bioRxiv directory

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 2014-08-26

28 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 2014-08-21

29 Inference of Cancer Progression Models with Biological Noise

Ilya Korsunsky;Daniele Ramazzotti;Giulio Caravagna;Bud Mishra;

10.1101/008326 — Bioinformatics — Posted on 2014-08-25

30 Inference of Cancer Progression Models with Biological Noise

Ilya Korsunsky;Daniele Ramazzotti;Giulio Caravagna;Bud Mishra;

10.1101/008326 — Bioinformatics — Posted on 2014-08-22

31 Genome-wide Comparative Analysis Reveals Possible Common Ancestors of NBS Domain Containing Genes in Hybrid Citrus sinensis Genome and Original Citrus clementina Genome

Yunsheng Wang;Lijuan Zhou;Dazhi Li;Amy Lawton-Rauh;Pradip K. Srimani;Liangying Dai;Yongping Duan;Feng Luo;

10.1101/008219 — Genomics — Posted on 2014-08-20

32 Dead or just asleep? Variance of microsatellite allele distributions in the human Y-chromosome.

Joe Flood;

10.1101/008227 — Genetics — Posted on 2014-08-21

33 Protein folding and binding can emerge as evolutionary spandrels through structural coupling

Michael Manhart;Alexandre V Morozov;

10.1101/008250 — Evolutionary Biology — Posted on 2014-08-20

34 Coordinated Evolution of Influenza A Surface Proteins

Alexey D. Neverov;Sergey Kryazhimskiy;Joshua B. Plotkin;Georgii A. Bazykin;

10.1101/008235 — Evolutionary Biology — Posted on 2014-08-20

35 Emergent speciation by multiple Dobzhansky-Muller incompatibilities

Tiago Paixão;Kevin E. Bassler;Ricardo B. R. Azevedo;

10.1101/008268 — Evolutionary Biology — Posted on 2014-08-21

36 Emergent speciation by multiple Dobzhansky-Muller incompatibilities

Tiago Paixão;Kevin E. Bassler;Ricardo B. R. Azevedo;

10.1101/008268 — Evolutionary Biology — Posted on 2014-08-20

37 Dual autogenous control of the multiple antibiotic resistance phenotype in Escherichia coli

Guillermo Rodrigo;Djordje Bajic;Ignacio Elola;Juan F Poyatos;

10.1101/008169 — Systems Biology — Posted on 2014-08-19

38 Statistical mechanics of multistable perception

Gurinder Singh Atwal;

10.1101/008177 — Neuroscience — Posted on 2014-08-19

39 Genome sequencing of the perciform fish Larimichthys crocea provides insights into stress adaptation

Jingqun Ao;Yinnan Mu;Li-Xin Xiang;DingDing Fan;MingJi Feng;Shicui Zhang;Qiong Shi;Lv-Yun Zhu;Ting Li;Yang Ding;Li Nie;Qiuhua Li;Wei-ren Dong;Liang Jiang;Bing Sun;XinHui Zhang;Mingyu Li;Hai-Qi Zhang;ShangBo Xie;YaBing Zhu;XuanTing Jiang;Xianhui Wang;Pengfei Mu;Wei Chen;Zhen Yue;Zhuo Wang;Jun Wang;Jian-Zhong Shao;Xinhua Chen;

10.1101/008136 — Genomics — Posted on 2014-08-18

40 The genomic landscape of polymorphic human nuclear mitochondrial insertions

Gargi Dayama;Sarah B Emery;Jeffrey M Kidd;Ryan E Mills;

10.1101/008144 — Genomics — Posted on 2014-08-19

41 Quantitative Genetics and Modularity in cranial and mandibular morphology of Calomys expulsus

Guilherme Garcia;Rui Cerqueira;Erika Hingst-Zaher;Gabriel Marroig;

10.1101/008151 — Evolutionary Biology — Posted on 2014-08-19

42 An amino acid polymorphism in the Drosophila insulin receptor demonstrates pleiotropic and adaptive function in life history traits

Annalise B. Paaby;Alan O. Bergland;Emily L. Behrman;Paul S. Schmidt;

10.1101/008193 — Evolutionary Biology — Posted on 2014-08-19

43 Side-binding proteins modulate actin filament dynamics

Alvaro H. Crevenna;Marcelino Arciniega;Aurelie Dupont;Kaja Kowalska;Oliver Lange;Roland Wedlich-Soldner;Don C. Lamb;

10.1101/008128 — Biophysics — Posted on 2014-08-18

44 CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional Data

Daniele Ramazzotti;Giulio Caravagna;Loes Olde Loohuis;Alex Graudenzi;Ilya Korsunsky;Giancarlo Mauri;Marco Antoniotti;Bud Mishra;

