bioRxiv directory

1 Landscape structure and management alter the outcome of a pesticide ERA: evaluating impacts of endocrine disruption using the ALMaSS European Brown Hare model

Madis Vasser;Markus Kängsepp;Jaan Aru;

10.1101/025817 — Neuroscience — Posted on 2015-08-31

3 Genome-wide characterization of PRE-1 reveals a hidden evolutionary relationship between suidae and primates

Hao Yu;Qingyan Wu;Jing Zhang;Ying Zhang;Chao Lu;Yunyun Cheng;Zhihui Zhao;Andreas Windemuth;Di Liu;Linlin Hao;

10.1101/025791 — Genomics — Posted on 2015-08-31

4 The genetics of Bene Israel from India reveals both substantial Jewish and Indian ancestry

Yedael Y. Waldman;Arjun Biddanda;Natalie R. Davidson;Paul Billing-Ross;Maya Dubrovsky;Christopher L. Campbell;Carole Oddoux;Eitan Friedman;Gil Atzmon;Eran Halperin;Harry Ostrer;Alon Keinan;

10.1101/025809 — Genetics — Posted on 2015-08-31

5 The mysterious orphans of Mycoplasmataceae

Tatiana Tatarinova;Inna Lysnyansky;Yuri Nikolsky;Alexander Bolshoy;

10.1101/025700 — Evolutionary Biology — Posted on 2015-08-29

6 Phylogenetic community structure metrics and null models: a review with new methods and software

Eliot T Miller;Damien R Farine;Christopher H Trisos;

10.1101/025726 — Ecology — Posted on 2015-08-29

7 Do we need demographic data to forecast population responses to climate change?

Andrew T. Tredennick;Peter B. Adler;

10.1101/025742 — Ecology — Posted on 2015-08-30

8 Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

Michael I Love;John B Hogenesch;Rafael A Irizarry;

10.1101/025767 — Bioinformatics — Posted on 2015-08-29

9 Genome scaffolding with PE-contaminated mate-pair libraries

Kristoffer Sahlin;Rayan Chikhi;Lars Arvestad;

10.1101/025650 — Bioinformatics — Posted on 2015-08-29

10 Tissue-specific tagging of endogenous loci in Drosophila melanogaster

Kate Koles;Anna R Yeh;Avital A Rodal;

10.1101/025635 — Neuroscience — Posted on 2015-08-28

11 DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

Hector Urbina;Douglas G. Scofield;Matias Cafaro;Anna Rosling;

10.1101/025668 — Microbiology — Posted on 2015-08-28

12 The site-frequency spectrum associated with Xi-coalescents

Jochen Blath;Mathias C Cronjager;Bjarki Eldon;Matthias Hammer;

10.1101/025684 — Evolutionary Biology — Posted on 2015-08-28

13 Simultaneously inferring T cell fate and clonality from single cell transcriptomes

Michael J.T. Stubbington;Tapio Lönnberg;Valentina Proserpio;Simon Clare;Anneliese O. Speak;Gordon Dougan;Sarah A. Teichmann;

10.1101/025676 — Bioinformatics — Posted on 2015-08-28

14 Genome wide estimates of mutation rates and spectrum in Schizosaccharomyces pombe indicate CpG sites are highly mutagenic despite the absence of DNA methylation

Megan G Behringer;David W Hall;

10.1101/025601 — Genetics — Posted on 2015-08-27

15 Implications of simplified linkage equilibrium SNP simulation

Sang Hong Lee;

10.1101/025619 — Genetics — Posted on 2015-08-27

16 Resurrection of the island rule – human-driven extinctions have obscured a basic evolutionary pattern

Søren Faurby;Jens-Christian Svenning;

10.1101/025486 — Ecology — Posted on 2015-08-27

17 Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

Philipp Eser;Leonhard Wachutka;Kerstin C Maier;Carina Demel;Mariana Boroni;Srignanakshi Iyer;Patrick Cramer;Julien Gagneur;

10.1101/025585 — Genomics — Posted on 2015-08-26

18 Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on museum collection specimens.

Tomasz Suchan;Camille Pitteloud;Nadezhda Gerasimova;Anna Kostikova;Sarah Schmid;Nils Arrigo;Mila Pajkovic;Michał Ronikier;Nadir Alvarez;

10.1101/025551 — Genomics — Posted on 2015-08-26

19 Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting

David Mavor;Participants in UCSF PUBS Class;James Fraser;

10.1101/025452 — Systems Biology — Posted on 2015-08-25

20 Systems Biology Approach to Model the Life Cycle of Trypanosoma cruzi

Alejandra Carrea;Luis Diambra;

10.1101/025510 — Systems Biology — Posted on 2015-08-25

21 On the widespread and critical impact of systematic bias and batch effects in single-cell RNA-Seq data

Stephanie C Hicks;Mingxiang Teng;Rafael A Irizarry;

10.1101/025528 — Genomics — Posted on 2015-08-25

22 Mapping quantitative trait loci underlying function-valued traits using functional principal component analysis and multi-trait mapping

Il-Youp Kwak;Candace R. Moore;Edgar P. Spalding;Karl W Broman;

10.1101/025577 — Genetics — Posted on 2015-08-26

23 Mapping quantitative trait loci underlying function-valued traits using functional principal component analysis and multi-trait mapping

Il-Youp Kwak;Candace R. Moore;Edgar P. Spalding;Karl W Broman;

10.1101/025577 — Genetics — Posted on 2015-08-26

24 Fitness-valley crossing with generalized parent-offspring transmission

Matthew Osmond;Sarah P Otto;

10.1101/025502 — Evolutionary Biology — Posted on 2015-08-26

25 Leaf traits drive differences in biomass partitioning among major plant functional types

Remko A Duursma;Daniel S Falster;

10.1101/025361 — Ecology — Posted on 2015-08-25

26 Inferring social structure and its drivers from refuge use in the desert tortoise, a relatively solitary species

Pratha Sah;Kenneth E. Nussear;Todd C. Esque;Christina M. Aiello;Peter J. Hudson;Shweta Bansal;

10.1101/025494 — Ecology — Posted on 2015-08-25

27 Multivariate State Hidden Markov Models for Mark-Recapture Data

Devin S. Johnson;Jeffrey L. Laake;Sharon R. Melin;Robert L. DeLong;

10.1101/025569 — Ecology — Posted on 2015-08-29

28 Multivariate State Hidden Markov Models for Mark-Recapture Data

Devin S. Johnson;Jeffrey L. Laake;Sharon R. Melin;Robert L. DeLong;

10.1101/025569 — Ecology — Posted on 2015-08-26

29 Re-examining the relationship between virus and microbial cell abundances in the global oceans

Charles H. Wigington;Derek L. Sonderegger;Corina P.D. Brussaard;Alison Buchan;Jan F. Finke;Jed Fuhrman;Jay T. Lennon;Mathias Middelboe;Curtis A. Suttle;Charles Stock;William H. Wilson;K. Eric Wommack;Steven W. Wilhelm;Joshua S. Weitz;

10.1101/025544 — Ecology — Posted on 2015-08-26

30 Further genetic diversification in multiple tumors and an evolutionary perspective on therapeutics

Yong Tao;Zheng Hu;Shaoping Ling;Shiou-Hwie Yeh;Weiwei Zhai;Ke Chen;Chunyan Li;Yu Wang;Kaile Wang;Hurng-Yi Wang;Eric A Hungate;Kenan Onel;Jiang Liu;Changqing Zeng;Richard R Hudson;Pei-Jer Chen;Xuemei Lu;Chung-I Wu;

