bioRxiv directory

Scott C Ritchie;Peter Würtz;Artika P Nath;Gad Abraham;Aki S Havulinna;Antti J Kangas;Pasi Soininen;Kristiina Aalto;Ilkka Seppälä;Emma Raitoharju;Marko Salmi;Mikael Maksimow;Satu Männistö;Mika Kähönen;Markus Juonala;Terho Lehtimäki;Sirpa Jalkanen;Markus Perola;Olli Raitakari;Veikko Salomaa;Mika Ala-Korpela;Johannes Kettunen;Michael Inouye;

10.1101/018655 — Genomics — Posted on 2015-04-28

14 Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns

Tychele Turner;Christopher Douville;Dewey Kim;Peter D Stenson;David N Cooper;Aravinda Chakravarti;Rachel Karchin;

10.1101/018648 — Genetics — Posted on 2015-04-27

15 Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans

Can Cenik;Elif Sarinay Cenik;Gun W Byeon;Fabian Grubert;Sophie I Candille;Damek Spacek;Bilal Alsallakh;Hagen Tilgner;Carlos L Araya;Hua Tang;Emiliano Ricci;Michael P Snyder;

10.1101/018572 — Genomics — Posted on 2015-04-26

16 Selection for Intermediate Genotypes Enables a Key Innovation in Phage Lambda

Alita Burmeister;Richard Lenski;Justin Meyer;

10.1101/018606 — Evolutionary Biology — Posted on 2015-04-27

17 Regime shifts in the Anthropocene: drivers, risks, and resilience

Juan Carlos Carlos Rocha;Garry D Peterson;Reinette Oonsie Biggs;

10.1101/018549 — Ecology — Posted on 2015-04-28

18 Big city, small world: Density, contact rates, and transmission of dengue across Pakistan.

Moritz U. G. Kraemer;T. Alex Perkins;Derek A.T. Cummings;Rubeena Zakar;Simon I. Hay;David L. Smith;Robert C. Reiner;

10.1101/018481 — Ecology — Posted on 2015-04-27

19 Evaluating different passive optical clearing protocols for two-photon deep tissue imaging in adult intact visceral and neuronal organs

R.C Vlieg;C Gillespie;W M Steve Lee;

10.1101/018622 — Bioengineering — Posted on 2015-04-27

20 Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.

Phelim Bradley;N Claire Gordon;Timothy M Walker;Laura Dunn;Simon Heys;Bill Huang;Sarah Earle;Louise J Pankhurst;Luke Anson;Mariateresa de Cesare;Paolo Piazza;Antonina A Votintseva;Tanya Golubchik;Daniel J Wilson;David H Wyllie;Roland Diel;Stefan Niemann;Silke Feuerriegel;Thomas A Kohl;Nazir Ismail;Shaheed V Omar;E Grace Smith;David Buck;Gil McVean;A Sarah Walker;Tim Peto;Derrick Crook;Zamin Iqbal;

10.1101/018564 — Genomics — Posted on 2015-04-26

21 Pluripotency Conversion of Gene Studied from Quantum Folding Theory

Liaofu Luo;

10.1101/018580 — Biophysics — Posted on 2015-04-26

22 Acute and chronic gregarisation are associated with distinct DNA methylation fingerprints in desert locusts

Eamonn B Mallon;Harindra E Amarasinghe;Swidbert R Ott;

10.1101/018499 — Zoology — Posted on 2015-04-24

23 Metagenome-assembled genomes uncover a global brackish microbiome

Luisa W Hugerth;John Larsson;Johannes Alneberg;Markus V Lindh;Catherine Legrand;Jarone Pinhassi;Anders F Andersson;

10.1101/018465 — Microbiology — Posted on 2015-04-24

24 Metagenome-assembled genomes uncover a global brackish microbiome

Luisa W Hugerth;John Larsson;Johannes Alneberg;Markus V Lindh;Catherine Legrand;Jarone Pinhassi;Anders F Andersson;

10.1101/018465 — Microbiology — Posted on 2015-04-23

25 Elephantid genomes reveal the molecular bases of Woolly Mammoth adaptations to the arctic

Vincent Lynch;Oscar C. Bedoya-Reina;Aakrosh Ratan;Michael Sulak;Daniela I. Drautz-Moses;George H. Perry;Webb Miller;Stephan C. Schuster;

10.1101/018366 — Genomics — Posted on 2015-04-23

26 Measuring the Landscape of CpG Methylation of Individual Repetitive Elements

Yuta Suzuki;Jonas Korlach;Stephen W. Turner;Tatsuya Tsukahara;Junko Taniguchi;Hideaki Yurino;Wei Qu;Jun Yoshimura;Yuji Takahashi;Jun Mitsui;Shoji Tsuji;Hiroyuki Takeda;Shinichi Morishita;

