bioRxiv directory

Hiroaki Sakai;Ken Naito;Eri Ogiso-Tanaka;Yu Takahashi;Kohtaro Iseki;Chiaki Muto;Kazuhito Satou;Kuniko Teruya;Akino Shiroma;Makiko Shimoji;Takashi Hirano;Takeshi Itoh;Akito Kaga;Norihiko Tomooka;

10.1101/021634 — Genomics — Posted on 2015-06-29

10 Life history evolution in response to changes in metapopulation structure in an arthropod herbivore

Annelies De Roissart;Nicky Wybouw;David Renault;Thomas Van Leeuwen;Dries Bonte;

10.1101/021683 — Evolutionary Biology — Posted on 2015-06-29

11 Evolution of organismal stoichiometry in a 50,000-generation experiment with Escherichia coli

Caroline B. Turner;Brian D. Wade;Justin R. Meyer;Richard E. Lenski;

10.1101/021360 — Evolutionary Biology — Posted on 2015-06-29

12 SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

Diego Mallo;Leonardo de Oliveira Martins;David Posada;

10.1101/021709 — Evolutionary Biology — Posted on 2015-06-30

13 Mitotic chromosome compaction via active loop extrusion

Anton Goloborodko;John F. Marko;Leonid Mirny;

10.1101/021642 — Biophysics — Posted on 2015-06-29

14 A simple method for automated equilibration detection in molecular simulations

John D Chodera;

10.1101/021659 — Biophysics — Posted on 2015-06-29

15 Mitochondrial DNA Copy Number Variation Across Human Cancers

Ed Reznik;Martin Miller;Yasin Senbabaoglu;Nadeem Riaz;William Lee;Chris Sander;

10.1101/021535 — Genomics — Posted on 2015-06-27

16 Adaptive evolution is substantially impeded by Hill-Robertson interference in Drosophila

David Castellano;Marta Coronado;Jose Campos;Antonio Barbadilla;Adam Eyre-Walker;

10.1101/021600 — Evolutionary Biology — Posted on 2015-06-27

17 Comprehensive nucleosome mapping of the human genome in cancer progression

Brooke Druliner;Daniel Vera;Ruth Johnson;Xiaoyang Ruan;Lynne Apone;Eileen Dimalanta;Fiona Stewart;Lisa Boardman;Jonathan H. Dennis;

10.1101/021618 — Cancer Biology — Posted on 2015-06-27

18 Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference

Rob Patro;Geet Duggal;Michael I Love;Rafael A Irizarry;Carl Kingsford;

10.1101/021592 — Bioinformatics — Posted on 2015-06-27

19 TransRate: reference free quality assessment of de-novo transcriptome assemblies

Richard D Smith-Unna;Chris Boursnell;Rob Patro;Julian M Hibberd;Steven Kelly;

10.1101/021626 — Bioinformatics — Posted on 2015-06-27

20 Connecting small RNAs and Aging

Joshua Elkington;

10.1101/021584 — Molecular Biology — Posted on 2015-06-26

21 Ordering structured populations in multiplayer cooperation games

Jorge Peña;Bin Wu;Arne Traulsen;

10.1101/021550 — Evolutionary Biology — Posted on 2015-06-26

22 Modeling small RNA competition in C. elegans

Joshua Elkington;

10.1101/021576 — Bioinformatics — Posted on 2015-06-26

23 Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data

John D O'Brien;Lucas Amenga-Etego;Ruiqi Li;

10.1101/021519 — Genomics — Posted on 2015-06-29

24 Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data

John D O'Brien;Lucas Amenga-Etego;Ruiqi Li;

10.1101/021519 — Genomics — Posted on 2015-06-25

25 Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

David E Weinberg;Premal Shah;Stephen W Eichhorn;Jeffrey A Hussmann;Joshua B Plotkin;David P Bartel;

10.1101/021501 — Genomics — Posted on 2015-06-26

26 SSCM: A method to analyze and predict the pathogenicity of sequence variants

Sharad Vikram;Matthew D Rasmussen;Eric A Evans;Imran S Haque;

10.1101/021527 — Bioinformatics — Posted on 2015-06-26

27 On enhancing variation detection through pan-genome indexing

Daniel Valenzuela;Niko Välimäki;Esa Pitkänen;Veli Mäkinen;

10.1101/021444 — Bioinformatics — Posted on 2015-06-26

28 On enhancing variation detection through pan-genome indexing

Daniel Valenzuela;Niko Välimäki;Esa Pitkänen;Veli Mäkinen;

10.1101/021444 — Bioinformatics — Posted on 2015-06-25

29 In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency

Nicolo Fusi;Ian Smith;John Doench;Jennifer Listgarten;

10.1101/021568 — Bioinformatics — Posted on 2015-06-26

30 Variability in group size and the evolution of collective action

Jorge Peña;Georg Nöldeke;

10.1101/021485 — Evolutionary Biology — Posted on 2015-06-25

31 A novel test for detecting gene-gene interactions in trio studies

Brunilda Balliu;Noah Zaitlen;

10.1101/021469 — Genetics — Posted on 2015-06-25

32 Some remarks on moments for stochastic chemical kinetics

Eduardo Sontag;Abhyudai Singh;

10.1101/021410 — Systems Biology — Posted on 2015-06-24

33 Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-step Task.