10.1101/025429 — Cancer Biology — Posted on 2015-08-25

31 A comparative analysis of network mutation burdens across 21 tumor types augments discovery from cancer genomes

Heiko Horn;Michael S. Lawrence;Jessica Xin Hu;Elizabeth Worstell;Nina Ilic;Yashaswi Shrestha;Eejung Kim;Atanas Kamburov;Alireza Kashani;William C. Hahn;Jesse S. Boehm;Gad Getz;Kasper Lage;

10.1101/025445 — Cancer Biology — Posted on 2015-08-25

32 OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data

Ning Leng;Jeea Choi;Li-Fang Chu;James Thomson;Christina Kendziorski;Ron Stewart;

10.1101/025437 — Bioinformatics — Posted on 2015-08-25

33 Control of sensory ectopic spike initiation by descending modulatory projection neurons

Carola Städele;Wolfgang Stein;

10.1101/025114 — Neuroscience — Posted on 2015-08-24

34 Construction of relatedness matrices using genotyping-by-sequencing data

Ken G Dodds;John C McEwan;Rudiger Brauning;Rayna M Anderson;Tracey C van Stijn;Theodor Kristjánsson;Shannon M Clarke;

10.1101/025379 — Genetics — Posted on 2015-08-24

35 Phylogeographic Inference Using Approximate Likelihoods

Brian C O'Meara;Nathan D Jackson;Ariadna E Morales-Garcia;Bryan C Carstens;

10.1101/025353 — Evolutionary Biology — Posted on 2015-08-24

36 The beetle amnion and serosa functionally interact as apposed epithelia

Stefan Koelzer;Maarten Hilbrant;Thorsten Horn;Kristen A. Panfilio;

10.1101/025247 — Developmental Biology — Posted on 2015-08-24

37 Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age

Nikolay A Ivanov;Ran Tao;Joshua G Chenoweth;Anna Brandtjen;Michelle I Mighdoll;John D Genova;Ronald D McKay;Yankai Jia;Daniel R Weinberger;Joel E Kleinman;Thomas M Hyde;Andrew E Jaffe;

10.1101/025288 — Cell Biology — Posted on 2015-08-25

38 Differential transcript usage from RNA-seq data: isoform pre-filtering improves performance of count-based methods

Charlotte Soneson;Katarina L Matthes;Malgorzata Nowicka;Charity W Law;Mark D Robinson;

10.1101/025387 — Bioinformatics — Posted on 2015-08-24

39 Modelizing Drosophila melanogaster longevity curves using a new discontinuous 2-Phases of Aging model

Hervé Tricoire;Michael Rera;

10.1101/025411 — Bioinformatics — Posted on 2015-08-31

40 Modelizing Drosophila melanogaster longevity curves using a new discontinuous 2-Phases of Aging model

Hervé Tricoire;Michael Rera;

10.1101/025411 — Bioinformatics — Posted on 2015-08-25

41 Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia

David J Winter;Maria A Pacheco;Andres Felipe A Vallejo;Rachel S. Schwartz;Myriam Arevalo-Herrera;Socrates Herrera;Reed Cartwright;Ananias Escalante;

10.1101/025338 — Genomics — Posted on 2015-08-23

42 Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis

David Ellison;Andrew Mugler;Matthew Brennan;Sung Hoon Lee;Robert Huebner;Eliah Shamir;Laura A Woo;Joseph Kim;Patrick Amar;Ilya Nemenman;Andrew J Ewald;Andre Levchenko;

10.1101/025346 — Biophysics — Posted on 2015-08-23

43 A novel recombinant DNA system for high efficiency affinity purification of proteins in Saccharomyces cerevisiae

Brian H Carrick;Lixuan HaO;Philip J Smaldino;David R Engelke;

10.1101/025205 — Molecular Biology — Posted on 2015-08-21

44 Snake venom gland cDNA sequencing using the Oxford Nanopore MinION portable DNA sequencer

John F Mulley;Adam D Hargreaves;

10.1101/025148 — Genetics — Posted on 2015-08-22

45 The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals

Günter Vogt;Cassandra Falckenhayn;Anne Schrimpf;Katharina Schmid;Katharina Hanna;Jörn Panteleit;Mark Helm;Ralf Schulz;Frank Lyko;

10.1101/025254 — Evolutionary Biology — Posted on 2015-08-23

46 The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals

Günter Vogt;Cassandra Falckenhayn;Anne Schrimpf;Katharina Schmid;Katharina Hanna;Jörn Panteleit;Mark Helm;Ralf Schulz;Frank Lyko;

10.1101/025254 — Evolutionary Biology — Posted on 2015-08-21

47 A transient ischemic environment induces reversible compaction of chromatin

Ina Kirmes;Aleksander Szczurek;Kirti Prakash;Iryna Charapitsa;Christina Heiser;Michael Musheev;Florian Schock;Karolina Fornalczyk;Dongyu Ma;Udo Birk;Christoph Cremer;George Reid;

10.1101/025221 — Cell Biology — Posted on 2015-08-21

48 Why cancer cells have a more hyperpolarised mitochondrial membrane potential and emergent prospects for therapy

Michael D Forrest;

10.1101/025197 — Cancer Biology — Posted on 2015-08-21

49 A Graph Theoretical Approach to Data Fusion

Justina Žurauskienė;Paul DW Kirk;Michael PH Stumpf;

10.1101/025262 — Bioinformatics — Posted on 2015-08-21

50 Integrating Gene Synthesis and Microfluidic Protein Analysis for Rapid Protein Engineering

Matthew C Blackburn;Ekaterina Petrova;Bruno E Correia;Sebastian Josef Maerkl;

10.1101/025239 — Bioengineering — Posted on 2015-08-21

51 Pollen contaminated with field-relevant levels of cyhalothrin affects honey bee survival, nutritional physiology, and pollen consumption behavior

Adam G Dolezal;Jimena Carrillo-Tripp;Wyatt Allen Miller;Bryony B Bonning;Amy L Toth;

10.1101/025189 — Animal Behavior and Cognition — Posted on 2015-08-21

52 The rediscovery of Strix butleri (Hume, 1878) in Oman and Iran, with molecular resolution of the identity of Strix omanensis Robb, van den Berg and Constantine, 2013

Magnus S. Robb;George Sangster;Mansour Aliabadian;Arnoud B. van den Berg;Mark Constantine;Martin Irestedt;Ali Khani;Seyed Babak Musavi;João M. G. Nunes;Maïa Sarrouf Willson;Alyn J. Walsh;

10.1101/025122 — Zoology — Posted on 2015-08-20

53 A statistical approach reveals designs for the most robust stochastic gene oscillators

Mae Woods;Miriam Leon;Ruben Perez-Carrasco;Chris P Barnes;

10.1101/025056 — Synthetic Biology — Posted on 2015-08-20

54 Efficient Disruption and Replacement of an Effector Gene in the Oomycete Phytophthora sojae using CRISPR/Cas9

Yufeng Fang;Brett M Tyler;

10.1101/025023 — Microbiology — Posted on 2015-08-20

55 Shift and adapt: the costs and benefits of karyotype variations

Aleeza C Gerstein;Judith Berman;

10.1101/025171 — Microbiology — Posted on 2015-08-20

56 Using Ancient Samples in Projection Analysis

Melinda A Yang;Montgomery Slatkin;