10.1101/018531 — Genomics — Posted on 2015-04-24

27 Predicting genetic interactions from Boolean models of biological networks

Laurence Calzone;Emmanuel Barillot;Andrei Zinovyev;

10.1101/018507 — Genetics — Posted on 2015-04-24

28 Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs

Michael B Doud;Orr Ashenberg;Jesse Bloom;

10.1101/018457 — Evolutionary Biology — Posted on 2015-04-23

29 THE REGIME SHIFTS DATABASE: A FRAMEWORK FOR ANALYZING REGIME SHIFTS IN SOCIAL-ECOLOGICAL SYSTEMS

Reinette Oonsie Biggs;Garry D Peterson;Juan Carlos Carlos Rocha;

10.1101/018473 — Ecology — Posted on 2015-04-23

30 SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers

Adwait Sathe;Xiaotu Ma;Michael Zhang;

10.1101/018515 — Cancer Biology — Posted on 2015-04-24

31 A quasi-digital approach to peptide sequencing using tandem nanopores with endo- and exo-peptidases

G Sampath;

10.1101/018432 — Bioengineering — Posted on 2015-04-27

32 A quasi-digital approach to peptide sequencing using tandem nanopores with endo- and exo-peptidases

G Sampath;

10.1101/018432 — Bioengineering — Posted on 2015-04-24

33 Reverse-correlation analysis of navigation dynamics in Drosophila larva using optogenetics

Luis Hernandez-Nunez;Jonas Belina;Mason Klein;Guangwei Si;Lindsey Claus;John R Carlson;Aravinthan D.T. Samuel;

10.1101/018408 — Neuroscience — Posted on 2015-04-22

34 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 2015-04-22

35 Tribolium castaneum as a model for microRNA evolution, expression and function during short germband development

Maria Ninova;Matthew Ronshaugen;Sam Griffiths-Jones;

10.1101/018424 — Developmental Biology — Posted on 2015-04-22

36 A cell-free framework for biological systems engineering

Henrike Niederholtmeyer;Zachary Sun;Yutaka Hori;Enoch Yeung;Amanda Verpoorte;Richard M Murray;Sebastian J Maerkl;

10.1101/018317 — Synthetic Biology — Posted on 2015-04-21

37 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 2015-04-21

38 On the structure of population activity under fluctuations in attentional state

Alexander S Ecker;George H Denfield;Matthias Bethge;Andreas S Tolias;

10.1101/018226 — Neuroscience — Posted on 2015-04-21

39 Social feedback and the emergence of rank in animal society

Elizabeth Hobson;Simon DeDeo;

10.1101/018374 — Animal Behavior and Cognition — Posted on 2015-04-21

40 Latent developmental and evolutionary shapes embedded within the grapevine leaf

Daniel H Chitwood;Laura L Klein;Regan O'Hanlon;Steven Chacko;Matthew Greg;Cassandra Kitchen;Allison J Miller;Jason P Londo;

10.1101/018291 — Plant Biology — Posted on 2015-04-21

41 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 2015-04-20

42 Genetic Basis of Transcriptome Diversity in Drosophila melanogaster

Wen Huang;Mary Anna Carbone;Michael Magwire;Jason Peiffer;Richard Lyman;Eric Stone;Robert Anholt;Trudy Mackay;

10.1101/018325 — Genetics — Posted on 2015-04-21

43 Bandage: interactive visualisation of de novo genome assemblies

Ryan R Wick;Mark B Schultz;Justin Zobel;Kathryn E Holt;

10.1101/018333 — Bioinformatics — Posted on 2015-04-21

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

Kana Shimizu;Koji Nuida;Gunnar Rätsch;

10.1101/018267 — Genomics — Posted on 2015-04-21

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

Kana Shimizu;Koji Nuida;Gunnar Rätsch;

10.1101/018267 — Genomics — Posted on 2015-04-20

46 Relationship between LD Score and Haseman-Elston Regression

Brendan Bulik-Sullivan;

10.1101/018283 — Genetics — Posted on 2015-04-20

47 benchNGS : An approach to benchmark short reads alignment tools

Farzana Rahman;Mehedi Hassan;Alona Martin Kryshchenko;Inna Dubchak;Nikolai Nickolai Alexandrov;Tatiana Tatarinova;

10.1101/018234 — Bioinformatics — Posted on 2015-04-18

48 Low levels of transposable element activity in Drosophila mauritiana: causes and consequences

Robert Kofler;Christian Schlötterer;

10.1101/018218 — Evolutionary Biology — Posted on 2015-04-20

49 Low levels of transposable element activity in Drosophila mauritiana: causes and consequences

Robert Kofler;Christian Schlötterer;

10.1101/018218 — Evolutionary Biology — Posted on 2015-04-17

50 benchmarkR: an R package for benchmarking genome-scale methods

Xiaobei Zhou;Charity W Law;Mark D Robinson;

