bioRxiv directory

David Valle-Garcia;Zulekha A. Qadeer;Domhnall S. McHugh;Flavia G. Ghiraldini;Asif H. Chowdhury;Dan Hasson;Michael A. Dyer;Felix Recillas-Targa;Emily Bernstein;

10.1101/027789 — Genomics — Posted on 2015-09-29

10 Tying down loose ends in the Chlamydomonas genome

Frederick R. Cross;

10.1101/027797 — Genomics — Posted on 2015-09-29

11 Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population

Elise B Robinson;Beate St Pourcain;Verneri Anttila;Jack Kosmicki;Brendan Bulik-Sullivan;Jakob Grove;Julian Maller;Kaitlin E Samocha;Stephan Sanders;Stephan Ripke;Joanna Martin;Mads V Hollegaard;Thomas Werge;David M Hougaard;Benjamin M Neale;David Evans;David Skuse;Preben Bo Mortensen;Anders Borglum;Angelica Ronald;George Davey Smith;Mark J Daly;

10.1101/027771 — Genetics — Posted on 2015-09-29

12 Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population

10.1101/027771 — Genetics — Posted on 2015-09-29

13 Genetic structure of island and mainland populations of a Neotropical bumble bee species

Flavio O Francisco;Leandro R Santiago;Yuri M Mizusawa;Benjamin P Oldroyd;Maria C Arias;

10.1101/027813 — Evolutionary Biology — Posted on 2015-09-29

14 COMADRE: a global database of animal demography

Roberto Salguero Gomez;Owen Jones;Ruth Archer;Christoph Bein;Hendrink de Burh;Claudia Farack;Fraence Gottschalk;Alexander Hartmann;Anne Henning;Gabriel Hoppe;Gesa Roemer;Tara Ruoff;Veronika Sommer;Julia Wille;Jakob Voigt;Stefan Zeh;Dirk Vieregg;Yvonne Buckley;Judy Che-Castaldo;David Hodgson;Alexander Scheuerlein;Hal Caswell;James Vaupel;

10.1101/027821 — Ecology — Posted on 2015-09-29

15 Automated discovery of relationships, models and principles in ecology

Pedro Cardoso;Paulo AV Borges;Jose C Carvalho;Francois Rigal;Rosalina Gabriel;Jose Cascalho;Luis Correia;

10.1101/027839 — Ecology — Posted on 2015-09-30

16 Automated discovery of relationships, models and principles in ecology

Pedro Cardoso;Paulo AV Borges;Jose C Carvalho;Francois Rigal;Rosalina Gabriel;Jose Cascalho;Luis Correia;

10.1101/027839 — Ecology — Posted on 2015-09-29

17 Fractality and Entropic Scaling in the Chromosomal Distribution of Conserved Noncoding Elements in the Human Genome

Dimitris Polychronopoulos;Labrini Athanasopoulou;Yannis Almirantis;

10.1101/027763 — Genomics — Posted on 2015-09-28

18 On the causes of evolutionary transition:transversion bias

Arlin Stoltzfus;Ryan W. Norris;

10.1101/027722 — Evolutionary Biology — Posted on 2015-09-28

19 Investigation of the cellular reprogramming phenomenon referred to as stimulus-triggered acquisition of pluripotency (STAP)

Hitoshi Niwa;

10.1101/027730 — Cell Biology — Posted on 2015-09-28

20 A benchmark of gene expression tissue-specificity metrics

Nadezda Kryuchkova;Marc Robinson-Rechavi;

10.1101/027755 — Bioinformatics — Posted on 2015-09-28

21 Mechanism-based sirtuin enzyme activation

Xiangying Guan;Alok Upadhyay;Raj Chakrabarti;

10.1101/027243 — Biochemistry — Posted on 2015-09-28

22 Elevating the status of code in ecology

K. A. S. Mislan;Jeffrey M. Heer;Ethan P. White;

10.1101/027110 — Ecology — Posted on 2015-09-28

23 An Option Space for Early Neural Evolution

Gaspar Jekely;Fred Keijzer;Peter Godfrey Smith;

10.1101/027425 — Evolutionary Biology — Posted on 2015-09-28

24 MG7: Configurable and scalable 16S metagenomics data analysis

Alexey Alekhin;Evdokim Kovach;Marina Manrique;Pablo Pareja-Tobes;Eduardo Pareja;Raquel Tobes;Eduardo Pareja-Tobes;

10.1101/027714 — Bioinformatics — Posted on 2015-09-28

25 Principles of studying a cell - a non-boastful paper for all molecular biologists

Han Chen;Xionglei He;

10.1101/027680 — Systems Biology — Posted on 2015-09-27

26 CRISPR/Cas9-Assisted Transformation-Efficient Reaction (CRATER), a novel method for selective transformation

Lynn J. Rothschild;Daniel T. Greenberg;Jack R. Takahashi;Kirsten A. Thompson;Akshay J. Maheshwari;Ryan E. Kent;Griffin McCutcheon;Joseph D. Shih;Charles L. Calvet;Tyler D. Devlin;Tina Ju;Daniel P. Kunin;Erica K. Lieberman;Thai Nguyen;Forrest G. Tran;Daniel Z. Xiang;Kosuke Fujishima;

10.1101/027664 — Synthetic Biology — Posted on 2015-09-27

27 Design Space Exploration of the Violacein Pathway in Escherichia coli Based Transcription Translation Cell-Free System (TX-TL)