10.1101/025015 — Genomics — Posted on 2015-08-20

57 Timing and scope of genomic expansion within Annelida: evidence from homeoboxes in the genome of the earthworm Eisenia fetida

Allison S Zwarycz;Carlos W Nossa;Nicholas H Putnam;Joseph Ryan;

10.1101/025130 — Genomics — Posted on 2015-08-20

58 R2d2 drives selfish sweeps in the house mouse

John P Didion;Andrew Parker Morgan;Liran Yadgary;Timothy A Bell;Rachel Clara McMullan;Lydia Ortiz de Solorzano;Janice Britton-Davidian;Carol J Bult;Karl J Campbell;Riccardo Castiglia;Yung-Hao Ching;Amanda J Chunco;James J Crowley;Elissa J Chesler;John E French;Sofia I Gabriel;Daniel M Gatti;Theodore Garland;Eva B Giagia-Athanasopoulou;Mabel D Giménez;Sofia A Grize;İslam Gündüz;Andrew Holmes;Heidi C Hauffe;Jeremy S Herman;James M Holt;Kunji Hua;Wesley J Jolley;Anna K Lindholm;María J López-Fuster;George Mitsainas;Maria Mathias;Leonard McMillan;M Graça Ramalhinho;Barbara Rehermann;Stephan P Ross

10.1101/024851 — Genetics — Posted on 2015-08-21

59 R2d2 drives selfish sweeps in the house mouse

10.1101/024851 — Genetics — Posted on 2015-08-21

60 R2d2 drives selfish sweeps in the house mouse

10.1101/024851 — Genetics — Posted on 2015-08-20

61 A simple approach for maximizing the overlap of phylogenetic and comparative data

Matthew W. Pennell;Richard G. FitzJohn;William K. Cornwell;

10.1101/024992 — Evolutionary Biology — Posted on 2015-08-20

62 Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

Jason Munshi-South;Christine P Zolnik;Stephen E Harris;

10.1101/025007 — Evolutionary Biology — Posted on 2015-08-20

63 Genomic and gene-expression comparisons among phage-resistant type-IV pilus mutants of Pseudomonas syringae pathovar phaseolicola

Mark J Sistrom;Derek Park;Heath O'Brien;Zheng Wang;David Guttman;Jeffrey P. Townsend;Paul Turner;

10.1101/025106 — Evolutionary Biology — Posted on 2015-08-20

64 Super-resolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes

Kirti Prakash;David Fournier;Stefan Redl;Gerrit Best;Máté Borsos;René Ketting;KiKuë Tachibana-Konwalski;Christoph Cremer;Udo Birk;

10.1101/023432 — Biophysics — Posted on 2015-08-20

65 Statistical Inference of a Convergent Antibody Repertoire Response to Influenza Vaccine

Nicolas Strauli;Ryan Hernandez;

10.1101/025098 — Bioinformatics — Posted on 2015-08-20

66 SFS_CODE: More Efficient and Flexible Forward Simulations

Ryan D. Hernandez;Lawrence H. Uricchio;

10.1101/025064 — Bioinformatics — Posted on 2015-08-20

67 Classifying Aging as a Disease in the context of ICD-11

Alex Zhavoronkov;Bhupinder Bhullar;

10.1101/024877 — Scientific Communication and Education — Posted on 2015-08-18

68 The human experience with intravenous levodopa

Shan H Siddiqi;Natalia K Abraham;Christopher L Geiger;Morvarid Karimi;Joel S Perlmutter;Kevin J Black;

10.1101/024794 — Neuroscience — Posted on 2015-08-18

69 Transcriptomic Characterization of Soybean Roots in Response to Bradyrhizobium Infection by RNA Sequencing

He Qingyuan;Yang Hongyan;Wu Ping;Li Zhengpeng;Wang Songhua;Zhu Changwei;

10.1101/024224 — Genomics — Posted on 2015-08-20

70 Transcriptomic Characterization of Soybean Roots in Response to Bradyrhizobium Infection by RNA Sequencing

He Qingyuan;Yang Hongyan;Wu Ping;Li Zhengpeng;Wang Songhua;Zhu Changwei;

10.1101/024224 — Genomics — Posted on 2015-08-19

71 A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Adam Kuester;Ariana Wilson;Shu-mei Chang;Regina Baucom;

10.1101/024950 — Evolutionary Biology — Posted on 2015-08-20

72 A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Adam Kuester;Ariana Wilson;Shu-mei Chang;Regina Baucom;

10.1101/024950 — Evolutionary Biology — Posted on 2015-08-18

73 Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions

Alexandru Al. Ecovoiu;Iulian Constantin Ghionoiu;Andrei Mihai Ciuca;Attila Cristian Ratiu;

10.1101/024976 — Bioinformatics — Posted on 2015-08-18

74 WMP: A novel comprehensive wheat miRNA database, including related bioinformatics software

Mohamed Amine Remita;Etienne Lord;Zahra Agharbaoui;Mickael Leclercq;Mohamed Badawi;Vladirmir Makarenkov;Fathey Sarhan;Abdoulaye Banire Diallo;

10.1101/024893 — Bioinformatics — Posted on 2015-08-18

75 CG methylation covaries with differential gene expression between leaf and floral bud tissues of Brachypodium distachyon

Kyria Roessler;Shohei Takuno;Brandon Gaut;

10.1101/024935 — Genomics — Posted on 2015-08-17

76 An extensive comparison of species-abundance distribution models.

Elita Baldridge;Xiao Xiao;Ethan P. White;

10.1101/024802 — — Posted on 2015-08-18

77 Antithetic Integral Feedback: A new motif for robust perfect adaptation in noisy biomolecular networks

Corentin Briat;Ankit Gupta;Mustafa Khammash;

10.1101/024919 — Systems Biology — Posted on 2015-08-17

78 Quorum-sensing synchronization of synthetic toggle switches: A design based on monotone dynamical systems theory

Evgeni Nikolaev;Eduardo Sontag;

10.1101/024810 — Synthetic Biology — Posted on 2015-08-17

79 TET1 Modulates H4K16 Acetylation by Interacting with hMOF to Regulate Expression of DNA Repair Genes and Oncogenic Transformation

Jianing Zhong;Xianfeng Li;Wanshi Cai;Yan Wang;Shanshan Dong;Jian’an Zhang;Jie Yang;Kangli Wang;Fengbiao Mao;Cheng Zeng;Yuanyuan Li;Jinyu Wu;Huanming Yang;Xingzhi Xu;Zhong Sheng Sun;

10.1101/024844 — Molecular Biology — Posted on 2015-08-17

80 Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential In HLA-Matched and Mismatched Donor-Recipient Pairs

Badar Abdul Razzaq;Allison Scalora;Vishal Koparde;Jeremy Meier;Musa Mahmood;Salman Salman;Max Jameson-Lee;Myrna Serrano;Nihar Sheth;Mark Voelkner;David Kobulnicky;Catherine Roberts;Andrea Ferreira-Gonzalez;Masoud Manjili;Gregory Buck;Michael Neale;Amir Toor;

10.1101/024828 — Immunology — Posted on 2015-08-17

81 A genomic region containing RNF212 and CPLX1 is associated with sexually-dimorphic recombination rate variation in wild Soay sheep (Ovis aries).

