch: robust matching of small variant datasets using flexible scoring schemes

Sun, C.; Medvedev, P.

10.1101/062943 — bioinformatics — Posted on 2016-12-13

436 Insights on the importance of salinity from the first cultured freshwater SAR11 (LD12) representative

Henson, M. W.; Lanclos, V. C.; Thrash, J. C.

10.1101/093567 — microbiology — Posted on 2016-12-13

437 A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma

Way, G. P.; Allaway, R. J.; Bouley, S. J.; Fadul, C. E.; Sanchez, Y.; Greene, C. S.

10.1101/075382 — genomics — Posted on 2016-12-13

438 CrowdVariant: a crowdsourcing approach to classify copy number variants

Greenside, P.; Zook, J.; Salit, M.; Poplin, R.; Cule, M.; DePristo, M.

10.1101/093526 — genomics — Posted on 2016-12-13

439 Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques

Prall, T. M.; Graham, M. E.; Karl, J. A.; Wiseman, R. W.; Ericsen, A. J.; Raveendran, M.; Harris, R. A.; Muzny, D. M.; Gibbs, R. A.; Rogers, J.; O'Connor, D. H.

10.1101/093559 — genetics — Posted on 2016-12-13

440 Detecting ancient positive selection in humans using extended lineage sorting

Peyregne, S.; Dannemann, M.; Pruefer, K.

10.1101/092999 — genetics — Posted on 2016-12-13

441 CTCF and Cohesin Regulate Chromatin Loop Stability with Distinct Dynamics

Hansen, A. S.; Pustova, I.; Cattoglio, C.; Tjian, R.; Darzacq, X.

10.1101/093476 — biophysics — Posted on 2016-12-13

442 Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance

Oda, T.; Lim, K.; Tomii, K.

10.1101/092742 — bioinformatics — Posted on 2016-12-13

443 Incorporating calibrated functional assay data into the BRCA1 Ex-UV database

Thompson, B. A.; Bell, R.; Welm, B. E.; Burn, J.; Tavtigian, S.

10.1101/079418 — genetics — Posted on 2016-12-13

444 Induced defenses alter the strength and direction of natural selection on reproductive traits in common milkweed

Thompson, K. A.; Cory, K. A.; Johnson, M. T. J.

10.1101/093609 — evolutionary biology — Posted on 2016-12-13

Patterson, M.; Bernard, T.; Kahn, D.

10.1101/093591 — evolutionary biology — Posted on 2016-12-13

446 CONTINUATION: Evaluation of adaptive somatic models in a gold standard whole genome somatic dataset

Campagne, F.

10.1101/093534 — bioinformatics — Posted on 2016-12-13

447 Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

10.1101/093468 — genomics — Posted on 2016-12-13

448 Genetic overlap between educational attainment, schizophrenia and autism

Warrier, V.; Bethlehem, R. A. I.; Geschwind, D.; Baron-Cohen, S.

10.1101/093575 — genetics — Posted on 2016-12-12

449 A bioinformatic panel to interrogate thousands of ExAC variants with minor reference allele that are missed by conventional variant calling

Koko, M.; Abdallah, M. O. E.; Amin, M.; Ibrahim, M.

10.1101/093450 — genomics — Posted on 2016-12-12

450 Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer

Goncalves, E.; Fraguais, A.; Garcia-Alonso, L.; Cramer, T.; Saez-Rodriguez, J.; Beltrao, P.

10.1101/093369 — genomics — Posted on 2016-12-12

451 Protein phosphatase 1 down regulates ZYG-1 levels to limit centrioleduplication

Peel, N.; Iyer, J.; Naik, A.; Dougherty, M. P.; Decker, M.; O'Connell, K. F.

10.1101/093492 — cell biology — Posted on 2016-12-12

452 BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

de Santiago, I.; Liu, ; O'Reilly, M.; Yuan, K.; Chilamakuri, C. S.; Ponder, B. A.; Meyer, K. B.; Markowetz, F.

10.1101/093393 — cancer biology — Posted on 2016-12-12

453 Charge influences substrate recognition and self-assembly of hydrophobic FG sequences

Chen, W. G.; Witten, J.; Grindy, S. C.; Holten-Andersen, N.; Ribbeck, K.

10.1101/090159 — biophysics — Posted on 2016-12-12

454 CTCF and Cohesin Regulate Chromatin Loop Stability with Distinct Dynamics

Hansen, A. S.; Pustova, I.; Cattoglio, C.; Tjian, R.; Darzacq, X.

10.1101/093476 — biophysics — Posted on 2016-12-12

455 Stochastic Model for Direction Changes of Swimming Bacteria

Fier, G.; Hansmann, D.; Buceta, R. C.

10.1101/093435 — biophysics — Posted on 2016-12-12

456 The impact of a simple α helical transmembrane peptide on lipid membrane dynamics

Olsinova, M.; Jurkiewicz, P.; Sykora, J.; Sabo, J.; Hof, M.; Cwiklik, L.; Cebecauer, M.

10.1101/093377 — biophysics — Posted on 2016-12-12

457 Correcting Chimeric Crosstalk in Single Cell RNA-seq Experiments

Dixit, A.

10.1101/093237 — bioinformatics — Posted on 2016-12-12

458 Detecting telomere elongation in longitudinal datasets: Analysis of a proposal by Simons, Stulp and Nakagawa

Nettle, D.; Bateson, M.

10.1101/093344 — epidemiology — Posted on 2016-12-12

459 Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation

Dillinger, S.; Straub, T.; Nemeth, A.

10.1101/054908 — genomics — Posted on 2016-12-12

460 MicroRNA exocytosis by large dense-core vesicle fusion

Gumurdu, A.; Yildiz, R.; Eren, E.; Karakulah, G.; Unver, T.; Genc, S.; Park, Y.

10.1101/093278 — neuroscience — Posted on 2016-12-12

461 Optimizing for generalization in the decoding of internally generated activity in the hippocampus

van der Meer, M.; Carey, A. A.; Tanaka, Y.

10.1101/066670 — neuroscience — Posted on 2016-12-12

462 Evolutionary variations in the biofilm-associated protein BslA from the genus Bacillus

Morris, R. J.; Schor, M.; Gillespie, R. M. C.; Ferreira, A. S.; Bromley, K. M.; Baldauf, L.; Arnaouteli, S.; Sukhodub, T.; Ostrowski, A.; Hobley, L.; Earl, C.; Stanley-Wall, N. R.; MacPhee, C. E.

10.1101/091884 — microbiology — Posted on 2016-12-12

463 Close genetic relationships between a spousal pair with autism-affected children and high minor allele content in cases in autism-associated SNPs

Zhu, Z.; Lu, X.; Yuan, D.; Huang, S.

10.1101/073452 — genomics — Posted on 2016-12-12

464 High-Throughput Sequencing of Transposable Elements Insertions Suggests Adaptive Evolution of the Invasive Asian Tiger Mosquito Towards Temperate Environments

Goubert, C.; Henri, H.; Minard, G.; Valiente Moro, C.; Mavingui, P.; Vieira, C.; Boulesteix, M.

10.1101/049197 — genomics — Posted on 2016-12-12

465 Splice Expression Variation Analysis (SEVA) for Differential Gene Isoform Usage in Cancer

Afsari, B.; Guo, T.; Considine, M.; Florea, L.; Kelley, D.; Flam, E.; Ha, P.; Geman, D.; Ochs, M. F.; Califano, J. A.; Gaykalova, D. A.; Favorov, A. V.; Fertig, E. J.

10.1101/091637 — genomics — Posted on 2016-12-12

466 The sek-1 p38 MAP kinase pathway regulates Gq signaling in C. elegans

Hoyt, J. M.; Wilson, S. K.; Kasa, M.; Rise, J. S.; Topalidou, I.; Ailion, M.

10.1101/093252 — genetics — Posted on 2016-12-12

467 The CARD-CC/Bcl10/paracaspase signaling complex is functionally conserved since the last common ancestor of planulozoa.

Staal, J.; Driege, Y.; Borghi, A.; Hulpiau, P.; Lievens, L.; Gul, I.; Sundararaman, S.; Goncalves, A.; Dhondt, I.; Braeckman, B.; Technau, U.; Saeys, Y.; Van Roy, F.; Beyaert, R.

10.1101/046789 — evolutionary biology — Posted on 2016-12-12

468 Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Osmanovic, D.; Kessler, D. A.; Rabin, Y.; Soen, Y.

10.1101/093120 — evolutionary biology — Posted on 2016-12-12

469 Projected spread of Zika virus in the Americas

Zhang, Q.; Sun, K.; Chinazzi, M.; Pastore-Piontti, A.; Dean, N. E.; Rojas, D. P.; Merler, S.; Mistry, D.; Poletti, P.; Rossi, L.; Bray, M.; Halloran, M. E.; Longini, I. M.; Vespignani, A.

10.1101/066456 — epidemiology — Posted on 2016-12-12

470 TAF10 is required for the integrity of TFIID and SAGA complexes but is initially dispensable for somitogenesis in the mouse embryo

Bardot, P.; Vincent, S. D.; Fournier, M.; Hubaud, A.; Joint, M.; Tora, L.; Pourquie, O.

10.1101/071324 — developmental biology — Posted on 2016-12-12

471 Parkin knockout inhibits neuronal development via regulation of proteasomal degradation of p21

Park, M. H.; Lee, H. J.; Lee, H. L.; Son, D. J.; Ju, J. H.; Hyun, B. K.; Jung, S. H.; Song, J.-K.; Lee, D.-H.; Hwang, C.-J.; Han, S. B.; Kim, S.; Hong, J. T.

10.1101/093294 — cell biology — Posted on 2016-12-12

472 BioMake: a GNU Make-compatible utility for declarative workflow management

Holmes, I. H.; Mungall, C. J.

10.1101/093245 — bioinformatics — Posted on 2016-12-12

473 Designing fecal microbiota transplant trials that account for differencesin donor stool efficacy

Olesen, S. W.; Gurry, T.; Alm, E. J.

10.1101/065383 — bioinformatics — Posted on 2016-12-12

474 Genetic variation and RNA structure regulate microRNA biogenesis

Fernandez, N.; Cordiner, R. A.; Young, R. S.; Hug, N.; Macias, S.; Caceres, J. F.

10.1101/093179 — biochemistry — Posted on 2016-12-12

475 Preliminary investigation of Incorporation and Viability of Crystal Violet in Aspergillus flavus

Paula, L. C. P. d.; Franco, D. G.; Marchetti, C. R.; Giannesi, G. C.; Zanoelo, F. F.; Oliveira, C. S. d.

10.1101/091108 — biochemistry — Posted on 2016-12-12

476 Familial heterogeneity in breast cancer predisposition: a study of 22 Utah families

O'Brien, E.; Kerber, R. A.; White, R. L.

10.1101/092841 — cancer biology — Posted on 2016-12-12

477 VHL inactivation without hypoxia is sufficient to achieve genome hypermethylation

Artemov, A. V.; Zhigalova, N.; Zhenilo, S.; Mazur, A. M.; Prokhortchouk, E. B.

10.1101/093310 — cancer biology — Posted on 2016-12-12

478 Protein Collapse is Encoded in the Folded State Architecture

Samanta, H. S.; Zhuravlev, P.; Hinczewski, M.; Hori, N.; Chakrabarti, S.; Thirumalai, D.

