bioRxiv directory

1 Hypothesis-free identification of modulators of genetic risk factors

Daria Zhernakova;Patrick Deelen;Martijn Vermaat;Maarten van Iterson;Michiel van Galen;Wibowo Arindrarto;Peter van t Hof;Hailiang Mei;Freerk van Dijk;Harm-Jan Westra;Marc Jan Bonder;Jeroen van Rooij;Marijn Verkerk;P. Mila Jhamai;Matthijs Moed;Szymon M. Kielbasa;Jan Bot;Irene Nooren;René Pool;Jenny van Dongen;Jouke J. Hottenga;Coen D.A. Stehouwer;Carla J.H. van der Kallen;Casper G. Schalkwijk;Alexandra Zhernakova;Yang Li;Ettje F. Tigchelaar;Marian Beekman;Joris Deelen;Diana van Heemst;Leonard H. van den Berg;Albert Hofman;André G. Uitterlinden;Marleen M.J. van Greevenbroek;Jan H. Veldink;Dorret

10.1101/033217 — Genetics — Posted on 2015-11-30

2 A Bayesian network approach for modeling mixed features in TCGA ovarian cancer data

Qingyang Zhang;Ji-Ping Wang;

10.1101/033332 — Systems Biology — Posted on 2015-11-30

3 Segmental interpolation surface: a tool to dissect environmental effects on plant water-use efficiency in drought prone scenarios

Gaston Quero;Sebastian Simondi;Omar Borsani;

10.1101/033308 — Plant Biology — Posted on 2015-11-30

4 Disease variants alter transcription factor levels and methylation of their binding sites

Marc Jan Bonder;René Luijk;Daria Zhernakova;Matthijs Moed;Patrick Deelen;Martijn Vermaat;Maarten van Iterson;Freerk van Dijk;Michiel van Galen;Jan Bot;Roderick C. Slieker;P. Mila Jhamai;Michael Verbiest;H. Eka D. Suchiman;Marijn Verkerk;Ruud van der Breggen;Jeroen van Rooij;Nico Lakenberg;Wibowo Arindrarto;Szymon M. Kielbasa;Iris Jonkers;Peter van t Hof;Irene Nooren;Marian Beekman;Joris Deelen;Diana van Heemst;Alexandra Zhernakova;Ettje F. Tigchelaar;Morris A. Swertz;Albert Hofman;André G. Uitterlinden;René Pool;Jenny van Dongen;Jouke J. Hottenga;Coen D.A. Stehouwer;Carla J.H. van der Kallen;C

10.1101/033084 — Genomics — Posted on 2015-11-30

5 Automated long-term recording and analysis of neural activity in behaving animals

Ashesh K Dhawale;Rajesh Poddar;Evi Kopelowitz;Valentin Normand;Steffen Wolff;Bence Olveczky;

10.1101/033266 — Neuroscience — Posted on 2015-11-30

6 Genome-wide and single-base resolution DNA methylomes of the Sea Lamprey (Petromyzon marinus) Reveal Gradual Transition of the Genomic Methylation Pattern in Early Vertebrates

Zhao Zhang;Gangbiao Liu;Yangyun Zhou;James P. B. Lloyd;David W. McCauley;Weiming Li;Xun Gu;Zhixi Su;

10.1101/033233 — Evolutionary Biology — Posted on 2015-11-30

7 Fish population dynamics and diversity in boreal and temperate reservoirs: A quantitative synthesis

Katrine Turgeon;Christopher T. Solomon;Christian Nozais;Irene Gregory-Eaves;

10.1101/033282 — — Posted on 2015-11-30

8 Immigration rates during population density reduction in a coral reef fish

Katrine Turgeon;Donald L. Kramer;

10.1101/033274 — Ecology — Posted on 2015-11-30

9 An Improved Genome Assembly of Azadirachta indica A. Juss.

Neeraja M Krishnan;Prachi Jain;Saurabh Gupta;Arun K Hariharan;Binay Panda;

10.1101/033290 — Bioinformatics — Posted on 2015-11-30

10 Efficient coalescent simulation and genealogical analysis for large sample sizes

Jerome Kelleher;Alison M Etheridge;Gil McVean;

10.1101/033118 — Evolutionary Biology — Posted on 2015-11-30

11 Efficient coalescent simulation and genealogical analysis for large sample sizes

Jerome Kelleher;Alison M Etheridge;Gil McVean;

10.1101/033118 — Evolutionary Biology — Posted on 2015-11-30

12 Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins

Toshitsugu Fujita;Miyuki Yuno;Hodaka Fujii;

10.1101/033241 — Biochemistry — Posted on 2015-11-30

13 Automatic segmentation of Drosophila neural compartments using GAL4 expression data reveals novel visual pathways

Karin Panser;Laszlo Tirian;Florian Schulze;Santiago Villalba;Gregory SXE Jefferis;Katja Buehler;Andrew D Straw;

10.1101/032292 — Neuroscience — Posted on 2015-11-29

14 Revolutionising Public Health Reference Microbiology using Whole Genome Sequencing: Salmonella as an exemplar

Philip Ashton;Satheesh Nair;Tansy Peters;Rediat Tewolde;Martin Day;Michel Doumith;Jonathan Green;Claire Jenkins;Anthony Underwood;Catherine Arnold;Elizabeth de Pinna;Tim Dallman;Kathie Grant;

10.1101/033225 — Microbiology — Posted on 2015-11-29

15 Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.

Nicolas Galtier;

10.1101/033043 — Evolutionary Biology — Posted on 2015-11-29

16 Two Independent and Highly Efficient Open Source TKF91 Implementations

Nikolai Baudis;Pierre Barbera;Sebastian Graf;Sarah Lutteropp;Daniel Opitz;Tomas Flouri;Alexandros Stamatakis;

10.1101/033191 — Bioinformatics — Posted on 2015-11-29

17 The role of deleterious substitutions in crop genomes

Thomas J Y Kono;Fengli Fu;Mohsen Mohammadi;Paul J Hoffman;Chaochih Liu;Robert M Stupar;Kevin P Smith;Peter Tiffin;Justin C Fay;Peter L Morrell;

10.1101/033175 — Genetics — Posted on 2015-11-28

18 BAGEL: A computational framework for identifying essential genes from pooled library screens.

Traver Hart;Jason Moffat;

10.1101/033068 — Systems Biology — Posted on 2015-11-27

19 Meiotic interactors of a mitotic gene TAO3 revealed by functional analysis of its rare variant

Saumya Gupta;Aparna Radhakrishnan;Rachana Nitin;Pandu Raharja-Liu;Gen Lin;Lars M Steinmetz;Julien Gagneur;Himanshu Sinha;

10.1101/033167 — Genetics — Posted on 2015-11-27

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

Cuong Dang;Antonio Peon;Pedro Ballester;

10.1101/033092 — Bioinformatics — Posted on 2015-11-27

21 NOVEL INTRONIC NON-CODING RNAS CONTRIBUTE TO MAINTENANCE OF PHENOTYPE IN SACCHAROMYCES CEREVISIAE

Katarzyna B Hooks;Samina Naseeb;Sam Griffiths-Jones;Daniela Delneri;

10.1101/033076 — Genetics — Posted on 2015-11-27

22 Diversity of immune strategies explained by adaptation to pathogen statistics

Andreas Mayer;Thierry Mora;Olivier Rivoire;Aleksandra M Walczak;

10.1101/033159 — Evolutionary Biology — Posted on 2015-11-27

23 Sequenceserver: a modern graphical user interface for custom BLAST databases

Anurag Priyam;Ben J Woodcroft;Vivek Rai;Alekhya Munagala;Ismail Moghul;Filip Ter;Mark Anthony Gibbins;HongKee Moon;Guy Leonard;Wolfgang Rumpf;Yannick Wurm;

10.1101/033142 — Bioinformatics — Posted on 2015-11-27

24 Interactions retain the co-phylogenetic matching that communities lost

Timothee Poisot;Daniel Stouffer;

10.1101/033050 — Evolutionary Biology — Posted on 2015-11-26

25 A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogenous ribonucleoprotein C on cleavage and polyadenylation

Andreas J Gruber;Ralf Schmidt;Andreas R Gruber;Georges Martin;Souvik Ghosh;Manuel Belmadani;Walter Keller;Mihaela Zavolan;

10.1101/033001 — Genomics — Posted on 2015-11-26

26 Genome-wide expression profiling Drosophila melanogaster deficiency heterozygotes reveals diverse genomic responses.

Hangnoh Lee;Dong-Yeon Cho;Cale Whitworth;Robert Eisman;Melissa Phelps;John Roote;Thomas Kaufman;Kevin Cook;Steven Russell;Teresa M Przytycka;Brian Oliver;

10.1101/032920 — Genetics — Posted on 2015-11-26

27 Can functional traits explain phylogenetic signal in the composition of a plant community?

Daijiang Li;Anthoy R Ives;Donald M Waller;

10.1101/032938 — Ecology — Posted on 2015-11-30

28 Can functional traits explain phylogenetic signal in the composition of a plant community?

Daijiang Li;Anthoy R Ives;Donald M Waller;

10.1101/032938 — Ecology — Posted on 2015-11-26

29 AGOUTI: improving genome assembly and annotation using transcriptome data

Simo V Zhang;Luting Zhuo;Matthew W Hahn;

10.1101/033019 — Bioinformatics — Posted on 2015-11-26

30 Rich chromatin structure prediction from Hi-C data

Laraib Iqbal Malik;Rob Patro;

10.1101/032953 — Bioinformatics — Posted on 2015-11-26

31 How reliable are ligand-centric methods for Target Fishing?

Antonio Peon;Cuong Dang;Pedro Ballester;

10.1101/032946 — Bioinformatics — Posted on 2015-11-26

32 A phylogenetically diverse class of blind type 1 opsins

Erin A Becker;Andrew I Yao;Phillip M Seitzer;Tobias Kind;Ting Wang;Rich Eigenheer;Katie S. Y. Shao;Vladimir Yarov-Yarovoy;Marc T Facciotti;

10.1101/033027 — Molecular Biology — Posted on 2015-11-26

33 The limitations of in vitro experimentation in understanding biofilms and chronic infection

Aled E L Roberts;Kasper N Kragh;Thomas Bjarnsholt;Stephen P Diggle;

10.1101/032987 — Microbiology — Posted on 2015-11-27

34 The limitations of in vitro experimentation in understanding biofilms and chronic infection

Aled E L Roberts;Kasper N Kragh;Thomas Bjarnsholt;Stephen P Diggle;

10.1101/032987 — Microbiology — Posted on 2015-11-26

35 Exopolysaccharide biosynthetic glycoside hydrolases can be utilized to disrupt and prevent Pseudomonas aeruginosa biofilms

Perrin Baker;Preston J HIll;Brendan D Snarr;Noor Alnabelseya;Mathew J Pestrak;Mark J Lee;Laura K Jennings;John Tam;Roman Melnyk;Matthew R Parsek;Donald C Sheppard;Daniel J Wozniak;P. Lynne Howell;