Thomas Akam;Rui Costa;Peter Dayan;

10.1101/021428 — Neuroscience — Posted on 2015-06-24

34 Discovery of methylation loci and analyses of differential methylation from replicated high-throughput sequencing data

Thomas J Hardcastle;

10.1101/021436 — Bioinformatics — Posted on 2015-06-24

35 Effects of MDMA on socioemotional feelings, authenticity, and autobiographical disclosure in healthy volunteers in a controlled setting

Matthew J Baggott;Jeremy R Coyle;Jennifer D Siegrist;Kathleen J Garrison;Gantt P Galloway;John E Mendelson;

10.1101/021329 — Pharmacology and Toxicology — Posted on 2015-06-29

36 Effects of MDMA on socioemotional feelings, authenticity, and autobiographical disclosure in healthy volunteers in a controlled setting

Matthew J Baggott;Jeremy R Coyle;Jennifer D Siegrist;Kathleen J Garrison;Gantt P Galloway;John E Mendelson;

10.1101/021329 — Pharmacology and Toxicology — Posted on 2015-06-23

37 Mechanical morphogenesis and the development of neocortical organisation

Ophélie Foubet;Roberto Toro;

10.1101/021311 — Neuroscience — Posted on 2015-06-23

38 Synthetic datasets and community tools for the rapid testing of ecological hypotheses

Timothee Poisot;Dominique Gravel;Shawn Leroux;Spencer A Wood;Marie-Josée Fortin;Benjamin Baiser;Alyssa R Cirtwill;Miguel B Araujo;Daniel B Stouffer;

10.1101/021402 — Ecology — Posted on 2015-06-23

39 Stochastic evolutionary games in dynamic populations

Weini Huang;Christoph Hauert;Arne Traulsen;

10.1101/021378 — Evolutionary Biology — Posted on 2015-06-23

40 Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model-Choice By Simulation-Trained Discriminant Analysis

Jeet Sukumaran;Evan P. Economo;L. Lacey Knowles;

10.1101/021303 — Evolutionary Biology — Posted on 2015-06-22

41 Genetic basis underlying connection between hyperglycemia and dyslipidemia in Apoe-deficient mice

Qian Wang;Andrew Grainger;Ani Manichaikul;Emily Farber;Suna Onengut-Gumuscu;Weibin Shi;

10.1101/021287 — Genetics — Posted on 2015-06-21

42 Could rare amino acids regulate enzymes abundance?

valentina agoni;

10.1101/021295 — Cell Biology — Posted on 2015-06-21

43 A New Mutation-Profile-Based Method for Understanding the Evolution of Cancer Somatic Mutations

Zhan Zhou;Yangyun Zou;Gangbiao Liu;Jingqi Zhou;Shiming Zhao;Zhixi Su;Gu Xun;

10.1101/021147 — Cancer Biology — Posted on 2015-06-20

44 Exon capture optimization in large-genome amphibians

Evan McCartney-Melstad;Genevieve G. Mount;H. Bradley Shaffer;

10.1101/021253 — Genomics — Posted on 2015-06-19

45 A targeted subgenomic approach for phylogenomics based on microfluidic PCR and high throughput sequencing

Simon Uribe-Convers;Matthew L Settles;David C Tank;

10.1101/021246 — Evolutionary Biology — Posted on 2015-06-19

46 Metacommunities in Dynamic Landscapes

Charles Novaes de Santana;Jan Klecka;Gian Marco Palamara;Carlos J. Melián;

10.1101/021220 — Ecology — Posted on 2015-06-26

47 Metacommunities in Dynamic Landscapes

Charles Novaes de Santana;Jan Klecka;Gian Marco Palamara;Carlos J. Melián;

10.1101/021220 — Ecology — Posted on 2015-06-22

48 Metacommunities in Dynamic Landscapes

Charles Novaes de Santana;Jan Klecka;Gian Marco Palamara;Carlos J. Melián;

10.1101/021220 — Ecology — Posted on 2015-06-19

49 A seasonal copepod ‘lipid pump’ promotes carbon sequestration in the deep North Atlantic

Sigrun H. Jonasdottir;Andre W. Visser;Katherine Richardson;Michael R. Heath;

10.1101/021279 — Ecology — Posted on 2015-06-19

50 Inference under a Wright-Fisher model using an accurate beta approximation

Paula Tataru;Thomas Bataillon;Asger Hobolth;

10.1101/021261 — Bioinformatics — Posted on 2015-06-19

51 TESS: Bayesian inference of lineage diversification rates from (incompletely sampled) molecular phylogenies in R

Sebastian Höhna;Michael R. May;Brian R. Moore;

10.1101/021238 — Bioinformatics — Posted on 2015-06-19

52 Decoding the Population Activity of Grid Cells for Spatial Localization and Goal-Directed Navigation

Martin Stemmler;Alexander Mathis;Andreas VM Herz;

10.1101/021204 — Neuroscience — Posted on 2015-06-22

53 Decoding the Population Activity of Grid Cells for Spatial Localization and Goal-Directed Navigation

Martin Stemmler;Alexander Mathis;Andreas VM Herz;

10.1101/021204 — Neuroscience — Posted on 2015-06-19

54 Hi-Cpipe: a pipeline for high-throughput chromosome capture

Giancarlo Castellano;François Le Dily;Antonio Hermoso Pulido;Miguel Beato;Guglielmo Roma;

10.1101/020636 — Bioinformatics — Posted on 2015-06-19

55 Variation-preserving normalization unveils blind spots in gene expression profiling

Carlos P. Roca;Susana I. L. Gomes;Mónica J. B. Amorim;Janeck J. Scott-Fordsmand;