Phuc H.B. Nguyen;Yong Wu;Shaobin Guo;Richard M Murray;

10.1101/027656 — Synthetic Biology — Posted on 2015-09-27

28 Evolutionary assembly patterns of prokaryotic genomes

Maximilian Press;Christine Queitsch;Elhanan Borenstein;

10.1101/027649 — Evolutionary Biology — Posted on 2015-09-27

29 Behavioral flexibility and problem solving in an invasive bird

Corina J Logan;

10.1101/027706 — Animal Behavior and Cognition — Posted on 2015-09-27

30 Tyrosination of α-Tubulin Controls The Initiation of Processive Dynein-Dynactin Motility

Richard J McKenney;Walter Huynh;Ronald D. Vale;Minhaj Sirajuddin;

10.1101/027631 — Biophysics — Posted on 2015-09-25

31 Design of the TRONCO BioConductor Package for TRanslational ONCOlogy

Marco Antoniotti;Giulio Caravagna;Luca De Sano;Alex Graudenzi;Giancarlo Mauri;Bud Mishra;Daniele Ramazzotti;

10.1101/027524 — Bioinformatics — Posted on 2015-09-25

32 The impact of host metapopulation structure on the population genetics of colonizing bacteria

Elina Numminen;Michael U Gutmann;Mikhail Shubin;Pekka Marttinen;Guillaume Meric;Willem van Schaik;Teresa Coque;Fernando Baquero;Rob Willems;Samuel K Sheppard;Edward J Feil;William P Hanage;Jukka Corander;

10.1101/027581 — Genetics — Posted on 2015-09-25

33 One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification

Samuel S Minot;Niklas Krumm;Nicholas B Greenfield;

10.1101/027607 — Bioinformatics — Posted on 2015-09-28

34 One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification

Samuel S Minot;Niklas Krumm;Nicholas B Greenfield;

10.1101/027607 — Bioinformatics — Posted on 2015-09-25

35 Estimating diversification rates from the fossil record

Gilles Didier;Marine Fau;Michel Laurin;

10.1101/027599 — Evolutionary Biology — Posted on 2015-09-25

36 Effects of diet on plumage coloration and pigment deposition in red and yellow domestic canaries

Rebecca Koch;Kevin McGraw;Geoffrey Hill;

10.1101/027532 — Physiology — Posted on 2015-09-24

37 Mixed Effects Models for Resampled Network Statistics Improves Statistical Power to Find Differences in Multi-Subject Functional Connectivity

Manjari Narayan;Genevera I Allen;

10.1101/027516 — Neuroscience — Posted on 2015-09-24

38 Accelerating gene discovery by phenotyping whole-genome sequenced multi- mutation strains and using the sequence kernel association test (SKAT)

Tiffany A Timbers;Stephanie J Garland;Swetha Mohan;Stephane Flibotte;Mark Edgley;Quintin Muncaster;Vinci Au;Erica Li-Leger;Federico Rosell;Jerry Cai;Suzanne Rademakers;Gert Jansen;Donald G Moerman;Michel R Leroux;

10.1101/027540 — Genomics — Posted on 2015-09-24

39 Temporal regulation of dUTP biosynthesis limits uracil incorporation during early DNA replication

Jay R. Hesselberth;Debra Suzi Bryan;

10.1101/027508 — Genomics — Posted on 2015-09-24

40 A Serial Multiplex Immunogold Labeling Method for Identifying Peptidergic Neurons in Connectomes

Reza Shahidi;Elizabeth Williams;Markus Conzelmann;Albina Asadulina;Csaba Veraszto;Sanja Jasek;Luis A Bezares-Calderon;Gaspar Jekely;

10.1101/027458 — Neuroscience — Posted on 2015-09-23

41 Variants in the FTO and CDKAL1 loci have recessive effects on risk of obesity and type 2 diabetes respectively

Andrew R Wood;Jessica Tyrell;Robin Beaumont;Samuel E Jones;Marcus A Tuke;Katherine S Ruth;The GIANT consortium;Hanieh Yaghootkar;Rachel Freathy;Anna Murray;Timothy M Frayling;Michael N Weedon;

10.1101/027490 — Genetics — Posted on 2015-09-25

42 Variants in the FTO and CDKAL1 loci have recessive effects on risk of obesity and type 2 diabetes respectively

Andrew R Wood;Jessica Tyrell;Robin Beaumont;Samuel E Jones;Marcus A Tuke;Katherine S Ruth;The GIANT consortium;Hanieh Yaghootkar;Rachel Freathy;Anna Murray;Timothy M Frayling;Michael N Weedon;

10.1101/027490 — Genetics — Posted on 2015-09-24

43 Social selection parapatry in an Afrotropical sunbird

Jay P McEntee;Joshua Penalba;Chacha Werema;Elia Mulungu;Maneno Mbilinyi;David Moyer;Louis Hansen;Jon Fjeldsaa;Rauri C.K. Bowie;

10.1101/027417 — Evolutionary Biology — Posted on 2015-09-23

44 Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk

Rudiger Brauning;Paul J Fisher;Alan F McCulloch;Russell J Smithies;James F Ward;Matthew J Bixley;Cindy T Lawley;Suzanne J Rowe;John C McEwan;