10.1101/018200 — Bioinformatics — Posted on 2015-04-17

51 Fulfilling the promise of Mendelian randomization

Joseph Pickrell;

10.1101/018150 — Genetics — Posted on 2015-04-16

52 Is there such a thing as Landscape Genetics?

Rodney J Dyer;

10.1101/018192 — Evolutionary Biology — Posted on 2015-04-16

53 Cancer stem cell plasticity as tumor growth promoter and catalyst of population collapse

Jan Poleszczuk;Heiko Enderling;

10.1101/018184 — Cancer Biology — Posted on 2015-04-16

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

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

10.1101/018143 — Bioinformatics — Posted on 2015-04-22

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

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

10.1101/018143 — Bioinformatics — Posted on 2015-04-16

56 Intensity matching in cuttlefish

Andres Laan;

10.1101/018176 — Animal Behavior and Cognition — Posted on 2015-04-16

57 Measuring the Contribution of Genomic Predictors to Improving Estimator Precision in Randomized trials

Prasad Patil;Michael A Rosenblum;Jeffrey T Leek;

10.1101/018168 — Bioinformatics — Posted on 2015-04-16

58 Enumeration of coliform bacteria and characterization of Escherichia coli isolated from Staff Club swimming pool in Ile-Ife, Nigeria

Tolutope Oluseyi Akeju;

10.1101/018127 — Microbiology — Posted on 2015-04-15

59 Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

Ben Busby;Allissa Dillman;Claire L. Simpson;Ian Fingerman;Sijung Yun;David M. Kristensen;Lisa Federer;Naisha Shah;Matthew C. LaFave;Laura Jimenez-Barron;Manusha Pande;Wen Luo;Brendan Miller;Cem Mayden;Dhruva Chandramohan;Kipper Fletez-Brant;Paul W. Bible;Sergej Nowoshilow;Alfred Chan;Eric JC Galvez;Jeremy Chignell;Joseph N. Paulson;Manoj Kandpal;Suhyeon Yoon;Esther Asaki;Abhinav Nellore;Adam Stine;Robert Sanders;Jesse Becker;Matt Lesko;Mordechai Abzug;Eugene Yaschenko;

10.1101/018085 — Genomics — Posted on 2015-04-16

60 Capturing heterotachy through multi-gamma site models

Remco Bouckaert;Peter Lockhart;

10.1101/018101 — Evolutionary Biology — Posted on 2015-04-15

61 A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

Qiongshi Lu;Yiming Hu;Jiehuan Sun;Yuwei Cheng;Kei-Hoi Cheung;Hongyu Zhao;

10.1101/018093 — Bioinformatics — Posted on 2015-04-15

62 Impact of the species compartment definition on quantitative modeling of microbial communities

Marko Budinich;Jeremie Bourdon;Damien Eveillard;

10.1101/018010 — Systems Biology — Posted on 2015-04-15

63 Natural selection defines the cellular complexity

Han Chen;Xionglei He;

10.1101/018069 — Evolutionary Biology — Posted on 2015-04-15

64 Association of TSH level above 2.1 mlU/L and first trimester pregnancy loss in anti-TPO antibody negative women

Yisrat Jahan;Enayetur Raheem;Mohammad Akteruzzaman;M Anwar Hussain;Rezaul Karim;Rifat Ara Jahan;

10.1101/018051 — Scientific Communication and Education — Posted on 2015-04-14

65 Phylogenetic analysis supports a link between DUF1220 domain number and primate brain expansion

Fabian Zimmer;Stephen H Montgomery;

10.1101/018077 — Evolutionary Biology — Posted on 2015-04-14

66 The design and analysis of binary variable traits in common garden genetic experiments of highly fecund species to assess heritability

Sarah W Davies;Samuel Scarpino;Thanapat Pongwarin;James Scott;Mikhail V Matz;

10.1101/018044 — Evolutionary Biology — Posted on 2015-04-17

67 The design and analysis of binary variable traits in common garden genetic experiments of highly fecund species to assess heritability

Sarah W Davies;Samuel Scarpino;Thanapat Pongwarin;James Scott;Mikhail V Matz;

10.1101/018044 — Evolutionary Biology — Posted on 2015-04-14

68 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 2015-04-15

69 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 2015-04-14

70 Rapid quantitative pharmacodynamic imaging with Bayesian estimation

Jonathan M Koller;M. Jonathan Vachon;G. Larry Bretthorst;Kevin J Black;

10.1101/017921 — Pharmacology and Toxicology — Posted on 2015-04-13

71 Fast ventral stream neural activity enables rapid visual categorization

Maxime Cauchoix;Sébastien M Crouzet;Denis Fize;Thomas Serre;

10.1101/017897 — Neuroscience — Posted on 2015-04-13

72 The African wolf is a missing link in the wolf-like canid phylogeny

Eli K. Rueness;Pål Trosvik;Anagaw Atickem;Claudio Sillero-Zubiri;Emiliano Trucchi;

