bioRxiv directory

Joerg Hagmann;Claude Becker;Jonas Müller;Oliver Stegle;Rhonda C Meyer;Korbinian Schneeberger;Joffrey Fitz;Thomas Altmann;Joy Bergelson;Karsten Borgwardt;Detlef Weigel;

10.1101/009225 — Genomics — Posted on 2014-09-16

49 An introduction to LifeLines DEEP: study design and baseline characteristics

Ettje F Tigchelaar;Alexandra Zhernakova;Jackie A.M. Dekens;Gerben Hermes;Agnieszka Baranska;Zlatan Mujagic;Morris A Swertz;Angélica M Muñoz;Patrick Deelen;Maria C Cénit;Lude Franke;Salome Scholtens;Ronald P Stolk;Cisca Wijmenga;Edith J.M. Feskens;

10.1101/009217 — Genomics — Posted on 2014-09-16

50 Inference of Gorilla demographic and selective history from whole genome sequence data

Kimberly F. McManus;Joanna L. Kelley;Shiya Song;Krishna Veeramah;August E. Woerner;Laurie S. Stevison;Oliver A. Ryder;Great Ape Genome Project;Jeffrey M. Kidd;Jeffrey D. Wall;Carlos D. Bustamante;Michael F. Hammer;

10.1101/009191 — Genomics — Posted on 2014-09-17

51 Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

John Beaulaurier;Shijia Zhu;Robert Sebra;Xue-Song Zhang;Chaggai Rosenbluh;Gintaras Deikus;Nan Shen;Diana Munera;Matthew K Waldor;Martin Blaser;Andrew Chess;Eric Schadt;Gang Fang;

10.1101/007823 — Microbiology — Posted on 2014-09-17

52 Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression

Maxwell W Libbrecht;Ferhat Ay;Michael M Hoffman;David M Gilbert;Jeffrey A Bilmes;William Stafford Noble;

10.1101/009209 — Genomics — Posted on 2014-09-16

53 Functional Antagonism Between CELF and Mbnl Proteins in the Cytoplasm

Eric T. Wang;Amanda J. Ward;Jennifer Cherone;Thomas T. Wang;Jimena Giudice;Thomas A. Cooper;Christopher B. Burge;

10.1101/009183 — Genomics — Posted on 2014-09-16

54 Non-crossover gene conversions show strong GC bias and unexpected clustering in humans

Amy L. Williams;Giulio Geneovese;Thomas Dyer;Nicolas Altemose;Katherine Truax;Goo Jun;Nick Patterson;Simon R. Myers;Joanne E. Curran;Ravi Duggirala;John Blangero;David Reich;Molly Przeworski;the T2D-GENES Consortium;

10.1101/009175 — Genetics — Posted on 2014-09-18

55 Non-crossover gene conversions show strong GC bias and unexpected clustering in humans

10.1101/009175 — Genetics — Posted on 2014-09-16

56 DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication

Karo Michaelian;Norberto Santillán Padilla;

10.1101/009126 — Biophysics — Posted on 2014-09-16

57 Oncogenic mutations of the EGF-Receptor ectodomain reveal an unexpected mechanism for ligand-independent activation

LAURA ORELLANA;ADAM HOSPITAL;MODESTO OROZCO;

10.1101/009068 — Biophysics — Posted on 2014-09-16

58 Interpretable per Case Weighted Ensemble Method for Cancer Associations

Adrin Jalali;Nico Pfeifer;

10.1101/008185 — Bioinformatics — Posted on 2014-09-15

59 Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

Matthew D MacManes;Michael B Eisen;

10.1101/009134 — Genomics — Posted on 2014-09-29

60 Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

Matthew D MacManes;Michael B Eisen;

10.1101/009134 — Genomics — Posted on 2014-09-15

61 Behavioral individuality reveals genetic control of phenotypic variability

Julien F Ayroles;Sean M Buchanan;Chelsea Jenney;Kyobi Skutt-Kakaria;Jennifer Grenier;Andrew G Clark;Daniel L Hartl;Benjamin L de Bivort;

10.1101/009027 — Genetics — Posted on 2014-09-12

62 Behavioral individuality reveals genetic control of phenotypic variability

Julien F Ayroles;Sean M Buchanan;Chelsea Jenney;Kyobi Skutt-Kakaria;Jennifer Grenier;Andrew G Clark;Daniel L Hartl;Benjamin L de Bivort;

10.1101/009027 — Genetics — Posted on 2014-09-11

63 Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands

Joyce Y Kao;Asif Zubair;Matthew P Salomon;Sergey V Nuzhdin;Daniel Campo;