10.1101/027318 — Genomics — Posted on 2015-09-23

45 Phototaxis and the origin of visual eyes

Nadine Randel;Gaspar Jekely;

10.1101/027466 — Evolutionary Biology — Posted on 2015-09-23

46 Parental effects and the evolution of phenotypic memory

Bram Kuijper;Rufus A Johnstone;

10.1101/027441 — Evolutionary Biology — Posted on 2015-09-23

47 Summer temperature can predict the distribution of wild yeast populations

Heather A. Robinson;Ana Pinharanda;Douda Bensasson;

10.1101/027433 — Evolutionary Biology — Posted on 2015-09-23

48 Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer Progression

Giulio Caravagna;Alex Graudenzi;DANIELE RAMAZZOTTI;Rebeca Sanz-Pamplona;Luca De Sano;Giancarlo Mauri;Victor Moreno;Marco Antoniotti;Bud Mishra;

10.1101/027359 — Bioinformatics — Posted on 2015-09-24

49 Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer Progression

Giulio Caravagna;Alex Graudenzi;DANIELE RAMAZZOTTI;Rebeca Sanz-Pamplona;Luca De Sano;Giancarlo Mauri;Victor Moreno;Marco Antoniotti;Bud Mishra;

10.1101/027359 — Bioinformatics — Posted on 2015-09-23

50 TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data

Luca De Sano;Giulio Caravagna;DANIELE RAMAZZOTTI;Alex Graudenzi;Giancarlo Mauri;Bud Mishra;Marco Antoniotti;

10.1101/027474 — Bioinformatics — Posted on 2015-09-24

51 TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data

Luca De Sano;Giulio Caravagna;DANIELE RAMAZZOTTI;Alex Graudenzi;Giancarlo Mauri;Bud Mishra;Marco Antoniotti;

10.1101/027474 — Bioinformatics — Posted on 2015-09-23

52 Suboptimal larval habitats modulate oviposition of the malaria vector mosquito Anopheles gambiae

Eunho Suh;Dong-Hwan Choe;Ahmed M Saveer;Laurence J Zwiebel;

10.1101/027367 — Physiology — Posted on 2015-09-25

53 Suboptimal larval habitats modulate oviposition of the malaria vector mosquito Anopheles gambiae

Eunho Suh;Dong-Hwan Choe;Ahmed M Saveer;Laurence J Zwiebel;

10.1101/027367 — Physiology — Posted on 2015-09-22

54 Speciation driven by hybridization and chromosomal plasticity in a wild yeast

Jean-Baptiste Leducq;Lou Nielly-Thibault;Guillaume Charron;Chris Eberlein;Jukka-Pekka Verta;Pedram Samani;Kayla Sylvester;Chris Todd Hittinger;Graham Bell;Christian R Landry;

10.1101/027383 — Genomics — Posted on 2015-09-22

55 FINEMAP: Efficient variable selection using summary data from genome-wide association studies

Christian Benner;Chris C.A. Spencer;Samuli Ripatti;Matti Pirinen;

10.1101/027342 — Genetics — Posted on 2015-09-22

56 Glial and neuronal Semaphorin signaling instruct the development of a functional myotopic map for Drosophila walking

Durafshan Sakeena Syed;Swetha B.M.;O. Venkateswara Reddy;Heinrich Reichert;VijayRaghavan K.;

10.1101/027375 — Developmental Biology — Posted on 2015-09-24

57 Glial and neuronal Semaphorin signaling instruct the development of a functional myotopic map for Drosophila walking

Durafshan Sakeena Syed;Swetha B.M.;O. Venkateswara Reddy;Heinrich Reichert;VijayRaghavan K.;

10.1101/027375 — Developmental Biology — Posted on 2015-09-22

58 Glucose modulates Drosophila longevity and immunity independent of the microbiota.

Anthony Galenza;Jaclyn Hutchinson;Bart Hazes;Shelagh Campbell;Edan Foley;

10.1101/027326 — Immunology — Posted on 2015-09-22

59 ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Gabriel E. Zentner;Sivakanthan Kasinathan;Beibei Xin;Remo Rohs;Steven Henikoff;

10.1101/027334 — Genomics — Posted on 2015-09-22

60 Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

Richard E Lenski;Michael J Wiser;Noah Ribeck;Zachary D Blount;Joshua R Nahum;James Jeffrey Morris;Luis Zaman;Caroline B Turner;Brian D Wade;Rohan Maddamsetti;Alita R Burmeister;Elizabeth J Baird;Jay Bundy;Nkrumah A Grant;Kyle J Card;Maia Rowles;Kiyana Weatherspoon;Spiridon E Papoulis;Rachel Sullivan;Colleen Clark;Joseph S Mulka;Neerja Hajela;

10.1101/027391 — Evolutionary Biology — Posted on 2015-09-22

61 Enhancing burst activation and propagation in cultured neuronal networks by photo-stimulation

Ghazaleh Afshar;Ahmed El Hady;Theo Geisel;Walter Stuehmer;Fred Wolf;

10.1101/027177 — Neuroscience — Posted on 2015-09-18

62 Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-Random Features of Cortical Synaptic Wiring.