10.1101/070920 — biophysics — Posted on 2016-12-12

479 Stability and plasticity of contextual modulation in the mouse visual cortex

Ranson, A.

10.1101/069880 — neuroscience — Posted on 2016-12-12

480 MtrA is an essential regulator that coordinates antibiotic production and sporulation in Streptomyces species

Som, N. F.; Heine, D.; Munnoch, J. T.; Holmes, N. A.; Knowles, F.; Chandra, G.; Seipke, R. F.; Hoskisson, P. A.; Wilkinson, B.; Hutchings, M. I.

10.1101/090399 — microbiology — Posted on 2016-12-12

481 Recent thymic emigrants produce antimicrobial IL-8, express complement receptors and are precursors of a tissue-homing Th8 lineage of memory cells

Pekalski, M. L.; Rubio Garcia, A.; Ferreira, R. C.; Rainbow, D. B.; Smyth, D. J.; Mashar, M.; Brady, J.; Savinykh, N.; Castro Dopico, X.; Mahmood, S.; Duley, S.; Stevens, H. E.; Walker, N. M.; Cutler, A. J.; Waldron-Lynch, F.; Dunger, D. B.; Shannon-Lowe, C.; Coles, A. J.; Jones, J. L.; Wallace, C.; Todd, J. A.; Wicker, L. S.

10.1101/059535 — immunology — Posted on 2016-12-12

482 Deploying dengue-suppressing Wolbachia: robust models predict slow but effective spatial spread in Aedes aegypti

Turelli, M.; Barton, N.

10.1101/093229 — zoology — Posted on 2016-12-11

483 Historian: accurate reconstruction of ancestral sequences and evolutionary rates

Holmes, I. H.

10.1101/093161 — bioinformatics — Posted on 2016-12-11

484 Cell-to-cell variability in the yeast pheromone response: high throughput screen identifiesgenes with different effects on transmitted signal and response

Pesce, C. G.; Peria, W.; Zdraljevic, S.; Rockwell, D.; Yu, R. C.; Colman-Lerner, A.; Brent, R.

10.1101/093187 — systems biology — Posted on 2016-12-11

485 Cell-to-cell variability in the yeast pheromone response: Cytoplasmic microtubule functionstabilizes signal generation and promotes accurate fate choice

Pesce, G.; Zdraljevic, S.; Bush, A.; Repetto, V.; Peria, W.; Yu, R. C.; Colman-Lerner, A.; Brent, R.

10.1101/093195 — systems biology — Posted on 2016-12-11

486 The computations underlying human confidence reports are probabilistic, but not Bayesian

Adler, W. T.; Ma, W. J.

10.1101/093203 — neuroscience — Posted on 2016-12-11

487 Transcriptional signatures of connectomic subregions of the human striatum

Parkes, L.; Fulcher, B.; Yucel, M.; Fornito, A.

10.1101/089458 — neuroscience — Posted on 2016-12-11

488 RL mechanisms of short-term plasticity of auditory cortex

Krugliakova, E.; Gorin, A.; Shestakova, A.; Fedele, T.; Klucharev, V.

10.1101/093138 — neuroscience — Posted on 2016-12-11

489 Microbial Genome-Wide Association Studies: Lessons from Human GWAS

Power, R.; Parkhill, J.; de Oliveira, T.

10.1101/093211 — genomics — Posted on 2016-12-11

490 Detecting ancient positive selection in humans using extended lineage sorting

Peyregne, S.; Dannemann, M.; Prufer, K.

10.1101/092999 — genetics — Posted on 2016-12-11

491 Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Osmanovic, D.; Kessler, D. A.; Rabin, Y.; Soen, Y.

10.1101/093120 — evolutionary biology — Posted on 2016-12-11

492 Conserved Non-exonic Elements: A Novel Class of Marker for Phylogenomics

Edwards, S. V.; Cloutier, A.; Baker, A. J.

10.1101/093070 — evolutionary biology — Posted on 2016-12-11

493 Fitness landscapes reveal simple strategies for steering evolution to minimize antibiotic resistance

Smith, M.; Cobey, S.

10.1101/093153 — evolutionary biology — Posted on 2016-12-11

494 Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

Baker, Z.; Schumer, M.; Haba, Y.; Holland, C.; Rosenthal, G. G.; Przeworski, M.

10.1101/093096 — evolutionary biology — Posted on 2016-12-11

495 Use of phenylacetonitrile plus acetic acid to monitor Pandemis pyrusana (Lepidoptera: Tortricidae) in apple

El-Sayed, A.; Suckling, D. M.

10.1101/092452 — ecology — Posted on 2016-12-11

496 Using social media to quantify spatial and temporal dynamics of wildlife tourism activities

Mancini, F.; Coghill, G. M.; Lusseau, D.

10.1101/093112 — ecology — Posted on 2016-12-11

497 Non Diaphanous Formin Delphilin Acts as a Barbed End Capping Protein

Dutta, P.; MAITI, S.

10.1101/093104 — cell biology — Posted on 2016-12-11

498 Cox-nnet: an artificial neural network Cox regression for prognosis prediction

Ching, T.; Zhu, X.; Garmire, L.

10.1101/093021 — bioinformatics — Posted on 2016-12-11

499 Microbial regime changes and indicators of eutrophication on the Mississippi River identified via a human-powered 2900 km transect

Henson, M. W.; Hanssen, J.; Spooner, G.; Flemming, P.; Pukonen, M.; Stahr, F.; Thrash, J. C.

10.1101/091512 — microbiology — Posted on 2016-12-11

500 Recombinant DNA resources for the comparative genomics of Ancylostoma ceylanicum.

Kapulkin, W. J.; Magalska, A.; Janecka, E.; Ciesielski, A.; Lobocka, M.; Behnke, J.; Wedrychowicz, H.

10.1101/092494 — genomics — Posted on 2016-12-11

501 The Evolution of Primate Body Size: Left-skewness, Maximum Size, and Cope’s Rule

Tillquist, R. C.; Shoemaker, L. G.; Knight, K. B.; Clauset, A.

10.1101/092866 — evolutionary biology — Posted on 2016-12-11

502 The centrosome is a selective phase that nucleates microtubules by concentrating tubulin

Woodruff, J. B.; Ferreira Gomes, B.; Widlund, P. O.; Mahamid, J.; Hyman, A. A.

10.1101/093054 — cell biology — Posted on 2016-12-10

503 KIF21A influences breast cancer metastasis and survival

Lucanus, A. J.; Yip, G. W.; King, V.

10.1101/093047 — cancer biology — Posted on 2016-12-10

504 Recent thymic emigrants produce antimicrobial IL-8, express complement receptors and are precursors of a tissue-homing Th8-like memory subset

10.1101/059535 — immunology — Posted on 2016-12-10

505 Genome-wide methylation data mirror ancestry information

Rahmani, E.; Shenhav, L.; Schweiger, R.; Yousefi, P.; Huen, K.; Eskenazi, B.; Eng, C.; Huntsman, S.; Hu, D.; Galanter, J.; Oh, S.; Waldenberger, M.; Strauch, K.; Grallert, H.; Meitinger, T.; Gieger, C.; Holland, N.; Burchard, E.; Zaitlen, N.; Halperin, E.

10.1101/066340 — genetics — Posted on 2016-12-10

506 C. elegans chromosomes connect to centrosomes by anchoring into the spindle network

Redemann, S.; Baumgart, J.; Lindow, N.; Fuerthauer, S.; Nazockdast, E.; Kratz, A.; Prohaska, S.; Brugues, J.; Shelley, M.; Mueller-Reichert, T.

10.1101/060855 — cell biology — Posted on 2016-12-10

507 SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology

Petkau, A.; Mabon, P.; Sieffert, C.; Knox, N.; Cabral, J.; Iskander, M.; Iskander, M.; Weedmark, K.; Zaheer, R.; Katz, L. S.; Nadon, C.; Reimer, A.; Taboada, E.; Beiko, R. G.; Hsiao, W.; Brinkman, F.; Graham, M.; The IRIDA Consortium, ; Van Domselaar, G.

10.1101/092940 — bioinformatics — Posted on 2016-12-10

508 Neurons in the mouse deep superior colliculus encode orientation/direction through suppression and extract selective visual features

Ito, S.; Feldheim, D. A.; Litke, A. M.

10.1101/092981 — neuroscience — Posted on 2016-12-09

509 Early survival and delayed death of developmentally-born dentate gyrus neurons

Cahill, S. P.; Yu, R. Q.; Green, D. C.; Todorova, E. V.; Snyder, J. S.

10.1101/092957 — neuroscience — Posted on 2016-12-09

510 Variability and stability of large-scale cortical oscillation patterns

Cox, R.; Schapiro, A.; Stickgold, R.

10.1101/093005 — neuroscience — Posted on 2016-12-09

511 Random versus maximum entropy models of neural population activity

Ferrari, U.; Obuchi, T.; Mora, T.

10.1101/092973 — neuroscience — Posted on 2016-12-09

512 A framework to interpret short tandem repeat variation in humans

Gymrek, M.; Willems, T.; Reich, D. E.; Erlich, Y.

10.1101/092734 — genetics — Posted on 2016-12-09

513 Optimizing Communication of Emergency Response Adaptive Randomization Clinical Trials to Potential Participants

Meurer, W. J.; Haidar, D.; Tehranisa, J.; McEvoy, B.

10.1101/091819 — clinical trials — Posted on 2016-12-07

514 Antisocial rewarding in structured populations

dos Santos, M.; Pena, J.

10.1101/092932 — evolutionary biology — Posted on 2016-12-09

515 Impact of implementation choices on quantitative predictions of cell-based computational models

Kursawe, J.; Baker, R. E.; Fletcher, A. G.

10.1101/092924 — biophysics — Posted on 2016-12-09

516 Easy and Accurate Reconstruction of Whole HIV Genomes from Short-Read Sequence Data

Wymant, C.; Blanquart, F.; Gall, A.; Bakker, M.; Bezemer, D.; Croucher, N. J.; Golubchik, T.; Hall, M.; Hillebregt, M.; Ong, S. H.; Albert, J.; Bannert, N.; Fellay, J.; Fransen, K.; Gourlay, A.; Grabowski, M. K.; Gunsenheimer-Bartmeyer, B.; Gunthard, H.; Kivela, P.; Kouyos, R.; Laeyendecker, O.; Liitsola, K.; Meyer, L.; Porter, K.; Ristola, M.; van Sighem, A.; Vanham, G.; Berkhout, B.; Cornelissen, M.; Kellam, P.; Reiss, P.; Fraser, C.

10.1101/092916 — bioinformatics — Posted on 2016-12-09

517 SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology

10.1101/092940 — bioinformatics — Posted on 2016-12-09

518 Evidence for Philopatry and Homing in a New World Elapid Snake

Hall, A. S.; Vazquez-Quinto, A. M. K.; Ramirez-Velazquez, A.; Smith, E. N.

10.1101/092833 — zoology — Posted on 2016-12-09

519 On the origin of nonequivalent states: how we can talk about preprints

Neylon, C.; Pattinson, D.; Bilder, G.; Lin, J.