10.1101/009092 — Evolutionary Biology — Posted on 2014-09-13

64 Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Alan O. Bergland;Ray Tobler;Josefa Gonzalez;Paul Schmidt;Dmitri Petrov;

10.1101/009084 — Evolutionary Biology — Posted on 2014-09-13

65 Conservation and structural analysis of the Xenopus laevis phospho-proteome

Jeffrey R Johnson;Silvia D Santos;Tasha Johnson;Ursula Pieper;Andrej Sali;Nevan J Krogan;Pedro Beltrao;

10.1101/009100 — Evolutionary Biology — Posted on 2014-09-14

66 Average genome size estimation enables accurate quantification of gene family abundance and sheds light on the functional ecology of the human microbiome

Stephen Nayfach;Katherine S Pollard;

10.1101/009001 — Bioinformatics — Posted on 2014-09-11

67 General markers of conscious visual perception and their timing

Renate Rutiku;Jaan Aru;Annika Tallinn;Talis Bachmann;

10.1101/008995 — Neuroscience — Posted on 2014-09-11

68 Intrinsic cortical dynamics dominate population responses to natural images across human visual cortex

Linda Henriksson;Seyed-Mahdi Khaligh-Razavi;Kendrick Kay;Nikolaus Kriegeskorte;

10.1101/008961 — Neuroscience — Posted on 2014-09-12

69 Evolving mutation rate advances invasion speed of sexual species

Marleen M. P. Cobben;Alexander Kubisch;

10.1101/008979 — Evolutionary Biology — Posted on 2014-09-11

70 The Sea Lamprey Meiotic Map Resolves Ancient Vertebrate Genome Duplications

Jeramiah Smith;

10.1101/008953 — Genomics — Posted on 2014-09-10

71 Extensive Decoupling of Metabolic Genes in Cancer

Ed Reznik;Chris Sander;

10.1101/008946 — Systems Biology — Posted on 2014-09-09

72 Mechanisms for multiple activity modes of VTA dopamine neurons

Andrew M. Oster;Philippe Faure;Boris S. Gutkin;

10.1101/008920 — Neuroscience — Posted on 2014-09-09

73 Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

Laure Frésard;Sophie Leroux;Pierre-François Roux;C Klopp;Stéphane Fabre;Diane Esquerré;Patrice Dehais;Anis Djari;David Gourichon;Sandrine Lagarrigue;Frédérique Pitel;

10.1101/008912 — Genomics — Posted on 2014-09-09

74 Systematic Imaging Reveals Features of Localized mRNAs and Their Changing Subcellular Destinations in Development

Helena Jambor;Vineeth Surendranath;Alex T. Kalinka;Pavel Mejstrik;Stephan Saalfeld;Pavel Tomancak;

10.1101/008938 — Developmental Biology — Posted on 2014-09-09

75 SPOILS OF WAR AND PEACE: ENEMY ADOPTION AND QUEEN-RIGHT COLONY FUSION FOLLOW COSTLY INTRASPECIFIC CONFLICT IN ACACIA ANTS

Kathleen P. Rudolph;Jay P. McEntee;

10.1101/008904 — Animal Behavior and Cognition — Posted on 2014-09-08

76 MDTraj: a modern, open library for the analysis of molecular dynamics trajectories

Robert T McGibbon;Kyle A Beauchamp;Christian R Schwantes;Lee-Ping Wang;Carlos X Hernández;Matthew P Harrigan;Thomas J Lane;Jason M Swails;Vijay S Pande;

10.1101/008896 — Bioinformatics — Posted on 2014-09-09

77 Myoinhibitory peptide regulates feeding in the marine annelid Platynereis

Elizabeth A Williams;Markus Conzelmann;Gáspár Jékely;

10.1101/008854 — Zoology — Posted on 2014-09-08

78 Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics

Irene Gallego Romero;Bryan J Pavlovic;Irene Hernando-Herraez;Nicholas E Banovich;Courtney L Kagan;Jonathan E Burnett;Constance H Huang;Amy Mitrano;Claudia I Chavarria;Inbar F Ben-Nun;Yingchun Li;Karen Sabatini;Trevor R Leonardo;Mana Parast;Tomas Marques-Bonet;Louise C Laurent;Jeanne F Loring;Yoav Gilad;

10.1101/008862 — Evolutionary Biology — Posted on 2014-09-08

79 Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics

10.1101/008862 — Evolutionary Biology — Posted on 2014-09-06

80 Epigenomic co-localization and co-evolution reveal a key role for 5hmC as a communication hub in the chromatin network of ESCs

