bioRxiv directory

Akihiro Shimokawa;Yuki Tonooka;Misato Matsumoto;Hironori Ara;Hiroshi Suzuki;Naoki Yamauchi;Masayoshi Shigyo;

10.1101/003103 — Plant Biology — Posted on 2014-02-28

3 High Bacterial Load Predicts Poor Outcomes in Patients with Idiopathic Pulmonary Fibrosis

Philip Molyneaux;Michael Cox;Saffron Willis-Owen;Kirsty Russell;Patrick Mallia;Anne-Marie Russell;Sebastian Johnston;Athol Wells;William Cookson;Toby Maher;Miriam Moffatt;

10.1101/003145 — Microbiology — Posted on 2014-02-28

4 A novel inference of the fundamental biodiversity number for multiple immigration-limited communities

Champak Beeravolu Reddy;François Munoz;Pierre Couteron;

10.1101/003137 — Ecology — Posted on 2014-02-28

5 Genomic Repeat Element Analyzer for Mammals (GREAM)

Darshan S Chandrashekar;Poulami Dey;Kshitish K Acharya;

10.1101/003111 — Bioinformatics — Posted on 2014-02-28

6 DNA methylation modulates transcription factor occupancy chiefly at sites of high intrinsic cell-type variability

Matthew Maurano;Hao Wang;Sam John;Anthony Shafer;Theresa Canfield;Kristen Lee;John A Stamatoyannopoulos;

10.1101/003061 — Genomics — Posted on 2014-02-27

7 On a solution of the biodiversity paradox and a competitive coexistence principle

Lev V. Kalmykov;Vyacheslav L. Kalmykov;

10.1101/003095 — Ecology — Posted on 2014-02-27

8 Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

Boryana Doyle;Geoffrey Fudenberg;Maxim Imakaev;Leonid Mirny;

10.1101/003087 — Biophysics — Posted on 2014-02-26

9 Genetic drift opposes mutualism during spatial population expansion

Melanie JI Mueller;Beverly I Neugeboren;David R Nelson;Andrew W Murray;

10.1101/003012 — Evolutionary Biology — Posted on 2014-02-25

10 Neanderthals had our de novo genes.

John Stewart Taylor;

10.1101/003004 — Evolutionary Biology — Posted on 2014-02-25

11 A tug-of-war between driver and passenger mutations in cancer and other adaptive processes

Christopher Dennis McFarland;Leonid A Mirny;Kirill S Korolev;

10.1101/003053 — Cancer Biology — Posted on 2014-02-26

12 Extensive translation of small ORFs revealed by polysomal ribo-Seq

Julie L Aspden;Ying Chen Eyre-Walker;Rose J. Phillips;Michele Brocard;Unum Amin;Juan Couso;

10.1101/002998 — Genomics — Posted on 2014-02-24

13 Genetic drift suppresses bacterial conjugation in spatially structured populations

Peter D. Freese;Kirill S. Korolev;Jose I Jimenez;Irene A. Chen;

10.1101/002980 — Biophysics — Posted on 2014-02-24

14 T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Anna-Sophie Fiston-Lavier;Maite G. Barrón;Dmitri A. Petrov;Josefa González;

10.1101/002964 — Bioinformatics — Posted on 2014-02-24

15 Efficient synergistic single-cell genome assembly

Narjes S. Movahedi;Zeinab Taghavi;Mallory Embree;Harish Nagarajan;Karsten Zengler;Hamidreza Chitsaz;

10.1101/002972 — Bioinformatics — Posted on 2014-02-24

16 Population diversification in a yeast metabolic program promotes anticipation of environmental shifts

Ophelia S Venturelli;Ignacio Zuleta;Richard M Murray;Hana El-Samad;

10.1101/002907 — Systems Biology — Posted on 2014-02-21

17 Spatial Information in Large-Scale Neural Recordings

Thaddeus R Cybulski;Joshua I Glaser;Adam H Marblestone;Bradley M Zamft;Edward S Boyden;George M Church;Konrad P Kording;

10.1101/002923 — Neuroscience — Posted on 2014-02-21

18 LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies

Brendan Bulik-Sullivan;Po-Ru Loh;Hilary Finucane;Stephan Ripke;Jian Yang;Schizophrenia Working Group Psychiatric Genomics Consortium;Nick Patterson;Mark J Daly;Alkes L Price;Benjamin M Neale;