10.1101/032714 — Microbiology — Posted on 2015-11-26

36 Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City

Stephen E. Harris;Alexander T. Xue;Diego Alvarado-Serrano;Joel T. Boehm;Tyler Joseph;Michael J. Hickerson;Jason Munshi-South;

10.1101/032979 — Evolutionary Biology — Posted on 2015-11-26

37 A quantitative interaction between signal detection in attention and reward/aversion behavior

Vijay Viswanathan;Byoung Woo Kim;John P Sheppard;Hao Ying;Kalyan Raman;Myung Joo Lee;Sang Lee;Frank Mulhern;Martin P Block;Bobby Calder;Dale T Mortensen;Anne J Blood;Hans C Breiter;

10.1101/032912 — Animal Behavior and Cognition — Posted on 2015-11-26

38 DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases

Nuria Queralt Rosinach;Janet Pinero;Alex Bravo Serrano;Ferran Sanz;Laura I Furlong;

10.1101/032961 — Bioinformatics — Posted on 2015-11-26

39 Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress

Zhe Cheng;Guoshou Teo;Sabrina Krueger;Tara Rock;Hiromi W.L. Koh;Hyungwon Choi;Christine Vogel;

10.1101/032797 — Systems Biology — Posted on 2015-11-26

40 Increased avidity for Dpp/BMP2 maintains the proliferation of eye progenitors in Drosophila

Marta Neto;Fernando Casares;

10.1101/032995 — Developmental Biology — Posted on 2015-11-26

41 FecalSeq: methylation-based enrichment for noninvasive population genomics from feces

Kenneth L Chiou;Christina M Bergey;

10.1101/032870 — Genomics — Posted on 2015-11-25

42 Early farmers from across Europe directly descended from Neolithic Aegeans

Zuzana Hofmanová;Susanne Kreutzer;Garrett Hellenthal;Christian Sell;Yoan Diekmann;David Díez del Molino;Lucy van Dorp;Saioa López;Athanasios Kousathanas;Vivian Link;Karola Kirsanow;Lara M Cassidy;Rui Martiniano;Melanie Strobel;Amelie Scheu;Kostas Kotsakis;Paul Halstead;Sevi Triantaphyllou;Nina Kyparissi-Apostolika;Dushanka-Christina Urem-Kotsou;Christina Ziota;Fotini Adaktylou;Shyamalika Gopalan;Dean M Bobo;Laura Winkelbach;Jens Blöcher;Martina Unterländer;Christoph Leuenberger;Çiler Çilingiroğlu;Barbara Horejs;Fokke Gerritsen;Stephen Shennan;Daniel G Bradley;Mathias Currat;Krishna Veeramah;Da

10.1101/032763 — Genomics — Posted on 2015-11-25

43 An evaluation of methods correcting for cell type heterogeneity in DNA methylation studies

Kevin McGregor;Sasha Bernatsky;Ines Colmegna;Marie Hudson;Tomi Pastinen;Aurélie Labbe;Celia Greenwood;

10.1101/032185 — Bioinformatics — Posted on 2015-11-25

44 Quantitative proteome-based guidelines for intrinsic disorder characterization

Michael Vincent;Mark Whidden;Santiago Schnell;

10.1101/032847 — Bioinformatics — Posted on 2015-11-25

45 Cell-type and state-dependent synchronization among rodent areas S1BF, V1, perirhinal cortex and hippocampus CA1

Martin Vinck;Jeroen J Bos;Laura Van Mourik-Donga;Krista Oplaat;Gerbrand A Klein;Jadin C Jackson;Luc J Gentet;Cyriel M.A. Pennartz;

10.1101/032904 — Neuroscience — Posted on 2015-11-25

46 Spread of the pandemic Zika virus lineage is associated with NS1 codon usage adaptation in humans

Caio Cesar de Melo Freire;Atila Iamarino;Daniel Ferreira de Lima Neto;Amadou Alpha Sall;Paolo Marinho de Andrade Zanotto;

10.1101/032839 — Microbiology — Posted on 2015-11-25

47 Characteristics of DNA methylation and gene expression in regulatory features on the Infinium 450k Beadchip

David Martino;Richard Saffery;

10.1101/032862 — Genetics — Posted on 2015-11-25

48 Quantifying polygenic effects in genome-wide association studies using generalized estimating equations

Julian Hecker;Dmitry Prokopenko;Christoph Lange;Heide Löhlein Fier;

10.1101/032854 — Bioinformatics — Posted on 2015-11-25

49 speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution

Alexander Zizka;Alexandre Antonelli;

10.1101/032755 — Evolutionary Biology — Posted on 2015-11-24

50 Rapid evolution of the inter-sexual genetic correlation for fitness in Drosophila melanogaster

Julie M Collet;Sara Fuentes;Jack Hesketh;Mark S Hill;Paolo Innocenti;Edward H Morrow;Kevin Fowler;Max Reuter;

10.1101/032664 — Evolutionary Biology — Posted on 2015-11-24

Radoslaw Cichy;Dimitrios Pantazis;Aude Oliva;

10.1101/032656 — Neuroscience — Posted on 2015-11-24

52 Genetic Associations with Subjective Well-Being Also Implicate Depression and Neuroticism

Aysu Okbay;Bart M. L. Baselmans;Jan-Emmanuel De Neve;Patrick Turley;Michel G. Nivard;Mark A. Fontana;Fleur S. W. Meddens;Richard Karlsson Linnér;Cornelius A. Rietveld;Jaime Derringer;Jacob Gratten;James J. Lee;Jimmy Z. Liu;Ronald de Vlaming;Dalton C. Conley;George Davey Smith;Albert Hofman;Magnus Johannesson;David I. Laibson;Sarah E. Medland;Michelle N. Meyer;Joseph K. Pickrell;Tonu Esko;Robert F. Krueger;Jonathan P. Beauchamp;Philipp D. Koellinger;Daniel J. Benjamin;Meike Bartels;David Cesarini;Social Science Genetic Association Consortium;

10.1101/032789 — Genetics — Posted on 2015-11-24

53 Fast and accurate construction of confidence intervals for heritability

Regev Schweiger;Shachar Kaufman;Reijo Laaksonen;Marcus E Kleber;Winfried März;Eleazar Eskin;Saharon Rosset;Eran Halperin;

10.1101/031492 — Genetics — Posted on 2015-11-24

54 The Implications of Small Stem Cell Niche Sizes and the Distribution of Fitness Effects of New Mutations in Aging and Tumorigenesis

Vincent L. Cannataro;Scott A. McKinley;Colette M. St. Mary;

10.1101/032813 — Evolutionary Biology — Posted on 2015-11-24

55 Analysis of the optimality of the Standard Genetic Code.

Balaji Kumar;Supreet Saini;

10.1101/032748 — Evolutionary Biology — Posted on 2015-11-24

56 A comparison of one-rate and two-rate inference frameworks for site-specific dN/dS estimation

Stephanie Spielman;Suyang Wan;Claus O Wilke;

10.1101/032805 — Evolutionary Biology — Posted on 2015-11-24

57 Expression weighted cell type enrichments reveal genetic and cellular nature of major brain disorders

Nathan Gerald Skene;Seth Grant;

10.1101/032680 — Neuroscience — Posted on 2015-11-23

58 Dynamics of scene representations in the human brain revealed by magnetoencephalography and deep neural networks

Radoslaw Martin Cichy;Aditya Khosla;Dimitrios Pantazis;Aude Oliva;

10.1101/032623 — Neuroscience — Posted on 2015-11-23

59 Virility does not Imply Immensity: Testis size, Accessory Gland Size and Ejaculate depletion pattern do not Evolve in Response to Experimental Manipulation of Sex Ratio in Drosophila melanogaster

Chechi;Zeeshan Ali Syed;N G Prasad;

10.1101/032649 — Evolutionary Biology — Posted on 2015-11-23

60 G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch

Osman Doluca;Oktay I Kaplan;Burak Berber;Nezih Hekim;

10.1101/032615 — Bioinformatics — Posted on 2015-11-24

61 G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch

Osman Doluca;Oktay I Kaplan;Burak Berber;Nezih Hekim;

10.1101/032615 — Bioinformatics — Posted on 2015-11-23

62 Activation of G proteins by guanine nucleotide exchange factors relies on GTPase activity

Rob J Stanley;Geraint MH Thomas;

10.1101/032607 — Biochemistry — Posted on 2015-11-23

63 YGR042W/MTE1 Functions in Double-Strand Break Repair with MPH1

Askar Yimit;TaeHyung Kim;Ranjith Anand;Sarah Meister;Jiongwen Ou;James Haber;Zhaolei Zhang;Grant W Brown;

10.1101/032581 — Genetics — Posted on 2015-11-30

64 YGR042W/MTE1 Functions in Double-Strand Break Repair with MPH1

Askar Yimit;TaeHyung Kim;Ranjith Anand;Sarah Meister;Jiongwen Ou;James Haber;Zhaolei Zhang;Grant W Brown;

10.1101/032581 — Genetics — Posted on 2015-11-23

65 The Ionotropic Receptors IR21a and IR25a mediate cool sensing in Drosophila

Lina Ni;Mason Klein;Kathryn Svec;Gonzalo Budelli;Elaine C Chang;Richard Benton;Aravi DT Samuel;Paul A Garrity;

10.1101/032540 — Neuroscience — Posted on 2015-11-22

66 BioJS-HGV Viewer: Genetic Variation Visualizer

Saket Choudhary;Leyla Garcia;Andrew Nightingale;Maria-Jesus Martin;

10.1101/032573 — Bioinformatics — Posted on 2015-11-23

67 BioJS-HGV Viewer: Genetic Variation Visualizer

Saket Choudhary;Leyla Garcia;Andrew Nightingale;Maria-Jesus Martin;

10.1101/032573 — Bioinformatics — Posted on 2015-11-22

68 Elevated gene expression of most microglial markers, and reduced expression of most pyramidal neuron and interneuron markers, in postmortem autism cortex

Rebeca Borges-Monroy;Chris Ponting;T. Grant Belgard;

10.1101/032557 — Neuroscience — Posted on 2015-11-21

69 Frequency-dependent representation of reinforcement-related information in the human medial and lateral prefrontal cortex

Elliot Smith;Garrett Banks;Charles Mikell;Shaun Patel;Sydney Cash;Emad Eskandar;Sameer Sheth;

10.1101/029058 — Neuroscience — Posted on 2015-11-21

70 Estimating Effect Sizes and Expected Replication Probabilities from GWAS Summary Statistics

Dominic Holland;Yunpeng Wang;Wesley K Thompson;Andrew Schork;Chi-Hua Chen;Min-Tzu Lo;Aree Witoelar;Thomas Werge;Michael O'Donovan;Ole A Andreassen;Anders Dale;