10.1101/021212 — Genomics — Posted on 2015-06-19

56 MDMA impairs response to water intake in healthy volunteers

Matthew J Baggott;Kathleen J Garrison;Jeremy R Coyle;Gantt P Galloway;Allan J Barnes;Marilyn A Huestis;John E Mendelson;

10.1101/021113 — Pharmacology and Toxicology — Posted on 2015-06-18

57 The discovery, distribution and evolution of viruses associated with Drosophila melanogaster

Claire L Webster;Fergal M Waldron;Shaun Robertson;Daisy Crowson;Giada Ferrari;Juan F Quintana;Jean-Michel Brouqui;Elizabeth H Bayne;Ben Longdon;Amy H Buck;Brian P Lazzaro;Jewelna Akorli;Penelope R Haddrill;Darren J Obbard;

10.1101/021154 — Microbiology — Posted on 2015-06-18

58 Genome Editing in Caenorhabditis briggsae using the CRISPR/Cas9 System

Elizabeth Culp;Cory Richman;Devika Sharanya;Bhagwati Gupta;

10.1101/021121 — Genetics — Posted on 2015-06-18

59 PaxtoolsR: Pathway Analysis in R Using Pathway Commons

Augustin Luna;Özgün Babur;Bülent Arman Aksoy;Emek Demir;Chris Sander;

10.1101/021105 — Bioinformatics — Posted on 2015-06-18

60 PrediXcan: Trait Mapping Using Human Transcriptome Regulation

Eric R Gamazon;Heather E Wheeler;Kaanan Shah;Sahar V Mozaffari;Keston Aquino-Michaels;Robert J Carroll;Anne E Eyler;Joshua C Denny;Dan L Nicolae;Nancy J Cox;Hae Kyung Im;GTEx Consortium;

10.1101/020164 — Genomics — Posted on 2015-06-17

61 Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli

Caroline B. Turner;Zachary D. Blount;Daniel H. Mitchell;Richard E. Lenski;

10.1101/020958 — Evolutionary Biology — Posted on 2015-06-17

62 Biographika: rich interactive data visualizations on the web for the research community

Pablo Pareja Tobes;Eduardo Pareja Tobes;Marina Manrique;Eduardo Pareja;Raquel Tobes;

10.1101/021063 — Bioinformatics — Posted on 2015-06-17

63 Stimulus induced visual cortical networks are recapitulated by spontaneous local and inter-areal synchronization

Christopher Lewis;Conrado Bosmann;Thilo Womelsdorf;Pascal Fries;

10.1101/021055 — Neuroscience — Posted on 2015-06-16

64 CTFFIND4: Fast and accurate defocus estimation from electron micrographs

Alexis Rohou;Nikolaus Grigorieff;

10.1101/020917 — Biophysics — Posted on 2015-06-16

65 Correspondence between resting state activity and brain gene expression

Guang-Zhong Wang;T. Grant Belgard;Deng Mao;Leslie Chen;Stefano Berto;Todd Preuss;Hanzhang Lu;Daniel Geschwind;Genevieve Konopka;

10.1101/021071 — Neuroscience — Posted on 2015-06-17

66 Correspondence between resting state activity and brain gene expression

Guang-Zhong Wang;T. Grant Belgard;Deng Mao;Leslie Chen;Stefano Berto;Todd Preuss;Hanzhang Lu;Daniel Geschwind;Genevieve Konopka;

10.1101/021071 — Neuroscience — Posted on 2015-06-16

67 Signatures of Dobzhansky-Muller Incompatibilities in the Genomes of Recombinant Inbred Lines

Maria Colomé-Tatché;Frank Johannes;

10.1101/021006 — Genetics — Posted on 2015-06-16

68 Leveraging distant relatedness to quantify human mutation and gene conversion rates

Pier Francesco Palamara;Laurent Francioli;Giulio Genovese;Peter Wilton;Alexander Gusev;Hilary Finucane;Sriram Sankararaman;Shamil Sunyaev;

10.1101/020776 — Genetics — Posted on 2015-06-16

69 Environmental fluctuations do not select for increased variation or population-based resistance in Escherichia coli

Shraddha Madhav Karve;Kanishka Tiwary;S Selveshwari;Sutirth Dey;

10.1101/021030 — Evolutionary Biology — Posted on 2015-06-16

70 Variability in cellular gene expression profiles and homeostatic regulation

Yuriy Mishchenko;

10.1101/021048 — Cell Biology — Posted on 2015-06-16

71 Sequence evidence for common ancestry of eukaryotic endomembrane coatomers

Vasilis J. Promponas;Katerina R. Katsani;Benjamin J. Blencowe;Christos A. Ouzounis;

10.1101/020990 — Bioinformatics — Posted on 2015-06-16

72 Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing

Hiroki Ando;Sebastien Lemire;Diana Pires;Timothy Lu;

10.1101/020891 — Synthetic Biology — Posted on 2015-06-15

73 Linkage disequilibrium between single nucleotide polymorphisms and hypermutable loci

Sterling Sawaya;Matt Jones;Matt Keller;

10.1101/020909 — Genetics — Posted on 2015-06-15

74 An accurate genetic clock

David H Hamilton;

10.1101/020933 — Genetics — Posted on 2015-06-19

75 An accurate genetic clock

David H Hamilton;