Daniel Miner;Jochen Triesch;

10.1101/027268 — Neuroscience — Posted on 2015-09-21

63 Task learning reveals neural signatures of internal models in rodent prefrontal cortex

Abhinav Singh;Adrien Peyrache;Mark Humphries;

10.1101/027102 — Neuroscience — Posted on 2015-09-21

64 Complete assembly of novel environmental bacterial genomes by MinIONTM sequencing

Daniel J Turner;Xiaoguang Dai;Simon Mayes;Sissel Juul;

10.1101/026930 — Microbiology — Posted on 2015-09-19

65 Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Kerstin Howe;Philipp Schiffer;Julia Zielinski;Thomas Wiehe;Gavin Laird;John Marioni;Onuralp Soylemez;Fyodor Kondrashov;Maria Leptin;

10.1101/027151 — Genomics — Posted on 2015-09-18

66 Conversion of Genomic DNA to Proxy Constructs Suitable for Accurate Nanopore Sequencing

Dimitra Tsavachidou;

10.1101/027284 — Genomics — Posted on 2015-09-21

67 MTG2: An efficient algorithm for multivariate linear mixed model analysis based on genomic information

Sang Hong Lee;Julius van der Werf;

10.1101/027201 — Genetics — Posted on 2015-09-18

68 A cost analysis of a cancer genetic service model in the UK

Ingrid Slade;Helen Hanson;Angela George;Kelly Kohut;Ann Strydom;Sarah Wordsworth;Nazneen Rahman;MCG Programme;

10.1101/027185 — Genetics — Posted on 2015-09-18

69 Systematic Review of the Research on Morphological Modularity

Borja Esteve-Altava;

10.1101/027144 — Evolutionary Biology — Posted on 2015-09-21

70 Rolling the Dice Twice: Evolving Reconstructed Ancient Proteins in Extant Organisms

Betul Kacar;

10.1101/027003 — Evolutionary Biology — Posted on 2015-09-21

71 Spatially-constrained growth enhances conversional meltdown

Maxim O. Lavrentovich;Mary E. Wahl;David R. Nelson;Andrew W. Murray;

10.1101/027292 — Evolutionary Biology — Posted on 2015-09-21

72 Simultaneous enhancement of multiple stability properties using two-parameter control methods in Drosophila melanogaster

Sudipta Tung;Abhishek Mishra;Sutirth Dey;

10.1101/027169 — Ecology — Posted on 2015-09-18

73 In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River

Matthew Cannon;James Hester;Amanda Shalkhauser;Ernest R Chan;Kyle Logue;Scott T Small;David Serre;

10.1101/027235 — Ecology — Posted on 2015-09-18

74 The potential of electricity transmission corridors in forested areas as bumble bee habitat

Bruce Hill;Ignasi Bartomeus;

10.1101/027078 — Ecology — Posted on 2015-09-21

75 The potential of electricity transmission corridors in forested areas as bumble bee habitat

Bruce Hill;Ignasi Bartomeus;

10.1101/027078 — Ecology — Posted on 2015-09-18

76 ZNF191 Inhibits Hepatocellular Carcinoma Metastasis via DLG1-mediated YAP1 Inactivation

Di Wu;Guoyuan Liu;Songmin Jiang;Long Yu;

10.1101/027060 — Cancer Biology — Posted on 2015-09-18

77 Laplacian eigenmaps and principal curves for high resolution pseudotemporal ordering of single-cell RNA-seq profiles

Kieran Campbell;Chris P Ponting;Caleb Webber;

10.1101/027219 — Bioinformatics — Posted on 2015-09-18

78 Genomic variant calling: Flexible tools and a diagnostic data set

Michael Lawrence;Melanie A Huntley;Eric Stawiski;Art Owen;Thomas D Wu;Leonard D Goldstein;Yi Cao;Jeremiah Degenhardt;Jason Young;Joseph Guillory;Sherry Heldens;Marlena Jackson;Somasekar Seshagiri;Robert Gentleman;

10.1101/027227 — Bioinformatics — Posted on 2015-09-18

79 WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system

Nathan Wong;Weijun Liu;Xiaowei Wang;

10.1101/026971 — Bioinformatics — Posted on 2015-09-18

80 Haplotype synthesis analysis in public reference data reveals functional variants underlying known genome-wide associated susceptibility loci

Andre Lacour;Tim Becker;

10.1101/027276 — Bioinformatics — Posted on 2015-09-21

81 Cortical idiosyncrasies predict the perception of object size

Christina Moutsiana;Benjamin de Haas;Andriani Papageorgiou;Jelle A van Dijk;Annika Balraj;John A Greenwood;D. Sam Schwarzkopf;

10.1101/026989 — Neuroscience — Posted on 2015-09-16

82 Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

Jean Fan;Neeraj Salathia;Rui Liu;Gwen Kaeser;Yun Yung;Joseph L Herman;Fiona Kaper;Jian-Bing Fan;Kun Zhang;Jerold Chun;Peter Kharchenko;

10.1101/026948 — Genomics — Posted on 2015-09-16

83 Single-cell phenotyping of human induced pluripotent stem cells by high-throughput imaging

Hans Christian Volz;Florian Heigwer;Tatjana Wuest;Marta Galach;Jochen Utikal;Hugo A. Katus;Michael Boutros;

10.1101/026955 — Genomics — Posted on 2015-09-16

84 The UCSC Genome Browser database: 2016 update

Matthew L. Speir;Ann S. Zweig;Kate R. Rosenbloom;Brian J. Raney;Benedict Paten;Parisa Nejad;Brian T. Lee;Katrina Learned;Donna Karolchik;Angie S. Hinrichs;Steve Heitner;Rachel A. Harte;Maximilian Haeussler;Luvina Guruvadoo;Pauline A. Fujita;Christopher Eisenhart;Mark Diekhans;Hiram Clawson;Jonathan Casper;Galt P. Barber;David Haussler;Robert M. Kuhn;W. James Kent;