David Juan;Juliane Perner;Enrique Carrillo de Santa Pau;Simone Marsili;David Ochoa;Ho-Ryun Chung;Martin Vingron;Daniel Rico;Alfonso Valencia;

10.1101/008821 — Bioinformatics — Posted on 2014-09-06

81 DiffVar: A new method for detecting differential variability with application to methylation in cancer and aging

Belinda Phipson;Alicia Oshlack;

10.1101/008847 — Bioinformatics — Posted on 2014-09-06

82 Synthetic logic circuits using RNA aptamer against T7 RNA polymerase

Jongmin Kim;Juan F Quijano;Enoch Yeung;Richard M Murray;

10.1101/008771 — Synthetic Biology — Posted on 2014-09-04

83 The projection of a test genome onto a reference population and applications to humans and archaic hominins

Melinda A Yang;Kelley Harris;Montgomery Slatkin;

10.1101/008805 — Genomics — Posted on 2014-09-04

84 A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

Jennifer Lachowiec;Xia Shen;Christine Queitsch;Örjan Carlborg;

10.1101/008789 — Genomics — Posted on 2014-09-04

85 Cross-population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

Xiaoquan Wen;Francesca Luca;Roger Pique-Regi;

10.1101/008797 — Genetics — Posted on 2014-09-04

86 Mixed Model with Correction for Case-Control Ascertainment Increases Association Power

tristan hayeck;Noah Zaitlen;Po-Ru Loh;Bjarni Vilhjalmsson;Samuela Pollack;Alexander Gusev;Jian Yang;Guo-Bo Chen;Michael E. Goddard;Peter M. Visscher;Nick Patterson;Alkes Price;

10.1101/008755 — Genetics — Posted on 2014-09-04

87 The dark side of theoretical ecology

Lev V. Kalmykov;

10.1101/008813 — — Posted on 2014-09-04

88 Glucose-lactate metabolic cooperation in cancer: insights from a spatial mathematical model and implications for targeted therapy

Jessica McGillen;Catherine J Kelly;Alicia Martinez-Gonzalez;Natasha K Martin;Eamonn A Gaffney;Philip K Maini;Victor M Perez-Garcia;

10.1101/008839 — Cancer Biology — Posted on 2014-09-04

89 Leveraging transcript quantification for fast computation of alternative splicing profiles

Gael P Alamancos;Amadís Pagès;Juan L Trincado;Nicolás Bellora;Eduardo Eyras;

10.1101/008763 — Bioinformatics — Posted on 2014-09-04

90 Tracing the genetic origin of Europe’s first farmers reveals insights into their social organization

Anna Szécsényi-Nagy;Guido Brandt;Victoria Keerl;János Jakucs;Wolfgang Haak;Sabine Möller-Rieker;Kitti Köhler;Balázs Mende;Marc Fecher;Krisztián Oross;Tibor Paluch;Anett Osztás;Viktória Kiss;György Pálfi;Erika Molnár;Katalin Sebők;András Czene;Tibor Paluch;Mario Šlaus;Mario Novak;Nives Pećina-Šlaus;Brigitta Ősz;Vanda Voicsek;Krisztina Somogyi;Gábor Tóth;Bernd Kromer;Eszter Bánffy;Kurt Alt;

10.1101/008664 — Genetics — Posted on 2014-09-03

91 OncoRep: An n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing

Tobias Meißner;Kathleen M. Fisch;Louis Gioia;Andrew I. Su;

10.1101/008748 — Bioinformatics — Posted on 2014-09-03

92 A high resolution 7-Tesla resting-state fMRI test-retest dataset with cognitive and physiological measures

Krzysztof Jacek Gorgolewski;Natacha Mendes;Domenica Wilfling;Elisabeth Wladimirow;Claudine J. Gauthier;Tyler Bonnen;Florence J. M. Ruby;Robert Trampel;Pierre-Louis Bazin;Roberto Cozatl;Jonathan Smallwood;Daniel S. Margulies;

10.1101/008706 — Neuroscience — Posted on 2014-09-03

93 A Consistent Estimator of the Evolutionary Rate

Krzysztof Bartoszek;Serik Sagitov;

10.1101/008714 — Evolutionary Biology — Posted on 2014-09-02

94 Rate and cost of adaptation in the Drosophila genome

Stephan Schiffels;Michael Lässig;Ville Mustonen;

10.1101/008680 — Evolutionary Biology — Posted on 2014-09-02

95 Direct gamete sequencing reveals no evidence for segregation distortion in house mouse hybrids

Russ Corbett-Detig;Emily Jacobs-Palmer;Daniel Hartl;Hopi Hoekstra;