10.1101/008110 — Bioinformatics — Posted on 2014-08-19

45 Understanding Admixture Fractions

Mason Liang;Rasmus Nielsen;

10.1101/008078 — Evolutionary Biology — Posted on 2014-08-16

46 Transposable elements contribute to activation of maize genes in response to abiotic stress

Irina Makarevitch;Amanda J Waters;Patrick T West;Michelle C Stitzer;Jeffrey Ross-Ibarra;Nathan M Springer;

10.1101/008052 — Genomics — Posted on 2014-08-15

47 Long-read, whole genome shotgun sequence data for five model organisms

Kristi E Kim;Paul Peluso;Primo Baybayan;Patricia Jane Yeadon;Charles Yu;William Fisher;Chen-Shan Chin;Nicole A Rapicavoli;David R Rank;Joachim Li;David Catcheside;Susan E Celniker;Adam M Phillippy;Casey M Bergman;Jane M Landolin;

10.1101/008037 — Genomics — Posted on 2014-08-15

48 Long-read, whole genome shotgun sequence data for five model organisms

10.1101/008037 — Genomics — Posted on 2014-08-15

49 Long-read, whole genome shotgun sequence data for five model organisms

10.1101/008037 — Genomics — Posted on 2014-08-15

50 Orb prevents autophagy in the Drosophila germline through translational repression of Atg12 mRNA

Isabelle Busseau;Stephanie Pierson;Dany Severac;Christelle Dantec;Martine Simonelig;

10.1101/007971 — Developmental Biology — Posted on 2014-08-15

51 The impact of radio-tags on Ruby-throated Hummingbirds (Archilochus colubris)

Theodore J Zenzal;Robert H Diehl;Frank R Moore;

10.1101/008029 — Zoology — Posted on 2014-08-14

52 Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo

Max Staller;Ben J. Vincent;Meghan D.J. Bragdon;Tara Lydiard-Martin;Zeba Wunderlich;Javier Estrada;Angela DePace;

10.1101/007922 — Systems Biology — Posted on 2014-08-13

53 Growth of Primary and Lateral Roots of Vicia faba L. in the Solution of Calcium Sulfate

Michael Pyshnov;

10.1101/007716 — Plant Biology — Posted on 2014-08-08

54 Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets

Patrick Danaher;Robin Lynn White;Erin Hanson;Jack Ballantyne;

10.1101/007898 — Genomics — Posted on 2014-08-12

55 Estimating strength of polygenic selection with principal components analysis of spatial genetic variation

Davide Piffer;

10.1101/008011 — Genetics — Posted on 2014-08-14

56 A codon model of nucleotide substitution with selection on synonymous codon usage

Laura Kubatko;Premal Shah;Radu Herbei;Michael Gilchrist;

10.1101/007849 — Evolutionary Biology — Posted on 2014-08-12

57 A Distance Method to Reconstruct Species Trees In the Presence of Gene Flow

Lingfei Cui;Laura Kubatko;

10.1101/007955 — Evolutionary Biology — Posted on 2014-08-14

58 How cultural transmission facilitates a long juvenile learning period

Ryan Baldini;

10.1101/007930 — Evolutionary Biology — Posted on 2014-08-14

59 Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing

Konstantin Berlin;Sergey Koren;Chen-Shan Chin;James Drake;Jane M Landolin;Adam M Phillippy;

10.1101/008003 — Bioinformatics — Posted on 2014-08-14

60 The importance of study design for detecting differentially abundant features in high-throughput experiments

Huaien Luo;Juntao Li;Kuan Hui Burton Chia;Paul Robson;Niranjan Nagarajan;

10.1101/007948 — Bioinformatics — Posted on 2014-08-14

61 RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research

Andrew S. Warren;Cristina Aurrecoechea;Brian Brunk;Prerak Desai;Scott Emrich;Gloria I. Giraldo-Calderón;Omar Harb;Deborah Hix;Daniel Lawson;Dustin Machi;Chunhong Mao;Michael McClelland;Eric Nordberg;Maulik Shukla;Leslie B. Vosshall;Alice R. Wattam;Rebecca Will;Hyun Seung Yoo;Bruno Sobral;

10.1101/007963 — Bioinformatics — Posted on 2014-08-14

62 RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research

10.1101/007963 — Bioinformatics — Posted on 2014-08-14

63 A quantitative analysis of objective feather colour assessment: measurements in the lab are more reliable than in the field

Iker Vaquero-Alba;Andrew McGowan;Daniel Pincheira-Donoso;Matthew R. Evans;Sasha R.X. Dall;