10.1101/092817 — scientific communication and education — Posted on 2016-12-09

520 Yorkie is required to restrict the injury responses in planarians

Lin, A. Y. T.; Pearson, B. J.

10.1101/092353 — molecular biology — Posted on 2016-12-09

521 Paradoxes in Leaky Microbial Trade

Kallus, Y.; Miller, J.; Libby, E.

10.1101/092882 — microbiology — Posted on 2016-12-09

522 Evaluation on Efficient Detection of Structural Variants at Low Coverage by Long-Read Sequencing

Fang, L.; Hu, J.; Wang, D.; Wang, K.

10.1101/092544 — genomics — Posted on 2016-12-09

523 The Evolution of Primate Body Size: Left-skewness, Maximum Size, and Cope’s Rule

Tilquist, R. C.; Shoemaker, L. G.; Knight, K. B.; Clauset, A.

10.1101/092866 — evolutionary biology — Posted on 2016-12-09

524 Direct and context-dependent effects of light, temperature, and phytoplankton shape bacterial community composition

Paver, S.; Kent, A.

10.1101/091967 — ecology — Posted on 2016-12-09

525 Familial heterogeneity in breast cancer predisposition: a study of 22 Utah families

O'Brien, E.; Kerber, R. A.; White, R. L.

10.1101/092841 — cancer biology — Posted on 2016-12-09

526 High-dimensional regression over disease subgroups

Dondelinger, F.; Mukherjee, S.; The Alzheimer's Disease Neuroimaging Initiative,

10.1101/092825 — bioinformatics — Posted on 2016-12-09

527 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 2016-12-09

528 Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate

Jasinska, A. J.; Zelaya, I.; Service, S. K.; Peterson, C.; Cantor, R. M.; Choi, O.-W.; DeYoung, J.; Eskin, E.; Fairbanks, L. A.; Fears, S.; Furterer, A.; Huang, Y. S.; Ramensky, V.; Schmitt, C. A.; Svardal, H.; Jorgensen, M. J.; Kaplan, J. R.; Villar, D.; Aken, B. L.; Flicek, P.; Nag, R.; Wong, E. S.; Blangero, J.; Dyer, T. D.; Bogomolov, M.; Benjamini, Y.; Weinstock, G. M.; Dewar, K.; Sabatti, C.; Wilson, R. K.; Jentsch, J. D.; Warren, W.; Coppola, G.; Woods, R. P.; Freimer, N. B.

10.1101/092874 — genetics — Posted on 2016-12-09

529 Paleochronic reversion in Psophocarpus, the decompression function in floral anatomic fields

Benya, E. G. F.

10.1101/070540 — plant biology — Posted on 2016-12-09

530 MultiCellDS: a standard and a community for sharing 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. M. H.; 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.

10.1101/090696 — systems biology — Posted on 2016-12-09

531 Genomic determinants of protein abundance variation in colorectal cancer cells

Roumeliotis, T. I.; Williams, S. P.; Goncalves, E.; Zamanzad Ghavidel, F.; Aben, N.; Michaut, M.; Schubert, M.; Wright, J. C.; Yang, M.; Alsinet, C.; Dienstmann, R.; Guinney, J.; Beltrao, P.; Brazma, A.; Stegle, O.; Adams, D. J.; Wessels, L.; Saez-Rodriguez, J.; McDermott, U.; Choudhary, J. S.

10.1101/092767 — systems biology — Posted on 2016-12-09

532 In vivo magnetic recording of neuronal activity

Caruso, L.; Wunderle, T.; Lewis, C. M.; Valadeiro, J.; Trauchessec, V.; Trejo-Rosillo, J.; Amaral, J. P.; Ni, J.; Fermon, C.; Cardoso, S.; Freitas, P. P.; Fries, P.; Pannetier-Lecoeur, M.

10.1101/092569 — neuroscience — Posted on 2016-12-09

533 A framework to interpret short tandem repeat variation in humans

Gymrek, M.; Willems, T.; Erlich, Y.; Reich, D. E.

10.1101/092734 — genetics — Posted on 2016-12-09

534 Practical Use of Methods for Imputation of HLA Alleles from SNP Genotype Data

Motyer, A.; Vukcevic, D.; Dilthey, A.; Donnelly, P.; McVean, G.; Leslie, S.

10.1101/091009 — genetics — Posted on 2016-12-09

535 DYNC1H1 mutations associated with neurological diseases compromise processivity of dynein-dynactin-cargo adaptor complexes

Hoang, H. T.; Schlager, M. A.; Carter, A. P.; Bullock, S. L.

10.1101/092791 — cell biology — Posted on 2016-12-09

536 Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance

Oda, T.; Lim, K.; Tomii, K.

10.1101/092742 — bioinformatics — Posted on 2016-12-09

537 Phenotypic plasticity can facilitate evolutionary rescue

Carja, O.; Plotkin, J. B.

10.1101/092718 — evolutionary biology — Posted on 2016-12-09

538 Ancient coexistence of norepinephrine, tyramine, and octopamine signaling in bilaterians

Bauknecht, P.; Jekely, G.

10.1101/063743 — evolutionary biology — Posted on 2016-12-09

539 Phenotypic plasticity promotes recombination and gene clustering in periodic environments

Gulisija, D.; Plotkin, J.

10.1101/092700 — evolutionary biology — Posted on 2016-12-09

540 Genome-level parameters describe the pan-nuclear fractal nature of eukaryotic interphase chromosomal arrangement

Fatakia, S. N.; Rao, B. J.

10.1101/083121 — evolutionary biology — Posted on 2016-12-09

541 Plant Cysteine Oxidases are Dioxygenases that Directly Enable Arginyl Transferase-Catalyzed Arginylation of N-End Rule Targets

White, M. D.; Klecker, M.; Hopkinson, R.; Weits, D.; Mueller, C.; Naumann, C.; O Neill, R.; Wickens, J.; Yang, J.; Brooks-Bartlett, J. C.; Garman, E. F.; Grossmann, T. N.; Dissmeyer, N.; Flashman, E.

10.1101/069336 — biochemistry — Posted on 2016-12-09

542 Cas13b is a Type VI-B CRISPR-associated RNA-Guided RNase differentially regulated by accessory proteins Csx27 and Csx28

Smargon, A.; Cox, D. B. T.; Pyzocha, N.; Zheng, K.; Slaymaker, I. M.; Gootenberg, J. S.; Abudayyeh, O. A.; Essletzbichler, P.; Shmakov, S.; Makarova, K. S.; Koonin, E. V.; Zhang, F.

10.1101/092577 — microbiology — Posted on 2016-12-09

543 The Dachsous/Fat/Four-jointed pathway implements axial long-range cell orientation

Mangione, F.; Martin-Blanco, E.

10.1101/092650 — developmental biology — Posted on 2016-12-09

544 LOCALIZER: subcellular localization prediction of plant and effector proteins in the plant cell

Sperschneider, J.; Catanzariti, A.-M.; DeBoer, K.; Petre, B.; Gardiner, D.; Singh, K.; Dodds, P.; Taylor, J.

10.1101/092726 — bioinformatics — Posted on 2016-12-09

545 Predicting binding free energies: Frontiers and benchmarks

Mobley, D. L.; Gilson, M. K.

10.1101/074625 — biophysics — Posted on 2016-12-08

546 Co-operation, competition and crowding: a discrete framework linking Allee kinetics, nonlinear diffusion, shocks and sharp-fronted travelling waves

Johnston, S.; Baker, R.; McElwain, S.; Simpson, M.

10.1101/077743 — biophysics — Posted on 2016-12-08

547 Serum extracellular vesicle depletion processes affect release and infectivity of HIV-1 in culture

Liao, Z.; Muth, D. C.; Eitan, E.; Travers, M.; Lehrmann, E.; Witwer, K. W.

10.1101/081687 — molecular biology — Posted on 2016-12-08

548 Flux through lipid synthesis dictates bacterial cell size.

Vadia, S.; Tse, J. L.; Wang, J. D.; Levin, P. A.

10.1101/092684 — microbiology — Posted on 2016-12-08

549 Pan-Cancer Analysis Reveals Technical Artifacts in The Cancer Genome Atlas (TCGA) Germline Variant Calls

Buckley, A. R.; Standish, K. A.; Bhutani, K.; Ideker, T.; Carter, H.; Harismendy, O.; Schork, N. J.

10.1101/092163 — genomics — Posted on 2016-12-08

550 Local genetic correlation gives insights into the shared genetic architecture of complex traits

Shi, H.; Mancuso, N.; Spendlove, S.; Pasaniuc, B.

10.1101/092668 — genetics — Posted on 2016-12-08

551 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 2016-12-08

552 IMPORT AND EXPORT OF GOLD NANOPARTICLES: EXCHANGE RATE IN CANCER CELLS AND FIBROBLASTS

Ivosev, V.; Jimenez Sanchez, G.; Abi Haidar, D.; Bazzi, R.; Roux, S.; Lacombe, S.

10.1101/092601 — cell biology — Posted on 2016-12-08

553 New single-molecule imaging of the eisosome BAR domain protein Pil1p reveals filament-like dynamics

Lacy, M.; Baddeley, D.; Berro, J.

10.1101/092536 — cell biology — Posted on 2016-12-08

554 Characterization of Dependencies Between Growth and Division in Budding Yeast

Mayhew, M. B.; Iversen, E. S.; Hartemink, A. J.

10.1101/082735 — bioinformatics — Posted on 2016-12-08

555 Evidence that the ventral stream codes the errors used in hierarchical inference and learning

Issa, E. B.; Cadieu, C. F.; DiCarlo, J. J.

10.1101/092551 — neuroscience — Posted on 2016-12-08

556 Resolving the Functional Significance of BRCA1 RING Domain Missense Substitutions

Paquette, A.; Tao, K.; Stark, A. W.; Rosenthal, J.; Bell, R.; Thompson, B. A.; Milash, B. A.; Gertz, J.; Varley, K. E.; Thomas, A.; Boucher, K.; Foulkes, W. D.; Goldgar, D. E.; Tavtigian, S. V.

10.1101/092619 — genetics — Posted on 2016-12-08

557 Tracking the embryonic stem cell transition from ground state pluripotency

Kalkan, T.; Olova, N.; Roode, M.; Mulas, C.; Lee, H. J.; Nett, I.; Marks, H.; Walker, R.; Stunnenberg, H. G.; Lilley, K.; Nichols, J.; Reik, W.; Bertone, P.; Smith, A.

10.1101/092510 — developmental biology — Posted on 2016-12-08

558 Fast and Stable Signal Deconvolution via Compressible State-Space Models

Kazemipour, A.; Liu, J.; Solarana, K.; Nagode, D. A.; Kanold, P. O.; Wu, M.; Babadi, B.

10.1101/092643 — bioengineering — Posted on 2016-12-08

559 Perfluorooctane sulfonate affects proliferation and differentiation of pluripotent human teratocarcinoma cells

Popovic, M.; Neilan, B. A.; Pomati, F.

10.1101/089698 — pharmacology and toxicology — Posted on 2016-12-08

560 Decoding the nonconscious dynamics of thought generation

Koenig-Robert, R.; Pearson, J.

10.1101/090712 — neuroscience — Posted on 2016-12-08

561 Recombinant DNA resources for the comparative genomics of Ancylostoma ceylanicum.

Kapulkin, W. J.; Magalska, A.; Janecka, E.; Ciesielski, A.; Lobocka, M.; Behnke, J.; Wedrychowicz, H.