Susan E Johnston;Camillo Bérénos;Jon Slate;Josephine M Pemberton;

10.1101/024869 — Genomics — Posted on 2015-08-17

82 The vgll3 locus controls age at maturity in wild and domesticated Atlantic salmon (Salmo salar L.) males

Fernando Ayllon;Erik Kjærner-Semb;Tomasz Furmanek;Vidar Wennevik;Monica F Solberg;Geir Dahle;Geir Lasse Taranger;Kevin A Glover;Markus S Almén;Carl J Rubin;Rolf B Edvardsen;Anna Wargelius;

10.1101/024927 — Genomics — Posted on 2015-08-17

83 The vgll3 locus controls age at maturity in wild and domesticated Atlantic salmon (Salmo salar L.) males

Fernando Ayllon;Erik Kjærner-Semb;Tomasz Furmanek;Vidar Wennevik;Monica F Solberg;Geir Dahle;Geir Lasse Taranger;Kevin A Glover;Markus S Almén;Carl J Rubin;Rolf B Edvardsen;Anna Wargelius;

10.1101/024927 — Genomics — Posted on 2015-08-17

84 Sex-dependent dominance at a single locus maintains variation in age at maturity in Atlantic salmon

Nicola J Barson;Tutku Aykanat;Kjetil Hindar;Matthew Baranski;Geir H Bolstad;Peder Fiske;Celeste Jacq;Arne Jensen;Susan E Johnston;Sten Karlsoon;Matthew Kent;Eero Niemelä;Torfinn Nome;Tor F Naesje;Panu Orell;Atso Romakkaniemi;Harald Saegrov;Kurt Urdal;Jaakko Erkinaro;Sigbjørn Lien;Craig R Primmer;

10.1101/024695 — Evolutionary Biology — Posted on 2015-08-20

85 Sex-dependent dominance at a single locus maintains variation in age at maturity in Atlantic salmon

10.1101/024695 — Evolutionary Biology — Posted on 2015-08-17

86 Sex-dependent dominance at a single locus maintains variation in age at maturity in Atlantic salmon

10.1101/024695 — Evolutionary Biology — Posted on 2015-08-17

87 Local population structure and patterns of Western Hemisphere dispersal for Coccidioides spp., the fungal cause of Valley Fever

David M Engelthaler;Chandler C Roe;Crystal M Hepp;Marcus Teixeira;Elizabeth M Driebe;James M Schupp;Lalitha Gade;Victor Waddell;Kenneth Komatsu;Eduardo Arathoon;Heidi Logemann;George R Thompson;Tom Chiller;Bridget Barker;Paul Keim;Anastastia P Litvintseva;

10.1101/024778 — Genomics — Posted on 2015-08-17

88 Data science identifies novel drug interactions that prolong the QT interval

Tal Lorberbaum;Kevin J Sampson;Raymond L Woosley;Robert S Kass;Nicholas P Tatonetti;

10.1101/024745 — Bioinformatics — Posted on 2015-08-17

89 Data science identifies novel drug interactions that prolong the QT interval

Tal Lorberbaum;Kevin J Sampson;Raymond L Woosley;Robert S Kass;Nicholas P Tatonetti;

10.1101/024745 — Bioinformatics — Posted on 2015-08-16

90 Optimal Point Process Filtering and Estimation of the Coalescent Process

Kris V Parag;Oliver G Pybus;

10.1101/024737 — Bioinformatics — Posted on 2015-08-16

91 Cookiecutter: a tool for kmer-based read filtering and extraction

Ekaterina Starostina;Gaik Tamazian;Pavel Dobrynin;Stephen O'Brien;Aleksey Komissarov;

10.1101/024679 — Bioinformatics — Posted on 2015-08-16

92 An integrative model of leukocyte genomics and organ dysfunction in heart failure patients requiring mechanical circulatory support

Nicholas Wisniewski;Galyna Bondar;Christoph Rau;Jay Chittoor;Eleanor Chang;Azadeh Esmaeili;Mario Deng;

10.1101/024646 — Genomics — Posted on 2015-08-14

93 Formation of Chromosomal Domains by Loop Extrusion

Geoffrey Fudenberg;Maxim Imakaev;Carolyn Lu;Anton Goloborodko;Nezar Abdennur;Leonid A Mirny;

10.1101/024620 — Genomics — Posted on 2015-08-14

94 Genome divergence and gene flow between Drosophila simulans and D. mauritiana

Sarah B. Kingan;Anthony J. Geneva;Jeffrey P. Vedanayagam;Daniel Garrigan;

10.1101/024711 — Evolutionary Biology — Posted on 2015-08-14

95 Evidence of a role for radiation-induced lysosomal damage in non-targeted effects: an experimental and theoretical analysis

Scott Bright;Alexander George Fletcher;David Fell;Munira A. Kadhim;

10.1101/024661 — Cell Biology — Posted on 2015-08-14

96 Modeling the overproduction of ribosomes when antibacterial drugs act on cells

Arijit Maitra;Ken A Dill;

10.1101/024703 — Biophysics — Posted on 2015-08-14

97 Can mindfulness meditation alter consciousness? An integrative interpretation

Jordi Manuello;Ugo Vercelli;Andrea Nani;Tommaso Costa;Franco Cauda;

10.1101/024174 — Neuroscience — Posted on 2015-08-13

98 Synergy of AMPA and NMDA receptor currents in dopaminergic neurons: a modeling study

Denis Zakharov;Lapis Christopher;Boris Gutkin;Alexey Kuznetsov;

10.1101/024653 — Neuroscience — Posted on 2015-08-14

99 Robust Estimates of Overall Immune-Repertoire Diversity from High-Throughput Measurements on Samples

Joseph Kaplinsky;Ramy Arnaout;

10.1101/024612 — Systems Biology — Posted on 2015-08-13

100 GreA and GreB enhance Escherichia coli RNA polymerase transcription rate in a reconstituted transcription-translation system

Lea L. De Maddalena;Henrike Niederholtmeyer;Matti Turtola;Zoe Swank;Georgiy A. Belogurov;Sebastian J. Maerkl;

10.1101/024604 — Synthetic Biology — Posted on 2015-08-13

101 Complete absence of thebaine biosynthesis under home-brew fermentation conditions

Drew Endy;Stephanie Galanie;Christina D Smolke;

10.1101/024299 — Synthetic Biology — Posted on 2015-08-13

102 BRAINformat: A Data Standardization Framework for Neuroscience Data

Oliver Rübel;Mr. Prabhat;Peter Denes;David Conant;Edward Chang;Kristofer Bouchard;

10.1101/024521 — Neuroscience — Posted on 2015-08-13

103 Hebbian Wiring Plasticity Generates Efficient Network Structures for Robust Inference with Synaptic Weight Plasticity

Naoki Hiratani;Tomoki Fukai;

10.1101/024406 — Neuroscience — Posted on 2015-08-13

104 Hebbian Wiring Plasticity Generates Efficient Network Structures for Robust Inference with Synaptic Weight Plasticity

Naoki Hiratani;Tomoki Fukai;

10.1101/024406 — Neuroscience — Posted on 2015-08-12

105 Crowdsourcing: Spatial clustering of low-affinity binding sites amplifies in vivo transcription factor occupancy

Justin Malin;Daphne Ezer;Xiaoyan Ma;Steve Mount;Hiren Karathia;Seung Gu Park;Boris Adryan;Sridhar Hannenhalli;

10.1101/024398 — Genomics — Posted on 2015-08-12

106 First intron length in mammals is associated with 5′ exon skipping rate

Seung Gu Park;Sridhar Hannenhalli;