10.1101/017996 — Evolutionary Biology — Posted on 2015-04-23

73 The African wolf is a missing link in the wolf-like canid phylogeny

Eli K. Rueness;Pål Trosvik;Anagaw Atickem;Claudio Sillero-Zubiri;Emiliano Trucchi;

10.1101/017996 — Evolutionary Biology — Posted on 2015-04-13

74 Concurrent origins of the genetic code and the homochirality of life, and the origin and evolution of biodiversity. Part II: Technical appendix

Dirson Jian Li;

10.1101/017988 — Evolutionary Biology — Posted on 2015-04-13

75 Concurrent origins of the genetic code and the homochirality of life, and the origin and evolution of biodiversity. Part I: Observations and explanations

Dirson Jian Li;

10.1101/017962 — Evolutionary Biology — Posted on 2015-04-13

76 Informed movement and dispersal in experimental metacommunities

Emanuel A. Fronhofer;Jan Klecka;Carlos J. Melián;Florian Altermatt;

10.1101/017954 — Ecology — Posted on 2015-04-13

77 Bayesian Modeling of Epigenetic Variation in Multiple Human Cell Types

Yu Zhang;Feng Yue;Ross C. Hardison;

10.1101/018028 — Bioinformatics — Posted on 2015-04-13

78 Interrogating conserved elements of diseases using Boolean combinations of orthologous phenotypes

John O Woods;Matthew Z Tien;Edward M Marcotte;

10.1101/017947 — Bioinformatics — Posted on 2015-04-13

79 Development of social behaviour in young zebrafish.

Elena Dreosti;Gonçalo Lopes;Adam R. Kampff;Stephen W. Wilson;

10.1101/017863 — Neuroscience — Posted on 2015-04-10

80 Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs

Gali Housman;Igor Ulitsky;

10.1101/017889 — Molecular Biology — Posted on 2015-04-10

81 Genome-wide analysis reveals novel regulators of growth in Drosophila melanogaster

Sibylle Chantal Vonesch;David Lamparter;Trudy FC Mackay;Sven Bergmann;Ernst Hafen;

10.1101/017855 — Genomics — Posted on 2015-04-10

82 MicroRNAs provide the first evidence of genetic link between diapause and aging in vertebrates

Luca Dolfi;Mario Baumgart;Marco Groth;Matthias Platzer;Alessandro Cellerino;

10.1101/017848 — Genomics — Posted on 2015-04-10

83 Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Favored Allele

Roy Ronen;Glenn Tesler;Ali Akbari;Shay Zakov;Noah A Rosenberg;Vineet Bafna;

10.1101/017871 — Evolutionary Biology — Posted on 2015-04-10

84 Brain composition in Heliconius butterflies, post-eclosion growth and experience dependent neuropil plasticity

Stephen H Montgomery;Richard M Merrill;Swidbert R Ott;

10.1101/017913 — Evolutionary Biology — Posted on 2015-04-15

85 Brain composition in Heliconius butterflies, post-eclosion growth and experience dependent neuropil plasticity

Stephen H Montgomery;Richard M Merrill;Swidbert R Ott;

10.1101/017913 — Evolutionary Biology — Posted on 2015-04-10

86 CIDANE: Comprehensive isoform discovery and abundance estimation

Stefan Canzar;Sandro Andreotti;David Weese;Knut Reinert;Gunnar W. Klau;

10.1101/017939 — Bioinformatics — Posted on 2015-04-12

87 Comment on “Two types of asynchronous activity in networks of excitatory and inhibitory spiking neurons”

Rainer Engelken;Farzad Farkhooi;David Hansel;Carl van Vreeswijk;Fred Wolf;

10.1101/017798 — Neuroscience — Posted on 2015-04-09

88 In vivo characterization of the connectivity and subcomponents of the human globus pallidus

Patrick Beukema;Timothy Verstynen;Fang-Cheng Yeh;

10.1101/017806 — Neuroscience — Posted on 2015-04-09

89 Comprehensive identification and characterization of conserved small ORFs in animals

Sebastian D Mackowiak;Henrik Zauber;Chris Bielow;Denise Thiel;Kamila Kutz;Lorenzo Calviello;Guido Mastrobuoni;Nikolaus Rajewsky;Stefan Kempa;Matthias Selbach;Benedikt Obermayer;

10.1101/017772 — Genomics — Posted on 2015-04-09

90 Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella

Kim A Steige;Johan Reimegård;Daniel Koenig;Douglas G Scofield;Tanja Slotte;

10.1101/017749 — Evolutionary Biology — Posted on 2015-04-09

91 Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella

Kim A Steige;Johan Reimegård;Daniel Koenig;Douglas G Scofield;Tanja Slotte;

10.1101/017749 — Evolutionary Biology — Posted on 2015-04-09

92 A Novel Mechanism for Color Vision: Pupil Shape and Chromatic Aberration Can Provide Spectral Discrimination for Color Blind Organisms.