10.1101/092494 — genomics — Posted on 2016-12-08

562 Paired CRISPR/Cas9 guide-RNAs enable high-throughput deletion scanning (ScanDel) of a Mendelian disease locus for functionally critical non-coding elements

Gasperini, M.; Findlay, G. M.; McKenna, A.; Milbank, J. H.; Lee, C.; Zhang, M. D.; Cusanovich, D. A.; Shendure, J.

10.1101/092445 — genomics — Posted on 2016-12-08

563 The detection of covariation of mRNA levels of large sets of genes across multiple human populations

Quan, Y.; Xie, C.; Williams, R. B. H.; Little, P.

10.1101/082842 — genetics — Posted on 2016-12-08

564 Mapping Autosomal Recessive Intellectual Disability: Combined Microarray and Exome Sequencing Identifies 26 Novel Candidate Genes in 192 Consanguineous Families

Harripaul, R.; Vasli, N.; Mikhailov, A.; Rafiq, M. A.; Mittal, K.; Windpassinger, C.; Sheikh, T.; Noor, A.; Mahmood, H.; Downey, S.; Johnson, M.; Vleuten, K.; Bell, L.; Ilyas, M.; Khan, F. S.; Khan, V.; Moradi, M.; Ayaz, M.; Naeem, F.; Heidari, A.; Ahmed, I.; Ghadami, S.; Agha, Z.; Zeinali, S.; Qamar, R.; Mozhdehipanah, H.; John, P.; Mir, A.; Ansar, M.; French, L.; Ayub, M.; Vincent, J. B.

10.1101/092346 — genetics — Posted on 2016-12-08

565 Mobile introns shape the genetic diversity of their host genes

Repar, J.; Warnecke, T.

10.1101/092585 — evolutionary biology — Posted on 2016-12-08

566 The architectural balance of the Ventral Nerve Cord depends on the level of JNK signaling activity

Karkali, K.; Panayotou, G.; Saunders, T. E.; Martin-Blanco, E.

10.1101/092486 — developmental biology — Posted on 2016-12-08

567 Detection and characterization of low and high genome coverage regions using an efficient running median and a double threshold approach.

Desvillechabrol, D.; Bouchier, C.; Kennedy, S.; Cokelaer, T.

10.1101/092478 — bioinformatics — Posted on 2016-12-08

568 Lysine methyltransferase SETD6 modifies histones and non-histone proteins

Binda, O.

10.1101/092031 — biochemistry — Posted on 2016-12-08

569 VIP36 preferentially binds to core-fucosylated N-glycans: a molecular docking study

Fiedler, K.

10.1101/092460 — biochemistry — Posted on 2016-12-08

570 Resting-state fMRI correlations: from link-wiseunreliability to whole brain stability

Pannunzi, M.; Hindriks, R.; Bettinardi, R. G.; 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 2016-12-08

571 The effect of crack cocaine addiction and age on the microstructure and morphology of the human striatum and thalamus using shape analysis and fast diffusion kurtosis imaging.

Garza-Villarreal, E. A.; Chakravarty, M. M.; Hansen, B.; Eskildsen, S. F.; Devenyi, G. A.; Castillo-Padilla, D.; Balducci-Garcia, T.; Reyes-Zamorano, E.; Jespersen, S. N.; Perez-Palacios, P.; Patel, R.; Gonzalez-Olvera, J. J.

10.1101/066647 — neuroscience — Posted on 2016-12-08

572 Systematic morphological profiling of human gene and allele function reveals Hippo-NF-κB pathway connectivity

Rohban, M. H.; Singh, S.; Wu, X.; Berthet, J. B.; Bray, M.-A.; Shrestha, Y.; Varelas, X.; Boehm, J. S.; Carpenter, A. E.

10.1101/092403 — systems biology — Posted on 2016-12-08

573 MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

10.1101/090456 — systems biology — Posted on 2016-12-08

574 Ancient coexistence of norepinephrine, tyramine, and octopamine signaling in bilaterians

Bauknecht, P.; Jekely, G.

10.1101/063743 — evolutionary biology — Posted on 2016-12-08

575 An overview on the DNA nucleotide compositions across kingdoms

Guo, Y.

10.1101/087569 — evolutionary biology — Posted on 2016-12-08

576 Adaptive and Non-adaptive Responses of Populations to Environmental Change

Coulson, T.; Kendall, B. E.; Barthold, J.; Plard, F.; Schindler, S.; Ozgul, A.; Gaillard, J.-M.

10.1101/090894 — evolutionary biology — Posted on 2016-12-08

577 Serum extracellular vesicle depletion processes affect release and infectivity of HIV-1 in culture

Liao, Z.; Muth, D. C.; Eitan, E.; Travers, M.; Lehrmann, E.; Witwer, K. W.

10.1101/081687 — molecular biology — Posted on 2016-12-08

578 Decoding Single Molecule Time Traces with Dynamic Disorder

Hwang, W.; Lee, I.-B.; Hong, S.-C.; Hyeon, C.

10.1101/092387 — biophysics — Posted on 2016-12-08

579 Do Regional Brain Volumes and Major Depressive Disorder Share Genetic Architecture: a study in Generation Scotland (n=19,762), UK Biobank (n=24,048) and the English Longitudinal Study of Ageing (n=5,766)

Wigmore, E. M.; Clarke, T.-K.; Adams, M. J.; Fernandez-Pujals, A. M.; Gibson, J.; Davies, G.; Hall, L. S.; Zeng, Y.; Thomson, P. A.; Hayward, C.; Smith, B. H.; Hocking, L. J.; Padmanabhan, S.; Deary, I. J.; Porteous, D. J.; Nicodemus, K. K.; McIntosh, A. M.

10.1101/059352 — genetics — Posted on 2016-12-08

580 A synthesis of over 9,000 mass spectrometry experiments reveals the core set of human protein complexes

Drew, K.; Lee, C.; Huizar, R. L.; Tu, F.; Borgeson, B.; McWhite, C. D.; Ma, Y.; Wallingford, J. B.; Marcotte, E. M.

10.1101/092361 — systems biology — Posted on 2016-12-07

581 Complete fold annotation of the human proteome using a novel structural feature space

Middleton, S.; Illuminati, J.; Kim, J.

10.1101/092379 — bioinformatics — Posted on 2016-12-07

582 Local Discriminant Hyperalignment for multi-subject fMRI data alignment

Yousefnezhad, M.; Zhang, D.

10.1101/092247 — neuroscience — Posted on 2016-12-07

583 Decoding visual stimuli in human brain by using Anatomical Pattern Analysis on fMRI images

Yousefnezhad, M.; Zhang, D.

10.1101/092221 — neuroscience — Posted on 2016-12-07

584 What rhythmic perception and amusia can tell us about vocal social communication in schizophrenia

Mitchell, R. L. C.; Gamez, K.; Bolgar, J.; Neustadter, E. S.; Calkins, M. E.; Moore, T. M.; Leitman, D. I.

10.1101/092098 — neuroscience — Posted on 2016-12-07

585 Influence Of Desire To Belong And Feelings Of Loneliness On Emotional Prosody Perception In Schizophrenia.

Mitchell, R.; Gamez, K.; Kohler, C.; Calkins, M. E.; Turetsky, B. I.; Leitman, D. I.

10.1101/092080 — neuroscience — Posted on 2016-12-07

586 Neural Homophily: Similar Neural Responses Predict Friendship

Parkinson, C.; Kleinbaum, A. M.; Wheatley, T.

10.1101/092130 — neuroscience — Posted on 2016-12-07

587 Neural codes of seeing architectural styles

Choo, H.; Nasar, J.; Nikrahei, B.; Walther, D. B.

10.1101/045245 — neuroscience — Posted on 2016-12-07

588 Genomic characterization of serial-passaged Ebola virus in a boa constrictor cell line

Fedewa, G.; Radoshitzky, S. R.; Chī, X.; Dŏng, L.; Spear, M.; Strauli, N.; Stenglein, M. D.; Hernandez, R.; Jahrling, P. B.; Kuhn, J. H.; DeRisi, J.

10.1101/091603 — genomics — Posted on 2016-12-07

589 Pan-Cancer Analysis Reveals Technical Artifacts in The Cancer Genome Atlas (TCGA) Germline Variant Calls

Buckley, A. R.; Standish, K. A.; Bhutani, K.; Ideker, T.; Harismendy, O.; Carter, H.; Schork, N. J.

10.1101/092163 — genomics — Posted on 2016-12-07

590 Updated reference genome sequence and annotation of Mycobacterium bovis AF2122/97

Malone, K. M.; Farrell, D.; Stuber, T. P.; Schubert, O. T.; Aebersold, R.; Robbe-Austerman, S.; Gordon, S. V.

10.1101/092122 — genomics — Posted on 2016-12-07

591 Genomic analysis of Mycobacterium tuberculosis reveals complex etiology of tuberculosis in Vietnam including frequent introduction and transmission of Beijing lineage and positive selection for EsxW Beijing variant

Holt, K. E.; McAdam, P.; Phan, V. K. T.; Dang, T. M. H.; Nguyen, N. L.; Nguyen, H. L.; Nguyen, T. Q. N.; Nguyen, T. T. T.; Thwaites, G.; Edwards, D. J.; Pham, K.; Farrar, J.; Khor, C. C.; Teo, Y. Y.; Inouye, M.; Caws, M.; Dunstan, S. J.

10.1101/092189 — genomics — Posted on 2016-12-07

592 Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome

Carlston, C. M.; O'Donnell-Luria, A.; Underhill, H. R.; Cummings, B. B.; Weisburd, B.; Minikel, E. V.; Birnbaum, D. P.; Exome Aggregation Consortium, ; Tvrdik, T.; MacArthur, D. G.; Mao, R.

10.1101/090720 — genetics — Posted on 2016-12-07

593 Recent evolution of cestode growth suppression by threespine stickleback

Weber, J. N.; Steinel, N. C.; Shim, K. C.; Bolnick, D. I.

10.1101/091942 — evolutionary biology — Posted on 2016-12-07

594 Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter

Harrigan, M. P.; McKiernan, K. A.; Shanmugasundaram, V.; Denny, R. A.; Pande, V. S.

10.1101/092155 — biophysics — Posted on 2016-12-07

595 A meta-analysis of bioinformatics softwarebenchmarks reveals that publication-bias undulyinfluences software accuracy

Gardner, P.; Paterson, J. M.; Ashari Ghomi, F.; Umu, S. U. U.; McGimpsey, S.; Pawlik, A.

10.1101/092205 — bioinformatics — Posted on 2016-12-07

596 Review: Population Structure in Genetic Studies: Confounding Factors and Mixed Models

Martin, L. S.; Eskin, E.

10.1101/092106 — bioinformatics — Posted on 2016-12-07

597 Optimized implementations of voxel-wise degree centrality and local functional connectivity density mapping in AFNI

Craddock, R.; Clark, D.

10.1101/067702 — bioinformatics — Posted on 2016-12-07

598 A Resource for Assessing Information Processing in the Developing Brain Using EEG and Eye Tracking

Langer, N.; Ho, E. J.; Alexander, L. M.; Xu, H. Y.; Jozanovic, R. K.; Henin, S.; Cohen, S.; Marcelle, E. T.; Parra, L. C.; Milham, M. P.; Kelly, S. P.