10.1101/032474 — Genetics — Posted on 2015-11-21

71 An in silico comparison of reduced-representation and sequence-capture protocols for phylogenomics

Rupert A. Collins;Tomas Hrbek;

10.1101/032565 — Evolutionary Biology — Posted on 2015-11-21

72 Polarized Cortical Tension drives Zebrafish Epiboly Movements

Amayra Hernandez-Vega;Maria Marsal;Philippe-Alexandre Pouille;Sebastien Tosi;Julien Colombelli;Tomas Luque;Daniel Navajas;Ignacio Pagonabarraga;Enrique Martin-Blanco;

10.1101/032284 — Developmental Biology — Posted on 2015-11-21

73 ASAP: A Machine-Learning Framework for Local Protein Properties

Dan Ofer;Nadav Brandes;Michal Linial;

10.1101/032532 — Bioinformatics — Posted on 2015-11-21

74 Timing of locomotor recovery modulated by the white gene in Drosophila

Chengfeng Xiao;R Meldrum Robertson;

10.1101/032490 — Neuroscience — Posted on 2015-11-21

75 Population size and the length of the chromosome blocks identical by descent over generations

Mathieu Tiret;Frederic Hospital;

10.1101/032482 — Evolutionary Biology — Posted on 2015-11-21

76 The relaxin receptor Lgr3 mediates growth coordination and developmental delay during Drosophila melanogaster imaginal disc regeneration

Jacob S. Jaszczak;Jacob B. Wolpe;Rajan Bhandari;Rebecca G. Jaszczak;Adrian Halme;

10.1101/032508 — Developmental Biology — Posted on 2015-11-21

77 Phenotypes in insect biodiversity research

Andrew R Deans;Istvan Miko;

10.1101/032425 — Zoology — Posted on 2015-11-20

78 Consistent estimation of complete neuronal connectivity in large neuronal populations using sparse "shotgun" neuronal activity sampling

Yuriy Mishchenko;

10.1101/032409 — Neuroscience — Posted on 2015-11-20

79 Mind the drift - improving sensitivity to fMRI pattern information by accounting for temporal pattern drift

Arjen Alink;Alexander Walther;Alexandra Krugliak;Jasper J.F. van den Bosch;Nikolaus Kriegeskorte;

10.1101/032391 — Neuroscience — Posted on 2015-11-20

80 Shared genomic variants: identification of transmission routes using pathogen deep sequence data

Colin J Worby;Marc Lipsitch;William P Hanage;

10.1101/032458 — Genomics — Posted on 2015-11-20

81 High-density SNP array and genome sequencing reveal signatures of selection in a divergent selection rat model for aerobic running capacity

Yu-yu Ren;Lauren G Koch;Steven L Britton;Nathan R Qi;Mary K Treutelaar;Charles F Burant;Jun Z Li;

10.1101/032441 — Genetics — Posted on 2015-11-20

82 Genome-wide analysis of over 106,000 individuals identifies 9 neuroticism-associated loci

Daniel J Smith;Valentina Escott-Price;Gail Davies;Mark ES Bailey;Lucia Colodro Conde;Joey Ward;Alexey Vedernikov;Riccardo Marioni;Breda Cullen;Donald Lyall;Saskia P Hagenaars;David CM Liewald;Michelle Luciano;Catharine R Gale;Stuart J Ritchie;Caroline Hayward;Barbara Nicholl;Brendan Bulik-Sullivan;Mark Adams;Baptiste Couvy-Duchesne;Nicholas Graham;Daniel Mackay;Jonathan Evans;Blair H Smith;David J Porteous;Sarah Medland;Nick Martin;Peter Holmans;Andrew M McIntosh;Jill P Pell;Ian J Deary;Michael O'Donovan;

10.1101/032417 — Genetics — Posted on 2015-11-25

83 Genome-wide analysis of over 106,000 individuals identifies 9 neuroticism-associated loci

10.1101/032417 — Genetics — Posted on 2015-11-20

84 BRANE Cut: Biologically-Related A priori Network Enhancement with Graph cuts for Gene Regulatory Network Inference

Aurélie Pirayre;Camille Couprie;Frédérique Bidard;Laurent Duval;Jean-Christophe Pesquet;

10.1101/032383 — Bioinformatics — Posted on 2015-11-20

85 Role of autoregulation and relative synthesis of operon partners in alternative sigma factor networks

Jatin Narula;Abhinav Tiwari;Oleg A. Igoshin;

10.1101/032359 — Systems Biology — Posted on 2015-11-20

86 Conjecture: Some auto-immune diseases are caused by the tissue, not a problem with the immune system

Harlan S Robins;

10.1101/032300 — Immunology — Posted on 2015-11-20

87 Data on the frequency of non-reproductive adults in a cross-cultural sample of small-scale human societies

Cody Ross;Paul Hooper;Monique Borgerhoff Mulder;

10.1101/032318 — Ecology — Posted on 2015-11-20

88 Genome-wide analysis of microRNA signature in lung adenocarcinoma with EGFR exon 19 deletion

Lixia Ju;Mingquan Han;Chao Zhao;Xuefei Li;

10.1101/032367 — Cancer Biology — Posted on 2015-11-20

89 In planta expression screens of candidate effector proteins from the wheat yellow rust fungus reveal processing bodies as a pathogen-targeted plant cell compartment

Benjamin Petre;Diane GO Saunders;Jan Sklenar;Cecile Lorrain;Ksenia V Krasileva;Joe Win;Sebastien Duplessis;Sophien Kamoun;

10.1101/032276 — Plant Biology — Posted on 2015-11-19

90 DISC1 regulates astrogenesis in the embryonic brain via modulation of RAS/MEK/ERK signaling through RASSF7

Shukun Wang;Qingli Liang;Huimin Qiao;Hong Li;Tianjin Shen;Fen Ji;Jianwei Jiao;

10.1101/032243 — Developmental Biology — Posted on 2015-11-19

91 From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

Sanaa Afroz Ahmed;Chien-Chi Lo;Po-E Li;Karen W Davenport;Patrick S.G. Chain;

10.1101/032250 — Bioinformatics — Posted on 2015-11-19

92 Temporal and spatial domain-specific transcriptomic analysis of a vital reproductive meristem in Arabidopsis thaliana

Gonzalo H Villarino;Miguel Flores-Vergara;Qiwen Hu;Bhupinder Sehra;Linda Robles;Javier Brumos;Anna Stepanova;Silvia Manrique;Lucia Colombo;Eva Sundberg;Steffen Heber;Robert G Franks;

10.1101/032128 — Plant Biology — Posted on 2015-11-18

93 Latitude delineates patterns of biogeography in terrestrial Streptomyces

Mallory J Choudoir;James R Doroghazi;Daniel H Buckley;

10.1101/032169 — Microbiology — Posted on 2015-11-18

94 Multiple Conformations of Gal3 Protein Drive the Galactose Induced Allosteric Activation of the GAL Genetic Switch of Saccharomyces cerevisiae

Rajesh Kumar Kar;Hungyo kharerin;Ranjith Padinhateeri;Jayadeva Bhat;

10.1101/032136 — Genetics — Posted on 2015-11-18

95 EcOH: In silico serotyping of E. coli from short read data

Danielle Ingle;Mary Valcanis;Alex Kuzevski;Marija Tauschek;Michael Inouye;Tim Stinear;Myron M Levine;Roy M Robins-Browne;Kathryn E. Holt;

10.1101/032151 — Microbiology — Posted on 2015-11-18

96 Centromere Detection of Human Metaphase Chromosome Images using a Candidate Based Method

Akila Subasinghe;Jagath Samarabandu;Yanxin Li;Ruth Wilkins;Farrah Flegal;Joan H.M. Knoll;Peter K. Rogan;

10.1101/032110 — Genetics — Posted on 2015-11-18

97 Potential impact of sexual transmission of Ebola virus on the epidemic in West Africa

Jessica Lee Abbate;Carmen Lia Murall;Heinz Richner;Christian L. Althaus;

10.1101/031880 — Ecology — Posted on 2015-11-25

98 Potential impact of sexual transmission of Ebola virus on the epidemic in West Africa

Jessica Lee Abbate;Carmen Lia Murall;Heinz Richner;Christian L. Althaus;

10.1101/031880 — Ecology — Posted on 2015-11-18

99 Neptune: A Tool for Rapid Microbial Genomic Signature Discovery

Eric Marinier;Rahat Zaheer;Chrystal Berry;Kelly A Weedmark;Michael Domaratzki;Philip Mabon;Natalie C Knox;Aleisha R Reimer;Morag R Graham;The LiDS-NG Consortium;Gary Van Domselaar;

10.1101/032227 — Bioinformatics — Posted on 2015-11-18

100 XMRF: An R package to Fit Markov Networks to High-Throughput Genetics Data

Ying-Wooi Wan;Genevera I. Allen;Yulia Baker;Eunho Yang;Pradeep Ravikumar;Zhandong Liu;

10.1101/032219 — Bioinformatics — Posted on 2015-11-18

101 Wikidata as a semantic framework for the Gene Wiki initiative

Sebastian Burgstaller-Muehlbacher;Andra Waagmeester;Elvira Mitraka;Julia Turner;Tim E. Putman;Justin Leong;Paul Pavlidis;Lynn Schriml;Benjamin M. Good;Andrew I. Su;

10.1101/032144 — Bioinformatics — Posted on 2015-11-19

102 Wikidata as a semantic framework for the Gene Wiki initiative

Sebastian Burgstaller-Muehlbacher;Andra Waagmeester;Elvira Mitraka;Julia Turner;Tim E. Putman;Justin Leong;Paul Pavlidis;Lynn Schriml;Benjamin M. Good;Andrew I. Su;

10.1101/032144 — Bioinformatics — Posted on 2015-11-18

103 Actin activates Pseudomonas aeruginosa ExoY nucleotidyl cyclase toxin and ExoY-like effector domains from MARTX toxins

Dorothee Raoux-Barbot;Cosmin Saveanu;Abdelkader Namane;Vasily Ogryzko;Lina Worpenberg;Souad Fellous;Elodie Assayag;Daniel Ladant;Louis Renault;Undine Mechold;

10.1101/032201 — Biochemistry — Posted on 2015-11-18

104 Integrating experimental data to calibrate quantitative cancer models

Heiko Enderling;

10.1101/032102 — Cancer Biology — Posted on 2015-11-17

105 MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies

Mohammed-Amin Madoui;Carole Dossat;Leo d'Agata;Edwin van der Vossen;Jan van Oeveren;Jean-Marc Aury;

10.1101/032045 — Genomics — Posted on 2015-11-17

106 Spatial selection and local adaptation jointly shape life-history evolution during range expansion

Katrien Van Petegem;Jeroen Boeye;Robby Stoks;Dries Bonte;

10.1101/031922 — Evolutionary Biology — Posted on 2015-11-17

107 Vectorization techniques for efficient agent-based model simulations of tumor growth

Jan Poleszczuk;Heiko Enderling;