Alexander L Stubbs;Christopher W Stubbs;

10.1101/017756 — Biophysics — Posted on 2015-04-22

93 A Novel Mechanism for Color Vision: Pupil Shape and Chromatic Aberration Can Provide Spectral Discrimination for Color Blind Organisms.

Alexander L Stubbs;Christopher W Stubbs;

10.1101/017756 — Biophysics — Posted on 2015-04-19

94 A Novel Mechanism for Color Vision: Pupil Shape and Chromatic Aberration Can Provide Spectral Discrimination for Color Blind Organisms.

Alexander L Stubbs;Christopher W Stubbs;

10.1101/017756 — Biophysics — Posted on 2015-04-10

95 A Novel Mechanism for Color Vision: Pupil Shape and Chromatic Aberration Can Provide Spectral Discrimination for Color Blind Organisms.

Alexander L Stubbs;Christopher W Stubbs;

10.1101/017756 — Biophysics — Posted on 2015-04-09

96 MEGSA: A powerful and flexible framework for analyzing mutual exclusivity of tumor mutations

Xing Hua;Paula L. Hyland;Jing Huang;Bin Zhu;Neil E. Caporaso;Maria Teresa Landi;Nilanjan Chatterjee;Jianxin Shi;

10.1101/017731 — Bioinformatics — Posted on 2015-04-09

97 An evaluation of the accuracy and speed of metagenome analysis tools

Stinus Lindgreen;Karen L Adair;Paul Gardner;

10.1101/017830 — Bioinformatics — Posted on 2015-04-09

98 Choosing subsamples for sequencing studies by minimizing the average distance to the closest leaf

Jonathan T. L. Kang;Peng Zhang;Sebastian Zöllner;Noah A. Rosenberg;

10.1101/017822 — Bioinformatics — Posted on 2015-04-09

99 Prototyping 1,4-butanediol (BDO) biosynthesis pathway in a cell-free transcription-translation (TX-TL) system

Yong Y Wu;Stephanie Culler;Julia Khandurina;Stephen Van Dien;Richard M Murray;

10.1101/017814 — Synthetic Biology — Posted on 2015-04-09

100 Multiple new species of Ophiocordyceps on ants

João Araújo;David P Hughes;

10.1101/017723 — Microbiology — Posted on 2015-04-18

101 Multiple new species of Ophiocordyceps on ants

João Araújo;David P Hughes;

10.1101/017723 — Microbiology — Posted on 2015-04-09

102 A Two-State Epistasis Model Reduces Missing Heritability of Complex Traits

Kerry L Bubb;Christine Queitsch;

10.1101/017491 — Genetics — Posted on 2015-04-08

103 A Two-State Epistasis Model Reduces Missing Heritability of Complex Traits

Kerry L Bubb;Christine Queitsch;

10.1101/017491 — Genetics — Posted on 2015-04-08

104 Phylogenetic tree inference from local gene content

Galina Glazko;Michael Gensheimer;Arcady Mushegian;

10.1101/017699 — Bioinformatics — Posted on 2015-04-08

105 Changes in postural syntax characterize sensory modulation and natural variation of C. elegans locomotion

Roland F. Schwarz;Robyn Branicky;Laura J. Grundy;William R. Schafer;André E.X. Brown;

10.1101/017707 — Animal Behavior and Cognition — Posted on 2015-04-08

106 Tissue-specific Enrichment of Lymphoma Risk Loci in Regulatory Elements

James E Hayes;Gosia Trynka;Joseph Vijai;Kenneth Offit;Soumya Raychaudhuri;Robert Klein;

10.1101/017657 — Genetics — Posted on 2015-04-07

107 Adaptive evolution of anti-viral siRNAi genes in bumblebees

Sophie Helbing;Michael Lattorff;

10.1101/017681 — Evolutionary Biology — Posted on 2015-04-07

108 The Impact of High-Performance Computing Best Practice Applied to Next-Generation Sequencing Workflows

Pierre Carrier;Bill Long;Richard Walsh;Jef Dawson;Carlos P. Sosa;Brian Haas;Timothy Tickle;Thomas William;

10.1101/017665 — Bioinformatics — Posted on 2015-04-07

109 Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Xiaobei Zhou;Mark D Robinson;

10.1101/017673 — Bioinformatics — Posted on 2015-04-20

110 Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Xiaobei Zhou;Mark D Robinson;

10.1101/017673 — Bioinformatics — Posted on 2015-04-07

111 Simulation of population development in the predator-prey system under changing conditions of interaction

Alexandr N. Tetearing;

10.1101/016964 — Systems Biology — Posted on 2015-04-06

112 Mutual predators: A descriptive cross-sectional study to identify prevalence and co-relation of Hepatitis C Virus and Human Immunodeficiency Virus type-1 coinfection