10.1101/092213 — neuroscience — Posted on 2016-12-07

599 Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments

Jenior, M. L.; Leslie, J. L.; Young, V. B.; Schloss, P.

10.1101/092304 — microbiology — Posted on 2016-12-07

600 Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing

Neparaczki, E.; Kocsy, K.; Toth, G. E.; Maroti, Z.; Kalmar, T.; Bihari, P.; Nagy, I.; Palfi, G.; Molnar, E.; Rasko, I.; Torok, T.

10.1101/092239 — genetics — Posted on 2016-12-07

601 The emergence, evolution, and diversification of the miR390-TAS3-ARF pathway in land plants

Xia, R.; Xu, J.; Meyers, B. C.

10.1101/090647 — evolutionary biology — Posted on 2016-12-07

602 Codon based co-occurrence network motifs in human mitochondria

Shinde, P.; Sarkar, C.; Jalan, S.

10.1101/092262 — evolutionary biology — Posted on 2016-12-07

603 An Estradiol-Inducible Promoter Enables Fast, Graduated Control of Gene Expression in Fission Yeast

Ohira, M.; Hendrickson, D. G.; McIsaac, R. S.; Rhind, N.

10.1101/092338 — cell biology — Posted on 2016-12-07

604 Summary of muscle parameters for Hill-based muscle modeling in the human lower limb

Miller, R. H.

10.1101/090944 — bioengineering — Posted on 2016-12-07

605 C. elegans detect the color of pigmented food sources to guide foraging decisions.

Ghosh, D. D.; Jin, X.; Nitabach, M.

10.1101/092072 — neuroscience — Posted on 2016-12-07

606 Population history of the Sardinian people inferred from whole-genome sequencing

Chiang, C. W. K.; Marcus, J. H.; Sidore, C.; Al-Asadi, H.; Zoledziewska, M.; Pitzalis, M.; Busonero, F.; Maschio, A.; Pistis, G.; Steri, M.; Angius, A.; Lohmueller, K. E.; Abecasis, G. R.; Schlessinger, D.; Cucca, F.; Novembre, J.

10.1101/092148 — genetics — Posted on 2016-12-07

607 Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets

De Kumar, B.; Parker, H. J.; Paulson, A.; Parrish, M. E.; Pushel, I.; Slaughter, B. D.; Unruh, J. R.; Zeitlinger, J. B.; Krumlauf, R.

10.1101/092296 — developmental biology — Posted on 2016-12-07

608 Ras/ERK-signalling promotes tRNA synthesis and growth via the RNA polymerase III repressor Maf1 in Drosophila

Sriskanthadevan-Pirahas, S.; Deshpande, R.; Lee, B.; Grewal, S.

10.1101/092114 — developmental biology — Posted on 2016-12-07

609 Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data

Foster, Z. S. L.; Sharpton, T.; Grunwald, N. J.

10.1101/071019 — bioinformatics — Posted on 2016-12-07

610 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.; Iori, K.; Maguire, J. R.; Ready, K.; Evans, E. A.; Kang, H. P.; Haque, I. S.

10.1101/088252 — genetics — Posted on 2016-12-07

611 Cannabis use and risk of schizophrenia:a Mendelian randomization study

Vaucher, J.; Keating, B. J.; Lasserre, A. M.; Gan, W.; Lyall, D.; Ward, J.; Smith, D. J.; Pell, J.; Sattar, N.; Pare, G.; Holmes, M.

10.1101/092015 — epidemiology — Posted on 2016-12-07

612 Specific expression and function of the Six3 optix in serially homologous organs

Al-Khatib, A.; Siomava, N.; Posnien, N.; Casares, F.

10.1101/091793 — developmental biology — Posted on 2016-12-07

613 When are inter-individual brain-behavior correlations informative?

Lebreton, M.; Palminteri, S.

10.1101/036772 — neuroscience — Posted on 2016-12-07

614 Testing pseudo-linear models of responses to naturalscenes in primate retina

Heitman, A.; Brackbill, N.; Greschner, M.; Sher, A.; Litke, A. M.; Chichilnisky, E. J.

10.1101/045336 — neuroscience — Posted on 2016-12-07

615 Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry

Schiff, S.; Tsuji, J.; Wu, L.; Venkiteswaran, J.; Molot, L.; Elgood, R.; Paterson, M.; Neufeld, J. D.

10.1101/054478 — microbiology — Posted on 2016-12-07

616 Complement receptor 2 and IL-8 production identifies in adults and neonates naive T cells recently arising from the thymus and a Th8-like subset of memory T cells

10.1101/059535 — immunology — Posted on 2016-12-07

617 Overcoming evolved resistance to population-suppressing homing-based gene drives

Marshall, J.; Buchman, A.; Sanchez C., H. M.; Akbari, O. S.

10.1101/088427 — evolutionary biology — Posted on 2016-12-07

618 Alzheimer’s disease pathogenesis is dependent on neuronal receptor PTPσ

Gu, Y.; Shu, Y.; Corona, A.; Xu, K.; Yi, A. F.; Chen, S.; Luo, M.; Flanagan, J. G.; Tremblay, M.; Landreth, G. E.; Nelson, R.; Silver, J.; Shen, Y.

10.1101/079806 — neuroscience — Posted on 2016-12-06

619 Genome-Wide Association Study Reveals First Locus for Anorexia Nervosa and Metabolic Correlations

Duncan, L.; Yilmaz, Z.; Walters, R.; Goldstein, J.; Anttila, 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 2016-12-06

620 Investigating side effect modules in the interactome and their use in drug adverse effect discovery

Guney, E.

10.1101/089730 — systems biology — Posted on 2016-12-06

621 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 2016-12-06

622 No evidence for genome editing of the endogenous DNA in mouse zygotes and HEK293T human cell line using the DNA-guided Natronobacterium gregoryi Argonaute (NgAgo).

Khin, N. C.; Lowe, J. L.; Lora, J. M.; Burgio, G.

10.1101/091678 — molecular biology — Posted on 2016-12-06

623 Genetic determinants of chromatin accessibility and gene regulation in T cell activation across human individuals

Cheng, C. S.; Gate, R. E.; Aiden, A. P.; Siba, A.; Tabaka, M.; Lituiev, D.; Machol, I.; Subramaniam, M.; Shammim, M.; Hougen, K. L.; Wortman, I.; Huang, S.-C.; Durand, N. C.; Feng, T.; De Jager, P. L.; Chang, H. Y.; Lieberman Aiden, E.; Benoist, C.; Beer, M. A.; Ye, C. J.; Regev, A.

10.1101/090241 — genomics — Posted on 2016-12-06

624 Non-linear tradeoffs allow cooperation to evolve from Prisoner’s Dilemma to Snow Drift

Chao, L.; Elena, S.

10.1101/091041 — evolutionary biology — Posted on 2016-12-06

625 Non-random inversion landscapes in prokaryotic genomes are shaped by heterogeneous selection pressures

Repar, J.; Warnecke, T.

10.1101/092056 — evolutionary biology — Posted on 2016-12-06

626 The adaptive significance of phasic colony cycles in army ants

Garnier, S.; Kronauer, D. J. C.

10.1101/091934 — evolutionary biology — Posted on 2016-12-06

627 A Phylogenetic Analysis of Shape Covariance Structure in the Anthropoid Skull

Garcia, G.; de Oliveira, F. B.; Marroig, G.

10.1101/090910 — evolutionary biology — Posted on 2016-12-06

628 Community-level facilitation by macroalgal foundation species peaks at an intermediate level of environmental stress

Scrosati, R. A.

10.1101/091777 — ecology — Posted on 2016-12-06

629 Resource-Driven Encounters and the Induction of Disease Among Consumers

Borchering, R. K.; Bellan, S. E.; Flynn, J. M.; Pulliam, J. R. C.; McKinley, S. A.

10.1101/091850 — ecology — Posted on 2016-12-06

630 Homeostasis Back and Forth: An Eco-Evolutionary Perspective of Cancer

Basanta, D.; Anderson, A.

10.1101/092023 — cancer biology — Posted on 2016-12-06

631 Cell Dynamics in the Wound Healing Process in Tumor Environment After Treatments

Shahriyari, L.

10.1101/080895 — cancer biology — Posted on 2016-12-06

632 Melittin-induced alterations in morphology and deformability of human red blood cells using quantitative phase imaging techniques

Hur, J.; Kim, K.; Lee, S.; Park, H.; Park, Y.

10.1101/091991 — biophysics — Posted on 2016-12-06

633 Rice protein models from the Nutritious Rice for the World Project

Hung, L.-H.; Samudrala, R.

10.1101/091975 — plant biology — Posted on 2016-12-06

634 Spatiotemporal characterization of the neural correlates of outcome valence and surprise during reward learning in humans

Fouragnan, E.; Queirazza, F.; Retzler, C.; Mullinger, K. J.; Philiastides, M. G.

10.1101/091710 — neuroscience — Posted on 2016-12-06

635 Expanding the language network: Domain-specific hippocampal recruitment during high-level linguistic processing

Blank, I.; Duff, M. C.; Brown-Schmidt, S.; Fedorenko, E.

10.1101/091900 — neuroscience — Posted on 2016-12-06

636 Identification of Klebsiella capsule synthesis loci from whole genome data

Wyres, K.; Wick, R. R.; Gorrie, C.; Jenney, A.; Follador, R.; Thomson, N. R.; Holt, K. E.

10.1101/071415 — genomics — Posted on 2016-12-06

637 Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder

Andrews, S. V.; Ellis, S. E.; Bakulski, K. M.; Sheppard, B.; Croen, L. A.; Hertz-Picciotto, I.; Newschaffer, C. J.; Feinberg, A. P.; Arking, D. E.; Ladd-Acosta, C.; Fallin, M. D.

10.1101/091330 — genomics — Posted on 2016-12-06

638 Understanding genetic changes underlying the molybdate resistance and the glutathione production in Saccharomyces cerevisiae wine strains using an evolution-based strategy

Mezzetti, F.; Fay, J. C.; Giudici, P.; De Vero, L.

10.1101/092007 — genomics — Posted on 2016-12-06

639 Differences in the rare variant spectrum among human populations

Mathieson, I.; Reich, D. E.

10.1101/063578 — genetics — Posted on 2016-12-06

640 Colonization and transmission of the gut microbiotaof the burying beetle, Nicrophorus vespilloides,through development

Wang, Y.; Rozen, D.

10.1101/091702 — ecology — Posted on 2016-12-06

641 Critical transitions and the fragmenting of global forests

Saravia, L. A.; Doyle, S.; Bond-Lamberty, B.

10.1101/091751 — ecology — Posted on 2016-12-06

642 Summary of muscle parameters for Hill-based muscle modeling in the human lower limb

Miller, R.

10.1101/090944 — bioengineering — Posted on 2016-12-06

643 A new law of human perception

Wei, X.-X.; Stocker, A. A.

10.1101/091918 — animal behavior and cognition — Posted on 2016-12-06

644 Visualizing the Structure of RNA-seq Expression Data usingGrade of Membership Models

Dey, K. K.; Hsiao, C. J.; Stephens, M.