10.1101/002931 — Genomics — Posted on 2014-02-21

19 Functional normalization of 450k methylation array data improves replication in large cancer studies

Jean-Philippe Fortin;Aurelie Labbe;Mathieu Lemire;Brent W. Zanke;Thomas J. Hudson;Elana J. Fertig;Celia M.T. Greenwood;Kasper D. Hansen;

10.1101/002956 — Bioinformatics — Posted on 2014-02-23

20 No evidence that natural selection has been less effective at removing deleterious mutations in Europeans than in West Africans

Ron Do;Daniel Balick;Heng Li;Ivan Adzhubei`;Shamil Sunyaev;David Reich;

10.1101/002865 — Evolutionary Biology — Posted on 2014-02-20

21 Mapping the structure of drosophilid behavior

Gordon J Berman;Daniel M Choi;William Bialek;Joshua W Shaevitz;

10.1101/002873 — Evolutionary Biology — Posted on 2014-02-20

22 An experimentally determined evolutionary model dramatically improves phylogenetic fit

Jesse D Bloom;

10.1101/002899 — Evolutionary Biology — Posted on 2014-02-20

23 Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I Love;Wolfgang Huber;Simon Anders;

10.1101/002832 — Bioinformatics — Posted on 2014-02-19

24 HTSeq - A Python framework to work with high-throughput sequencing data

Simon Anders;Paul Theodor Pyl;Wolfgang Huber;

10.1101/002824 — Bioinformatics — Posted on 2014-02-20

25 A GWAS platform built on iPlant cyber-infrastructure

Liya Wang;Doreen Ware;Carol Lushbough;Nirav Merchant;Lincoln Stein;

10.1101/002881 — Bioinformatics — Posted on 2014-02-20

26 Widespread signals of convergent adaptation to high altitude in Asia and America

Matthieu Foll;Oscar E. Gaggiotti;Josephine T. Daub;Alexandra Vatsiou;Laurent Excoffier;

10.1101/002816 — Genetics — Posted on 2014-02-19

27 Widespread signals of convergent adaptation to high altitude in Asia and America

Matthieu Foll;Oscar E. Gaggiotti;Josephine T. Daub;Alexandra Vatsiou;Laurent Excoffier;

10.1101/002816 — Genetics — Posted on 2014-02-19

28 Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa

Chiara Barbieri;Mário Vicente;Sandra Oliveira;Koen Bostoen;Jorge Rocha;Mark Stoneking;Brigitte Pakendorf;

10.1101/002808 — Evolutionary Biology — Posted on 2014-02-18

29 ESCRT-0 is not required for ectopic Notch activation and tumor suppression in Drosophila

Emiliana Tognon;Nadine Wollscheid;Katia Cortese;Carlo Tacchetti;thomas vaccari;

10.1101/002790 — Developmental Biology — Posted on 2014-02-18

30 Fluorescent sensors for activity and regulation of the nitrate transceptor CHL1/NRT1.1 and oligopeptide transporters

Cheng Hsun Ho;Wolf B. Frommer;

10.1101/002741 — Cell Biology — Posted on 2014-02-18

31 A Novel Approach for Multi-Domain and Multi-Gene Family Identification Provides Insights into Evolutionary Dynamics of Disease Resistance Genes in Core Eudicot Plants

Johannes A. Hofberger;Beifei Zhou;Haibao Tang;Jonathan DG Jones;M. Eric Schranz;

10.1101/002766 — Genomics — Posted on 2014-02-17

32 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 2014-02-19

33 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 2014-02-17

34 Immune stimulation reduces sleep and memory ability in Drosophila melanogaster

Eamonn Mallon;Akram Alghamdi;Robert Holdbrook;Ezio Rosato;

10.1101/002717 — Zoology — Posted on 2014-02-14

35 Synthesis and patterning of tunable multiscale materials with engineered cells

Allen Y Chen;Urartu O.S. Seker;Michelle Y Lu;Robert J Citorik;Timothy Lu;

10.1101/002659 — Synthetic Biology — Posted on 2014-02-14

36 Neuroanatomical diversity of corpus callosum and brain volume in the Autism Brain Imaging Data Exchange (Abide) project

Aline Lefebvre;Anita Beggiato;Thomas Bourgeron;Roberto Toro;

10.1101/002691 — Neuroscience — Posted on 2014-02-15

37 Neuroanatomical diversity of corpus callosum and brain volume in the Autism Brain Imaging Data Exchange (Abide) project

Aline Lefebvre;Anita Beggiato;Thomas Bourgeron;Roberto Toro;