Fouzia Ashraf;Dalaq Aiysha;Muhammad Tajamal;Shahzeb Shahzeb Javed;Saamia Saamia Tahir;Omar Ali;Mahmood Shaukat;

10.1101/017574 — Pathology — Posted on 2015-04-06

113 Echo state networks with multiple read-out modules

Andres Laan;

10.1101/017558 — Neuroscience — Posted on 2015-04-06

114 Genome of octoploid plant maca (Lepidium meyenii) illuminates genomic basis for high altitude adaptation in the central Andes

Jun Sheng;Wei Chen;Yang Dong;Liangsheng Zhang;Jing Zhang;Yang Tian;Liang Yan;Guanghui Zhang;Xiao Wang;Yan Zeng;Jiajin Zhang;Xiao Ma;Yuntao Tan;Ni Long;Yangzi Wang;Yujin Ma;Yu Xue;Shumei Hao;Shengchao Yang;Wen Wang;

10.1101/017590 — Genomics — Posted on 2015-04-06

115 Genomic prediction of celiac disease targeting HLA-positive individuals

Gad Abraham;Alexia Rohmer;Jason A Tye-Din;Michael Inouye;

10.1101/017608 — Genomics — Posted on 2015-04-06

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

Fernando Racimo;

10.1101/017566 — Evolutionary Biology — Posted on 2015-04-06

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

Fernando Racimo;

10.1101/017566 — Evolutionary Biology — Posted on 2015-04-06

118 Phylogenomic analyses support traditional relationships within Cnidaria

Felipe Zapata;Freya E Goetz;Stephen A Smith;Mark Howison;Stefan Siebert;Samuel Church;Steven M Sanders;Cheryl Lewis Ames;Catherine S McFadden;Scott C France;Marymegan Daly;Allen G Collins;Steven HD Haddock;Casey Dunn;Paulyn Cartwright;

10.1101/017632 — Evolutionary Biology — Posted on 2015-04-06

119 Rich structure landscapes in both natural and artificial RNAs revealed by mutate-and-map analysis

Pablo Cordero;Rhiju Das;

10.1101/017624 — Biochemistry — Posted on 2015-04-06

120 An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types

Sunho Park;Seung-Jun Kim;Donghyeon Yu;Samuel Pena-Llopis;Jianjiong Gao;Jin Suk Park;Hao Tang;Beibei Chen;Jiwoong Kim;Jessie Norris;Xinlei Wang;Min Chen;Minsoo Kim;Jeongsik Yong;Zabi WarDak;Kevin S Choe;Michael Story;Timothy K. Starr;Jae-Ho Cheong;Tae Hyun Hwang;

10.1101/017582 — Bioinformatics — Posted on 2015-04-06

121 Mycobacterial infection induces a specific human innate immune response

John D Blischak;Ludovic Tailleux;Amy Mitrano;Luis B Barreiro;Yoav Gilad;

10.1101/017483 — Genomics — Posted on 2015-04-03

122 Denisovan Ancestry in East Eurasian and Native American Populations.

Pengfei Qin;Mark Stoneking;

10.1101/017475 — Evolutionary Biology — Posted on 2015-04-03

123 Phenotypic Covariation And Morphological Diversification In The Ruminant Skull

Annat Haber;

10.1101/017533 — Evolutionary Biology — Posted on 2015-04-06

124 Phenotypic Covariation And Morphological Diversification In The Ruminant Skull

Annat Haber;

10.1101/017533 — Evolutionary Biology — Posted on 2015-04-04

125 Evolutionarily induced alternative states and coexistence in systems with apparent competition

Sebastian Schreiber;Swati Patel;

10.1101/017525 — Ecology — Posted on 2015-04-03

126 A quantitative review of relationships between ecosystem services

Heera Lee;Sven Lautenbach;

10.1101/017467 — Ecology — Posted on 2015-04-04

127 Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap

Hao Wang;Joel McManus;Carl Kingsford;

10.1101/017509 — Bioinformatics — Posted on 2015-04-04

128 A mathematical framework for statistical decision confidence

Balázs Hangya;Joshua I. Sanders;Adam Kepecs;

10.1101/017400 — Neuroscience — Posted on 2015-04-01

129 Abundant contribution of short tandem repeats to gene expression variation in humans

Melissa Gymrek;Thomas Willems;Haoyang Zeng;Barak Markus;Mark J Daly;Alkes L Price;Jonathan Pritchard;Yaniv Erlich;

10.1101/017459 — Genomics — Posted on 2015-04-02

130 CRISPR with independent transgenes is a safe and robust alternative to autonomous gene drives in basic research

Fillip Port;Nadine Muschalik;Simon L Bullock;