10.1101/020933 — Genetics — Posted on 2015-06-15

76 Identification of Slco1a6 as a candidate gene that broadly affects gene expression in mouse pancreatic islets

Jianan Tian;Mark P. Keller;Angie T. Oler;Mary E. Rabaglia;Kathryn L. Schueler;Donald S. Stapleton;Aimee Teo Broman;Wen Zhao;Christina Kendziorski;Brian S. Yandell;Bruno Hagenbuch;Karl W Broman;Alan D. Attie;

10.1101/020974 — Genetics — Posted on 2015-06-16

77 Identification of Slco1a6 as a candidate gene that broadly affects gene expression in mouse pancreatic islets

10.1101/020974 — Genetics — Posted on 2015-06-15

78 Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

Jennifer Marie Shelton;Michelle C Coleman;Nic Herndon;Nanyan Lu;Ernest T Lam;Thomas Anantharaman;Palak Sheth;Susan J Brown;

10.1101/020966 — Bioinformatics — Posted on 2015-06-15

79 Striatal dynamics explain duration judgments

Thiago S. Gouvêa;Tiago Monteiro;Asma Motiwala;Sofia Soares;Christian K. Machens;Joseph J. Paton;

10.1101/020883 — Neuroscience — Posted on 2015-06-15

80 Systematic identification of significantly mutated regions reveals a rich landscape of functional molecular alterations across cancer genomes

Carlos L. Araya;Can Cenik;Jason A. Reuter;Gert Kiss;Vijay S. Pande;Michael P. Snyder;William J. Greenleaf;

10.1101/020875 — Genomics — Posted on 2015-06-15

81 Overcoming analytical reliability issues in clinical proteomics using rank-based network approaches

Wilson Wen Bin Goh;Limsoon Wong;

10.1101/020867 — Bioinformatics — Posted on 2015-06-15

82 MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA-seq data.

Greg Finak;Andrew McDavid;Masanao Yajima;Jingyuan Deng;Vivian Gersuk;Alex K Shalek;Chloe K Slichter;Hannah W Miller;M Julianna McElrath;Martin Prlic;Peter Linsley;Raphael Gottardo;

10.1101/020842 — Bioinformatics — Posted on 2015-06-15

83 Automated Contamination Detection in Single-Cell Sequencing

Markus Lux;Barbara Hammer;Alexander Sczyrba;

10.1101/020859 — Bioinformatics — Posted on 2015-06-15

84 Probing the fabric of the rare biosphere

Bibiana G. Crespo;Philip J. Wallhead;Ramiro Logares;Carlos Pedros-Alio;

10.1101/020818 — Microbiology — Posted on 2015-06-18

85 Probing the fabric of the rare biosphere

Bibiana G. Crespo;Philip J. Wallhead;Ramiro Logares;Carlos Pedros-Alio;

10.1101/020818 — Microbiology — Posted on 2015-06-12

86 MERS-CoV recombination: implications about the reservoir and potential for adaptation

Gytis Dudas;Andrew Rambaut;

10.1101/020834 — Evolutionary Biology — Posted on 2015-06-12

87 The Nature, Extent, and Consequences of Genetic Variation in the opa Repeats of Notch in Drosophila

Clinton Rice;Danielle Beekman;Liping Liu;Albert J Erives;

10.1101/020826 — Evolutionary Biology — Posted on 2015-06-12

88 A novel method to enhance the sensitivity of marker detection using a refined hierarchical prior of tissue similarities

Shahin Mohammadi;Ananth Grama;

10.1101/020685 — Systems Biology — Posted on 2015-06-11

89 Environmental DNA reveals that rivers are conveyer belts of biodiversity information

Kristy Deiner;Emanuel A. Fronhofer;Elvira Meachler;Jean-Claude Walser;Florian Altermatt;

10.1101/020800 — Ecology — Posted on 2015-06-11

90 bModelTest: Bayesian phylogenetic site model averaging and model comparison

Remco Bouckaert;Alexei Drummond;

10.1101/020792 — Bioinformatics — Posted on 2015-06-11

91 Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

David M Rocke;Luyao Ruan;Yilun Zhang;J. Jared Gossett;Blythe Durbin-Johnson;Sharon Aviran;

10.1101/020784 — Bioinformatics — Posted on 2015-06-11

92 Thiosulfate-hydrogen peroxide redox oscillator as pH driver for ribozyme activity in the RNA world

Rowena Ball;John Brindley;

10.1101/020693 — Molecular Biology — Posted on 2015-06-10

93 Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap

Ivan Sovic;Mile Sikic;Andreas Wilm;Shannon Nicole Fenlon;Swaine Chen;Niranjan Nagarajan;

10.1101/020719 — Genomics — Posted on 2015-06-10

94 The migration game in habitat network: the case of tuna

Patrizio Mariani;Vlastimil Krivan;Brian R MacKenzie;Christian Mullon;

10.1101/020743 — Ecology — Posted on 2015-06-10

95 Discrete Distributional Differential Expression (D3E) - A Tool for Gene Expression Analysis of Single-cell RNA-seq Data

Mihails Delmans;Martin Hemberg;

10.1101/020735 — Bioinformatics — Posted on 2015-06-10

96 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 2015-06-10

97 Cellular reprogramming dynamics follow a simple one-dimensional reaction coordinate

Sai Teja Pusuluri;Alex H. Lang;Pankaj Mehta;Horacio E. Castillo;

10.1101/020677 — Systems Biology — Posted on 2015-06-09

98 Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables

Lindsay V Clark;Andrea Drauch Schreier;

10.1101/020610 — Bioinformatics — Posted on 2015-06-09

99 Landauer in the age of synthetic biology: energy consumption and information processing in biochemical networks

Pankaj Mehta;Alex H Lang;David J Schwab;