10.1101/032086 — Systems Biology — Posted on 2015-11-17

108 Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

Logan Kistler;Oliver Smith;Roselyn Ware;Garry Momber;Richard Bates;Paul Garwood;Simon Fitch;Mark Pallen;Vincent Gaffney;Robin Allaby;

10.1101/032060 — Genomics — Posted on 2015-11-18

109 Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

Logan Kistler;Oliver Smith;Roselyn Ware;Garry Momber;Richard Bates;Paul Garwood;Simon Fitch;Mark Pallen;Vincent Gaffney;Robin Allaby;

10.1101/032060 — Genomics — Posted on 2015-11-17

110 Diversity of fate outcomes in cell pairs under lateral inhibition

Nara Guisoni;Rosa Martinez Corral;Jordi Garcia-Ojalvo;Joaquin de Navascues;

10.1101/032078 — Developmental Biology — Posted on 2015-11-17

111 The State of Software in Evolutionary Biology

Diego Darriba;Tomas Flouri;Alexandros Stamatakis;

10.1101/031930 — Evolutionary Biology — Posted on 2015-11-16

112 Kaiju: Fast and sensitive taxonomic classification for metagenomics

Peter Menzel;Kim Lee Ng;Anders Krogh;

10.1101/031229 — Bioinformatics — Posted on 2015-11-16

113 Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls

Yi-Juan Hu;Peizhou Liao;Henry Richard Johnston;Andrew Allen;Glen Satten;

10.1101/032037 — Bioinformatics — Posted on 2015-11-16

114 A statistical approach to genome size evolution: Observations and explanations

Dirson Jian Li;

10.1101/031963 — Evolutionary Biology — Posted on 2015-11-16

115 The Genetic Equidistance Phenomenon at the Proteomic Level

Denghui Luo;Shi Huang;

10.1101/031914 — Evolutionary Biology — Posted on 2015-11-16

116 Learning structure in gene expression data using deep architectures, with an application to gene clustering

Aman Gupta;Haohan Wang;Madhavi Ganapathiraju;

10.1101/031906 — Bioinformatics — Posted on 2015-11-16

117 Effective QTL Discovery Incorporating Genomic Annotations

Xiaoquan Wen;

10.1101/032003 — Genetics — Posted on 2015-11-16

118 Towards a study of gene regulatory constraints to morphological evolution of the Drosophila ocellar region

Daniel Aguilar-Hidalgo;David Becerra-Alonso;Diana Garcia-Morales;Fernando Casares;

10.1101/031948 — Developmental Biology — Posted on 2015-11-16

119 Mass graphs and their applications in top-down proteomics

Qiang Kou;Si Wu;Nikola Tolić;Ljiljana Pasa-Tolić;Xiaowen Liu;

10.1101/031997 — Bioinformatics — Posted on 2015-11-16

120 Wikidata: A platform for data integration and dissemination for the life sciences and beyond

Elvira Mitraka;Andra Waagmeester;Sebastian Burgstaller-Muehlbacher;Lynn M Schriml;Andrew I Su;Benjamin M Good;

10.1101/031971 — Bioinformatics — Posted on 2015-11-16

121 Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in the Chlamydomonas reinhardtii plastid genome

Rob W Ness;Susanne A Kraemer;Nick Colegrave;Peter D Keightley;

10.1101/031898 — Genomics — Posted on 2015-11-16

122 Marker-based estimates reveal significant non-additive effects in clonally propagated cassava (Manihot esculenta): implications for the prediction of total genetic value and the selection of varieties

Marnin Wolfe;Peter Kulakow;Ismail Y Rabbi;Jean-Luc Jannink;

10.1101/031864 — Genomics — Posted on 2015-11-16

123 Strong Selection is Necessary for Evolution of Blindness in Cave Dwellers

Reed A. Cartwright;Rachel S Schwartz;Alexandra L. Merry;Megan M. Howell;

10.1101/031872 — Evolutionary Biology — Posted on 2015-11-16

124 A protein aggregation-dependent scaling-free synaptic facilitation rule for neural network simulations

Michele Sanguanini;Antonino Cattaneo;

10.1101/031856 — Neuroscience — Posted on 2015-11-15

125 Ant and mite diversity drives toxin variation in the Little Devil poison frog

Jenna R McGugan;Gary D Byrd;Alexandre B Roland;Stephanie N Caty;Nisha Kabir;Elicio E Tapia;Sunia A Trauger;Luis A Coloma;Lauren O'Connell;

10.1101/031849 — — Posted on 2015-11-15

126 Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations

Caitlin McHugh;Timothy A Thornton;Lisa Brown;

10.1101/031831 — Genetics — Posted on 2015-11-14

127 A new model of human dispersal

Trevor G Underwood;

10.1101/031674 — Genetics — Posted on 2015-11-14

128 Towards extracting supporting information about predicted protein-protein interactions

Adam Roth;Sandeep Subramanian;Madhavi Ganapathiraju;

10.1101/031591 — Bioinformatics — Posted on 2015-11-14

129 Biomechanics of shear-sensitive adhesion in climbing animals: peeling, pre-tension and sliding-induced changes in interface strength

David Labonte;Walter Federle;

10.1101/031773 — Zoology — Posted on 2015-11-14

130 Hyper-variability in Circulating Insulin Levels and Physiological Outcomes to High Fat Feeding in Male Ins1-/-:Ins2+/- Mice in a Specific Pathogen-free Facility

Nicole M Templeman;Arya Mehran;James Johnson;

10.1101/031799 — Physiology — Posted on 2015-11-14

131 Cortical state and natural movie responses in cat visual cortex

Martin A Spacek;Nicholas V Swindale;

10.1101/031765 — Neuroscience — Posted on 2015-11-14

132 An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria

Stephen Nayfach;Beltran Rodriguez-Mueller;Nandita Garud;Katherine S Pollard;

10.1101/031757 — Genomics — Posted on 2015-11-14

133 Natural selection reduces linked neutral divergence between distantly related species

Tanya Phung;Christian Huber;Kirk Lohmueller;

10.1101/031740 — Genomics — Posted on 2015-11-14

134 DataJoint: managing big scientific data using MATLAB or Python

Dimitri Yatsenko;Jacob Reimer;Alexander S Ecker;Edgar Y Walker;Fabian Sinz;Philipp Berens;Andreas Hoenselaar;Ronald James Cotton;Athanassios S. Siapas;Andreas S. Tolias;

10.1101/031658 — Bioinformatics — Posted on 2015-11-14

135 Shared generative rules of locomotor behavior in arthropods and vertebrates

Alex Gomez-Marin;Efrat Oron;Anna Gakamsky;Dan Valente;Yoav Benjamini;Ilan Golani;

10.1101/031716 — Animal Behavior and Cognition — Posted on 2015-11-14

136 Hyper-variability in Circulating Insulin and Physiological Outcomes in Male High Fat-fed Ins1-/-:Ins2+/- Mice in a Conventional Facility

Arya Mehran;Nicole M Templeman;Xiaoke Hu;James Johnson;

10.1101/031807 — Physiology — Posted on 2015-11-14

137 pong: fast analysis and visualization of latent clusters in population genetic data

Aaron A Behr;Katherine Z Liu;Gracie Liu-Fang;Priyanka Nakka;Sohini Ramachandran;

10.1101/031815 — Genomics — Posted on 2015-11-14

138 Health and population effects of rare gene knockouts in adult humans with related parents

Vagheesh Narasimhan;Karen Hunt;Dan Mason;Christopher L Baker;Konrad Karczewski;Michael Barnes;Anthony Barnett;Chris Bates;Srikanth Bellary;Nick Bockett;Kristina Giorda;Chris Griffiths;Harry Hemingway;Zhilong Jia;Ann Kelly;Hajrah Khawaja;Monkol Lek;Shaun McCarthy;Rosie McEachan;Kenneth Paigen;Costas Parisinos;Eamonn Sheridan;Laura Southgate;Louise Tee;Mark Thomas;Yali Xue;Michael Schnall-Levin;Petko M Petkov;Chris Tyler-Smith;Eamonn Maher;Richard Trembath;Daniel MacArthur;John Wright;Richard Durbin;David van Heel;

10.1101/031641 — Genomics — Posted on 2015-11-14

139 Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications

Wei Gu;Emily D Crawford;Brian D O'Donovan;Michael R Wilson;Eric D Chow;Hanna Retallack;Joseph L DeRisi;

10.1101/031708 — Genomics — Posted on 2015-11-20

140 Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications

Wei Gu;Emily D Crawford;Brian D O'Donovan;Michael R Wilson;Eric D Chow;Hanna Retallack;Joseph L DeRisi;

10.1101/031708 — Genomics — Posted on 2015-11-14

141 Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions

Steven H Wu;Rachel S Schwartz;David J Winter;Don Conrad;Reed A Cartwright;

10.1101/031724 — Genomics — Posted on 2015-11-14

142 A short remark on Ontogenetic model and its analytical solution

Ya Li;Ji Huan He;

10.1101/031732 — Genetics — Posted on 2015-11-14

143 Hybrid dysgenesis in Drosophila simulans associated with a rapid global invasion of the P-element

Tom Hill;Christian Schlotterer;Andrea J Betancourt;

10.1101/031781 — Evolutionary Biology — Posted on 2015-11-14

144 Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

Anil Raj;Sidney Wang;Heejung Shim;Arbel Harpak;Yang I Li;Brett Englemann;Matthew Stephens;Yoav Gilad;Jonathan K Pritchard;

10.1101/031617 — Genomics — Posted on 2015-11-25

145 Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

Anil Raj;Sidney Wang;Heejung Shim;Arbel Harpak;Yang I Li;Brett Englemann;Matthew Stephens;Yoav Gilad;Jonathan K Pritchard;

10.1101/031617 — Genomics — Posted on 2015-11-13

146 A spectral analysis approach to detect actively translated open reading frames in high-resolution ribosome profiling data

Lorenzo Calviello;Neelanjan Mukherjee;Emanuel Wyler;Henrik Zauber;Antje Hirsekorn;Matthias Selbach;Markus Landthaler;Benedikt Obermayer;Uwe Ohler;

10.1101/031625 — Genomics — Posted on 2015-11-13

147 Recent demography drives changes in linked selection across the maize genome

Timothy Mathes Beissinger;Li Wang;Kate Crosby;Arun Durvasula;Matthew B Hufford;Jeff Ross-Ibarra;

10.1101/031666 — Evolutionary Biology — Posted on 2015-11-13

148 Isolation-by-Drift: Quantifying the Respective Contributions of Genetic Drift and Gene Flow in Shaping Spatial Patterns of Genetic Differentiation

Jerome Prunier;Vincent Dubut;Lounes Chikhi;Simon Blanchet;

10.1101/031633 — Evolutionary Biology — Posted on 2015-11-13

149 MAGELLAN: a tool to explore small fitness landscapes

Sophie Brouillet;Harry Annoni;Luca Ferretti;Guillaume Achaz;