10.1101/017384 — Genetics — Posted on 2015-04-01

131 Autosomal dominant multiple pterygium syndrome is caused by mutations in MYH3

Jessica X Chong;Lindsay C Burrage;Anita E Beck;Colby T Marvin;Margaret J McMillin;Kathryn M Shively;Kati J Buckingham;Carlos A Bacino;Mahim Jain;Yasemin Alanay;Susan A Berry;John C Carey;Richard A Gibbs;Brendan H Lee;Deborah Krakow;Jay Shendure;Deborah A Nickerson;University Washington Center Mendelian Genomics;Michael J Bamshad;

10.1101/017434 — Genetics — Posted on 2015-04-03

132 Historic and prehistoric human-driven extinctions have reshaped global mammal diversity patterns

Søren Faurby;Jens-Christian Svenning;

10.1101/017368 — Ecology — Posted on 2015-04-01

133 Un-complicating protein complex prediction.

Konstantinos Koutroumpas;François Képès;

10.1101/017376 — Bioinformatics — Posted on 2015-04-01

134 Whole Genome Regulatory Variant Evaluation for Transcription Factor Binding

Haoyang Zeng;Tatsunori Hashimoto;Daniel D. Kang;David K. Gifford;

10.1101/017392 — Bioinformatics — Posted on 2015-04-01

135 On the Optimal Use of Isotherm Models for the Characterization of Biosorption of Lead Onto Algae

F. Brouers;Tariq Al-Musawi;

10.1101/017426 — Bioengineering — Posted on 2015-04-01

136 Non-dichotomous inference using bootstrapped evidence

D. Sam Schwarzkopf;

10.1101/017327 — Neuroscience — Posted on 2015-04-03

137 Crossvalidation in brain imaging analysis

Nikolaus Kriegeskorte;

10.1101/017418 — Neuroscience — Posted on 2015-04-01

138 External Microbiota of Western United States Bats: Does It Matter Where You Are From?

Ara Kooser;Jason C Kimble;Jesse M Young;Debbie C Buecher;Ernest W Valdez;Andrea Porras-Alfaro;Diana E Northup;

10.1101/017319 — Microbiology — Posted on 2015-04-14

139 External Microbiota of Western United States Bats: Does It Matter Where You Are From?

Ara Kooser;Jason C Kimble;Jesse M Young;Debbie C Buecher;Ernest W Valdez;Andrea Porras-Alfaro;Diana E Northup;

10.1101/017319 — Microbiology — Posted on 2015-04-06

140 The Evolution of Cooperation by the Hankshaw Effect

Sarah P Hammarlund;Brian D Connelly;Katherine J Dickinson;Benjamin Kerr;

10.1101/016667 — Evolutionary Biology — Posted on 2015-04-01

141 RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints

Yi Zhong;Theofanis Karaletsos;Philipp Drewe;Vipin Thankam T Sreedharan;David Kuo;Kamini Singh;Hans-Guido Wendel;Gunnar Rätsch;

10.1101/017111 — Bioinformatics — Posted on 2015-04-10

142 Index-based map-to-sequence alignment in large eukaryotic genomes

Davide Verzotto;Axel M Hillmer;Audrey S M Teo;Niranjan Nagarajan;

10.1101/017194 — Bioinformatics — Posted on 2015-04-06

143 RNAseq in the mosquito maxillary palp: a little antennal RNA goes a long way

David C. Rinker;Xiaofan Zhou;Ronald Jason Pitts;Patrick L. Jones;Antonis Rokas;LJ Zwiebel;

10.1101/016998 — Genomics — Posted on 2015-04-02

144 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-04-03

145 Sensitivity analysis of Wnt β-catenin based transcription complex might bolster power-logarithmic psychophysical law and reveal preserved gene gene interactions

Shriprakash Sinha;

10.1101/015834 — Systems Biology — Posted on 2015-04-20

146 Sensitivity analysis of Wnt β-catenin based transcription complex might bolster power-logarithmic psychophysical law and reveal preserved gene gene interactions

Shriprakash Sinha;

10.1101/015834 — Systems Biology — Posted on 2015-04-19

147 Sensitivity analysis of Wnt β-catenin based transcription complex might bolster power-logarithmic psychophysical law and reveal preserved gene gene interactions

Shriprakash Sinha;

10.1101/015834 — Systems Biology — Posted on 2015-04-12

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

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

10.1101/015545 — Plant Biology — Posted on 2015-04-08

149 Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor

Emmanuel Lorenzo Cornejo de los Santos;Joseph T Meyerowitz;Stephen L Mayo;Richard M Murray;

10.1101/015438 — Synthetic Biology — Posted on 2015-04-30

150 FGF/MAPK signaling sets the switching threshold of a bistable circuit controlling cell fate decisions in ES cells

Christian Schröter;Pau Rué;Jonathan P Mackenzie;Alfonso Martinez Arias;

10.1101/015404 — Developmental Biology — Posted on 2015-04-21

151 A multi-method approach for proteomic network inference in 11 human cancers

Yasin Şenbabaoğlu;Selçuk Onur Sümer;Giovanni Ciriello;Nikolaus Schultz;Chris Sander;