10.1101/007914 — Animal Behavior and Cognition — Posted on 2014-08-13

64 A quantitative analysis of objective feather colour assessment: measurements in the lab are more reliable than in the field

Iker Vaquero-Alba;Andrew McGowan;Daniel Pincheira-Donoso;Matthew R. Evans;Sasha R.X. Dall;

10.1101/007914 — Animal Behavior and Cognition — Posted on 2014-08-12

65 A versatile two-step CRISPR- and RMCE-based strategy for efficient genome engineering in Drosophila

Xu Zhang;Wouter Koolhaas;Frank Schnorrer;

10.1101/007864 — Developmental Biology — Posted on 2014-08-11

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

Jomar Fajardo Rabajante;Ariel Lagdameo Babierra;

10.1101/007831 — Systems Biology — Posted on 2014-08-11

67 Expanding xylose metabolism in yeast for plant cell wall conversion to biofuels

Xin Li;Vivian Y Yu;Yuping Lin;Kulika Chomvong;Raíssa Estrela;Julie M Liang;Elizabeth Znameroski;Joanna Feehan;Soo Rin Kim;Yong-Su Jin;N Louise Glass;Jamie Cate;

10.1101/007807 — Synthetic Biology — Posted on 2014-08-09

68 NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases

Marta Costa;James D. Manton;Aaron D. Ostrovsky;Steffen Prohaska;Gregory S.X.E. Jefferis;

10.1101/006346 — Neuroscience — Posted on 2014-08-09

69 Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life

Santiago Herrera;Paula H. Reyes-Herrera;Timothy M. Shank;

10.1101/007781 — Genomics — Posted on 2014-08-08

70 Efficient Bayesian mixed model analysis increases association power in large cohorts

Po-Ru Loh;George Tucker;Brendan K Bulik-Sullivan;Bjarni J Vilhjalmsson;Hilary K Finucane;Daniel I Chasman;Paul M Ridker;Benjamin M Neale;Bonnie Berger;Nick Patterson;Alkes L Price;

10.1101/007799 — Genetics — Posted on 2014-08-09

71 Mapping migration in a songbird using high-resolution genetic markers

Kristen C Ruegg;Eric Anderson;Kristina Paxton;Vanessa Apkenas;Sirena Lao;Rodney Siegel;Dave DeSante;Frank Moore;Thomas B Smith;

10.1101/007757 — Ecology — Posted on 2014-08-08

72 Seasonality dynamics of avian influenza occurrences in Central and West Africa

Trevon Fuller;Mariette Ducatez;Kevin Njabo;Emanuel Couacy-Hymann;Tony Chasar;G L Aplogan;Sirena Lao;F Awoume;A Tehou;Q Langeois;Scott Krauss;Thomas B Smith;

10.1101/007740 — Ecology — Posted on 2014-08-08

73 Benchmarking undedicated cloud computing providers for analysis of genomic datasets.

Seyhan Yazar;George EC Gooden;David A Mackey;Alex Hewitt;

10.1101/007724 — Bioinformatics — Posted on 2014-08-07

74 Spatial distribution and seasonal fluctuations of Drosophila on Santa Catalina Island with an emphasis on the repleta species group

Joyce Y Kao;Sergey V Nuzhdin;

10.1101/007732 — Ecology — Posted on 2014-08-07

75 Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression

Jessica K. Polka;Pamela A. Silver;

10.1101/007773 — Microbiology — Posted on 2014-08-09

76 Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression

Jessica K. Polka;Pamela A. Silver;

10.1101/007773 — Microbiology — Posted on 2014-08-08

77 Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression

Jessica K. Polka;Pamela A. Silver;

10.1101/007773 — Microbiology — Posted on 2014-08-08

78 Postmating reproductive barriers contribute to the incipient sexual isolation of US and Caribbean Drosophila melanogaster

Joyce Y Kao;Seana Lymer;Sea H Hwang;Albert Sung;Sergey V Nuzhdin;

10.1101/007765 — Evolutionary Biology — Posted on 2014-08-07

79 Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels

Patrick Deelen;Daria Zhernakova;Mark de Haan;Marijke van der Sijde;Marc Jan Bonder;Juha Karjalainen;K. Joeri van der Velde;Kristin M. Abbott;Jingyuan Fu;Cisca Wijmenga;Richard J. Sinke;Morris A. Swertz;Lude Franke;

10.1101/007633 — Genetics — Posted on 2014-08-01

80 Ontogeny of aerial righting and wing flapping in juvenile birds

Dennis Evangelista;Sharlene Cam;Tony Huynh;Igor Krivitskiy;Robert Dudley;