10.1101/002691 — Neuroscience — Posted on 2014-02-14

38 Genomic V-gene repertoire in reptiles

David N Olivieri;Bernardo von Haeften;Christian Sánchez-Espinel;Jose Faro;Francisco Gambón-Deza;

10.1101/002618 — Immunology — Posted on 2014-02-12

39 The immunologic V-gene repertoire in mammals

David N Olivieri;Bernardo von Haeften;Christian Sánchez-Espinel;Francisco Gambón-Deza;

10.1101/002667 — Immunology — Posted on 2014-02-13

40 Cell specific eQTL analysis without sorting cells

Harm-Jan Westra;Danny Arends;Tõnu Esko;Marjolein J. Peters;Claudia Schurmann;Katharina Schramm;Johannes Kettunen;Hanieh Yaghootkar;Benjamin Fairfax;Anand Kumar Andiappan;Yang Li;Jingyuan Fu;Juha Karjalainen;Mathieu Platteel;Marijn Visschedijk;Rinse Weersma;Silva Kasela;Lili Milani;Liina Tserel;Pärt Peterson;Eva Reinmaa;Albert Hofman;André G. Uitterlinden;Fernando Rivadeneira;Georg Homuth;Astrid Petersmann;Roberto Lorbeer;Holger Prokisch;Thomas Meitinger;Christian Herder;Michael Roden;Harald Grallert;Samuli Ripatti;Markus Perola;Adrew R. Wood;David Melzer;Luigi Ferrucci;Andrew B. Singleton;Dena

10.1101/002600 — Genetics — Posted on 2014-02-12

41 Differential gene expression and alternative splicing in insect immune specificity

Carolyn Riddell;Juan David Lobaton Garces;Sally Adams;Seth M Barribeau;David Twell;Eamonn Mallon;

10.1101/002709 — Evolutionary Biology — Posted on 2014-02-15

42 Differential gene expression and alternative splicing in insect immune specificity

Carolyn Riddell;Juan David Lobaton Garces;Sally Adams;Seth M Barribeau;David Twell;Eamonn Mallon;

10.1101/002709 — Evolutionary Biology — Posted on 2014-02-14

43 Evolutionary rates for multivariate traits: the role of selection and genetic variation

William Pitchers;Jason B. Wolf;Tom Tregenza;John Hunt;Ian Dworkin;

10.1101/002683 — Evolutionary Biology — Posted on 2014-02-14

44 Evolutionary rates for multivariate traits: the role of selection and genetic variation

William Pitchers;Jason B. Wolf;Tom Tregenza;John Hunt;Ian Dworkin;

10.1101/002683 — Evolutionary Biology — Posted on 2014-02-14

45 mangal - making ecological network analysis simple

Timothée E Poisot;Benjamin Baiser;Jennifer A Dunne;Sonia Kéfi;Francois Massol;Nicolas Mouquet;Tamara N Romanuk;Daniel B Stouffer;Spencer A Wood;Dominique Gravel;

10.1101/002634 — Ecology — Posted on 2014-02-12

46 Production of systemically circulating Hedgehog by the intestine couples nutrition to growth and development

Jonathan Rodenfels;Oksana Lavrynenko;Sophie Ayciriex;Julio L Sampaio;Maria Carvalho;Andrej Shevchenko;Suzanne Eaton;

10.1101/002626 — Developmental Biology — Posted on 2014-02-14

47 Non-specificity of Pitstop 2 in clathrin-mediated endocytosis

Anna K Willox;Yasmina M.E. Sahraoui;Stephen J Royle;

10.1101/002675 — Cell Biology — Posted on 2014-02-13

48 A reassessment of consensus clustering for class discovery

Yasin Şenbabaoğlu;George Michailidis;Jun Z Li;

10.1101/002642 — Bioinformatics — Posted on 2014-02-15

49 A reassessment of consensus clustering for class discovery

Yasin Şenbabaoğlu;George Michailidis;Jun Z Li;

10.1101/002642 — Bioinformatics — Posted on 2014-02-14

50 Spectacle: Faster and more accurate chromatin state annotation using spectral learning

Jimin Song;Kevin C Chen;

10.1101/002725 — Bioinformatics — Posted on 2014-02-14

51 Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora

Robert J Williamson;Emily B Josephs;Adrian E Platts;Khaled M Hazzouri;Annabelle Haudry;Mathieu Blanchette;Stephen I Wright;

10.1101/002428 — Evolutionary Biology — Posted on 2014-02-10

52 Estimating the evolution of human life history traits in age-structured populations

Ryan Baldini;