10.1101/031583 — Evolutionary Biology — Posted on 2015-11-13

150 Whole genome sequencing of 56 Mimulus individuals illustrates population structure and local selection

Joshua Robert Puzey;John H Willis;John K Kelly;

10.1101/031575 — Evolutionary Biology — Posted on 2015-11-13

151 Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin

Xiaoxia Ge;Marilyn R. Gunner;

10.1101/031609 — Biophysics — Posted on 2015-11-13

152 Rising out of the ashes: additive genetic variation for susceptibility to Hymenoscyphus fraxineus in Fraxinus excelsior

Facundo Muñoz;Benoit Marçais;Jean Dufour;Arnaud Dowkiw;

10.1101/031393 — Pathology — Posted on 2015-11-16

153 Rising out of the ashes: additive genetic variation for susceptibility to Hymenoscyphus fraxineus in Fraxinus excelsior

Facundo Muñoz;Benoit Marçais;Jean Dufour;Arnaud Dowkiw;

10.1101/031393 — Pathology — Posted on 2015-11-12

154 Environmental unpredictability and inbreeding depression select for mixed dispersal syndromes

Jorge Hidalgo;Rafael Rubio de Casas;Miguel A. Munoz;

10.1101/031351 — Evolutionary Biology — Posted on 2015-11-12

155 Species sorting along a subsidy gradient alters community stability

Mario E Muscarella;Stuart E Jones;Jay T Lennon;

10.1101/031476 — Ecology — Posted on 2015-11-16

156 Species sorting along a subsidy gradient alters community stability

Mario E Muscarella;Stuart E Jones;Jay T Lennon;

10.1101/031476 — Ecology — Posted on 2015-11-12

157 Maternal expression of the novel centrosome assembly factor Wdr8 is required for vertebrate embryonic mitosis and development

Daigo Inoue;Manuel Stemmer;Thomas Thumberger;Joachim Wittbrodt;Oliver J Gruss;

10.1101/031336 — Cell Biology — Posted on 2015-11-12

158 Scan-o-matic: high-resolution microbial phenomics at a massive scale

Martin Zackrisson;Johan Hallin;Lars-Göran Ottosson;Peter Dahl;Esteban Fernandez-Parada;Erik Ländström;Luciano Fernandez-Ricaud;Petra Kaferle;Andreas Skyman;Stig Omholt;Uros Petrovic;Jonas Warringer;Anders Blomberg;

10.1101/031443 — Microbiology — Posted on 2015-11-12

159 Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.

Tim Putman;Sebastian Burgstaller;Andra Waagmeester;Chunlei Wu;Andrew I Su;Benjamin Good;

10.1101/031286 — Genomics — Posted on 2015-11-12

160 Human knockouts in a cohort with a high rate of consanguinity

Danesh Saleheen;Pradeep Natarajan;Wei Zhao;Asif Rasheed;Sumeet Khetarpal;Hong-Hee Won;Konrad J Karczewski;Anne H ODonnell-Luria;Kaitlin E Samocha;Namrata Gupta;Mozzam Zaidi;Maria Samuel;Atif Imran;Shahid Abbas;Faisal Majeed;Madiha Ishaq;Saba Akhtar;Kevin Trindade;Megan Mucksavage;Nadeem Qamar;Khan S Zaman;Zia Yaqoob;Tahir Saghir;Syed NH Rizvi;Anis Memon;Nadeem H Mallick;Mohammad Ishaq;Syed Z Rasheed;Fazal ur Rehman Memon;Khalid Mahmood;Naveeduddin Ahmed;Ron Do;Daniel G MacArthur;Stacey Gabriel;Eric S Lander;Mark J Daly;Philippe Frossard;John Danesh;Daniel J Rader;Sekar Kathiresan;

10.1101/031518 — Genomics — Posted on 2015-11-12

161 Characterization of expression quantitative trait loci in extensively phenotyped pedigrees ascertained for bipolar disorder

Christine Peterson;Susan Service;Anna Jasinska;Fuying Gao;Ivette Zelaya;Terri Teshiba;Carrie Bearden;Victor Reus;Gabriel Macaya;Carlos López-Jaramillo;Marina Bogomolov;Yoav Benjamini;Eleazar Eskin;Giovanni Coppola;Nelson Freimer;Chiara Sabatti;

10.1101/031427 — Genomics — Posted on 2015-11-12

162 Surprisingly weak coordination between leaf structure and function among closely-related tomato species

Christopher D Muir;Miquel Ángel Conesa;Emilio Roldán;Arántzazu Molins;Jeroni Galmés;

10.1101/031328 — Evolutionary Biology — Posted on 2015-11-12

163 Are all global alignment algorithms and implementations correct?

Tomáš Flouri;Kassian Kobert;Torbjørn Rognes;Alexandros Stamatakis;

10.1101/031500 — Bioinformatics — Posted on 2015-11-12

164 Auxin signaling is a common factor underlying natural variation in tomato shade avoidance

Susan M Bush;Leonela Carriedo;Fulop Daniel;Yasunori Ichihashi;Mike F Covington;Ravi Kumar;Aashish Ranjan;Daniel H Chitwood;Lauren Headland;Daniele L Filiault;Jose M Jimenez-Gomez;Neelima R Sinha;Julin N Maloof;

10.1101/031088 — Plant Biology — Posted on 2015-11-23

165 Auxin signaling is a common factor underlying natural variation in tomato shade avoidance

10.1101/031088 — Plant Biology — Posted on 2015-11-12

166 An association between sexes of successive siblings in the data from Demographic and Health Survey program

Mikhail Monakhov;

10.1101/031344 — Physiology — Posted on 2015-11-24

167 An association between sexes of successive siblings in the data from Demographic and Health Survey program

Mikhail Monakhov;

10.1101/031344 — Physiology — Posted on 2015-11-16

168 An association between sexes of successive siblings in the data from Demographic and Health Survey program

Mikhail Monakhov;

10.1101/031344 — Physiology — Posted on 2015-11-12

169 An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

Daniel Portik;Lydia Smith;Ke Bi;

10.1101/031468 — Genomics — Posted on 2015-11-12

170 Overview: Modeling Heterogeneous Tumor Tissue as a Multiphase Material

Hermann B Frieboes;

10.1101/031534 — Biophysics — Posted on 2015-11-12

171 Rapid Genotype Refinement for Whole-Genome Sequencing Data using Multi-Variate Normal Distributions

Rudy Arthur;Jared O'Connell;Ole Schulz-Trieglaff;Anthony J Cox;

10.1101/031484 — Bioinformatics — Posted on 2015-11-12

172 Connecting Boolean Integrase Logic gates to a novel alkane control signal via engineered level matching.

Thomas Folliard;Jerome Bonnet;John Ward;Frank Baganz;Christopher Grant;Drew Endy;

10.1101/031542 — Synthetic Biology — Posted on 2015-11-12

173 A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer

Eliseos J Mucaki;Natasha G Caminsky;Ami M Perri;Ruipeng Lu;Alain Laederach;Matthew Halvorsen;Joan H.M. Knoll;Peter K Rogan;

10.1101/031419 — Genetics — Posted on 2015-11-11

174 Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

Jenny Chen;Alexander A. Shishkin;Xiaopeng Zhu;Sabah Kadri;Itay Maza;Jacob H Hanna;Aviv Regev;Manuel Garber;

10.1101/031385 — Evolutionary Biology — Posted on 2015-11-11

175 Incomplete protection against dengue virus type 2 re-infection in Peru

Brett M. Forshey;Robert C. Reiner;Sandra Olkowski;Amy C. Morrison;Angelica Espinoza;Kanya C. Long;Stalin Vilcarromero;Wilma Casanova;Helen J. Wearing;Eric S. Halsey;Tadeusz J. Kochel;Thomas W. Scott;Steven T. Stoddard;

10.1101/023747 — Immunology — Posted on 2015-11-11

176 Genome-wide association and prediction reveals the genetic architecture of cassava mosaic disease resistance and prospects for rapid genetic improvement

Marnin Wolfe;Ismail Y Rabbi;Chiedozie Egesi;Martha Hamblin;Robert Kawuki;Peter Kulakow;Roberto Lozano;Dunia Pino Del Carpio;Punna Ramu;Jean-Luc Jannink;

10.1101/031179 — Genomics — Posted on 2015-11-11

177 Micro-Pharmacodynamics: Bridging In Vitro and In Vivo Experimental Scales in Testing Drug Efficacy and Resistance

Katarzyna A Rejniak;

10.1101/031294 — Systems Biology — Posted on 2015-11-11

178 Progressive lengthening of 3′ untranslated regions of mRNAs by alternative cleavage and polyadenylation in cellular senescence of mouse embryonic fibroblasts

Miao Han;Guo liang Lv;Hong bo Nie;Ting Shen;Yi chi Niu;Xue ping Li;Meng Chen;Xia Zheng;Wei Li;Chen Ding;Gang Wei;Jun Gu;Xiao Li Tian;Yu fang Zheng;Xin hua Liu;Jin feng Hu;Wei Tao;Ting Ni;

10.1101/031302 — Genomics — Posted on 2015-11-11

179 Extending the Stress-Gradient hypothesis: greater adaptation between teosinte and soil biota at higher stress sites

Anna M O'Brien;Ruairidh J.H. Sawers;Jeffrey Ross-Ibarra;Sharon Y Strauss;

10.1101/031195 — Ecology — Posted on 2015-11-11

180 Modeling Small Non-canonical RNA Motifs with the Rosetta FARFAR Server

Joseph David Yesselman;Rhiju Das;

10.1101/031278 — Biophysics — Posted on 2015-11-11

181 Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome

Bin Zhang;Peter Wolynes;

10.1101/031260 — Biophysics — Posted on 2015-11-11

182 Validation of Illumina’s Isaac variant calling workflow

Liudmila Sergeevna Mainzer;Brad A. Chapman;Oliver Hofmann;Gloria Rendon;Zachary D. Stephens;Victor Jongeneel;

10.1101/031021 — Bioinformatics — Posted on 2015-11-26

183 Validation of Illumina’s Isaac variant calling workflow

Liudmila Sergeevna Mainzer;Brad A. Chapman;Oliver Hofmann;Gloria Rendon;Zachary D. Stephens;Victor Jongeneel;

10.1101/031021 — Bioinformatics — Posted on 2015-11-13

184 Isaac, the Illumina variant calling workflow

Liudmila Sergeevna Mainzer;Brad A. Chapman;Oliver Hofmann;Gloria Rendon;Zachary D. Stephens;Victor Jongeneel;

10.1101/031021 — Bioinformatics — Posted on 2015-11-11

185 Reconstitution of CO2 regulation of SLAC1 anion channel and function of CO2-permeable PIP2;1 aquaporin as carbonic anhydrase 4 interactor

Cun Wang;Honghong Hu;Xue Qin;Brian Zeise;Danyun Xu;Wouter-Jan Rappel;Walter F Boron;Julian I Schroeder;

10.1101/030296 — Plant Biology — Posted on 2015-11-13

186 Reconstitution of CO2 regulation of SLAC1 anion channel and function of CO2-permeable PIP2;1 aquaporin as carbonic anhydrase 4 interactor

Cun Wang;Honghong Hu;Xue Qin;Brian Zeise;Danyun Xu;Wouter-Jan Rappel;Walter F Boron;Julian I Schroeder;

10.1101/030296 — Plant Biology — Posted on 2015-11-10

187 Shared genetic aetiology between cognitive functions and physical and mental health in UK Biobank (N = 112 151) and 24 GWAS consortia.