10.1101/027037 — Genomics — Posted on 2015-09-17

85 Inference of complex population histories using whole-genome sequences from multiple populations

Matthias Steinrücken;John A. Kamm;Yun S. Song;

10.1101/026591 — Evolutionary Biology — Posted on 2015-09-16

86 Non-null Effects of the Null Range in Biogeographic Models: Exploring Parameter Estimation in the DEC Model

Kathryn A Massana;Jeremy M Beaulieu;Nicholas J Matzke;Brian C O'Meara;

10.1101/026914 — Evolutionary Biology — Posted on 2015-09-16

87 Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations

Marcus M Dillon;Nicholas P Rouillard;Brian Van Dam;Romain Gallet;Vaughn S Cooper;

10.1101/027086 — Evolutionary Biology — Posted on 2015-09-17

88 Construction of the third generation Zea mays haplotype map

Robert Bukowski;Xiaosen Guo;Yanli Lu;Cheng Zou;Bing He;Zhengqin Rong;Bo Wang;Dawen Xu;Bicheng Yang;Chuanxiao Xie;Longjiang Fan;Shibin Gao;Xun Xu;Gengyun Zhang;Yingrui Li;Yinping Jiao;John Doebley;Jeffrey Ross-Ibarra;Vince Buffalo;Cinta M Romay;Edward S Buckler;Yunbi Xu;Jinsheng Lai;Doreen Ware;Qi Sun;

10.1101/026963 — Bioinformatics — Posted on 2015-09-16

89 Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

Jeremy A. Frank;Yao Pan;Ave Tooming-Klunderud;Vincent G.H. Eijsink;Alice C. McHardy;Alexander J. Nederbragt;Phillip B. Pope;

10.1101/026922 — Bioinformatics — Posted on 2015-09-16

90 A pathway-centric view of spatial proximity in the 3D nucleome across cell lines

Hiren Karathia;Carl Kingsford;Michelle Girvan;Sridhar Hannenhalli;

10.1101/027045 — Bioinformatics — Posted on 2015-09-17

91 The neurotranscriptome of the Aedes aegypti mosquito

Benjamin J Matthews;Carolyn S McBride;Matthew DeGennaro;Orion Despo;Leslie B Vosshall;

10.1101/026823 — Neuroscience — Posted on 2015-09-15

92 Extensive sequencing of seven human genomes to characterize benchmark reference materials

Justin M Zook;David Catoe;Jennifer McDaniel;Lindsay Vang;Noah Spies;Arend Sidow;Ziming Weng;Yuling Liu;Chris Mason;Noah Alexander;Dhruva Chandramohan;Elizabeth Henaff;Feng Chen;Erich Jaeger;Ali Moshrefi;Khoa Pham;William Stedman;Tiffany Liang;Michael Saghbini;Zeljko Dzakula;Alex Hastie;Han Cao;Gintaras Deikus;Eric Schadt;Robert Sebra;Ali Bashir;Rebecca M Truty;Christopher C Chang;Natali Gulbahce;Keyan Zhao;Srinka Ghosh;Fiona Hyland;Yutao Fu;Mark Chaisson;Jonathan Trow;Chunlin Xiao;Stephen T Sherry;Alexander W Zaranek;Madeleine Ball;Jason Bobe;Preston Estep;George M Church;Patrick Marks;Sofia K

10.1101/026468 — Genomics — Posted on 2015-09-15

93 Widespread shortening of 3’ untranslated regions and increased exon inclusion characterize the human macrophage response to infection

Athma A Pai;Golshid Baharian;Ariane Page Sabourin;Jessica F Brinkworth;Yohann Nedelec;Joseph W Foley;Jean-Christophe Grenier;Katherine J Siddle;Anne Dumaine;Vania Yotova;Zachary P Johnson;Robert E Lanford;Christopher B Burge;Luis B Barreiro;

10.1101/026831 — Genomics — Posted on 2015-09-15

94 Using Cell line and Patient samples to improve Drug Response Prediction

Cheng Zhao;Ying Li;Zhaleh Safikhani;Benjamin Haibe-Kains;Anna Goldenberg;

10.1101/026534 — Bioinformatics — Posted on 2015-09-15

95 Bayesian Gaussian Process Latent Variable Models for pseudotime inference in single-cell RNA-seq data

Kieran Campbell;Christopher Yau;

10.1101/026872 — Bioinformatics — Posted on 2015-09-15

96 IDENTIFICATION OF GENOMIC REGIONS CARRYING A CAUSAL MUTATION IN UNORDERED GENOMES

Pilar Corredor-Moreno;Ed Chalstrey;Carlos A Lugo;Dan MacLean;

10.1101/026856 — Bioinformatics — Posted on 2015-09-15

97 Diffantom: whole-brain diffusion MRI phantoms derived from real datasets of the Human Connectome Project

Oscar Esteban;Emmanuel Caruyer;Alessandro Daducci;Meritxell Bach-Cuadra;Maria-J. Ledesma-Carbayo;Andres Santos;