10.1101/002584 — Evolutionary Biology — Posted on 2014-02-19

53 Estimating the evolution of human life history traits in age-structured populations

Ryan Baldini;

10.1101/002584 — Evolutionary Biology — Posted on 2014-02-11

54 Social, spatial and temporal segregation in an ant society

Lauren E Quevillon;Ephraim M Hanks;Shweta Bansal;David P Hughes;

10.1101/002519 — Ecology — Posted on 2014-02-11

55 Sashimi plots: Quantitative visualization of alternative isoform expression from RNA-seq data

Yarden Katz;Eric T Wang;Jacob Stilterra;Schraga Schwartz;Bang Wong;Helga Thorvaldsdóttir;James T Robinson;Jill P Mesirov;Edoardo M Airoldi;Christopher B Burge;

10.1101/002576 — Bioinformatics — Posted on 2014-02-11

56 Noradrenergic plasticity of olfactory sensory neuron inputs to the main olfactory bulb

Dennis Eckmeier;Stephen David Shea;

10.1101/002550 — Neuroscience — Posted on 2014-02-09

57 Metabolic composition of anode community predicts electrical power in microbial fuel cells

Andre Gruning;Nelli J Beecroft;Claudio Avignone-Rossa;

10.1101/002337 — Microbiology — Posted on 2014-02-07

58 Epistasis within the MHC contributes to the genetic architecture of celiac disease

Ben Goudey;Gad Abraham;Eder Kikianty;Qiao Wang;Dave Rawlinson;Fan Shi;Izhak Haviv;Linda Stern;Adam Kowalczyk;Michael Inouye;

10.1101/002485 — Genomics — Posted on 2014-02-20

59 Epistasis within the MHC contributes to the genetic architecture of celiac disease

Ben Goudey;Gad Abraham;Eder Kikianty;Qiao Wang;Dave Rawlinson;Fan Shi;Izhak Haviv;Linda Stern;Adam Kowalczyk;Michael Inouye;

10.1101/002485 — Genomics — Posted on 2014-02-07

60 The roles of standing genetic variation and evolutionary history in determining the evolvability of anti-predator strategies

Jordan Fish;Daniel R O'Donnell;Abhijna Parigi;Ian Dworkin;Aaron P Wagner;

10.1101/002493 — Evolutionary Biology — Posted on 2014-02-07

61 Investigating speciation in face of polyploidization: what can we learn from approximate Bayesian computation approach?

Camille Roux;John Pannell;

10.1101/002527 — Evolutionary Biology — Posted on 2014-02-09

62 Within the fortress: A specialized parasite of ants is not evicted

Emilia S. Gracia;Charissa de Bekker;Jim Russell;Kezia Manlove;Ephraim Hanks;David P. Hughes;

10.1101/002501 — Ecology — Posted on 2014-02-12

63 Within the fortress: A specialized parasite of ants is not evicted

Emilia S. Gracia;Charissa de Bekker;Jim Russell;Kezia Manlove;Ephraim Hanks;David P. Hughes;

10.1101/002501 — Ecology — Posted on 2014-02-07

64 Automated ensemble assembly and validation of microbial genomes

Sergey Koren;Todd J Treangen;Christopher M Hill;Mihai Pop;Adam M Phillippy;

10.1101/002469 — Bioinformatics — Posted on 2014-02-07

65 Broadly tuned and respiration-independent inhibition in the olfactory bulb of awake mice

Brittany N Cazakoff;Billy Y B Lau;Kerensa L Crump;Heike Demmer;Stephen David Shea;

10.1101/002410 — Neuroscience — Posted on 2014-02-06

66 Biochemical ‘Cambrian’ explosion-implosions: the generation and pruning of genetic codes

Rodrick Wallace;

10.1101/002436 — Evolutionary Biology — Posted on 2014-02-06

67 Methods to study toxic transgenes in C. elegans: an analysis of protease-dead separase in the C. elegans embryo

Diana M Mitchell;Lindsey R Uehlein;Joshua Bembenek;

10.1101/002444 — Cell Biology — Posted on 2014-02-06

68 Genetic variants associated with motion sickness point to roles for inner ear development, neurological processes, and glucose homeostasis

Bethann S Hromatka;Joyce Y Tung;Amy K Kiefer;Chuong B Do;David A Hinds;Nicholas Eriksson;

10.1101/002386 — Genetics — Posted on 2014-02-04

69 Evolutionary dynamics of shared niche construction

Philip Gerlee;Alexander RA Anderson;