10.1101/020594 — Synthetic Biology — Posted on 2015-06-08

100 Estimating information flow through a memory system: the utility of meta-analytic methods for genetics

Tugce Yildizoglu;Jan-Marek Weislogel;Farhan Mohammad;Edwin S.-Y. Chan;Pryseley N. Assam;Adam Claridge-Chang;

10.1101/020586 — Neuroscience — Posted on 2015-06-08

101 Statistical Colocalization of Genetic Risk Variants for Related Autoimmune Diseases in the Context of Common Controls

Mary D Fortune;Hui Guo;Oliver Burren;Ellen Schofield;Neil M Walker;Maria Ban;Stephen J Sawcer;John Bowes;Jane Worthington;Anne Barton;Steve Eyre;John A Todd;Chris Wallace;

10.1101/020651 — Genomics — Posted on 2015-06-08

102 Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model streptomycetes

Pablo Cruz-Morales;Johannes F. Kopp;Christian E. Martinez-Guerrero;Luis A. Yanez-Guerra;Nelly Selem-Mojica;Hilda E. Ramos-Aboites;Jorg Feldmann;Francisco Barona-Gomez;

10.1101/020503 — Genomics — Posted on 2015-06-08

103 Genome-wide transcription factor activities are explained by intrinsic conformational dynamics of binding-sites and distal flanking-regions

Munazah Andrabi;Andrew Paul Hutchins;Diego Miranda-Saavedra;Hidetoshi Kono;Ruth Nussinov;Kenji Mizuguchi;Shandar Ahmad;

10.1101/020602 — Genomics — Posted on 2015-06-09

104 Genome-wide transcription factor activities are explained by intrinsic conformational dynamics of binding-sites and distal flanking-regions

Munazah Andrabi;Andrew Paul Hutchins;Diego Miranda-Saavedra;Hidetoshi Kono;Ruth Nussinov;Kenji Mizuguchi;Shandar Ahmad;

10.1101/020602 — Genomics — Posted on 2015-06-08

105 A gene for social immunity in the burying beetle Nicrophorus vespilloides?

William JP Palmer;Ana Duarte;Matthew Schrader;Jonathan P Day;Rebecca Kilner;Francis Jiggins;

10.1101/020644 — Genetics — Posted on 2015-06-08

106 WaspAtlas: A Nasonia vitripennis gene database

Nathaniel J Davies;Eran Tauber;

10.1101/020669 — Bioinformatics — Posted on 2015-06-08

107 Generic transcriptional response of E. coli to stress

Ranginee Choudhury;Saroj Kant Mohapatra;

10.1101/020578 — Microbiology — Posted on 2015-06-07

108 Ex vivo mycobacterial growth inhibition assay (MGIA) for tuberculosis vaccine testing - a protocol for mouse splenocytes

Andrea Andrea Zelmer;Rachel Tanner;Elena Stylianou;Sheldon Morris;Angelo Izzo;Ann Williams;Sally Sharpe;Ilaria Pepponi;Barry Walker;David A Hokey;Helen McShane;Michael Brennan;Helen Fletcher;

10.1101/020560 — Immunology — Posted on 2015-06-07

109 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 2015-06-07

110 The Nature, Extent, and Consequences of Cryptic Genetic Variation in the opa Repeats of Notch in Drosophila

Clinton Rice;Danielle Beekman;Liping Liu;Albert Erives;

10.1101/020529 — Genetics — Posted on 2015-06-10

111 The Nature, Extent, and Consequences of Cryptic Genetic Variation in the opa Repeats of Notch in Drosophila

Clinton Rice;Danielle Beekman;Liping Liu;Albert Erives;

10.1101/020529 — Genetics — Posted on 2015-06-09

112 The Nature, Extent, and Consequences of Cryptic Genetic Variation in the opa Repeats of Notch in Drosophila

Clinton Rice;Danielle Beekman;Liping Liu;Albert Erives;

10.1101/020529 — Genetics — Posted on 2015-06-07

113 Coalescent inference using serially sampled, high-throughput sequencing data from intra-host HIV infection

Kevin Dialdestoro;Jonas Andreas Sibbesen;Lasse Maretty;Jayna Raghwani;Astrid Gall;Paul Kellam;Oliver Pybus;Jotun Hein;Paul Jenkins;

10.1101/020552 — Genetics — Posted on 2015-06-07

114 Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population

Benjamin D Redelings;Seiji Kumagai;Liuyang Wang;Andrey Tatarenkov;Ann K. Sakai;Stephen G. Weller;Theresa M. Culley;John C. Avise;Marcy K. Uyenoyama;

10.1101/020537 — Evolutionary Biology — Posted on 2015-06-07

115 Limits of aerobic metabolism in cancer cells

Alexei Vazquez;

10.1101/020461 — Systems Biology — Posted on 2015-06-05

116 Cell-cell communication in yeast using auxin biosynthesis and auxin responsive CRISPR transcription factors

Arjun Khakhar;Nicholas Bolten;Jennifer Nemhauser;Eric Klavins;

10.1101/020487 — Synthetic Biology — Posted on 2015-06-05

117 Response to Comment on ”Two types of asynchronous activity in networks of excitatory and inhibitory spiking neurons”

Srdjan Ostojic;

10.1101/020354 — Neuroscience — Posted on 2015-06-05

118 Are Genetic Interactions Influencing Gene Expression Evidence for Biological Epistasis or Statistical Artifacts?

Alexandra Fish;John A. Capra;William S Bush;