10.1101/024463 — Genomics — Posted on 2015-08-12

107 Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the critical need for reference strain sequencing

Alexander L Greninger;Kevin Messacar;Thelma Dunnebacke-Dixon;Samia N Naccache;Scot Federman;Jerome Bouquet;David Mirsky;Yosuke Nomura;Shigeo Yagi;Carol Glaser;Michael Vollmer;Craig A. Press;Bette K Klenschmidt-DeMasters;Samuel R Dominguez;Charles Y Chiu;

10.1101/024455 — Genomics — Posted on 2015-08-12

108 Genomic analysis of allele-specific expression in the mouse liver

Ashutosh K Pandey;Robert W Williams;

10.1101/024588 — Genomics — Posted on 2015-08-13

109 A computational approach to estimating nondisjunction frequency in Saccharomyces cerevisiae

Daniel Chu;Sean M Burgess;

10.1101/024570 — Genetics — Posted on 2015-08-19

110 A computational approach to estimating nondisjunction frequency in Saccharomyces cerevisiae

Daniel Chu;Sean M Burgess;

10.1101/024570 — Genetics — Posted on 2015-08-18

111 A computational approach to estimating nondisjunction frequency in Saccharomyces cerevisiae

Daniel Chu;Sean M Burgess;

10.1101/024570 — Genetics — Posted on 2015-08-17

112 A computational approach to estimating nondisjunction frequency in Saccharomyces cerevisiae

Daniel Chu;Sean M Burgess;

10.1101/024570 — Genetics — Posted on 2015-08-14

113 A computational approach to estimating nondisjunction frequency in Saccharomyces cerevisiae

Daniel Chu;Sean M Burgess;

10.1101/024570 — Genetics — Posted on 2015-08-13

114 Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry

Pavel Flegontov;Piya Changmai;Anastassiya Zidkova;Maria D. Logacheva;Nefize Ezgi Altinisik;Olga Flegontova;Mikhail S. Gelfand;Evgeny S. Gerasimov;Ekaterina V. Khrameeva;Olga P. Konovalova;Tatiana Neretina;Yuri V. Nikolsky;George Starostin;Vita V. Stepanova;Igor V. Travinsky;Martin Triska;Petr Triska;Tatiana V. Tatarinova;

10.1101/024554 — Genetics — Posted on 2015-08-13

115 Gap gene regulatory dynamics evolve along a genotype network

Anton Crombach;Karl R Wotton;Eva Jimenez-Guri;Johannes Jaeger;

10.1101/024471 — Evolutionary Biology — Posted on 2015-08-12

116 Successful asexual lineages of the Irish potato Famine pathogen are triploid

Ying Li;Qian Zhou;Kun Qian;Theo van der Lee;Sanwen Huang;

10.1101/024596 — Evolutionary Biology — Posted on 2015-08-13

117 S/HIC: Robust identification of soft and hard sweeps using machine learning

Daniel R Schrider;Andrew D Kern;

10.1101/024547 — Evolutionary Biology — Posted on 2015-08-13

118 Oxygen changes drive non-uniform scaling in Drosophila melanogaster embryogenesis

Steven Gregory Kuntz;Michael B. Eisen;

10.1101/024208 — Developmental Biology — Posted on 2015-08-12

119 Comment on "Variation in cancer risk among tissues can be explained by the number of stem cell divisions"

Maxime Tarabichi;Vincent Detours;

10.1101/024497 — Cancer Biology — Posted on 2015-08-12

120 The role of oxygen in avascular tumor growth

David Robert Grimes;Pavitra Kannan;Alan McIntyre;Anthony Kavanagh;Abul Siddiky;Simon Wigfield;Adrian Harris;Mike Partridge;

10.1101/024562 — Cancer Biology — Posted on 2015-08-13

121 Fuzzy-FishNet: A highly precise distribution-free network approach for feature selection in clinical proteomics

Wilson Wen Bin Goh;

10.1101/024430 — Bioinformatics — Posted on 2015-08-12

122 Toward high-throughput predictive modeling of protein binding/unbinding kinetics

See Hong Chiu;Lei Xie;

10.1101/024513 — Bioinformatics — Posted on 2015-08-12

123 Fasta-O-Matic: a tool to sanity check and if needed reformat FASTA files

Jennifer Marie Shelton;Susan J Brown;

10.1101/024448 — Bioinformatics — Posted on 2015-08-21

124 Fasta-O-Matic: a tool to sanity check and if needed reformat FASTA files

Jennifer Marie Shelton;Susan J Brown;

10.1101/024448 — Bioinformatics — Posted on 2015-08-13

125 A Molecular Classification of Human Mesenchymal Stromal Cells

Florian Rohart;Elizabeth Mason;Nicholas Matigian;Rowland Mosbergen;Othmar Korn;Tyrone Chen;Suzanne Butcher;Jatin Patel;Kerry Atkinson;Kiarash Khosrotehrani;Nicholas Fisk;Kim-Anh Lê Cao;Christine A Wells;

10.1101/024414 — Systems Biology — Posted on 2015-08-11

126 A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

Judith Risse;Marian Thomson;Garry Blakely;Georgios Koutsovoulos;Mark Blaxter;Mick Watson;

10.1101/024323 — Genomics — Posted on 2015-08-11

127 Prediction of primary somatosensory neuron activity during active tactile exploration

Dario Campagner;Mathew H. Evans;Michael R. Bale;Andrew Erskine;Rasmus S. Petersen;

10.1101/024364 — Neuroscience — Posted on 2015-08-12

128 Prediction of primary somatosensory neuron activity during active tactile exploration

Dario Campagner;Mathew H. Evans;Michael R. Bale;Andrew Erskine;Rasmus S. Petersen;

10.1101/024364 — Neuroscience — Posted on 2015-08-10

129 Prediction of primary somatosensory neuron activity during active tactile exploration

Dario Campagner;Mathew H. Evans;Michael R. Bale;Andrew Erskine;Rasmus S. Petersen;

10.1101/024364 — Neuroscience — Posted on 2015-08-10

130 A conserved interaction between a C-terminal motif in Norovirus VPg and the HEAT-1 domain of eIF4G is essential for translation initiation

Eoin N Leen;Frédéric Sorgeloos;Samantha Correia;Yasmin Chaudhry;Fabien Cannac;Chiara pastore;Yingqi Xu;Stephen C Graham;Stephen J Matthews;Ian G Goodfellow;Stephen Curry;

10.1101/024349 — Molecular Biology — Posted on 2015-08-10

131 A common framework for identifying linkage rules across different types of interactions

Ignasi Bartomeus;Dominique Gravel;Jason Tylianakis;Marcelo Aizen;Ian Dickie;Maud Bernard-Verdier;

10.1101/024315 — Ecology — Posted on 2015-08-10

132 Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA

Emel Akdoğan;Mehmet Tardu;Görkem Garipler;Gülkız Baytek;İbrahim Halil Kavaklı;Cory D. Dunn;

10.1101/024331 — Genetics — Posted on 2015-08-14

133 Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA

Emel Akdoğan;Mehmet Tardu;Görkem Garipler;Gülkız Baytek;İbrahim Halil Kavaklı;Cory D. Dunn;

10.1101/024331 — Genetics — Posted on 2015-08-10

134 Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM

Anna Zhou;Alexis Rohou;Daniel G Schep;John V Bason;Martin G Montgomery;John E Walker;Nikolaus Grigorieff;John L Rubinstein;