10.1101/008672 — Evolutionary Biology — Posted on 2014-09-02

96 Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Jared A Grummer;Martha L. Calderón;Adrián Nieto Montes-de Oca;Eric N Smith;Fausto Méndez-de la Cruz;Adam Leaché;

10.1101/008623 — Evolutionary Biology — Posted on 2014-09-02

97 Dimorphic development in Streblospio benedicti: genetic analysis of morphological differences between larval types

Christina Zakas;Matthew V Rockman;

10.1101/008730 — Developmental Biology — Posted on 2014-09-02

98 A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD

Imran S Haque;Kyle A Beauchamp;Vijay S Pande;

10.1101/008631 — Biophysics — Posted on 2014-09-02

99 ProbAlign: a re-alignment method for long sequencing reads

Feng Zeng;Rui Jiang;Guoli Ji;Ting Chen;

10.1101/008698 — Bioinformatics — Posted on 2014-09-02

100 BoCluSt: bootstrap clustering stability algorithm for community detection in networks

Carlos Garcia;

10.1101/008656 — Bioinformatics — Posted on 2014-09-02

101 Modelling reactions catalysed by carbohydrate-active enzymes

Önder Kartal;Oliver Ebenhöh;

10.1101/008615 — Systems Biology — Posted on 2014-09-01

102 Conditional U1 Gene Silencing in Toxoplasma gondii

Manuela S Pieperhoff;Gurman S Pall;Elena Jimenez-Ruis;Sujaan Das;Eleanor H Wong;Joanne Heng;Sylke Mueller;Michael J Blackman;Markus Meissner;

10.1101/008649 — Molecular Biology — Posted on 2014-09-01

103 Mucosal effects of tenofovir 1% gel

Florian Hladik;Adam Burgener;Lamar Ballweber;Raphael Gottardo;Slim Fourati;James Y Dai;Mark J Cameron;Lucia Vojtech;Johanna Strobl;Sean M Hughes;Craig Hoesley;Philip Andrew;Sherri Johnson;Jeanna Piper;David R Friend;T Blake Ball;Ross D. Cranston;Kenneth H Mayer;M Juliana McElrath;Ian McGowan;

10.1101/008607 — Microbiology — Posted on 2014-09-01

104 An analytical approach to bistable biological circuit discrimination using real algebraic geometry

Dan Siegal-Gaskins;Elisa Franco;Tiffany Zhou;Richard M Murray;

10.1101/008581 — Systems Biology — Posted on 2014-09-04

105 Sensitivity of quantitative traits to mutational effects, number of loci, and population history

Joshua G. Schraiber;Michael J. Landis;

10.1101/008540 — Evolutionary Biology — Posted on 2014-09-04

106 Rational design and adaptive management of combination therapies for Hepatitis C virus infection

Ruian Ke;Claude Loverdo;Hangfei Qi;Ren Sun;James O Lloyd-Smith;

10.1101/008466 — Evolutionary Biology — Posted on 2014-09-08

107 Perturbation biology models predict c-Myc as an effective co-target in RAF inhibitor resistant melanoma cells

Anil Korkut;Weiqing Wang;Emek Demir;B?lent Arman Aksoy;Xiaohong Jing;Evan Molinelli;?zg?n Babur;Debra Bemis;David B Solit;Christine Pratilas;Chris Sander;

10.1101/008201 — Cancer Biology — Posted on 2014-09-11

108 Branching and oscillations in the epigenetic landscape of cell-fate determination

Jomar Fajardo Rabajante;Ariel Lagdameo Babierra;

10.1101/007831 — Systems Biology — Posted on 2014-09-13

109 Branching and oscillations in the epigenetic landscape of cell-fate determination

Jomar Fajardo Rabajante;Ariel Lagdameo Babierra;

10.1101/007831 — Systems Biology — Posted on 2014-09-04

110 Conservation of expression regulation throughout the animal kingdom

Michael Kuhn;Andreas Beyer;

10.1101/007252 — Bioinformatics — Posted on 2014-09-02

111 Chromosomal distribution of cyto-nuclear genes in a dioecious plant with sex chromosomes

Josh Hough;J Arvid Agren;Spencer CH Barrett;Stephen I Wright;

10.1101/007047 — Evolutionary Biology — Posted on 2014-09-05

112 Convergent Evolution During Local Adaptation to Patchy Landscapes

Peter L. Ralph;Graham Coop;

10.1101/006940 — Evolutionary Biology — Posted on 2014-09-08

113 Probabilities of Fitness Consequences for Point Mutations Across the Human Genome

Brad Gulko;Ilan Gronau;Melissa J Hubisz;Adam Siepel;

10.1101/006825 — Genomics — Posted on 2014-09-11

114 Detecting pairwise correlations in spike trains: an objective comparison of methods and application to the study of retinal waves.