10.1101/026898 — Bioinformatics — Posted on 2015-09-15

98 RNA polymerase errors cause splicing defects and can be regulated by differential expression of RNA polymerase subunits

Lucas B Carey;

10.1101/026799 — Genomics — Posted on 2015-09-14

99 Analytical limits of hybrid identification using genetic markers: an empirical and simulation study in Hippolais warblers

Jan O Engler;Soenke Twietmeyer;Jean Secondi;Ortwin Elle;Axel Hochkirch;

10.1101/026781 — Genetics — Posted on 2015-09-14

100 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions

Ying Zhou;Kai Yuan;Yaoliang Yu;Xumin Ni;Pengtao Xie;Eric P Xing;Shuhua Xu;

10.1101/026757 — Evolutionary Biology — Posted on 2015-09-14

101 Genetic structure of the stingless bee Tetragonisca angustula

Flavio O Francisco;Leandro R Santiago;Yuri M Mizusawa;Benjamin P Oldroyd;Maria C Arias;

10.1101/026740 — Evolutionary Biology — Posted on 2015-09-14

102 Species range expansion constrains the ecological niches of resident butterflies.

Hélène Audusseau;Maryline Le Vaillant;Niklas Janz;Sören Nylin;Bengt Karlsson;Reto Schmucki;

10.1101/026765 — Ecology — Posted on 2015-09-14

103 Distribution and abundance of the West Indian manatee (Trichechus manatus) in the Panama Canal

Giselle Muschett;Juliana Vianna;

10.1101/026724 — Zoology — Posted on 2015-09-13

104 How sex-biased dispersal affects conflict over parental investment

Bram Kuijper;Rufus A Johnstone;

10.1101/026732 — Evolutionary Biology — Posted on 2015-09-13

105 Prioritization of sites for plant species restoration in the Chilean Biodiversity Hotspot: A spatial multi-criteria decision analysis approach

Ignacio C Fernandez;Narkis S Morales;

10.1101/026716 — Ecology — Posted on 2015-09-13

106 Connectome of a model local cortical circuit flexibly shapes layer-dependent multi-frequency oscillations

Markus Helmer;Xue Jie Chen;Wei Wei;Fred Wolf;Demian Battaglia;

10.1101/026674 — Neuroscience — Posted on 2015-09-12

107 Model-free Estimation of Tuning Curves and Their Attentional Modulation, Based on Sparse and Noisy Data

Markus Helmer;Vladislav Kozyrev;Valeska Stephan;Stefan Treue;Theo Geisel;Demian Battaglia;

10.1101/026682 — Neuroscience — Posted on 2015-09-12

108 Stimuli reduce the dimensionality of cortical activity

Luca Mazzucato;Alfredo Fontanini;Giancarlo La Camera;

10.1101/026666 — Neuroscience — Posted on 2015-09-12

109 The effects of both recent and long-term selection and genetic drift are readily evident in North American barley breeding populations

Ana M Poets;Mohsen Mohammadi;Kiran Seth;Hongyun Wang;Thomas J.Y. Kono;Zhou Fang;Gary J Muehlbauer;Kevin P Smith;Peter L Morrell;

10.1101/026625 — Genetics — Posted on 2015-09-11

110 Selection on network dynamics drives differential rates of protein domain evolution

Brian K Mannakee;Ryan N Gutenkunst;

10.1101/026658 — Evolutionary Biology — Posted on 2015-09-11

111 Quantitative neuroanatomy for connectomics in Drosophila

Casey M Schneider-Mizell;Stephan Gerhard;Mark Longair;Tom Kazimiers;Feng Li;Maarten F. Zwart;Andrew Champion;Frank Midgley;Richard Fetter;Stephan Saalfeld;Albert Cardona;

10.1101/026617 — Neuroscience — Posted on 2015-09-10

112 Immunosequencing reveals diagnostic signatures of chronic viral infection in T cell memory

Ryan Emerson;William DeWitt;Marissa Vignali;Jenna Gravley;Cindy Desmarais;Christoper Carlson;John Hansen;Mark Rieder;Harlan Robins;

10.1101/026567 — Genomics — Posted on 2015-09-11

113 Immunosequencing reveals diagnostic signatures of chronic viral infection in T cell memory

Ryan Emerson;William DeWitt;Marissa Vignali;Jenna Gravley;Cindy Desmarais;Christoper Carlson;John Hansen;Mark Rieder;Harlan Robins;

10.1101/026567 — Genomics — Posted on 2015-09-10

114 Low base-substitution mutation rate in the germline genome of ciliate Tetrahymena thermophila

Hongan Long;David J Winter;Allan Y-C Chang;Way Sun;Steven H. Whu;Mariel Balboa;Ricardo BR Azevedo;Reed A Cartwright;Michael Lynch;Rebecca A Zufall;

10.1101/025536 — Evolutionary Biology — Posted on 2015-09-16

115 Low base-substitution mutation rate in the germline genome of ciliate Tetrahymena thermophila

Hongan Long;David J Winter;Allan Y-C Chang;Way Sun;Steven H. Whu;Mariel Balboa;Ricardo BR Azevedo;Reed A Cartwright;Michael Lynch;Rebecca A Zufall;

10.1101/025536 — Evolutionary Biology — Posted on 2015-09-10

116 Mapping phylogenetic trees to reveal distinct patterns of evolution

Michelle Kendall;Caroline Colijn;