Saskia P Hagenaars;Sarah E Harris;Gail Davies;William David Hill;David CM Liewald;Stuart J Ritchie;Riccardo E Marioni;Chloe Fawns-Ritchie;Breda Cullen;Rainer Malik;METASTROKE consortium;International Consortium for Blood Pressure GWAS;SpiroMeta consortium;CHARGE consortium Pulmonary Group;CHARGE consortium Aging and Longevity Group;Bradford B Worrall;Cathie LM Sudlow;Joanna M Wardlaw;John Gallacher;Jill Pell;Andrew M McIntosh;Daniel J Smith;Catharine R Gale;Ian J Deary;

10.1101/031120 — Genetics — Posted on 2015-11-10

188 MicrobiomeGWAS: a tool for identifying host genetic variants associated with microbiome composition

Xing Hua;Lei Song;Guoqin Yu;James J. Goedert;Christian C. Abnet;Maria T. Landi;Jianxin Shi;

10.1101/031187 — Bioinformatics — Posted on 2015-11-10

189 CRISPResso: sequencing analysis toolbox for CRISPR genome editing

Luca Pinello;Matthew C Canver;Megan D Hoban;Stuart H Orkin;Donald B Kohn;Daniel E Bauer;Guo-Cheng Yuan;

10.1101/031203 — Bioinformatics — Posted on 2015-11-10

190 Faster processing of moving compared to flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion

Manivannan Subramaniyan;Alexander S Ecker;Saumil S. Patel;James R. Cotton;Matthias Bethge;Philipp Berens;Andreas S. Tolias;

10.1101/031146 — Neuroscience — Posted on 2015-11-10

191 Pleiotropy between neuroticism and physical and mental health: findings from 108 038 men and women in UK Biobank

Catharine Gale;Saskia P Hagenaars;Gail Davies;W David Hill;David CM Liewald;Breda Cullen;International Consortium for Blood Pressure GWAS;CHARGE consortium Aging and Longevity Group;Jill Pell;Andrew M McIntosh;Daniel J Smith;Ian J Deary;Sarah Harris;

10.1101/031138 — Genetics — Posted on 2015-11-10

192 Collinearity Analysis of Allotetraploid Gossypium Tomentosum and Gossypium Darwinii

Fang Liu;Zhong-li Zhou;Chun-ying Wang;Yu-hong Wang;Xiao-yan Cai;Xing-xing Wang;Kun-bo Wang;Zheng-sheng Zhang;

10.1101/031104 — Evolutionary Biology — Posted on 2015-11-10

193 Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae (Carassius auratus red var. × Cyprinus carpio)

Li Ren;Wuhui Li;Chenchen Tang;Jun Xiao;Xiaojun Tan;Min Tao;Chun Zhang;Shaojun Liu;

10.1101/031096 — Evolutionary Biology — Posted on 2015-11-10

194 Dead or gone? Bayesian inference on mortality for the dispersing sex

Julia A Barthold;Craig Packer;Andrew J Loveridge;David W Macdonald;Fernando Colchero;

10.1101/031161 — — Posted on 2015-11-10

195 Physics-based multiscale mass transport model in drug delivery and tumor microenvironment

Arturas Ziemys;Milos Kojic;Mauro Ferrari;

10.1101/031252 — Cancer Biology — Posted on 2015-11-10

196 Modeling Transitions between Responsive and Resistant States in Breast Cancer with Application to Therapy Optimization

Chun Chen;John J. Tyson;William Baumann;

10.1101/031245 — Cancer Biology — Posted on 2015-11-10

197 Agent based models to investigate cooperation between cancer cells

Joao Xavier;William Chang;

10.1101/031070 — Cancer Biology — Posted on 2015-11-09

198 Evolving cohesion metrics of a research network on rare diseases: a longitudinal study over 14 years

Carlos Benito Amat;Francois Perruchas;

10.1101/030809 — Scientific Communication and Education — Posted on 2015-11-09

199 On the importance of being structured: instantaneous coalescence rates and a re-evaluation of human evolution

Olivier Mazet;Willy Rodríguez;Simona Grusea;Simon Boitard;Lounès Chikhi;

10.1101/031062 — Evolutionary Biology — Posted on 2015-11-09

200 Numerical simulation of population development using the function of the age distribution of birthrate

Alexandr N Tetearing;

10.1101/031047 — Bioinformatics — Posted on 2015-11-09

201 Identification of protein secretion systems in bacterial genomes

Sophie S Abby;Jean Cury;Julien Guglielmini;Bertrand Néron;Marie Touchon;Eduardo PC Rocha;

10.1101/031039 — Microbiology — Posted on 2015-11-09

202 Identification and analysis of integrons and cassette arrays in bacterial genomes

Jean Cury;Thomas Jové;Marie Touchon;Bertrand Néron;Eduardo P. C. Rocha;

10.1101/030866 — Bioinformatics — Posted on 2015-11-09

203 A computational model of inhibition of HIV-1 by interferon-alpha

Edward P Browne;Benjamin Letham;Cynthia Rudin;

10.1101/031005 — Microbiology — Posted on 2015-11-09

204 A multi-trait meta-analysis with imputed sequence variants reveals twelve QTL for mammary gland morphology in Fleckvieh cattle

Hubert Pausch;Reiner Emmerling;Hermann Schwarzenbacher;Ruedi Fries;

10.1101/030981 — Genetics — Posted on 2015-11-09

205 Exploring phylogenomic relationships within Myriapoda: should high matrix occupancy be the goal?

Rosa Fernandez;Gregory D Edgecombe;Gonzalo Giribet;

10.1101/030973 — Evolutionary Biology — Posted on 2015-11-09

206 Targeted mutations on 3D hub loci alter spatial interaction environment

Bo Ding;Lina Zheng;David Medovoy;Wei Wang;

10.1101/030999 — Biophysics — Posted on 2015-11-09

207 Haplotag: software for haplotype-based genotyping-by-sequencing analysis

Nicholas A Tinker;Wubishet A Bekele;Jiro Hattori;

10.1101/031013 — Bioinformatics — Posted on 2015-11-09

208 Climate and developmental plasticity: interannual variability in grapevine leaf morphology

Daniel H Chitwood;Susan M Rundell;Darren Y Li;Quaneisha L Woodford;Tommy T Yu;Jose R Lopez;Danny Greenblatt;Julie Kang;Jason P Londo;

10.1101/030957 — Plant Biology — Posted on 2015-11-10

209 Climate and developmental plasticity: interannual variability in grapevine leaf morphology

Daniel H Chitwood;Susan M Rundell;Darren Y Li;Quaneisha L Woodford;Tommy T Yu;Jose R Lopez;Danny Greenblatt;Julie Kang;Jason P Londo;

10.1101/030957 — Plant Biology — Posted on 2015-11-08

210 A pan-cancer analysis of prognostic genes

Jordan Anaya;Brian J Reon;Wei-Min Chen;Stefan Bekiranov;Anindya Dutta;

10.1101/030924 — Genomics — Posted on 2015-11-08

211 An Approximate Markov Model for the Wright-Fisher Diffusion

Anna Ferrer-Admetlla;Christoph Leuenberger;Jeffrey D Jensen;Daniel Wegmann;

10.1101/030940 — Genetics — Posted on 2015-11-08

212 Assisted reproduction causes intrauterus growth restriction by disrupting placental lipid metabolism

Yubao Wei;Shuqiang Chen;Xiuying Huang;Sin Man Lam;Guanghou Shui;Fangzhen Sun;

10.1101/030965 — Developmental Biology — Posted on 2015-11-08

213 Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions

Neda Vesselinova;Boian S. Alexandrov;Michael E. Wall;

10.1101/030908 — Systems Biology — Posted on 2015-11-07

214 Modularity and Morphometrics: Error Rates in Hypothesis Testing

Guilherme Garcia;Felipe Bandoni de Oliveira;Gabriel Marroig;

10.1101/030874 — Evolutionary Biology — Posted on 2015-11-07

215 Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

Mario Vallejo-Marin;Arielle Cooley;Michelle Qi;Madison Folmer;Michael McKain;Joshua Puzey;

10.1101/030932 — Evolutionary Biology — Posted on 2015-11-07

216 Evidence for the priming effect in a planktonic estuarine microbial community

Andrew Decker Steen;Lauren N. M. Quigley;Alison Buchan;

10.1101/030916 — Ecology — Posted on 2015-11-07

217 Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade cannabis flowers

Kevin McKernan;Jessica Spangler;Lei Zhang;Vasisht Tadigotla;Yvonne Helbert;Theodore Foss;Douglas Smith;

10.1101/030775 — Microbiology — Posted on 2015-11-06

218 Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

Nicole Stoesser;Anna Sheppard;Louise Pankhurst;Nicola de Maio;Catrin E Moore;Robert Sebra;Paul Turner;Luke W Anson;Andrew Kasarskis;Elizabeth M Batty;Veronica Kos;Daniel J Wilson;Rattanaphone Phetsouvanh;David Wyllie;Evgeni Sokurenko;Amee R Manges;Timothy J Johnson;Lance B Price;Timothy E. A. Peto;James R Johnson;Xavier Didelot;Ann Sarah Walker;Derrick W Crook;Modernising Medical Microbiology Informatics Group;

10.1101/030668 — Genomics — Posted on 2015-11-06

219 Convergent patterns of sex chromosome dosage compensation between lepidopteran species (WZ/ZZ) and eutherian mammals (XX/XY): insights from a moth neo-Z chromosome

Liuqi Gu;James Walters;Douglas Knipple;

10.1101/030767 — Genomics — Posted on 2015-11-06

220 Quantifying the unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects

James Zou;Gregory Valiant;Paul Valiant;Konrad Karczewski;Siu On Chan;Kaitlin Samocha;Monkol Lek;Exome Aggregation Consortium;Shamil Sunyaev;Mark Daly;Daniel MacArthur;

10.1101/030841 — Genetics — Posted on 2015-11-07

221 Quantifying the unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects

James Zou;Gregory Valiant;Paul Valiant;Konrad Karczewski;Siu On Chan;Kaitlin Samocha;Monkol Lek;Exome Aggregation Consortium;Shamil Sunyaev;Mark Daly;Daniel MacArthur;

10.1101/030841 — Genetics — Posted on 2015-11-06

222 Adaptation to an invasive host is collapsing a native ecotype

Meredith L Cenzer;