Catherine Sarah Cutts;Stephen J Eglen;

10.1101/006635 — Neuroscience — Posted on 2014-09-09

115 Reducing INDEL calling errors in whole-genome and exome sequencing data

Han Fang;Yiyang Wu;Giuseppe Narzisi;Jason A. O'Rawe;Laura T. Jimenez Barrón;Julie Rosenbaum;Michael Ronemus;Ivan Iossifov;Michael C. Schatz;Gholson J. Lyon;

10.1101/006148 — Bioinformatics — Posted on 2014-09-17

116 Recombination impacts damaging and disease mutation accumulation in human populations

Julie Hussin;Alan Hodgkinson;Youssef Idaghdour;Jean-Christophe Grenier;Jean-Philippe Goulet;Elias Gbeha;Elodie Hip-Ki;Philip Awadalla;

10.1101/006064 — Evolutionary Biology — Posted on 2014-09-10

117 Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)

Laura Vann;Thomas Kono;Tanja Pyha ̈j ̈arvi;Matthew B Hufford;Jeffrey Ross-Ibarra;

10.1101/005819 — Evolutionary Biology — Posted on 2014-09-11

118 Cancer-associated recurrent mutations in RNase III domains of DICER1

Bülent Arman Aksoy;Anders Jacobsen;Robert J Fieldhouse;William Lee;Emek Demir;Giovanni Ciriello;Nikolaus Schultz;Debora S Marks;Chris Sander;

10.1101/005686 — Cancer Biology — Posted on 2014-09-12

119 Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia

Simone Ecker;Vera Pancaldi;Daniel Rico;Alfonso Valencia;

10.1101/005637 — Cancer Biology — Posted on 2014-09-03

120 diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals

Paula Tataru;Jasmine A. Nirody;Yun S. Song;

10.1101/005082 — Bioinformatics — Posted on 2014-09-03

121 Pushed beyond the brink: Allee effects, environmental stochasticity, and extinction

Gregory Roth;Sebastian Schreiber;

10.1101/004887 — Ecology — Posted on 2014-09-02

122 Sequence co-evolution gives 3D contacts and structures of protein complexes

Thomas A. Hopf;Charlotta P.I. Schärfe;João P.G.L.M. Rodrigues;Anna G. Green;Chris Sander;Alexandre M.J.J. Bonvin;Debora S. Marks;

10.1101/004762 — Bioinformatics — Posted on 2014-09-15

123 Unravelling the diversity behind Ophiocordyceps unilateralis complex: Three new species of Zombie-Ant fungus from Brazilian Amazon

João Araújo;Harry C Evans;David M Geiser;William P Mackay;David P Hughes;

10.1101/003806 — Evolutionary Biology — Posted on 2014-09-29

124 Protected polymorphisms and evolutionary stability of patch-selection strategies in stochastic environments

Steve Evans;Alexandru Hening;Sebastian Schreiber;

10.1101/003780 — Evolutionary Biology — Posted on 2014-09-02

125 Exploring the spatially explicit predictions of the Maximum Entropy Theory of Ecology

Daniel McGlinn;Xiao Xiao;Justin Kitzes;Ethan P White;

10.1101/003657 — Ecology — Posted on 2014-09-02

126 Flexible analysis of transcriptome assemblies with Ballgown

Alyssa C Frazee;Geo Pertea;Andrew E Jaffe;Ben Langmead;Steven L Salzberg;Jeffrey T Leek;

10.1101/003665 — Bioinformatics — Posted on 2014-09-05

127 Genetic influences on translation in yeast

Frank W. Albert;Dale Muzzey;Jonathan S. Weissman;Leonid Kruglyak;

10.1101/003319 — Genetics — Posted on 2014-09-02

128 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 2014-09-16

129 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 2014-09-26

130 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 2014-09-30

131 U2AF1 mutations alter splice site recognition in hematological malignancies

Janine O Ilagan;Aravind Ramakrishnan;Brian Hayes;Michele E Murphy;Ahmad S Zebari;Philip Bradley;Robert K Bradley;

10.1101/001107 — Cancer Biology — Posted on 2014-09-29

132 A Population Genetic Signature of Polygenic Local Adaptation

Jeremy J Berg;Graham Coop;

10.1101/000026 — Genetics — Posted on 2014-09-08

Archive, 2014-09