10.1101/020479 — Genomics — Posted on 2015-06-05

119 The evolution, diversity and host associations of rhabdoviruses

Ben Longdon;Gemma GR Murray;William J Palmer;Jonathan P Day;Darren J Parker;John J Welch;Darren J Obbard;Francis M Jiggins;

10.1101/020107 — Evolutionary Biology — Posted on 2015-06-05

120 DISSECT: A new tool for analyzing extremely large genomic datasets

Oriol Canela-Xandri;Andy Law;Alan Gray;John A. Woolliams;Albert Tenesa;

10.1101/020453 — Bioinformatics — Posted on 2015-06-05

121 Single Cells of Pseudomonas aeruginosa Exhibit Electrotaxis and Durotaxis Behaviours

Lee Preiss;Suresh Neethirajan;

10.1101/020511 — Bioengineering — Posted on 2015-06-05

122 Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005–2010: Potential for Molecular Surveillance of New Outbreaks

Mohammad A. Alkhamis;Brian R. Moore;Andrés M. Perez;

10.1101/020339 — Evolutionary Biology — Posted on 2015-06-04

123 Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005–2010: Potential for Molecular Surveillance of New Outbreaks

Mohammad A. Alkhamis;Brian R. Moore;Andrés M. Perez;

10.1101/020339 — Evolutionary Biology — Posted on 2015-06-04

124 Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005–2010: Potential for Molecular Surveillance of New Outbreaks

Mohammad A. Alkhamis;Brian R. Moore;Andrés M. Perez;

10.1101/020339 — Evolutionary Biology — Posted on 2015-06-04

125 Bringing Down Cancer Aircraft: Searching For Essential Hypomutated Proteins In Skin Melanoma

Mikhail Pyatnitskiy;Dmitriy Karpov;Ekaterina Poverennaya;Andrey Lisitsa;Sergei Moshkovskii;

10.1101/020396 — Cancer Biology — Posted on 2015-06-04

126 When does high-dose antimicrobial chemotherapy prevent the evolution of resistance?

Troy Day;Andrew F. Read;

10.1101/020321 — Microbiology — Posted on 2015-06-03

127 Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

Alex L Greninger;Samia N Naccache;Scot Federman;Guixia Yu;Placide Mbala;Vanessa Bres;Jerome Bouquet;Doug Stryke;Sneha Somasekar;Jeffrey Linnen;Roger Dodd;Prime Mulembakani;Bradley Schneider;Jean-Jacques Muyembe;Susan Stramer;Charles Y Chiu;

10.1101/020420 — Genomics — Posted on 2015-06-05

128 Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

10.1101/020420 — Genomics — Posted on 2015-06-03

129 Evolution of ecological dominance of yeast species in high-sugar environments

Kathryn M Williams;Ping Liu;Justin C Fay;

10.1101/020370 — Evolutionary Biology — Posted on 2015-06-03

130 A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells

Juan Gonzalez-Vallinas;Amadís Pagès;Babita Singh;Eduardo Eyras;

10.1101/020362 — Bioinformatics — Posted on 2015-06-03

131 Cpipe: a shared variant detection pipeline designed for diagnostic settings

Simon Sadedin;Harriet Dashnow;Paul James;Melanie Bahlo;Denis C Bauer;Andrew Lonie;Sebastian Lunke;Ivan Macciocca;Jason Ross;Kirby R Siemering;Zornitza Stark;Sue White;Graham Taylor;Clara Gaff;Alicia Oshlack;Natalie Thorne;Melbourne Genomics Health Alliance;

10.1101/020388 — Bioinformatics — Posted on 2015-06-03

132 Segmenting Microarrays with Deep Neural Networks

Andrew L Jones;

10.1101/020404 — Bioinformatics — Posted on 2015-06-03

133 BEEtag : a low-cost, image-based tracking system for the study of animal behavior and locomotion

James Crall;Nick Gravish;Andrew M Mountcastle;Stacey A Combes;

10.1101/020347 — Animal Behavior and Cognition — Posted on 2015-06-03

134 Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

Jeanneth Mosquera-Rendon;Ana M. Rada-Bravo;Sonia Cardenas-Brito;Mauricio Corredor;Eliana Restrepo-Pineda;Alfonso Benitez-Paez;

10.1101/020305 — Genomics — Posted on 2015-06-02

135 The weighting is the hardest part: on the behavior of the likelihood ratio test and score test under weight misspecification in rare variant association studies

Camelia C. Minica;Giulio Genovese;Christina M. Hultman;René Pool;Jacqueline M. Vink;Conor V. Dolan;Benjamin M. Neale;

10.1101/020198 — Genetics — Posted on 2015-06-07

136 The weighting is the hardest part: on the behavior of the likelihood ratio test and score test under weight misspecification in rare variant association studies

Camelia C. Minica;Giulio Genovese;Christina M. Hultman;René Pool;Jacqueline M. Vink;Conor V. Dolan;Benjamin M. Neale;

10.1101/020198 — Genetics — Posted on 2015-06-03

137 The weighting is the hardest part: on the behavior of the likelihood ratio test and score test under weight misspecification in rare variant association studies

Camelia C. Minica;Giulio Genovese;Christina M. Hultman;René Pool;Jacqueline M. Vink;Conor V. Dolan;Benjamin M. Neale;

10.1101/020198 — Genetics — Posted on 2015-06-03

138 The weighting is the hardest part: on the behavior of the likelihood ratio test and score test under weight misspecification in rare variant association studies