10.1101/051631 — genetics — Posted on 2016-12-06

645 Life Cycle Perspectives on Human Health Impacts of Ionic Liquids

Mehrkesh, A.; Karunanithi, A. T.

10.1101/091454 — pharmacology and toxicology — Posted on 2016-12-04

646 Evolutionary variations in the biofilm-associated protein BslA from the genus Bacillus

Morris, R. J.; Schor, M.; Gillespie, R. M. C.; Ferreira, A. S.; Bromley, K. M.; Baldauf, L.; Arnaouteli, S.; Sukhodub, T.; Earl, C.; Stanley-Wall, N. R.; MacPhee, C. E.

10.1101/091884 — microbiology — Posted on 2016-12-06

647 Validating Regulatory Predictions from Diverse Bacteria with Mutant Fitness Data

Sagawa, S.; Price, M. N.; Deutschbauer, A. M.; Arkin, A. P.

10.1101/091405 — microbiology — Posted on 2016-12-06

648 Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in Alpha-Proteobacteria

Ardissone, S.; Redder, P.; Russo, G.; Frandi, A.; Fumeaux, C.; Patrignani, A.; Schlapbach, R.; Falquet, L.; Viollier, P. H.

10.1101/091785 — microbiology — Posted on 2016-12-06

649 Experimental evolution reveals favored adaptive routes to cell aggregation in yeast

Hope, E. A.; Amorosi, C. J.; Miller, A. W.; Dang, K.; Heil, C. S.; Dunham, M. J.

10.1101/091876 — genetics — Posted on 2016-12-06

650 The emergence, evolution, and diversification of the miR390-TAS3-ARF pathway in land plants

Xia, R.; Xu, J.; Meyers, B. C.

10.1101/090647 — evolutionary biology — Posted on 2016-12-06

651 OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics

Eastman, P.; Swails, J.; Chodera, J. D.; McGibbon, R. T.; Zhao, Y.; Beauchamp, K. A.; Wang, L.-P.; Simmonett, A. C.; Harrigan, M. P.; Brooks, B. R.; Pande, V. S.

10.1101/091801 — biophysics — Posted on 2016-12-06

652 The Aquarius/EMB-4 helicase licenses co-transcriptional gene silencing

Akay, A.; Di Domenico, T.; Suen, K. M.; Nabih, A.; Parada, G. E.; Larance, M.; Medhi, R.; Berkyurek, A. C.; Wedeles, C. J.; Zhang, X.; Ma, P.; Lamond, A. I.; Hemberg, M.; Claycomb, J. M.; Miska, E. A.

10.1101/089763 — molecular biology — Posted on 2016-12-05

653 The dynamic three-dimensional organization of the diploid yeast genome

Kim, S.; Liachko, I.; Brickner, D. G.; Cook, K.; Noble, W. S.; Brickner, J. H.; Shendure, J.; Dunham, M.

10.1101/091827 — genomics — Posted on 2016-12-05

654 Discovery of an autoimmunity-associated IL2RA enhancer by unbiased targeting of transcriptional activation

Simeonov, D. R.; Gowen, B. G.; Boontanrart, M.; Roth, T.; Lee, Y.; Chan, A.; Nguyen, M. L.; Gate, R. E.; Subramaniam, M.; Woo, J. M.; Mitros, T.; Ray, G. J.; Bray, N. L.; Curie, G. L.; Naddaf, N.; Boyer, E.; Van Gool, F.; Schumann, K.; Daly, M. J.; Fahr, K. K.; Ye, C.; Bluestone, J. A.; Anderson, M. S.; Corn, J. E.; Marson, A.

10.1101/091843 — genetics — Posted on 2016-12-05

655 Effect of obesity-linked FTO rs9939609 variant on physical activity and dietary patterns in physically active men and women

West, N. R.; Dorling, J.; Thackray, A. E.; Decombel, S. E.; Stensel, D. J.; Grice, S. J.

10.1101/091728 — genetics — Posted on 2016-12-05

656 The innate immune systems of malacostracan crustaceans exhibit both conserved and evolutionarily distinct components

Lai, A. G.; Aboobaker, A.

10.1101/091835 — evolutionary biology — Posted on 2016-12-05

657 Specific expression and function of the Six3 optix in serially homologous organs

Al-Khatib, A.; Siomava, N.; Posnien, N.; Casares, F.

10.1101/091793 — developmental biology — Posted on 2016-12-05

658 Reprogramming protein kinase substrate specificity through synthetic mutations

Lubner, J. M.; Church, G. M.; Chou, M. F.; Schwartz, D.

10.1101/091892 — biochemistry — Posted on 2016-12-05

659 Cushing’s Syndrome mutant PKAL205R exhibits altered substrate specificity

Lubner, J. M.; Dodge-Kafka, K. L.; Carlson, C. R.; Church, G. M.; Chou, M. F.; Schwartz, D.

10.1101/091231 — biochemistry — Posted on 2016-12-05

660 Unsupervised spike sorting for large scale, high density multielectrode arrays

Hilgen, G.; Sorbaro, M.; Pirmoradian, S.; Muthmann, J.-O.; Kepiro, I.; Ullo, S.; Juarez Ramirez, C.; Puente Encinas, A.; Maccione, A.; Berdondini, L.; Murino, V.; Sona, D.; Cella Zanacchi, F.; Bhalla, U.; Sernagor, E.; Hennig, M. H.

10.1101/048645 — neuroscience — Posted on 2016-12-05

661 Distinctive BOLD Connectivity Patterns in the Schizophrenia Brain: Machine-learning based comparison between various connectivity measures

Han, H.-B.

10.1101/084160 — neuroscience — Posted on 2016-12-05

662 Measuring MEG closer to the brain: Performance of on-scalp sensor arrays

Iivanainen, J.; Stenroos, M.; Parkkonen, L.

10.1101/073585 — neuroscience — Posted on 2016-12-05

663 MtrA is an essential regulator that coordinates antibiotic production and development in Streptomyces species

Som, N. F.; Heine, D.; Munnoch, J. T.; Holmes, N. A.; Knowles, F.; Chandra, G.; Seipke, R. F.; Hoskisson, P. A.; Wilkinson, B. W.; Hutchings, M. I.

10.1101/090399 — microbiology — Posted on 2016-12-05

664 Microbial regime changes and indicators of eutrophication on the Mississippi River identified via a human-powered 2900 km transect

Henson, M. W.; Hanssen, J.; Spooner, G.; Flemming, P.; Pukonen, M.; Stahr, F.; Thrash, J. C.

10.1101/091512 — microbiology — Posted on 2016-12-05

665 Splice Expression Variation Analysis (SEVA) for Differential Gene Isoform Usage in Cancer

Afsari, B.; Guo, T.; Considine, M.; Florea, L.; Kelly, D.; Flam, E.; Ha, P.; Geman, D.; Ochs, M. F.; Califano, J. A.; Gaykalova, D. A.; Favorov, A. V.; Fertig, E. J.

10.1101/091637 — genomics — Posted on 2016-12-05

666 High-Throughput Sequencing of Transposable Elements Insertions Suggests Evidence for Adaptive Evolution of the Invasive Asian Tiger Mosquito Towards Temperate Environments

Goubert, C.; Henri, H.; Minard, G.; Valiente Moro, C.; Mavingui, P.; Vieira, C.; Boulesteix, M.

10.1101/049197 — genomics — Posted on 2016-12-05

667 Incomplete dominance of deleterious alleles contributes 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 2016-12-05

668 Adaptive evolution by spontaneous domain fusion and protein relocalisation

Farr, A. D.; Rainey, P. B.

10.1101/091744 — evolutionary biology — Posted on 2016-12-05

Buckley, R. M.; Kortschak, R. D.; Raison, J. M.; Adelson, D. L.

10.1101/091652 — evolutionary biology — Posted on 2016-12-05

670 Revealing compartmentalised membrane diffusion in living cells with interferometric scattering microscopy

de Wit, G.; Albrecht, D.; Ewers, H.; Kukura, P.

10.1101/091736 — biophysics — Posted on 2016-12-05

671 Pathway-based dissection of the genomic heterogeneity of cancer hallmarks with SLAPenrich

Iorio, F.; Garcia-Alonso, L.; Brammeld, J.; Martincorena, I.; Wille, D. R.; McDermott, U.; Saez-Rodriguez, J.

10.1101/077701 — bioinformatics — Posted on 2016-12-05

672 Spatiotemporal characterization of the neural correlates of outcome valence and surprise during reward learning in humans

Fouragnan, E.; Queirazza, F.; Retzler, C.; Mullinger, K.; Philiastides, M.

10.1101/091710 — neuroscience — Posted on 2016-12-05

673 Impact of regulatory variation across human iPSCs and differentiated cells

Banovich, N. E.; Li, Y. I.; Raj, A.; Ward, M. C.; Greenside, P.; Calderon, D.; Tung, P. Y.; Burnett, J. E.; Myrthil, M.; Thomas, S. M.; Burrows, C. K.; Gallego Romero, I.; Pavlovic, B. J.; Kundaje, A.; Pritchard, J. K.; Gilad, Y.

10.1101/091660 — genomics — Posted on 2016-12-05

674 Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder

Andrews, S. V.; Ellis, S. E.; Bakulski, K. M.; Sheppard, B.; Croen, L. A.; Hertz-Picciotto, I.; Newschaffer, C. J.; Feinberg, A. P.; Arking, D. E.; Ladd-Acosta, C.; Fallin, M. D.

10.1101/091330 — genomics — Posted on 2016-12-05

675 Colonization and transmission of the gut microbiotaof the burying beetle, Nicrophorus vespolloides,through development

Wang, Y.; Rozen, D.

10.1101/091702 — ecology — Posted on 2016-12-05

676 Geographical restructuring of Arabidopsis thaliana’s genetic makeup in the Iberian Peninsula due to climate change based on genetic cluster membership

Marcer, A.; Fortin, M.-J.; Pico, F. X.

10.1101/091686 — ecology — Posted on 2016-12-05

677 The population genetics of human disease: the case of recessive, lethal mutations

Guerra Amorim, C. E.; Gao, Z.; Baker, Z.; Diesel, J. F.; Simons, Y. B.; Haque, I. S.; Pickrell, J.; Przeworski, M.

10.1101/091579 — genetics — Posted on 2016-12-04

678 SiFit: A Method for Inferring Tumor Trees from Single-Cell Sequencing Data under Finite-site Models

Zafar, H.; Tzen, A.; Navin, N.; Chen, K.; Nakhleh, L.

10.1101/091595 — bioinformatics — Posted on 2016-12-04

679 Engineered Cpf1 Enzymes with Altered PAM Specificities

Gao, L.; Cox, D. B. T.; Yan, W. X.; Manteiga, J.; Schneider, M.; Yamano, T.; Nishimasu, H.; Nureki, O.; Zhang, F.

10.1101/091611 — synthetic biology — Posted on 2016-12-04

680 Heterogeneous firing responses predict diverse couplings to presynaptic activity in mice layer V pyramidal neurons

Zerlaut, Y.; Destexhe, A.

10.1101/091587 — neuroscience — Posted on 2016-12-04

681 Monozygotic twin pairs discordant for amyotrophic lateral sclerosis carry both common and unique epigenetic differences relevant to disease

Young, P. E.; Kum Jew, S.; Buckland, M. E.; Pamphlett, R.; Suter, C. M.