10.1101/023770 — Biochemistry — Posted on 2015-08-11

135 Ancient trans-acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response

Yevgeniy Plavskin;Akitomo Nagashima;Pierre-François Perroud;Mitsuyasu Hasebe;Ralph S Quatrano;Gurinder S Atwal;Marja CP Timmermans;

10.1101/024307 — Plant Biology — Posted on 2015-08-10

136 Landscape and dynamics of transcription initiation in the malaria parasite Plasmodium falciparum

Sophie Adjalley;Christophe Chabbert;Bernd Klaus;Vicent Pelechano;Lars Steinmetz;

10.1101/024356 — Genomics — Posted on 2015-08-10

137 Endogenous human stem cell-associated retroviruses

Gennadi Glinsky;

10.1101/024273 — Genomics — Posted on 2015-08-10

138 Atp6v1b2 Plays Important Roles in the Early Development of Hearing, the Pectoral Fin, the Cardiovascular System, and the Swim Bladder of the Zebrafish, Supporting a Role for the Gene in Syndromic Hearing Loss

Yongyi Yuan;Xue Gao;Feng Xin;Pu Dai;

10.1101/024240 — Genetics — Posted on 2015-08-10

139 Distribution of gene tree histories under the coalescent model with gene flow

Yuan Tian;Laura Kubatko;

10.1101/023937 — Evolutionary Biology — Posted on 2015-08-10

140 Cross-species transmission and differential fate of an endogenous retrovirus in three mammal lineages

Xiaoyu Zhuo;Cedric Feschotte;

10.1101/024190 — Evolutionary Biology — Posted on 2015-08-10

141 Life history effects on the molecular clock of autosomes and sex chromosomes

Guy Amster;Guy Sella;

10.1101/024281 — Evolutionary Biology — Posted on 2015-08-17

142 Life history effects on the molecular clock of autosomes and sex chromosomes

Guy Amster;Guy Sella;

10.1101/024281 — Evolutionary Biology — Posted on 2015-08-10

143 Core variability in substitution rates and the basal sequence characteristics of the human genome

Aleksandr B. Sahakyan;Shankar Balasubramanian;

10.1101/024257 — Evolutionary Biology — Posted on 2015-08-10

144 Core variability in substitution rates and the basal sequence characteristics of the human genome

Aleksandr B. Sahakyan;Shankar Balasubramanian;

10.1101/024257 — Evolutionary Biology — Posted on 2015-08-10

145 Core variability in substitution rates and the basal sequence characteristics of the human genome

Aleksandr B. Sahakyan;Shankar Balasubramanian;

10.1101/024257 — Evolutionary Biology — Posted on 2015-08-10

146 Facing the heat: thermoregulation and behaviour of lowland species of a cold-dwelling butterfly genus, Erebia

Irena Kleckova;Jan Klecka;

10.1101/024265 — Ecology — Posted on 2015-08-10

147 Manta: Rapid detection of structural variants and indels for clinical sequencing applications

Xiaoyu Chen;Ole Schulz-Trieglaff;Richard Shaw;Bret Barnes;Felix Schlesinger;Anthony J. Cox;Semyon Kruglyak;Christopher T. Saunders;

10.1101/024232 — Bioinformatics — Posted on 2015-08-10

148 Targeted insertion in well-characterized Drosophila cell lines using φC31 integrase

Lucy Cherbas;Jennifer F. Hackney;Lei Gong;Claire Salzer;Eric Mauser;Dayu Zhang;Peter Cherbas;

10.1101/024216 — Bioengineering — Posted on 2015-08-08

149 Impact of the X chromosome and sex on regulatory variation

Kimberly R Kukurba;Princy Parsana;Kevin S Smith;Zachary Zappala;David A Knowles;Marie-Julie Favé;Xin Li;Xiaowei Zhu;James B Potash;Myrna M Weissman;Jianxin Shi;Anshul Kundaje;Douglas F Levinson;Philip Awadalla;Sara Mostafavi;Alexis Battle;Stephen B Montgomery;

10.1101/024117 — Genomics — Posted on 2015-08-07

150 Genome variation and meiotic recombination in Plasmodium falciparum: insights from deep sequencing of genetic crosses

Alistair Miles;Zamin Iqbal;Paul Vauterin;Richard Pearson;Susana Campino;Michel Theron;Kelda Gould;Daniel Mead;Eleanor Drury;John O'Brien;Valentin Ruano Rubio;Bronwyn MacInnis;Jonathan Mwangi;Upeka Samarakoon;Lisa Ranford-Cartwright;Michael Ferdig;Karen Hayton;Xinzhuan Su;Thomas Wellems;Julian Rayner;Gil McVean;Dominic Kwiatkowski;

10.1101/024182 — Genomics — Posted on 2015-08-07

151 Isolation-By-Distance-and-Time in a stepping-stone model

Nicolas Duforet-Frebourg;Montgomery Slatkin;

10.1101/024133 — Genetics — Posted on 2015-08-07

152 Integrative approaches for large-scale transcriptome-wide association studies

Alexander Gusev;Arthur Ko;Huwenbo Shi;Gaurav Bhatia;Wonil Chung;Brenda WJ Penninx;Rick Jansen;Eco JC de Geus;Dorret I Boomsma;Fred A Wright;Patrick F Sullivan;Elina Nikkola;Marcus Alvarez;Mete Civelek;Aldons J Lusis;Terho Lehtimaki;Emma Raitoharju;Mika Kahonen;Ilkka Seppala;Olli Raitakari;Johanna Kuusisto;Markku Laakso;Alkes L Price;Paivi Pajukanta;Bogdan Pasaniuc;

10.1101/024083 — Genetics — Posted on 2015-08-10

153 Integrative approaches for large-scale transcriptome-wide association studies

10.1101/024083 — Genetics — Posted on 2015-08-07

154 Integrative approaches for large-scale transcriptome-wide association studies

10.1101/024083 — Genetics — Posted on 2015-08-07

155 Mammalian development does not recapitulate suspected key transformations in the evolution of the mammalian middle ear

Héctor Ramirez-Chaves;Stephen Wroe;Lynne Selwood;Lyn Hinds;Chris Leigh;Daisuke Koyabu;Nikolay Kardjilov;Vera Weisbecker;

10.1101/023820 — Evolutionary Biology — Posted on 2015-08-07

156 More efficacious drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

Alison F Feder;Soo-Yon Rhee;Robert W Shafer;Dmitri A Petrov;Pleuni S Pennings;

10.1101/024109 — Evolutionary Biology — Posted on 2015-08-07

157 Fast and efficient QTL mapper for thousands of molecular phenotypes

Halit Ongen;Alfonso Buil;Andrew Brown;Emmanouil Dermitzakis;Olivier Delaneau;

10.1101/022301 — Bioinformatics — Posted on 2015-08-07

158 A digital approach to protein identification and quantity estimation using tandem nanopores, peptidases, and database search

G Sampath;

10.1101/024158 — Bioengineering — Posted on 2015-08-07

159 A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics

Guillaume Pare;Shihong Mao;Wei Deng;

10.1101/024067 — Genetics — Posted on 2015-08-07

160 A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics

Guillaume Pare;Shihong Mao;Wei Deng;

10.1101/024067 — Genetics — Posted on 2015-08-06

161 Inference and analysis of population structure using genetic data and network theory

Gili Greenbaum;Alan R. Templeton;Shirli Bar-David;

10.1101/024042 — Genetics — Posted on 2015-08-06

162 Decreased transcription factor binding levels nearby primate pseudogenes suggests regulatory degeneration

Gavin M Douglas;Michael D Wilson;Alan M Moses;

10.1101/024026 — Evolutionary Biology — Posted on 2015-08-06

163 An integrated transcriptomics and proteomics study of Head and Neck Squamous Cell Carcinoma – methodological and analytical considerations.