10.1101/002378 — Evolutionary Biology — Posted on 2014-02-05

70 A phase diagram for gene selection and disease classification

Hong-Dong Li;Qing-Song Xu;Yi-Zeng Liang;

10.1101/002360 — Bioinformatics — Posted on 2014-02-05

71 A phase diagram for gene selection and disease classification

Hong-Dong Li;Qing-Song Xu;Yi-Zeng Liang;

10.1101/002360 — Bioinformatics — Posted on 2014-02-04

72 SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data

Sandra Steyaert;Wim Van Criekinge;Ayla De Paepe;Simon Denil;Klaas Mensaert;Katrien Vandepitte;Wim Vanden Berghe;Geert Trooskens;Tim De Meyer;

10.1101/002352 — Bioinformatics — Posted on 2014-02-04

73 The organization and dynamics of corticostriatal pathways link the medial orbitofrontal cortex to future decisions

Timothy Verstynen;

10.1101/002311 — Neuroscience — Posted on 2014-02-03

74 Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data

Richard W Lusk;

10.1101/002279 — Genomics — Posted on 2014-02-06

75 Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms

Fernando Racimo;Joshua G Schraiber;

10.1101/002345 — Genetics — Posted on 2014-02-04

76 FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation.

Jerven Bolleman;Christopher J Mungall;Francesco Strozzi;Joachim Baran;Michel Dumontier;Raoul J P Bonnal;Robert Buels;Robert Hoehndorf;Takatomo Fujisawa;Toshiaki Katayama;Peter J A Cock;

10.1101/002121 — Bioinformatics — Posted on 2014-02-02

77 FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation.

Jerven Bolleman;Christopher J Mungall;Francesco Strozzi;Joachim Baran;Michel Dumontier;Raoul J P Bonnal;Robert Buels;Robert Hoehndorf;Takatomo Fujisawa;Toshiaki Katayama;Peter J A Cock;

10.1101/002121 — Bioinformatics — Posted on 2014-02-01

78 Modeling bi-modality improves characterization of cell cycle on gene expression in single cells

Lucas Dennis;Andrew McDavid;Patrick Danaher;Greg Finak;Michael Krouse;Alice Wang;Philippa Webster;Joseph Beechem;Raphael Gottardo;

10.1101/002295 — Bioinformatics — Posted on 2014-02-03

79 Improving Protein Docking with Constraint Programming and Coevolution Data

Ludwig Krippahl;Fábio Madeira;

10.1101/002329 — Bioinformatics — Posted on 2014-02-03

80 Significantly distinct branches of hierarchical trees: A framework for statistical analysis and applications to biological data

Guoli Sun;Alexander Krasnitz;

10.1101/002188 — Bioinformatics — Posted on 2014-02-12

81 Significantly distinct branches of hierarchical trees: A framework for statistical analysis and applications to biological data

Guoli Sun;Alexander Krasnitz;

10.1101/002188 — Bioinformatics — Posted on 2014-02-10

82 Linking indices for biodiversity monitoring to extinction risk theory

Michael A. McCarthy;Alana L. Moore;Jochen Krauss;John W Morgan;Christopher F. Clements;

10.1101/000760 — Ecology — Posted on 2014-02-07

83 Human genetics and clinical aspects of neurodevelopmental disorders

Gholson J Lyon;Jason O'Rawe;

10.1101/000687 — Genetics — Posted on 2014-02-20

84 Joint analysis of functional genomic data and genome-wide association studies of 18 human traits

Joseph Pickrell;

10.1101/000752 — Genomics — Posted on 2014-02-25

85 A data repository and analysis framework for spontaneous neural activity recordings in developing retina

Stephen Eglen;Michael Weeks;Mark Jessop;Jennifer Simonotto;Tom Jackson;Evelyne Sernagor;

10.1101/000455 — Neuroscience — Posted on 2014-02-18

86 An unmet actin requirement explains the mitotic inhibition of clathrin-mediated endocytosis

Satdip Kaur;Andrew B Fielding;Gisela Gassner;Nicholas J Carter;Stephen J Royle;

10.1101/001701 — Cell Biology — Posted on 2014-02-18

87 The Toxoplasma Acto-MyoA Motor Complex Is Important but Not Essential for Gliding Motility and Host Cell Invasion

Saskia Egarter;Nicole Andenmatten;Allison J Jackson;Jamie A Whitelaw;Gurmann Pall;Jennifer A Black;David JP Ferguson;Isabelle Tardieux;Alex Mogilner;Markus Meissner;

10.1101/001800 — Cell Biology — Posted on 2014-02-12

Archive, 2014-02