10.1101/026641 — Evolutionary Biology — Posted on 2015-09-11

117 A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment)

Matthew A Rittenhouse;Crawford W Revie;Amy Hurford;

10.1101/026583 — Ecology — Posted on 2015-09-10

118 Changes in Forest Composition, Stem Density, and Biomass from the Settlement Era (1800s) to Present in the Upper Midwestern United States

Simon Goring;David J Mladenoff;Charles V Cogbill;Sydne Record;Christopher J Paciorek;Stephen T Jackson;Michael Dietze;Andria Dawson;Jaclyn Matthes;Jason S McLachlan;John W Williams;

10.1101/026575 — — Posted on 2015-09-11

119 Changes in Forest Composition, Stem Density, and Biomass from the Settlement Era (1800s) to Present in the Upper Midwestern United States

Simon Goring;David J Mladenoff;Charles V Cogbill;Sydne Record;Christopher J Paciorek;Stephen T Jackson;Michael Dietze;Andria Dawson;Jaclyn Matthes;Jason S McLachlan;John W Williams;

10.1101/026575 — — Posted on 2015-09-10

120 Decomposing variability in protein levels from noisy expression, genome duplication and partitioning errors during cell-divisions

Mohammad Soltani;Cesar Augusto Vargas-Garcia;Duarte Antunes;Abhyudai Singh;

10.1101/026559 — Systems Biology — Posted on 2015-09-10

121 Standard melanoma-associated markers do not identify the MM127 metastatic melanoma cell line

Parvathi Haridas;Jacqui McGovern;Ahishek Kashyap;Sean McElwain;Matthew Simpson;

10.1101/026633 — Cancer Biology — Posted on 2015-09-11

122 Characterizing and comparing phylogenies from their Laplacian spectrum

Eric Lewitus;Helene Morlon;

10.1101/026476 — Systems Biology — Posted on 2015-09-09

123 Long-delay learning in intraoral conditioned taste aversion

Thomas A. Houpt;Jennifer A. Cassell;Stephanie McCormack;Bumsup Kwon;Gary Tiffany;Jeffrey Lorch;

10.1101/026500 — Neuroscience — Posted on 2015-09-09

124 Selection on heritable heterozygosity but no response to selection. Why?

Tim Coulson;Sonya Clegg;

10.1101/026492 — Evolutionary Biology — Posted on 2015-09-09

125 EvolQG - An R package for evolutionary quantitative genetics

Diogo Melo;Guilherme Garcia;Alex Hubbe;Ana Paula Assis;Gabriel Marroig;

10.1101/026518 — Evolutionary Biology — Posted on 2015-09-11

126 EvolQG - An R package for evolutionary quantitative genetics

Diogo Melo;Guilherme Garcia;Alex Hubbe;Ana Paula Assis;Gabriel Marroig;

10.1101/026518 — Evolutionary Biology — Posted on 2015-09-10

127 EvolQG - An R package for evolutionary quantitative genetics

Diogo Melo;Guilherme Garcia;Alex Hubbe;Ana Paula Assis;Gabriel Marroig;

10.1101/026518 — Evolutionary Biology — Posted on 2015-09-10

128 Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

Antonino Ingargiola;Ted Laurence;Robert Boutelle;Shimon Weiss;Xavier Michalet;

10.1101/026484 — Biophysics — Posted on 2015-09-14

129 Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

Antonino Ingargiola;Ted Laurence;Robert Boutelle;Shimon Weiss;Xavier Michalet;

10.1101/026484 — Biophysics — Posted on 2015-09-09

130 Structural constraints to information flow within cortical circuits: a TMS/EEG-dMRI study

Enrico Amico;Olivier Bodart;Olivia Gosseries;Lizette Heine;Mario Rosanova;Pieter Van Mierlo;Charlotte Martial;Marcello Massimini;Daniele Marinazzo;Steven Laureys;

10.1101/026419 — Neuroscience — Posted on 2015-09-09

131 Effects of reference databases’ refinements on the validity of molecular definitions of 15,371 candidate human-specific regulatory sequences

Gennadi Glinsky;

10.1101/026435 — Genomics — Posted on 2015-09-09

132 Efficient Integrative Multi-SNP Association Analysis using Deterministic Approximation of Posteriors

Xiaoquan Wen;Yeji Lee;Francesca Luca;Roger Pique-Regi;

10.1101/026450 — Genetics — Posted on 2015-09-09

133 Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action

Ence Yang;Gang Wang;Jizhou Yang;Beiyan Zhou;Yanan Tian;James J Cai;

10.1101/026393 — Genetics — Posted on 2015-09-09

134 Divergent MLS1 promoters lie on a fitness plateau for gene expression

Andrew C Bergen;Gerilyn M Olsen;Justin C Fay;

10.1101/026427 — Evolutionary Biology — Posted on 2015-09-09

135 Growing neuronal islands on multi-electrode arrays using an Accurate Positioning-μCP device

Robert Samhaber;Manuel Schottdorf;Ahmed El Hady;Kai Broeking;Andreas Daus;Christiane Thielemann;Walter Stuehmer;Fred Wolf;

10.1101/026401 — Bioengineering — Posted on 2015-09-09

136 Development of EST-SSR annotated database in olive (Olea europaea)

sami said adawy;morad mokhtar mokhtar;Alsamman Mahmoud Alsamman;Mahmoud m Sakr;

10.1101/026294 — Genomics — Posted on 2015-09-08

137 Modeling Continuous Admixture

Ying Zhou;Hongxiang Qiu;Shuhua Xu;

10.1101/026278 — Genetics — Posted on 2015-09-08

138 An Accurate Genetic Clock

David H Hamilton;

10.1101/026286 — Genetics — Posted on 2015-09-08

139 Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species.