10.1101/007708 — Animal Behavior and Cognition — Posted on 2014-08-06

81 NxTrim: optimized trimming of Illumina mate pair reads

Jared O'Connell;Ole Schulz-Trieglaff;Emma Carlson;Matthew M Hims;Niall A Gormley;Anthony J Cox;

10.1101/007666 — Bioinformatics — Posted on 2014-08-06

82 The evolution of cooperation under local regulation and non-additive gene action: building on Hamilton’s ideas

Roberto H. Schonmann;Robert Boyd;Renato Vicente;

10.1101/007682 — Evolutionary Biology — Posted on 2014-08-06

83 How to make a kin selection model when marginal fitness is non-linear?

Roberto H. Schonmann;Robert Boyd;Renato Vicente;

10.1101/007674 — Evolutionary Biology — Posted on 2014-08-06

84 Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents?

Bjarki Eldon;Matthias Birkner;Jochen Blath;Fabian Freund;

10.1101/007690 — Evolutionary Biology — Posted on 2014-08-06

85 In Silico Design of Self-Optimizing Integrated Metabolic and Gene Regulatory Networks

Timo Maarleveld;Bennet K NG;Herbert Sauro;Kyung Kim;

10.1101/007658 — Bioengineering — Posted on 2014-08-05

86 The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences

N. Ari Wijetunga;Fabien Delahaye;Yong Mei Zhao;Aaron Golden;Jessica C Mar;Francine H. Einstein;John M. Greally;

10.1101/007591 — Genomics — Posted on 2014-08-01

87 The impacts of historical barriers on floristic patterns of plant groups with different dispersal abilities in the Ryukyu Archipelago, Japan

Koh Nakamura;Rempei Suwa;Tetsuo Denda;Masatsugu Yokota;

10.1101/007617 — Ecology — Posted on 2014-08-07

88 The impacts of historical barriers on floristic patterns of plant groups with different dispersal abilities in the Ryukyu Archipelago, Japan

Koh Nakamura;Rempei Suwa;Tetsuo Denda;Masatsugu Yokota;

10.1101/007617 — Ecology — Posted on 2014-08-01

89 The architectural stratification and woody species diversity in subtropical evergreen broadleaf forests along a latitudinal thermal gradient of the Ryukyu Archipelago, Japan

Sm Feroz;Rempei Suwa;Koh Nakamura;Akio Hagihara;Masatsugu Yokota;

10.1101/007625 — Ecology — Posted on 2014-08-07

90 The architectural stratification and woody species diversity in subtropical evergreen broadleaf forests along a latitudinal thermal gradient of the Ryukyu Archipelago, Japan

Sm Feroz;Rempei Suwa;Koh Nakamura;Akio Hagihara;Masatsugu Yokota;

10.1101/007625 — Ecology — Posted on 2014-08-03

91 Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

Richard Wilton;Tamas Budavari;Ben Langmead;Sarah J Wheelan;Steven Salzberg;Alex Szalay;

10.1101/007641 — Bioinformatics — Posted on 2014-08-01

92 UniqTag: Content-derived unique and stable identifiers for gene annotation

Shaun D Jackman;Joerg Bohlmann;Inanc Birol;

10.1101/007583 — Bioinformatics — Posted on 2014-08-01

93 A comparison of control samples for ChIP-seq of histone modifications

Christoffer Flensburg;Sarah A Kinkel;Andrew Keniry;Marnie Blewitt;Alicia Oshlack;

10.1101/007609 — Bioinformatics — Posted on 2014-08-01

94 QuASAR: Quantitative Allele Specific Analysis of Reads

Chris Harvey;Gregory A Moyebrailean;Omar Davis;Xiaoquan Wen;Francesca Luca;Roger Pique-Regi;

10.1101/007492 — Bioinformatics — Posted on 2014-08-03

95 The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia

Bayazit Yunusbayev;Mait Metspalu;Ene Metspalu;Albert Valeev;Sergei Litvinov;Ruslan Valiev;Vita Akhmetova;Elena Balanovska;Oleg Balanovsky;Shahlo Turdikulova;Dilbar Dalimova;Pagbajabyn Nymadawa;Ardeshir Bahmanimehr;Hovhannes Sahakyan;Kristiina Tambets;Sardana Fedorova;Nikolay Barashkov;Irina Khidiatova;Evelin Mihailov;Rita Khusainova;Larisa Damba;Miroslava Derenko;Boris Malyarchuk;Ludmila Osipova;Mikhail Voevoda;Levon Yepiskoposyan;Toomas Kivisild;Elza Khusnutdinova;Richard Villems;