Anupama Rajan Bhat;Manoj Kumar Gupta;Priya Krithivasan;Kunal Dhas;Jayalakshmi Nair;Ram Bhupal Reddy;Sudheendra HV;Sandip Chavan;Harsha Vardhan;Sujatha Darsi;Lavanya Balakrishnan;Shanmukh Katragadda;Vikram Kekatpure;Amritha Suresh;Pramila Tata;Binay Panda;Moni A Kuriakose;Ravi Sirdeshmukh;

10.1101/024059 — Cancer Biology — Posted on 2015-08-06

164 DADA2: High resolution sample inference from amplicon data

Benjamin J Callahan;Paul J McMurdie;Michael J Rosen;Andrew W Han;Amy J Johnson;Susan P Holmes;

10.1101/024034 — Bioinformatics — Posted on 2015-08-06

165 Light-induced indeterminacy alters shade avoiding tomato leaf morphology

Daniel H. Chitwood;Ravi Kumar;Aashish Ranjan;Julie Pelletier;Brad Townsley;Yasunori Ichihashi;Ciera Martinez;Kristina Zumstein;John Harada;Julin Maloof;Neelima Sinha;

10.1101/024018 — Plant Biology — Posted on 2015-08-05

166 Disentangling sources of selection on exonic transcriptional enhancers

Rachel M Agoglia;Hunter B Fraser;

10.1101/024000 — Genetics — Posted on 2015-08-05

167 The impact of partitioning on phylogenomic accuracy

Diego Darriba;David Posada;

10.1101/023978 — Bioinformatics — Posted on 2015-08-19

168 The impact of partitioning on phylogenomic accuracy

Diego Darriba;David Posada;

10.1101/023978 — Bioinformatics — Posted on 2015-08-05

169 A circuit theory of protein structure

G Sampath;

10.1101/023994 — Bioengineering — Posted on 2015-08-05

170 How to develop objective-driven comprehensive science outreach initiatives aiming at multiple audiences

Sanjai Patel;Andreas Prokop;

10.1101/023838 — Genetics — Posted on 2015-08-05

171 Trait Evolution on Phylogenetic Networks

Dwueng-Chwuan Jhwueng;Brian O'Meara;

10.1101/023986 — Evolutionary Biology — Posted on 2015-08-05

172 The P25 protein of Potato virus X suppresses accumulation of 24nt siRNAs in the N. benthamiana transgenic line 16c

Shahinez Garcia;Christophe Himber;Olivier Voinnet;

10.1101/023895 — Plant Biology — Posted on 2015-08-04

173 Learning the human chromatin network from all ENCODE ChIP-seq data

Scott M. Lundberg;William B. Tu;Brian Raught;Linda Z. Penn;Michael M. Hoffman;Su-In Lee;

10.1101/023911 — Genomics — Posted on 2015-08-04

174 Werner syndrome helicase modulates G4 DNA-dependent transcription and opposes mechanistically distinct senescence-associated gene expression programs

Weiliang Tang;Ana I. Robles;Richard P. Beyer;Lucas T. Gray;Giang Hong Nguyen;Junko Oshima;Nancy Maizels;Curtis C. Harris;Raymond J. Monnat;

10.1101/023739 — Genetics — Posted on 2015-08-04

175 Werner syndrome helicase modulates G4 DNA-dependent transcription and opposes mechanistically distinct senescence-associated gene expression programs

Weiliang Tang;Ana I. Robles;Richard P. Beyer;Lucas T. Gray;Giang Hong Nguyen;Junko Oshima;Nancy Maizels;Curtis C. Harris;Raymond J. Monnat;

10.1101/023739 — Genetics — Posted on 2015-08-04

176 Infinitely Long Branches and an Informal Test of Common Ancestry

Leonardo de Oliveira Martins;David Posada;

10.1101/023903 — Evolutionary Biology — Posted on 2015-08-04

177 Correcting bias from stochastic insert size in read pair data — applications to structural variation detection and genome assembly

Kristoffer Sahlin;Mattias Frånberg;Lars Arvestad;

10.1101/023929 — Bioinformatics — Posted on 2015-08-04

178 Species Tree Estimation from Genome-wide Data with Guenomu

Leonardo de Oliveira Martins;David Posada;

10.1101/023861 — Genomics — Posted on 2015-08-03

179 Genomic DNA transposition induced by human PGBD5

Anton Henssen;Elizabeth Henaff;Eileen Jiang;Amy R Eisenberg;Julianne R Carson;Camila Villasante;Mondira Ray;Eric Still;Melissa Burns;Jorge Gandara;Cedric Feschotte;Christopher E. Mason;Alex Kentsis;

10.1101/023887 — Genomics — Posted on 2015-08-03

180 Population genomic scans reveal novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana

Billie Gould;John R Stinchcombe;

10.1101/023788 — Evolutionary Biology — Posted on 2015-08-03

181 Detection of adaptive shifts on phylogenies using shifted stochastic processes on a tree

Paul Bastide;Mahendra Mariadassou;Stéphane Robin;

10.1101/023804 — Evolutionary Biology — Posted on 2015-08-03

182 D3M: Detection of differential distributions of methylation levels

Yusuke Matsui;Masahiro Mizuta;Satoru Miyano;Teppei Shimamura;

10.1101/023879 — Bioinformatics — Posted on 2015-08-03

183 A decision underlies phototaxis in an insect.

E. Axel Gorostiza;Julien Colomb;Bjoern Brembs;

10.1101/023846 — Animal Behavior and Cognition — Posted on 2015-08-06

184 A decision underlies phototaxis in an insect.

E. Axel Gorostiza;Julien Colomb;Bjoern Brembs;

10.1101/023846 — Animal Behavior and Cognition — Posted on 2015-08-03

185 Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetry

Sarah E. Boyce;Joel Tellinghuisen;John D. Chodera;

10.1101/023796 — Biochemistry — Posted on 2015-08-03

186 Biomimetic and Non-biomimetic Extraction of Motor Control Signals Through Matched Filtering of Neural Population Dynamics

Islam S Badreldin;Karim G Oweiss;

10.1101/023689 — Neuroscience — Posted on 2015-08-01

187 Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

mathieu gautier;

10.1101/023721 — Genetics — Posted on 2015-08-02

188 Multilocus sex determination revealed in two populations of gynodioecious wild strawberry, Fragaria vesca subsp. bracteata

Tia-Lynn Ashman;Jacob Tennessen;Rebecca Dalton;Rajanikanth Govindarajulu;Mathew Koski;Aaron Liston;

10.1101/023713 — Genetics — Posted on 2015-08-02

189 Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines

John G. Cleary;Ross Braithwaite;Kurt Gaastra;Brian S Hilbush;Stuart Inglis;Sean A Irvine;Alan Jackson;Richard Littin;Mehul Rathod;David Ware;Justin M. Zook;Len Trigg;Francisco M. De La Vega;