10.1101/030858 — Evolutionary Biology — Posted on 2015-11-06

223 Patterns of transcriptional response to 1,25-dihydroxyvitamin D3 and bacterial lipopolysaccharide in primary human monocytes

Silvia N Kariuki;John D Blischak;Shigeki Nakagome;David B Witonsky;Anna Di Rienzo;

10.1101/030759 — Genetics — Posted on 2015-11-06

224 Fitness costs of herbicide resistance across natural populations of the common morning glory, Ipomoea purpurea

Megan van Etten;Adam Kuester;Shu-Mei Chang;Regina Baucom;

10.1101/030833 — Evolutionary Biology — Posted on 2015-11-06

225 Dynamic stem cell states: naive to primed pluripotency in rodents and humans

Leehee Weinberger;Muneef Ayyash;Noa Novershtern;Jacob H. Hanna;

10.1101/030676 — Developmental Biology — Posted on 2015-11-06

226 Simulating serial-target antibacterial drug synergies using flux balance analysis

Andrew S Krueger;Christian Munck;Gautam Dantas;George M Church;James Galagan;Joseph Lehar;Morten OA Sommer;

10.1101/030791 — Systems Biology — Posted on 2015-11-06

227 What’s in my pot? Real-time species identification on the MinION™

Sissel Juul;Fernando Izquierdo;Adam Hurst;Xiaoguang Dai;Amber Wright;Eugene Kulesha;Roger Pettett;Daniel J Turner;

10.1101/030742 — Genomics — Posted on 2015-11-06

228 Using genotype data to distinguish pleiotropy from heterogeneity: deciphering coheritability in autoimmune and neuropsychiatric diseases

Buhm Han;Jennie G Pouget;Kamil Slowikowski;Eli Stahl;Cue Hyunkyu Lee;Dorothee Diogo;Xinli Hu;Yu Rang Park;Eunji Kim;Peter K Gregersen;Solbritt Rantapaa Dahqvist;Jane Worthington;Steve Eyre;Lars Klareskog;Tom Huizinga;Wei-Min Chen;Suna Onengut-Gumuscu;Stephen S Rich;Major Depressive Disorder Working Group of the PGC;Naomi Wray;Soumya Raychaudhuri;

10.1101/030783 — Genomics — Posted on 2015-11-06

229 chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts

Birte Kehr;Páll Melsted;

10.1101/030825 — Bioinformatics — Posted on 2015-11-06

230 Dynamical state of the network determines the efficacy of single neuron properties in shaping the network activity

Ajith Sahasranamam;Ioannis Vlachos;Ad Aertsen;Arvind Kumar;

10.1101/030700 — Neuroscience — Posted on 2015-11-05

231 The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data

Sandeep J Joseph;Ben Li;Robert A Petit;Zhaohui Qin;Lyndsey Darrow;Timothy D Read;

10.1101/030692 — Genomics — Posted on 2015-11-05

232 On characterizing membrane protein clusters with model-free spatial correlation approaches

Arun Shivanandan;Jayakrishnan Unnikrishnan;Aleksandra Radenovic;

10.1101/030718 — Biophysics — Posted on 2015-11-09

233 On characterizing membrane protein clusters with model-free spatial correlation approaches

Arun Shivanandan;Jayakrishnan Unnikrishnan;Aleksandra Radenovic;

10.1101/030718 — Biophysics — Posted on 2015-11-05

234 ADAGE analysis of publicly available gene expression data collections illuminates Pseudomonas aeruginosa-host interactions

Jie Tan;John H Hammond;Deborah A Hogan;Casey S Greene;

10.1101/030650 — Bioinformatics — Posted on 2015-11-05

235 Common and phylogenetically widespread coding for peptides by bacterial small RNAs

Robin C Friedman;Stefan Kalkhof;Olivia Doppelt-Azeroual;Stephan Mueller;Martina Chovancova;Martin von Bergen;Benno Schwikowski;

10.1101/030619 — Microbiology — Posted on 2015-11-04

236 Low-temperature-specific effects of PHYTOCHROME C on the circadian clock in Arabidopsis suggest that PHYC underlies natural variation in biological timing

Kieron D Edwards;Francois Guerineau;Paul F Devlin;Andrew J Millar;

10.1101/030577 — Genetics — Posted on 2015-11-05

237 Low-temperature-specific effects of PHYTOCHROME C on the circadian clock in Arabidopsis suggest that PHYC underlies natural variation in biological timing

Kieron D Edwards;Francois Guerineau;Paul F Devlin;Andrew J Millar;

10.1101/030577 — Genetics — Posted on 2015-11-04

238 Hydroxide Once or Twice? A combined Neutron Crystallographic and Quantum Chemical Study of the Hydride Shift in D-Xylose Isomerase

Matt Challacombe;Nicolas Bock;Paul Langan;Andrey Kovalevsky;

10.1101/030601 — — Posted on 2015-11-04

239 Sub-tomogram averaging in RELION

Tanmay A.M. Bharat;Sjors H.W. Scheres;

10.1101/030544 — Molecular Biology — Posted on 2015-11-04

240 Crop diversity enhances disease suppressive potential in soils

Ariane L Peralta;Yanmei Sun;Marshall D McDaniel;Jay T Lennon;

10.1101/030528 — Microbiology — Posted on 2015-11-07

241 Crop diversity enhances disease suppressive potential in soils

Ariane L Peralta;Yanmei Sun;Marshall D McDaniel;Jay T Lennon;

10.1101/030528 — Microbiology — Posted on 2015-11-04

242 Evaluating disease similarity using latent Dirichlet allocation

James M Frick;Rajarshi Guha;Tyler Peryea;Noel T Southall;

10.1101/030593 — Bioinformatics — Posted on 2015-11-04

243 Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers

Alison Dawn Scott;Noah Stenz;David Baum;

10.1101/030585 — Plant Biology — Posted on 2015-11-03

244 The zebrafish goosepimples/myosin Vb mutant exhibits cellular attributes of human microvillus inclusion disease

Jaydeep Sidhaye;Clyde Pinto;Shweta Dharap;Tressa Jacob;Shobha Bhargava;Mahendra Sonawane;

10.1101/030536 — Developmental Biology — Posted on 2015-11-03

245 Systematic Functional Annotation and Visualization of Biological Networks

Anastasia Baryshnikova;

10.1101/030551 — Systems Biology — Posted on 2015-11-03

246 4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments

Ramya Raviram;Pedro P. Rocha;Christian L. Müller;Emily R. Miraldi;Sana Badri;Yi Fu;Emily Swanzey;Charlotte Proudhon;Valentina Snetkova;Richard Bonneau;Jane Skok;

10.1101/030569 — Bioinformatics — Posted on 2015-11-03

247 Various localized epigenetic marks predict expression across 54 samples and reveal underlying chromatin state enrichments

Lalita Devadas;Angela Yen;Manolis Kellis;

10.1101/030478 — Genetics — Posted on 2015-11-03

248 GBStools: A Unified Approach for Reduced Representation Sequencing and Genotyping

Thomas F Cooke;Muh-Ching Yee;Marina Muzzio;Alexandra Sockell;Ryan Bell;Omar E Cornejo;Joanna L Kelley;Graciela Bailliet;Claudio M Bravi;Carlos D Bustamante;Eimear Kenny;

10.1101/030494 — Genomics — Posted on 2015-11-03

249 Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine

Padhraig Gormley;Verneri Anttila;Bendik S Winsvold;Priit Palta;Tonu Esko;Tune H Pers;Kai-How Farh;Ester Cuenca-Leon;Mikko Muona;Nicholas A Furlotte;Tobias Kurth;Andres Ingason;George McMahon;Lannie Ligthart;Gisela M Terwindt;Mikko Kallela;Tobias M Freilinger;Caroline Ran;Scott G Gordon;Anine H Stam;Stacy Steinberg;Guntram Borck;Markku Koiranen;Lydia Quaye;Hieab HH Adams;Terho Lehtimaki;Antti-Pekka Sarin;Juho Wedenoja;David A Hinds;Julie E Buring;Markus Schurks;Paul M Ridker;Maria Gudlaug Hrafnsdottir;Hreinn Stefansson;Susan M Ring;Jouke-Jan Hottenga;Brenda WJH Penninx;Markus Farkkila;Ville Art

10.1101/030288 — Genetics — Posted on 2015-11-03

250 Resources for the comprehensive discovery of functional RNA elements

Balaji Sundararaman;Lijun Zhan;Steven Blue;Rebecca Stanton;Keri Elkins;Sara Olson;Xintao Wei;Eric L Van Nostrand;Stephanie C Huelga;Brendan M Smalec;Xiaofeng Wang;Eurie L Hong;Jean M Davidson;Eric Lecuyer;Brenton R Graveley;Gene W Yeo;

10.1101/030486 — Genomics — Posted on 2015-11-03

251 The Prolylhydroxylase PHD2 Modulates Centromere Function through the Hydroxylation of CENP-N

Sandra C Moser;Dalila Bensaddek;Brian Ortmann;Sonia Rocha;Angus I Lamond;Jason R Swedlow;

10.1101/030452 — Cell Biology — Posted on 2015-11-03

252 Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads

Ivan Sovic;Kresimir Krizanovic;Karolj Skala;Mile Sikic;

10.1101/030437 — Bioinformatics — Posted on 2015-11-13

253 Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads

Ivan Sovic;Kresimir Krizanovic;Karolj Skala;Mile Sikic;

10.1101/030437 — Bioinformatics — Posted on 2015-11-03

254 The Strength of Selection Against Neanderthal Introgression

Ivan Juric;Simon Aeschbacher;Graham Coop;

10.1101/030148 — Evolutionary Biology — Posted on 2015-11-21

255 Comprehensive cross-population analysis of high-grade serous ovarian cancer supports no more than three subtypes

Gregory P Way;James Rudd;Chen Wang;Habib Hamidi;Brooke L Fridley;Gottfried Konecny;Ellen L Goode;Casey S Greene;Jennifer A Doherty;

10.1101/030239 — Cancer Biology — Posted on 2015-11-18

256 MetaR: simple, high-level languages for data analysis with the R ecosystem

Fabien Campagne;William ER Digan;Manuele Simi;

10.1101/030254 — Bioinformatics — Posted on 2015-11-04

257 Adaptation to heavy-metal contaminated environments proceeds via selection on pre-existing genetic variation

Kevin M. Wright;Uffe Hellsten;Chenling Xu;Annie L. Jeong;Avinash Sreedasyam;Jarrod A. Chapman;Jeremy Schmutz;Graham Coop;Daniel S. Rokhsar;John H. Willis;

10.1101/029900 — Evolutionary Biology — Posted on 2015-11-07

258 A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city

Pedro Dorado-Morales;Cristina Vilanova;Juli Pereto;Franscisco M Codoner;Daniel Ramon;Manuel Porcar;

10.1101/029660 — Microbiology — Posted on 2015-11-30

259 Disruption of endosperm development is a major cause of hybrid seed inviability between Mimulus guttatus and M. nudatus