10.1101/005850 — Genetics — Posted on 2014-08-13

96 Exploiting evolutionary non-commutativity to prevent the emergence of bacterial antibiotic resistance

Daniel Nichol;Peter Jeavons;Alexander G Fletcher;Robert A Bonomo;Philip K Maini;Jerome L Paul;Robert A Gatenby;Alexander RA Anderson;Jacob G Scott;

10.1101/007542 — Evolutionary Biology — Posted on 2014-08-03

97 Selection of chromosomal DNA libraries using a multiplex CRISPR system in Saccharomyces cerevisiae

Owen W Ryan;Jeffrey M Skerker;Matthew J Maurer;Xin Li;Jordan C Tsai;Snigdha Poddar;Michael E Lee;Will DeLoache;John E Dueber;Adam P Arkin;Jamie Cate;

10.1101/007310 — Synthetic Biology — Posted on 2014-08-19

98 MINI REVIEW: Statistical methods for detecting differentially methylated loci and regions

Mark D Robinson;Abdullah Kahraman;Charity W Law;Helen Lindsay;Malgorzata Nowicka;Lukas M Weber;Xiaobei Zhou;

10.1101/007120 — Bioinformatics — Posted on 2014-08-29

99 Stress-Induced Mutagenesis and Complex Adaptation

Yoav Ram;Lilach Hadany;

10.1101/007096 — Evolutionary Biology — Posted on 2014-08-25

100 Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

Felipe Zapata;Nerida G. Wilson;Mark Howison;Sónia CS Andrade;Katharina M. Jörger;Michael Schrödl;Freya E. Goetz;Gonzalo Giribet;Casey W. Dunn;

10.1101/007039 — Evolutionary Biology — Posted on 2014-08-21

101 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 2014-08-23

102 Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Robin Andersson;Peter Refsing Andersen;Eivind Valen;Leighton Core;Jette Bornholdt;Mette Boyd;Torben Heick Jensen;Albin Sandelin;

10.1101/005447 — Genomics — Posted on 2014-08-29

103 The conserved PFT1 tandem repeat is crucial for proper flowering in Arabidopsis thaliana

Pauline Rival;Maximilian O Press;Jacob Bale;Tanya Grancharova;Soledad F Undurraga;Christine Queitsch;

10.1101/006437 — Genetics — Posted on 2014-08-04

104 Hsp90 promotes kinase evolution

Jennifer Lachowiec;Tzitziki Lemus;Elhanan Borenstein;Christine Queitsch;

10.1101/006411 — Evolutionary Biology — Posted on 2014-08-04

105 Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels.

Nicholas E Banovich;Xun Lan;Graham McVicker;Bryce Van de Geijn;Jacob F Degner;John D. Blischak;Julien Roux;Jonathan K. Pritchard;Yoav Gilad;

10.1101/006171 — Genomics — Posted on 2014-08-12

106 Restriction and recruitment - gene duplication and the origin and evolution of snake venom toxins

Adam D Hargreaves;Martin T Swain;Matthew J Hegarty;Darren W Logan;John F Mulley;

10.1101/006023 — Evolutionary Biology — Posted on 2014-08-25

107 A Tandem Cell for Nanopore-based DNA Sequencing with Exonuclease

G Sampath;

10.1101/005934 — Bioengineering — Posted on 2014-08-08

108 Untangling cross-frequency coupling in neuroscience

Juhan Aru;Jaan Aru;Viola Priesemann;Michael Wibral;Luiz Lana;Gordon Pipa;Wolf Singer;Raul Vicente;

10.1101/005926 — Neuroscience — Posted on 2014-08-25

109 Lighter: fast and memory-efficient error correction without counting

Li Song;Liliana Florea;Ben Langmead;

10.1101/005579 — Bioinformatics — Posted on 2014-08-07

110 Data-intensive modeling of forest dynamics

Jean F Lienard;Dominique Gravel;Nikolay Strigul;

10.1101/005009 — Ecology — Posted on 2014-08-06

111 Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community.

Diane Saunders;Kentaro Yoshida;Christine Sambles;Rachel Glover;Bernardo Clavijo;Manuel Corpas;Daniel Bunting;Suomeng Dong;Ghanasyam Rallapalli;Matthew Clark;David Swarbreck;Sarah Ayling;Matthew Bashton;Steve Collin;Tsuyoshi Hosoya;Anne Edwards;Lisa Crossman;Graham Etherington;Joe Win;Liliana Cano;David Studholme;J Allan Downie;Mario Caccamo;Sophien Kamoun;Dan MacLean;