10.1101/023754 — Bioinformatics — Posted on 2015-08-03

190 Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines

John G. Cleary;Ross Braithwaite;Kurt Gaastra;Brian S Hilbush;Stuart Inglis;Sean A Irvine;Alan Jackson;Richard Littin;Mehul Rathod;David Ware;Justin M. Zook;Len Trigg;Francisco M. De La Vega;

10.1101/023754 — Bioinformatics — Posted on 2015-08-02

191 Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations

Kiyoshi Ezawa;Dan Graur;Giddy Landan;

10.1101/023622 — Evolutionary Biology — Posted on 2015-08-04

192 Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part III: Algorithm for first approximation

Kiyoshi Ezawa;Dan Graur;Giddy Landan;

10.1101/023614 — Bioinformatics — Posted on 2015-08-04

193 Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part I: Theoretical basis

Kiyoshi Ezawa;Dan Graur;Giddy Landan;

10.1101/023598 — — Posted on 2015-08-04

194 Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part II: Perturbation analyses

Kiyoshi Ezawa;Dan Graur;Giddy Landan;

10.1101/023606 — Evolutionary Biology — Posted on 2015-08-04

195 destiny – diffusion maps for large-scale single-cell data in R

Philipp Angerer;Laleh Haghverdi;Maren Büttner;Fabian Theis;Carsten Marr;Florian Buettner;

10.1101/023309 — Bioinformatics — Posted on 2015-08-04

196 destiny – diffusion maps for large-scale single-cell data in R

Philipp Angerer;Laleh Haghverdi;Maren Büttner;Fabian Theis;Carsten Marr;Florian Buettner;

10.1101/023309 — Bioinformatics — Posted on 2015-08-03

197 Dendrites enable a robust mechanism for neuronal stimulus selectivity

Romain D. Cazé;Sarah Jarvis;Amanda Joy Foust;Simon R Schultz;

10.1101/023200 — Neuroscience — Posted on 2015-08-02

198 Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

Endre Sebestyén;Babita Singh;Belén Miñana;Amadís Pagès;Francesca Mateo;Miguel A Pujana;Juan Valcarcel;Eduardo Eyras;

10.1101/023010 — Cancer Biology — Posted on 2015-08-02

199 Monoallelic methylation and allele specific expression in a social insect

Zoe N Lonsdale;Kate Lee;Maria Kyriakidou;Harindra Amarasinghe;Despina Nathanael;Eamonn B Mallon;

10.1101/022657 — Evolutionary Biology — Posted on 2015-08-04

200 A New method to detect Event-Related Potentials based on Pearson’s Correlation

Patrizio Tressoldi;William Giroldini;Luciano Pederzoli;Marco Bilucaglia;Simone Melloni;

10.1101/022046 — Neuroscience — Posted on 2015-08-12

201 Livestock market data for modeling disease spread among US cattle

Ian T. Carroll;Shweta Bansal;

10.1101/021980 — Bioinformatics — Posted on 2015-08-03

202 Concerted activities of Mcm4, Sld3 and Dbf4 in control of origin activation and DNA replication fork progression

Yi-Jun Sheu;Justin B Kinney;Bruce Stillman;

10.1101/021832 — Genetics — Posted on 2015-08-18

203 A simple method for automated equilibration detection in molecular simulations

John D Chodera;

10.1101/021659 — Biophysics — Posted on 2015-08-17

204 On enhancing variation detection through pan-genome indexing

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

10.1101/021444 — Bioinformatics — Posted on 2015-08-03

205 CTFFIND4: Fast and accurate defocus estimation from electron micrographs

Alexis Rohou;Nikolaus Grigorieff;

10.1101/020917 — Biophysics — Posted on 2015-08-13

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

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

10.1101/020974 — Genetics — Posted on 2015-08-28

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

10.1101/020974 — Genetics — Posted on 2015-08-14

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

10.1101/020974 — Genetics — Posted on 2015-08-13

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

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

10.1101/020966 — Bioinformatics — Posted on 2015-08-18

210 Probing the fabric of the rare biosphere

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

10.1101/020818 — Microbiology — Posted on 2015-08-30

211 Probing the fabric of the rare biosphere

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

10.1101/020818 — Microbiology — Posted on 2015-08-30

212 The evolution, diversity and host associations of rhabdoviruses

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

10.1101/020107 — Evolutionary Biology — Posted on 2015-08-06

213 The evolution, diversity and host associations of rhabdoviruses

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

10.1101/020107 — Evolutionary Biology — Posted on 2015-08-05

214 A computational modelling approach for deriving biomarkers to predict cancer risk in premalignant disease

Andrew Dhawan;Trevor A Graham;Alexander G Fletcher;

10.1101/020222 — Cancer Biology — Posted on 2015-08-25

215 Shifts in diversification rates linked to biogeographic movement into new areas, an example of disparate continental distributions and a recent radiation in the Andes

Simon Uribe-Convers;David C Tank;

10.1101/019554 — Evolutionary Biology — Posted on 2015-08-17

216 The NADPH oxidase and microbial killing by neutrophils, with a particular emphasis on the proposed antimicrobial role of myeloperoxidase within the phagocytic vacuole

Adam P Levine;Anthony W Segal;

10.1101/019174 — Immunology — Posted on 2015-08-13

217 Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Abhinav Nellore;Leonardo Collado-Torres;Andrew E Jaffe;José Alquicira-Hernández;Jacob Pritt;James Morton;Jeffrey T Leek;Ben Langmead;

10.1101/019067 — Bioinformatics — Posted on 2015-08-12

218 Size Structures Sensory Hierarchy in Ocean Life

Erik Andreas Martens;Navish Wadhwa;Nis Sand Jacobsen;Christian Lindemann;Ken Haste Andersen;André Visser;

10.1101/018937 — Ecology — Posted on 2015-08-26

219 Invasive plants as novel food resources, the pollinators’ perspective

Ignasi Bartomeus;Jochen Fründ;Neal M. Williams;

10.1101/018952 — Ecology — Posted on 2015-08-27

220 Inferring species interactions from co-occurrence data with Markov networks

David J. Harris;

10.1101/018861 — Ecology — Posted on 2015-08-05

221 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 2015-08-05

222 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 2015-08-05

223 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 2015-08-24

224 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 2015-08-12

225 A quantitative review of relationships between ecosystem services

Heera Lee;Sven Lautenbach;

10.1101/017467 — Ecology — Posted on 2015-08-10

226 GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

Rubén Rellán-Álvarez;Guillaume Lobet;Heike Lindner;Pierre-Luc M Pradier;Jose Sebastian;Muh-Ching Yee;Yu Geng;Charlotte Trontin;Therese LaRue;Amanda Schrager Lavelle;Cara H Haney;Rita Nieu;Julin N Maloof;John P Vogel;José R Dinneny;

10.1101/016931 — Plant Biology — Posted on 2015-08-03

227 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-08-12

228 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-08-04

229 Mapping the Conformational Landscape of a Dynamic Enzyme by XFEL and Multitemperature Crystallography

Daniel A Keedy;Lillian R Kenner;Matthew Warkentin;Rahel Woldeyes;Michael C Thompson;Aaron S Brewster;Andrew H Van Benschoten;Elizabeth L Baxter;Jesse B Hopkins;Monarin Uervirojnangkoorn;Scott E McPhillps;Jinhu Song;Roberto Alonso-Mori;James M Holton;William I Weis;Axel T Brunger;S. Michael Soltis;Henrik Lemke;Ana Gonzalez;Nicholas K Sauter;Aina E Cohen;Henry van den Bedem;Robert E Thorne;James Fraser;