10.1101/015214 — Bioinformatics — Posted on 2015-04-15

152 Discovery of large genomic inversions using pooled clone sequencing

Marzieh Eslami Rasekh;Giorgia Chiatante;Mattia Miroballo;Joyce Tang;Mario Ventura;Chris T Amemiya;Evan E. Eichler;Francesca Antonacci;Can Alkan;

10.1101/015156 — Bioinformatics — Posted on 2015-04-22

153 The biological functions of Naa10—from amino-terminal acetylation to human disease

Max Doerfel;Gholson Lyon;

10.1101/014324 — Biochemistry — Posted on 2015-04-21

154 An Atlas of Genetic Correlations across Human Diseases and Traits

Brendan Bulik-Sullivan;Hilary K Finucane;Verneri Anttila;Alexander Gusev;Felix R Day;ReproGen Consortium;Psychiatric Genomics Consortium;Anorexia Nervosa Genetic Consortium Wellcome Trust Consortium 3;Laramie Duncan;John R.B. Perry;Nick Patterson;Elise Robinson;Mark J Daly;Alkes L Price;Benjamin M Neale;

10.1101/014498 — Genomics — Posted on 2015-04-06

155 Oscillatory signatures of crossmodal congruence effects: An EEG investigation employing a visuotactile pattern matching paradigm

Florian Göschl;Uwe Friese;Jonathan Daume;Peter König;Andreas K. Engel;

10.1101/014092 — Neuroscience — Posted on 2015-04-15

156 Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin

Austin G Meyer;Claus O Wilke;

10.1101/014183 — Evolutionary Biology — Posted on 2015-04-09

157 A pooling-based approach to mapping genetic variants associated with DNA methylation

Irene Miriam Kaplow;Julia L MacIsaac;Sarah M Mah;Lisa M McEwen;Michael S Kobor;Hunter B Fraser;

10.1101/013649 — Genomics — Posted on 2015-04-15

158 Geographic range size is predicted by plant mating system

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

10.1101/013417 — Evolutionary Biology — Posted on 2015-04-10

159 Rethinking inheritance, yet again: inheritomes, contextomes and dynamic phenotypes

N. G. Prasad;Sutirth Dey;Amitabh Joshi;T.N.C. Vidya;

10.1101/013367 — Evolutionary Biology — Posted on 2015-04-08

160 Asynchronous Rate Chaos in Spiking Neuronal Circuits

Omri Harish;David Hansel;

10.1101/013375 — Neuroscience — Posted on 2015-04-06

161 Division of Labor in Hand Usage Is Associated with Higher Hand Performance in Free-Ranging Bonnet Macaques, Macaca radiate

Madhur Mangalam;Nisarg Desai;Mewa Singh;

10.1101/013268 — Bioengineering — Posted on 2015-04-07

162 BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data

Andrey V. Kartashov;Artem Barski;

10.1101/012799 — Bioinformatics — Posted on 2015-04-20

163 Limits to adaptation along environmental gradients

Jitka Polechová;Nick Barton;

10.1101/012690 — Evolutionary Biology — Posted on 2015-04-08

164 Reproductive workers show queen-like gene expression in an intermediately eusocial insect, the buff-tailed bumble bee Bombus terrestris.

Mark C Harrison;Robert L Hammond;Eamonn B Mallon;

10.1101/012500 — Evolutionary Biology — Posted on 2015-04-22

165 Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus.

Rachel M Wright;Galina V Aglyamova;Eli Meyer;Mikhail V Matz;

10.1101/012211 — Genomics — Posted on 2015-04-17

166 Generalised empirical Bayesian methods for discovery of differential data in high-throughput biology

Thomas J Hardcastle;

10.1101/011890 — Bioinformatics — Posted on 2015-04-06

167 Inference of cell-cell interactions from population density characteristics and cell trajectories on static and growing domains

Robert Ross;Christian A Yates;Ruth E Baker;

10.1101/011080 — Systems Biology — Posted on 2015-04-11

168 E. coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity

Shraddha Madhav Karve;Sachit Daniel;Yashraj Chavhan;Abhishek Anand;Somendra Singh Kharola;Sutirth Dey;

10.1101/011007 — Evolutionary Biology — Posted on 2015-04-08

169 The Histology of Nanomia bijuga (Hydrozoa: Siphonophora)

Samuel H Church;Stefan Siebert;Pathikrit Bhattacharyya;Casey W Dunn;

10.1101/010868 — Zoology — Posted on 2015-04-02

170 Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

Aziz Belkadi;Alexandre Bolze;Yuval Itan;Aurelie Cobat;Quentin B Vincent;Alexander Antipenko;Lei Shang;Bertrand Boisson;Jean-Laurent Casanova;Laurent Abel;