Camelia C. Minica;Giulio Genovese;Christina M. Hultman;René Pool;Jacqueline M. Vink;Conor V. Dolan;Benjamin M. Neale;

10.1101/020198 — Genetics — Posted on 2015-06-02

139 Sequence capture of ultraconserved elements from bird museum specimens

John McCormack;Whitney L.E. Tsai;Brant C Faircloth;

10.1101/020271 — Evolutionary Biology — Posted on 2015-06-02

140 Myc-induced cell mixing is required for competitive tissue invasion and destruction

Eduardo Moreno;Romain Levayer;Barbara Hauert;

10.1101/020313 — Cell Biology — Posted on 2015-06-02

141 The next 20 years of genome research

Michael Schatz;

10.1101/020289 — Bioinformatics — Posted on 2015-06-02

142 Triplex Domain Finder: Detection of Triple Helix Binding Domains in Long Non-Coding RNAs

Sonja Hanzelmann;Chao-Chung Kuo;Marie Kalwa;Wolfgang Wagner;Ivan G. Costa;

10.1101/020297 — Bioinformatics — Posted on 2015-06-02

143 PIK3CA Mutational Analysis in Formalin-Fixed, Paraffin-Embedded Archival Tissues of Urothelial Carcinoma of Urinary Bladder

Alcides Chaux;Julie S. Cohen;Luciana Schultz;Roula Albadine;Sana Jadallah;Kathleen M. Murphy;Diana Teheri;Mark P. Schoenberg;George J. Netto;

10.1101/020263 — Pathology — Posted on 2015-06-16

144 PIK3CA Mutational Analysis in Formalin-Fixed, Paraffin-Embedded Archival Tissues of Urothelial Carcinoma of Urinary Bladder

Alcides Chaux;Julie S. Cohen;Luciana Schultz;Roula Albadine;Sana Jadallah;Kathleen M. Murphy;Diana Teheri;Mark P. Schoenberg;George J. Netto;

10.1101/020263 — Pathology — Posted on 2015-06-01

145 Approximately independent linkage disequilibrium blocks in human populations

Tomaz Berisa;Joseph K. Pickrell;

10.1101/020255 — Genomics — Posted on 2015-06-01

146 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 2015-06-01

147 OPERA-LG: Efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees

Song Gao;Denis Bertrand;Burton KH Chia;Niranjan Nagarajan;

10.1101/020230 — Bioinformatics — Posted on 2015-06-01

148 Pyvolve: a flexible Python module for simulating sequences along phylogenies

Stephanie J Spielman;Claus O Wilke;

10.1101/020214 — Bioinformatics — Posted on 2015-06-16

149 Pyvolve: a flexible Python module for simulating sequences along phylogenies

Stephanie J Spielman;Claus O Wilke;

10.1101/020214 — Bioinformatics — Posted on 2015-06-01

150 Post-transcriptional regulation across human tissues

Alexander Franks;Edoardo Airoldi;Nikolai Slavov;

10.1101/020206 — Systems Biology — Posted on 2015-06-23

151 A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary

Michael R. May;Sebastian Höhna;Brian R. Moore;

10.1101/020149 — Evolutionary Biology — Posted on 2015-06-02

152 A simple model-based approach to inferring and visualizing cancer mutation signatures

Yuichi Shiraishi;Georg Tremmel;Satoru Miyano;Matthew Stephens;

10.1101/019901 — Bioinformatics — Posted on 2015-06-01

153 Stochastic models of evidence accumulation in changing environments

Alan Veliz-Cuba;Zachary P Kilpatrick;Kresimir Josic;

10.1101/019398 — Neuroscience — Posted on 2015-06-13

154 Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION

John M Urban;Jacob Bliss;Charles E Lawrence;Susan A Gerbi;

10.1101/019281 — Genomics — Posted on 2015-06-22

155 ZIFA: Dimensionality reduction for zero-inflated single cell gene expression analysis

Christopher Yau;Emma Pierson;

10.1101/019141 — Bioinformatics — Posted on 2015-06-14

156 Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

Jean-Philippe Fortin;Kasper D Hansen;

10.1101/019000 — Genomics — Posted on 2015-06-03

157 A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years

Hang Zhou;Sile Hu;Rostislav Matveev;Qianhui Yu;Jing Li;Philipp Khaitovich;Li Jin;Michael Lachmann;Mark Stoneking;Qiaomei Fu;Kun Tang;

10.1101/018929 — Evolutionary Biology — Posted on 2015-06-19

158 A high-throughput RNA-seq approach to profile transcriptional responses

Gregory A Moyerbrailean;Gordon O Davis;Chris T Harvey;Donovan Watza;Xiaoquan Wen;Roger Pique-Regi;Francesca Luca;

10.1101/018416 — Genomics — Posted on 2015-06-09

159 Generating effective models and parameters for RNA genetic circuits

Chelsea Y Hu;Jeffrey D Varner;Julius B Lucks;

10.1101/018358 — Synthetic Biology — Posted on 2015-06-08

160 Efficient genotype compression and analysis of large genetic variation datasets

Ryan M Layer;Neil Kindlon;Konrad J Karczewski;Exome Aggregation Consortium ExAC;Aaron R Quinlan;

10.1101/018259 — Genomics — Posted on 2015-06-05

161 Ensembler: Enabling high-throughput molecular simulations at the superfamily scale

Daniel L Parton;Patrick B Grinaway;Sonya M Hanson;Kyle A Beauchamp;John D Chodera;