10.1101/090977 — neuroscience — Posted on 2016-12-04

682 BLISS: quantitative and versatile genome-wide profiling of DNA breaks in situ

Yan, W. X.; Mirzazadeh, R.; Garnerone, S.; Scott, D. A.; Schneider, M. W.; Kallas, T.; Custodio, J.; Wernersson, E.; Gao, L.; Li, Y.; Federova, Y.; Zetsche, B.; Zhang, F.; Bienko, M.; Crosetto, N.

10.1101/091629 — molecular biology — Posted on 2016-12-04

683 DNA Fountain enables a robust and efficient storage architecture

Erlich, Y.; Zielinski, D.

10.1101/074237 — synthetic biology — Posted on 2016-12-04

684 Real-time detection of PRT1-mediated ubiquitination via fluorescently labeled substrate probes

Mot, A. C.; Prell, E.; Klecker, M.; Naumann, C.; Faden, F.; Westermann, B.; Dissmeyer, N.

10.1101/062067 — plant biology — Posted on 2016-12-04

685 The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

Prince, D. J.; O'Rourke, S. M.; Thompson, T. Q.; Ali, O. A.; Lyman, H. S.; Saglam, I. K.; Hotaling, T. J.; Spidle, A. P.; Miller, M. R.

10.1101/056853 — genetics — Posted on 2016-12-04

686 Deep mutational scanning reveals characteristics important for targeting of the tail-anchored protein Fis1

Keskin, A.; Akdogan, E.; Dunn, C. D.

10.1101/045351 — cell biology — Posted on 2016-12-04

687 Prototyping a valinomycin biosynthesis pathway within a cell-free transcription-translation (TX-TL) system

Zhou, T.

10.1101/091520 — synthetic biology — Posted on 2016-12-04

688 Training qualitatively shifts the neural mechanisms that support attentional selection

Itthipuripat, S.; Cha, K.; Byers, A.; Serences, J. T.

10.1101/091413 — neuroscience — Posted on 2016-12-04

689 Stimulus visibility controls the balance between attention-induced changes in contrast appearance and decision bias

Itthipuripat, S.; Chang, K.-Y.; Bong, A.; Serences, J. T.

10.1101/091421 — neuroscience — Posted on 2016-12-04

690 The interaction of orientation-specific surround suppression and visual-spatial attention

Rokem, A.; Landau, A. N.

10.1101/091553 — neuroscience — Posted on 2016-12-04

691 A Novel DNA-binding Protein Coordinates Asymmetric Chromosome Replication and Chromosome Partitioning

Taylor, J.; Panis, G.; Viollier, P.; Marczynski, G.

10.1101/091496 — microbiology — Posted on 2016-12-04

692 Genome-wide survey of Pseudomonas aeruginosa PA14 reveals a role for the glyoxylate pathway and extracellular proteases in the limited utilization of mucin

Flynn, J. M.; Phan, C. Q.; Hunter, R. C.

10.1101/091462 — microbiology — Posted on 2016-12-04

693 Maximizing ecological and evolutionary insight from bisulfite sequencing data sets

Lea, A.; Vilgalys, T.; Durst, P.; Tung, J.

10.1101/091488 — genomics — Posted on 2016-12-04

694 Precise Quantification of Translation Inhibition by mRNA Structures that Overlap with the Ribosomal Footprint in N-terminal Coding Sequences

Espah Borujeni, A.; Cetnar, D.; Farasat, I.; Smith, A.; Lundgren, N.; Salis, H. M.

10.1101/091470 — genetics — Posted on 2016-12-04

695 The Phenotypic, Genotypic, & Environmental Drivers of Local Adaptation to a Harsh Granite Outcrop Environment in Mimulus

Ferris, K. G.; Willis, J. H.

10.1101/091538 — evolutionary biology — Posted on 2016-12-04

696 Zebrafish Nanog is not required in embryonic cells

Gagnon, J. A.; Obbad, K.; Schier, A. F.

10.1101/091504 — developmental biology — Posted on 2016-12-04

697 Mitogenome and nuclear DNA differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean

Leslie, M. S.; Archer, F. I.; Morin, P. A.

10.1101/091215 — zoology — Posted on 2016-12-04

698 mRNA turnover through CDS-targeting is the primary role of miRNA in the green alga Chlamydomonas.

Chung, B. Y.; Deery, M. J.; Groen, A. J.; Howard, J.; Baulcombe, D. C.

10.1101/088807 — molecular biology — Posted on 2016-12-04

699 Microbial regime changes and indicators of eutrophication on the Mississippi River identified via a human-powered 2900 km transect

Henson, M. W.; Hanssen, J.; Spooner, G.; Flemming, P.; Pukonen, M.; Stahr, F.; Thrash, J. C.

10.1101/091512 — microbiology — Posted on 2016-12-04

700 Cerebellar anodal tDCS increases implicit visuomotor remapping when strategic re-aiming is suppressed

Leow, L.-A.; Marinovic, W.; Riek, S.; Carroll, T.

10.1101/091397 — neuroscience — Posted on 2016-12-04

701 Germ granules prevent accumulation of somatic transcripts in the adult C. elegans germline

Knutson, A. K.; Egelhofer, T. A.; Rechtsteiner, A.; Strome, S.

10.1101/089433 — developmental biology — Posted on 2016-12-03

702 Summary of muscle parameters for Hill-based muscle modeling in the human lower limb

Miller, R.

10.1101/090944 — bioengineering — Posted on 2016-12-03

703 Resource Competition Shapes the Response of Genetic Circuits

Qian, Y.; Huang, H.-H.; Jimenez, J.; Del Vecchio, D.

10.1101/091306 — synthetic biology — Posted on 2016-12-03

704 Mindboggling morphometry of human brains

Klein, A.; Ghosh, S. S.; Bao, F. S.; Giard, J.; Hame, Y.; Stavsky, E.; Lee, N.; Rossa, B.; Reuter, M.; Chaibub Neto, E.; Keshavan, A.

10.1101/091322 — neuroscience — Posted on 2016-12-03

705 Compositional Inductive Biases in Function Learning

Schulz, E.; Tenenbaum, J. B.; Duvenaud, D.; Speekenbrink, M.; Gershman, S. J.

10.1101/091298 — animal behavior and cognition — Posted on 2016-12-03

706 Bacterial genome reduction as a result of short read sequence assembly

Williamson, C. H. D.; Sanchez, A.; Vazquez, A.; Gutman, J.; Sahl, J. W.

10.1101/091314 — genomics — Posted on 2016-12-03

707 Exploring the mutational robustness of nucleic acidsby searching genotype neighbourhoods in sequencespace

Zhou, Q.; Sun, X.; Xia, X.; Fan, Z.; Luo, Z.; Zhao, S.; Liang, H.; Shakhnovich, E.

10.1101/091389 — evolutionary biology — Posted on 2016-12-03

708 How Cancer Genomics Drives Cancer Biology: Does Synthetic Lethality Explain Mutually Exclusive Oncogenic Mutations?

Varmus, H.; Unni, A. M.; Lockwood, W. W.

10.1101/091173 — cancer biology — Posted on 2016-12-03

709 Monolayer-crystal streptavidin support films provide an internal standard of cryo-EM image quality

Han, B.-G.; Watson, Z. L.; Cate, J. H. D.; Glaeser, R. M.

10.1101/091355 — biophysics — Posted on 2016-12-03

710 Resonance modulation, annihilation and generation of anti-resonance and anti-phasonance in 3D neuronal systems: interplay of resonant and amplifying currents with slow dynamics

Rotstein, H. G.

10.1101/091207 — neuroscience — Posted on 2016-12-02

711 Nus factors have a widespread regulatory function in bacteria

Baniulyte, G.; Singh, N.; Benoit, C.; Johnson, R.; Ferguson, R.; Paramo, M.; Stringer, A.; Scott, A.; Lapierre, P.; Wade, J.

10.1101/091223 — microbiology — Posted on 2016-12-02

712 Pathways analyses of schizophrenia GWAS focusing on known and novel drug targets

Gaspar, H. A.; Breen, G.

10.1101/091264 — genomics — Posted on 2016-12-02

713 Genetic determinants of chromatin accessibility and gene regulation in T cell activation across human individuals

10.1101/090241 — genomics — Posted on 2016-12-02

714 Negative regulation of uPAR activity by a GPI-specific phospholipase C

van Veen, M.; Matas-Rico, E.; van de Wetering, K.; Leyton-Puig, D.; Kedziora, K. M.; Sidenius, N.; Jalink, K.; Perrakis, A.; Moolenaar, W. H.

10.1101/091272 — cell biology — Posted on 2016-12-02

715 Characterizing Xenopus tropicalis endurance capacities with multilevel transcriptomics

Richards, A. J.; Herrel, A.; Videlier, M.; Paszkiewicz, K.; Pollet, N.; Bonneaud, C.

10.1101/091280 — bioinformatics — Posted on 2016-12-02

716 Mechanism of ribosome rescue by ArfA and RF2

Demo, G.; Svidritskiy, E.; Madireddy, R.; Diaz-Avalos, R.; Grant, T.; Grigorieff, N.; Sousa, D.; Korostelev, A.

10.1101/091256 — biochemistry — Posted on 2016-12-02

717 Unsupervised extraction of functional gene expression signatures in the bacterial pathogen Pseudomonas aeruginosa with eADAGE

Tan, J.; Doing, G.; Lewis, K. A.; Price, C. E.; Chen, K. M.; Cady, K. C.; Perchuk, B.; Laub, M. T.; Hogan, D. A.; Greene, C. S.

10.1101/078659 — systems biology — Posted on 2016-12-02

718 Gene expression models based on a reference laboratory strain are bad predictors of Mycobacterium tuberculosis complex transcriptional diversity.

Chiner-Oms, A.; Gonzalez-Candelas, F.; Comas, I.

10.1101/091082 — systems biology — Posted on 2016-12-02

719 Multi-scale approaches for high-speed imaging and analysis of large neural populations

Friedrich, J.; Yang, W.; Soudry, D.; Mu, Y.; Ahrens, M. B.; Yuste, R.; Peterka, D. S.; Paninski, L.

10.1101/091132 — neuroscience — Posted on 2016-12-02

720 The Structured Coalescent and its Approximations

Mueller, N. F.; Rasmussen, D. A.; Stadler, T.

10.1101/091058 — evolutionary biology — Posted on 2016-12-02

721 Senescence gives insights into the morphogenetic evolution of anamniotes.

Villiard, E.; Denis, J.-F.; Hashemi, F. S.; Igelmann, S.; Ferbeyre, G.; Roy, S.

10.1101/091199 — developmental biology — Posted on 2016-12-02

722 Effective Cell Immunoablation in Undisrupted Developing Avian Embryos

Lopez Diaz, M.; Bujan Valera, J.; Cadorniga, C.

10.1101/091116 — developmental biology — Posted on 2016-12-02

723 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 2016-12-02

724 A Bayesian Heteroscedastic GLM with Application to fMRI Data with Motion Spikes

Eklund, A.; Lindquist, M. A.; Villani, M.