Elen Oneal;John H. Willis;Robert Franks;

10.1101/029223 — Evolutionary Biology — Posted on 2015-11-02

260 Osmophoresis - a possible mechanism for vesicle trafficking in tip-growing cells

Andrei Lipchinsky;

10.1101/029157 — Cell Biology — Posted on 2015-11-25

261 Osmophoresis - a possible mechanism for vesicle trafficking in tip-growing cells

Andrei Lipchinsky;

10.1101/029157 — Cell Biology — Posted on 2015-11-07

262 TP53 copy number expansion correlates with the evolution of increased body size and an enhanced DNA damage response in elephants

Michael Sulak;Lindsey Fong;Katelyn Mika;Sravanthi Chigurupati;Lisa Yon;Nigel P. Mongan;Richard D. Emes;Vincent J. Lynch;

10.1101/028522 — Genetics — Posted on 2015-11-24

263 in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies

Xiaofan Zhou;David Peris;Jacek Kominek;Cletus P Kurtzman;Chris Todd Hittinger;Antonis Rokas;

10.1101/028134 — Bioinformatics — Posted on 2015-11-01

264 Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

Jeffrey A Hussmann;Stephanie Patchett;Arlen Johnson;Sara Sawyer;William H Press;

10.1101/027938 — Genomics — Posted on 2015-11-25

265 A Serial Multiplex Immunogold Labeling Method for Identifying Peptidergic Neurons in Connectomes

Reza Shahidi;Elizabeth Williams;Markus Conzelmann;Albina Asadulina;Csaba Veraszto;Sanja Jasek;Luis A Bezares-Calderon;Gaspar Jekely;

10.1101/027458 — Neuroscience — Posted on 2015-11-27

266 Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk

Rudiger Brauning;Paul J Fisher;Alan F McCulloch;Russell J Smithies;James F Ward;Matthew J Bixley;Cindy T Lawley;Suzanne J Rowe;John C McEwan;

10.1101/027318 — Genomics — Posted on 2015-11-04

267 Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-Random Features of Cortical Synaptic Wiring.

Daniel Miner;Jochen Triesch;

10.1101/027268 — Neuroscience — Posted on 2015-11-23

268 The UCSC Genome Browser database: 2016 update

Matthew L. Speir;Ann S. Zweig;Kate R. Rosenbloom;Brian J. Raney;Benedict Paten;Parisa Nejad;Brian T. Lee;Katrina Learned;Donna Karolchik;Angie S. Hinrichs;Steve Heitner;Rachel A. Harte;Maximilian Haeussler;Luvina Guruvadoo;Pauline A. Fujita;Christopher Eisenhart;Mark Diekhans;Hiram Clawson;Jonathan Casper;Galt P. Barber;David Haussler;Robert M. Kuhn;W. James Kent;

10.1101/027037 — Genomics — Posted on 2015-11-06

269 Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

Antonino Ingargiola;Ted Laurence;Robert Boutelle;Shimon Weiss;Xavier Michalet;

10.1101/026484 — Biophysics — Posted on 2015-11-11

270 ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

Tarun Mall;John Eckstein;David Norris;Hiral Vora;Nowlan Freese;Ann E. Loraine;

10.1101/025924 — Bioinformatics — Posted on 2015-11-26

271 Multivariate State Hidden Markov Models for Mark-Recapture Data

Devin S. Johnson;Jeffrey L. Laake;Sharon R. Melin;Robert L. DeLong;

10.1101/025569 — Ecology — Posted on 2015-11-19

272 Multivariate State Hidden Markov Models for Mark-Recapture Data

Devin S. Johnson;Jeffrey L. Laake;Sharon R. Melin;Robert L. DeLong;

10.1101/025569 — Ecology — Posted on 2015-11-19

273 Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

Jason Munshi-South;Christine P Zolnik;Stephen E Harris;

10.1101/025007 — Evolutionary Biology — Posted on 2015-11-26

274 An extensive comparison of species-abundance distribution models.

Elita Baldridge;Xiao Xiao;Ethan P. White;

10.1101/024802 — — Posted on 2015-11-02

275 Antithetic Integral Feedback: A new motif for robust perfect adaptation in noisy biomolecular networks

Corentin Briat;Ankit Gupta;Mustafa Khammash;

10.1101/024919 — Systems Biology — Posted on 2015-11-23

276 Estimating the effect of competition on trait evolution using maximum likelihood inference

Jonathan Drury;Julien Clavel;Marc Manceau;Hélène Morlon;

10.1101/023473 — Evolutionary Biology — Posted on 2015-11-10

277 Structural modeling of the flagellum MS ring protein FliF reveals similarities to the type III secretion system and sporulation complex

Julien R. C. Bergeron;

10.1101/023564 — Biochemistry — Posted on 2015-11-04

278 EigenGWAS: finding loci under selection through genome-wide association studies of eigenvectors in structured populations

Guo-Bo Chen;Sang Hong Lee;Zhi-Xiang Zhu;Beben Benyamin;Matthew R Robinson;

10.1101/023457 — Genetics — Posted on 2015-11-17

279 Capabilities and Limitations of Tissue Size Control Through Passive Mechanical Forces

Jochen Kursawe;Pavel A. Brodskiy;Jeremiah J. Zartman;Ruth E. Baker;Alexander George Fletcher;

10.1101/023184 — Developmental Biology — Posted on 2015-11-23

280 Capabilities and Limitations of Tissue Size Control Through Passive Mechanical Forces

Jochen Kursawe;Pavel A. Brodskiy;Jeremiah J. Zartman;Ruth E. Baker;Alexander George Fletcher;

10.1101/023184 — Developmental Biology — Posted on 2015-11-07

281 Incomplete proteasomal degradation of green fluorescent proteins in the context of tandem fluorescent protein timers

Anton Khmelinskii;Matthias Meurer;Chi-Ting Ho;Birgit Besenbeck;Julia Fueller;Marius K Lemberg;Bernd Bukau;Axel Mogk;Michael Knop;

10.1101/023119 — Cell Biology — Posted on 2015-11-12

282 Nanoscale architecture of the axon initial segment reveals an organized and robust scaffold

Christophe Leterrier;Jean Potier;Ghislaine Caillol;Claire Debarnot;Fanny Rueda Boroni;Bénédicte Dargent;

10.1101/022962 — Neuroscience — Posted on 2015-11-06

283 Ordering structured populations in multiplayer cooperation games

Jorge Peña;Bin Wu;Arne Traulsen;

10.1101/021550 — Evolutionary Biology — Posted on 2015-11-30

284 Concordance and incongruence in preclinical anxiety models: systematic review and meta-analyses

Farhan Mohammad;Joses Ho;Chun Lei Lim;Jia Hern Woo;Dennis Jun Jie Poon;Bhumika Lamba;Adam Claridge-Chang;

10.1101/020701 — Animal Behavior and Cognition — Posted on 2015-11-18

285 RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

Julie Nadel;Rodoniki Athanasiadou;Christophe Lemetre;Neil Ari Wijetunga;Pilib Ó Broin;Hanae Sato;Zhengdong Zhang;Jeffrey Jeddeloh;Cristina Montagna;Aaron Golden;Cathal Seoighe;John M. Greally;

10.1101/020545 — Genomics — Posted on 2015-11-16

286 RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

Julie Nadel;Rodoniki Athanasiadou;Christophe Lemetre;Neil Ari Wijetunga;Pilib Ó Broin;Hanae Sato;Zhengdong Zhang;Jeffrey Jeddeloh;Cristina Montagna;Aaron Golden;Cathal Seoighe;John M. Greally;

10.1101/020545 — Genomics — Posted on 2015-11-02

287 A computational modelling approach for deriving biomarkers to predict cancer risk in premalignant disease

Andrew Dhawan;Trevor A Graham;Alexander G Fletcher;

10.1101/020222 — Cancer Biology — Posted on 2015-11-27

288 Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing

Minh Duc Cao;Devika Ganesamoorthy;Alysha Elliott;Huihui Zhang;Matthew Cooper;Lachlan Coin;

10.1101/019356 — Bioinformatics — Posted on 2015-11-15

289 GenOO: A Modern Perl Framework for High Throughput Sequencing analysis

Manolis Maragkakis;Panagiotis Alexiou;Zissimos Mourelatos;

10.1101/019265 — Bioinformatics — Posted on 2015-11-03

290 Surface-driven registration method for the structure-informed segmentation of diffusion MR images

Oscar Esteban;Dominique Zosso;Alessandro Daducci;Meritxell Bach-Cuadra;Maria J. Ledesma-Carbayo;Jean-Philippe Thiran;Andres Santos;

10.1101/018945 — Bioengineering — Posted on 2015-11-11

291 Inferring species interactions from co-occurrence data with Markov networks

David J. Harris;

10.1101/018861 — Ecology — Posted on 2015-11-26

292 Efficient Privacy-Preserving String Search and an Application in Genomics

Kana Shimizu;Koji Nuida;Gunnar Rätsch;

10.1101/018267 — Genomics — Posted on 2015-11-27

293 Fast principal components analysis reveals convergent evolution of ADH1B gene in Europe and East Asia

Kevin J Galinsky;Gaurav Bhatia;Po-Ru Loh;Stoyan Georgiev;Sayan Mukherjee;Nick J Patterson;Alkes L Price;

10.1101/018143 — Bioinformatics — Posted on 2015-11-09

294 Testing for ancient selection using cross-population allele frequency differentiation

Fernando Racimo;

10.1101/017566 — Evolutionary Biology — Posted on 2015-11-19

295 Testing for ancient selection using cross-population allele frequency differentiation

Fernando Racimo;

10.1101/017566 — Evolutionary Biology — Posted on 2015-11-19

296 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-11-13

297 Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection

Mark Christian Harrison;Eamonn B Mallon;Dave Twell;Robert L Hammond;

10.1101/016626 — Evolutionary Biology — Posted on 2015-11-23

298 ExoRNAi exposes contrasting roles for sugar exudation in host-finding by plant pathogens

Neil D Warnock;Leonie Wilson;Juan V Canet-Perez;Thomas Fleming;Colin C Fleming;Aaron G Maule;Johnathan J Dalzell;

10.1101/015545 — Plant Biology — Posted on 2015-11-13

299 Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

Mark Lipson;Po-Ru Loh;Sriram Sankararaman;Nick Patterson;Bonnie Berger;David Reich;

10.1101/015560 — Genetics — Posted on 2015-11-13

300 Large-scale non-targeted metabolomic profiling in three human population-based studies

Andrea Ganna;Tove Fall;Samira Salihovic;Woojoo Lee;Corey D Broeckling;Jitender Kumar;Sara Hägg;Markus Stenemo;Patrik K.E. Magnusson;Jessica Prenni;Lars Lind;Yudi Pawitan;Erik Ingelsson;

10.1101/002782 — Bioinformatics — Posted on 2015-11-12

Archive, 2015-11