10.1101/018036 — Bioinformatics — Posted on 2015-06-29

162 Echo state networks with multiple read-out modules

Andres Laan;

10.1101/017558 — Neuroscience — Posted on 2015-06-07

163 Transcriptome Differences between Alternative Sex Determining Genotypes in the House Fly, Musca domestica

Richard P Meisel;Jeffrey G Scott;Andrew G Clark;

10.1101/016774 — Genomics — Posted on 2015-06-01

164 Two variance component model improves genetic prediction in family data sets

George Tucker;Po-Ru Loh;Iona M MacLeod;Ben J Hayes;Michael E Goddard;Bonnie Berger;Alkes L Price;

10.1101/016618 — Genetics — Posted on 2015-06-10

165 Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis

Po-Ru Loh;Gaurav Bhatia;Alexander Gusev;Hilary K Finucane;Brendan K Bulik-Sullivan;Samuela J Pollack;Schizophrenia Working Group Psychiatric Genomics Consortium;Teresa R de Candia;Sang Hong Lee;Naomi R Wray;Kenneth S Kendler;Michael C O'Donovan;Benjamin M Neale;Nick Patterson;Alkes L Price;

10.1101/016527 — Genetics — Posted on 2015-06-05

166 Detecting hidden diversification shifts in models of trait-dependent speciation and extinction

Jeremy M Beaulieu;Brian C O'Meara;

10.1101/016386 — Evolutionary Biology — Posted on 2015-06-16

167 PoMo: An Allele Frequency-based Approach for Species Tree Estimation

Nicola De Maio;Dominik Schrempf;Carolin Kosiol;

10.1101/016360 — Evolutionary Biology — Posted on 2015-06-03

168 No association between plant mating system & geographic range overlap

Dena Grossenbacher;Ryan Briscoe Runquist;Emma Goldberg;Yaniv Brandvain;

10.1101/016261 — Evolutionary Biology — Posted on 2015-06-15

169 Dissection of a complex disease susceptibility region using a Bayesian stochastic search approach to fine mapping

Chris Wallace;Antony J Cutler;Nikolas Pontikos;Marcin L Pekalski;Oliver S Burren;Jason D Cooper;Arcadio Rubio Garcia;Ricardo C Ferreira;Hui Guo;Neil M Walker;Deborah J Smyth;Stephen S Rich;Suna Onengut-Gumuscu;Stephen S Sawcer;Maria Ban;Sylvia Richardson;John Todd;Linda Wicker;

10.1101/015164 — Genetics — Posted on 2015-06-10

170 Dissection of a complex disease susceptibility region using a Bayesian stochastic search approach to fine mapping

10.1101/015164 — Genetics — Posted on 2015-06-01

171 Transdermal neuromodulation of noradrenergic activity suppresses psychophysiological and biochemical stress responses in humans

William J. Tyler;Alyssa M. Boasso;Hailey M. Mortimore;Rhonda S. Silva;Jonathan D. Charlesworth;Michelle A. Marlin;Kirsten Aebersold;Linh Aven;Daniel Z. Wetmore;Sumon K. Pal;

10.1101/015032 — Neuroscience — Posted on 2015-06-03

172 Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription

Kaur Alasoo;Fernando Martinez Estrada;Christine Hale;Siamon Gordon;Fiona Powrie;Gordon Dougan;Subhankar Mukhopadhyay;Daniel Gaffney;

10.1101/014209 — Immunology — Posted on 2015-06-25

173 Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel

David Houle;Eladio J. Márquez;

10.1101/014936 — Genetics — Posted on 2015-06-11

174 The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly

Chuck Pepe-Ranney;Ed Hall;

10.1101/013938 — Ecology — Posted on 2015-06-19

175 The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly

Chuck Pepe-Ranney;Ed Hall;

10.1101/013938 — Ecology — Posted on 2015-06-09

176 Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation.

Charles Pepe-Ranney;Chantal Koechli;Ruth Potrafka;Cheryl Andam;Erin Eggleston;Ferran Garcia-Pichel;Daniel H Buckley;

10.1101/013813 — Microbiology — Posted on 2015-06-09

177 Independent molecular basis of convergent highland adaptation in maize

Shohei Takuno;Peter Ralph;Kelly Swarts;Rob J Elshire;Jeffrey C Glaubitz;Edward S. Buckler;Matthew B Hufford;Jeffrey Ross-Ibarra;

10.1101/013607 — Evolutionary Biology — Posted on 2015-06-09

178 A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair

Ivo Buchhalter;Barbara Hutter;Tyler S Alioto;Timothy A Beck;Paul C Boutros;Benedikt Brors;Adam P Butler;Sasithorn Chotewutmontri;Robert E Denroche;Sophia Derdak;Nicolle Diessl;Lars Feuerbach;Akihiro Fujimoto;Susanne Gröbner;Marta Gut;Nicholas J Harding;Michael Heinold;Lawrence E Heisler;Jonathan Hinton;Natalie Jäger;David Jones;Rolf Kabbe;Andrey Korshunov;John D McPherson;Andrew Menzies;Hidewaki Nakagawa;Christopher Previti;Keiran Raine;Paolo Ribeca;Sabine Schmidt;Rebecca Shepherd;Lucy Stebbings;Patrick S Tarpey;Jon W Teague;Laurie Tonon;David A Wheeler;Liu Xi;Takafumi N Yamaguchi;Anne-Sophie