10.1101/091066 — neuroscience — Posted on 2016-12-02

725 High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

Lee, S. T.; Kahn, S. A.; Delmont, T. O.; Hubert, N. A.; Morrison, H. G.; Antonopoulos, D. A.; Rubin, D. T.; Eren, A. M.

10.1101/090993 — microbiology — Posted on 2016-12-02

726 Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses

Van Leuven, J. T.; Ridenhour, B. J.; Miller, C. R.; Miura, T. A.

10.1101/090936 — immunology — Posted on 2016-12-02

727 How well do RNA-Seq differential gene expression tools perform in higher eukaryotes?

Froussios, K.; Schurch, N. J.; Mackinnon, K.; Gierlinski, M.; Duc, C.; Simpson, G. G.; Barton, G. J.

10.1101/090753 — genomics — Posted on 2016-12-02

728 Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps

Sailer, Z. R.; Harms, M. J.

10.1101/072256 — genetics — Posted on 2016-12-02

729 Joint inference of demography and mutation rates from polymorphism data and pedigrees

Parat, F.; Szilagyi, S. M.; Wegmann, D.; Tellier, A.

10.1101/091090 — genetics — Posted on 2016-12-02

730 Analyses of the core eukaryotic protein subunit of telomerase support extensive adaptation to different evolutionary and life histories in the Metazoa

Lai, A. G.; Pouchkina-Stantcheva, N.; Di Donfrancesco, A.; Kildisiute, G.; Sahu, S.; Aboobaker, A.

10.1101/091124 — evolutionary biology — Posted on 2016-12-02

731 The Tell-Tale Genome

BORTOLINI, E.; Pagani, L.; Crema, E. R.; Sarno, S.; Barbieri, C.; Boattini, A.; Sazzini, M.; Graca da Silva, S.; Martini, G.; Metspalu, M.; Pettener, D.; Luiselli, D.; Tehrani, J. J.

10.1101/091074 — evolutionary biology — Posted on 2016-12-02

732 Predicting off-target effects for end-to-end CRISPR guide design

Listgarten, J.; Weinstein, M.; Elibol, M.; Hoang, L.; Doench, J.; Fusi, N.

10.1101/078253 — bioinformatics — Posted on 2016-12-02

733 Each cell needs long double-stranded RNA for silencing by feeding RNAi in C. elegans

Raman, P.; Zaghab, S.; Traver, E.; Jose, A.

10.1101/066415 — genetics — Posted on 2016-12-02

734 Inferring Fitness Landscapes and Selection on Phenotypic States from Single-Cell Genealogical Data

Nozoe, T.; Kussell, E.; Wakamoto, Y.

10.1101/069260 — systems biology — Posted on 2016-12-02

735 Major host transitions are modulated through transcriptome-wide reprograming events in Schistocephalus solidus, a threespine stickleback parasite

Hebert, F.-O.; Grambauer, S.; Barber, I.; Landry, C.; Aubin-Horth, N.

10.1101/072769 — genomics — Posted on 2016-12-02

736 Adaptive and Non-adaptive Responses of Populations to Environmental Change

Coulson, T.; Kendall, B. E.; Barthold, J.; Plard, F.; Schindler, S.; Ozgul, A.; Gaillard, J.-M.

10.1101/090894 — evolutionary biology — Posted on 2016-12-02

737 Entropy and codon bias in HIV-1

Pandey, A.

10.1101/052274 — bioinformatics — Posted on 2016-12-02

738 Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees

Solomon, B.; Kingsford, C.

10.1101/086561 — genomics — Posted on 2016-12-02

739 Impact of climatic changes in the Late Pleistocene on migrations and extinctions of mammals in Europe: four case studies

Baca, M.; Nadachowski, A.; Lipecki, G.; Mackiewicz, P.; Marciszak, A.; Popović, D.; Socha, P.; Stefaniak, K.; Wojtal, P.

10.1101/090878 — evolutionary biology — Posted on 2016-12-02

740 Climate-driven range shifts in fragmented ecosystems

Cristofari, R.; Liu, X.; Bonadonna, F.; Cherel, Y.; Pistorius, P.; Le Maho, Y.; Raybaud, V.; Stenseth, N. C.; Le Bohec, C.; Trucchi, E.

10.1101/090852 — evolutionary biology — Posted on 2016-12-02

741 Summary of muscle parameters for Hill-based muscle modeling in the human lower limb

Miller, R.

10.1101/090944 — bioengineering — Posted on 2016-12-02

742 AllSome Sequence Bloom Trees

Sun, C.; Harris, R. S.; Chikhi, R.; Medvedev, P.

10.1101/090464 — bioinformatics — Posted on 2016-12-02

743 Long-read whole genome sequencing identifies causal structural variation in a Mendelian disease

Merker, J.; Wenger, A. M.; Sneddon, T.; Grove, M.; Waggott, D.; Utiramerur, S.; Hou, Y.; Lambert, C. C.; Eng, K. S.; Hickey, L.; Korlach, J.; Ford, J.; Ashley, E. A.

10.1101/090985 — genomics — Posted on 2016-12-02

744 Single-molecule sequencing of the Drosophila serrata genome

Allen, S. L.; Delaney, E. K.; Kopp, A.; Chenoweth, S. F.

10.1101/090969 — genomics — Posted on 2016-12-02

745 Taming the Late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA

Bennett, E. A.; Champlot, S.; Peters, J.; Arbuckle, B. S.; Guimaraes, S.; Pruvost, M.; Bar-David, S.; Davis, S. J. M.; Gautier, M.; Kaczensky, P.; Kuehn, R.; Mashkour, M.; Morales-Muniz, A.; Pucher, E.; Tournepiche, J.-F.; Uerpmann, H.-P.; Balasescu, A.; Germonpre, M.; Gunden, C. Y.; Hemami, M.-R.; Moulle, P.-E.; Oztan, A.; Uerpmann, M.; Walzer, C.; Grange, T.; Geigl, E.-M.

10.1101/090928 — evolutionary biology — Posted on 2016-12-02

746 Pervasive Antagonistic Interactions Among Hybrid Incompatibility Loci

Guerrero, R. F.; Nakazato, T.; Muir, C. D.; Josway, S.; Moyle, L. C.

10.1101/090886 — evolutionary biology — Posted on 2016-12-01

747 Adaptive and Non-adaptive Responses of Populations to Environmental Change

Coulson, T.; Kendall, B. E.; Barthold, J.; Plard, F.; Schindler, S.; Ozgul, A.; Gaillard, J.-M.

10.1101/090894 — evolutionary biology — Posted on 2016-12-01

748 Germ granules prevent accumulation of somatic transcripts in the adult C. elegans germline

Knutson, A. K.; Egelhofer, T. A.; Rechtsteiner, A.; Strome, S.

10.1101/089433 — developmental biology — Posted on 2016-12-01

749 Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer

O'Donnell, T.; Christie, E. L.; Ahuja, A.; Buros, J.; Aksoy, B. A.; Bowtell, D. D. L.; Snyder, A.; Hammerbacher, J.

10.1101/090134 — cancer biology — Posted on 2016-12-01

750 Alzheimer’s disease pathogenesis is dependent on neuronal receptor ΡΤΡσ

Gu, Y.; Shu, Y.; Corona, A.; Xu, K.; Yi, A. F.; Chen, S.; Luo, M.; Flanagan, J. G.; Tremblay, M.; Landreth, G. E.; Nelson, R.; Silver, J.; Shen, Y.

10.1101/079806 — neuroscience — Posted on 2016-12-01

751 High levels of antibiotic tolerance and persistence are induced by the commercial anti-microbial triclosan

Westfall, C. S.; Levin, P. A.

10.1101/090829 — microbiology — Posted on 2016-12-01

752 Identification and quantitative analysis of the major determinants of translation elongation rate variation

Dao Duc, K.; Song, Y. S.

10.1101/090837 — genomics — Posted on 2016-12-01

753 Finite-sites multiple mutations interference gives rise to wavelet-like oscillations of multilocus linkage disequilibrium

Garcia, V.; Glassberg, E. C.; Harpak, A.; Feldman, M. W.

10.1101/090571 — genetics — Posted on 2016-12-01

754 Structure and origin of the White Cap locus and its role in evolution of grain color in maize

Tan, B.-C.; Guan, J.-C.; Ding, S.; Wu, S.; Saunders, J. W.; Koch, K. E.; McCarty, D. R.

10.1101/082677 — genetics — Posted on 2016-12-01

755 The Bacterial Sequential Markov Coalescent

De Maio, N.; Wilson, D. J.

10.1101/090845 — evolutionary biology — Posted on 2016-12-01

756 New genes and functional innovation in mammals

Villanueva-Canas, J. L.; Ruiz-Orera, J.; Agea, I.; Gallo, M.; Andreu, D.; Alba, M.

10.1101/090860 — evolutionary biology — Posted on 2016-12-01

757 Cadm1 regulates airway stem cell growth and differentiation via modulation of Stat3 activity

Seedhar, P.; Sage, E.; Vallath, S.; Sturges, G.; Giangreco, A.

10.1101/090761 — cell biology — Posted on 2016-12-01

758 Discrete mutations in colorectal cancer correlate with defined microbial communities in the tumor microenvironment

Burns, M. B.; Montassier, E.; Abrahante, J.; Starr, T. K.; Knights, D.; Blekhman, R.

10.1101/090795 — cancer biology — Posted on 2016-12-01

759 BCFtools/csq: Haplotype-aware variant consequences

Danecek, P.; McCarthy, S. A.

10.1101/090811 — bioinformatics — Posted on 2016-12-01

760 Tumor Origin Detection with Tissue-Specific miRNA and DNA methylation Markers

Tang, W.; Wan, S.; Zou, Q.

10.1101/090746 — bioinformatics — Posted on 2016-12-01

761 Adipocyte Jak2 Mediates Growth Hormone-Induced Hepatic Insulin Resistance

Corbit, K.; Camporez, J. P. G.; Tran, J. L.; Wilson, C. G.; Lowe, D.; Nordstrom, S.; Ganeshan, K.; Perry, R. J.; Schulman, G.; Jurczak, M. J.; Weiss, E.

10.1101/076265 — physiology — Posted on 2016-12-01

762 Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-Seq peak callers

Teng, M.; Irizarry, R. A.

10.1101/090704 — genomics — Posted on 2016-12-01

763 Rapidly evolving homing CRISPR barcodes

Kalhor, R.; Mali, P.; Church, G. M.

10.1101/055863 — synthetic biology — Posted on 2016-12-01

764 Bayesian large-scale multiple regression with summary statistics from genome-wide association studies

Zhu, X.; Stephens, M.

10.1101/042457 — genetics — Posted on 2016-12-01

765 Modeling of axonal endoplasmic reticulum network by spastic paraplegia proteins

Yalçın, B; Zhao, L; Stofanko, M; O'Sullivan, N; Kang, Z; Roost, A; Thomas, M; Zaessinger, S; Blard, O; Patto, A; Baena, V; Terasaki, M; O'Kane, C

10.1101/069005 — cell biology — Posted on 2016-12-01

766 The unbalanced distribution of the amino aicds(Arg, Lys) in high pI proteins of complete proteomes, its origin and evolution

Xie, Z.

10.1101/090290 — bioinformatics — Posted on 2016-12-01

Archive, 2016-12