Jing Wang;Nathaniel R Street;Douglas G Scofield;Pär K Ingvarsson;

10.1101/026344 — Evolutionary Biology — Posted on 2015-09-08

140 General methods for evolutionary quantitative genetic inference from generalised mixed models.

Pierre de Villemereuil;Holger Schielzeth;Shinichi Nakagawa;Michael Morrissey;

10.1101/026377 — Evolutionary Biology — Posted on 2015-09-08

141 HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations

Antonio Carvajal-Rodríguez;

10.1101/026369 — Evolutionary Biology — Posted on 2015-09-08

142 Combining niche modelling, land use-change, and genetic information to assess the conservation status of Pouteria splendens populations in Central Chile

Narkis S Morales;Ignacio C Fernandez;Basilio A Carrasco;Cristina Orchard;

10.1101/026336 — Ecology — Posted on 2015-09-08

143 Passenger DNA alterations reduce cancer fitness in cell culture and mouse models

Christopher D McFarland;Julia A Yaglom;Jonathan W Wojtkowiak;Jacob G Scott;David L Morse;Michael Y Sherman;Leonid A Mirny;

10.1101/026302 — Cancer Biology — Posted on 2015-09-08

144 Integrated Genome Browser: visual analytics platform for genomics

Nowlan H. Freese;David C. Norris;Ann E. Loraine;

10.1101/026351 — Bioinformatics — Posted on 2015-09-15

145 Integrated Genome Browser: visual analytics platform for genomics

Nowlan H. Freese;David C. Norris;Ann E. Loraine;

10.1101/026351 — Bioinformatics — Posted on 2015-09-11

146 Integrated Genome Browser: visual analytics platform for genomics

Nowlan H. Freese;David C. Norris;Ann E. Loraine;

10.1101/026351 — Bioinformatics — Posted on 2015-09-08

147 Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve;Yann Ponty;Joao Paulo Peirera Zanetti;

10.1101/026310 — Bioinformatics — Posted on 2015-09-08

148 pcaReduce: Hierarchical Clustering of Single Cell Transcriptional Profiles

Justina Zurauskiene;Christopher Yau;

10.1101/026385 — Bioinformatics — Posted on 2015-09-08

149 Selection for mitochondrial quality drives the evolution of sexes with a dedicated germline

Arunas Radzvilavicius;Zena Hadjivasiliou;Nick Lane;Andrew Pomiankowski;

10.1101/026252 — Evolutionary Biology — Posted on 2015-09-07

150 Quantitative Genetics Meets Integral Projection Models: Unification of Widely Used Methods from Ecology and Evolution

Tim Coulson;Floriane Plard;Susanne Schindler;Arpat Ozgul;Jean-Michel Gaillard;

10.1101/026260 — Evolutionary Biology — Posted on 2015-09-07

151 Exact solutions of coupled multispecies linear reaction-diffusion equations on a uniformly growing domain

Matthew Simpson;Jesse Sharp;Liam Morrow;Ruth Baker;

10.1101/026229 — Biophysics — Posted on 2015-09-07

152 Prediction of Hfq in actinobacteria

Nagamani Bora;Alan C Ward;Wonyong Kim;

10.1101/026195 — Microbiology — Posted on 2015-09-06

153 Limits to adaptation in partially selfing species

Matthew Hartfield;Sylvain Glemin;

10.1101/026146 — Evolutionary Biology — Posted on 2015-09-06

154 Overlapping Genes and Size Constraints in Viruses - An Evolutionary Perspective

Nadav Brandes;Michal Linial;

10.1101/026203 — Evolutionary Biology — Posted on 2015-09-06

155 Revisiting inconsistency in large pharmacogenomic studies

Zhaleh Safikhani;Mark Freeman;Petr Smirnov;Nehme El-Hachem;Adrian She;Rene Quevedo;Anna Goldenberg;Nicolai Juul Birkbak;Christos Hatzis;Leming Shi;Andrew H Beck;Hugo JWL Aerts;John Quackenbush;Benjamin Haibe-Kains;

10.1101/026153 — Bioinformatics — Posted on 2015-09-11

156 Revisiting inconsistency in large pharmacogenomic studies

10.1101/026153 — Bioinformatics — Posted on 2015-09-06

157 Mechanistic modelling and Bayesian inference elucidates the variable dynamics of double-strand break repair

Chris P Barnes;Mae Woods;

10.1101/026070 — Systems Biology — Posted on 2015-09-07

158 Mechanistic modelling and Bayesian inference elucidates the variable dynamics of double-strand break repair

Chris P Barnes;Mae Woods;

10.1101/026070 — Systems Biology — Posted on 2015-09-04

159 Evolutionary quantitative genomics of Populus trichocarpa

Ilga Porth;Jaroslav Klapste;Athena D McKown;Jonathan La Mantia;Robert D Guy;Paer K Ingvarsson;Richard Hamelin;Shawn D Mansfield;Juergen Ehlting;Carl J Douglas;Yousry A El-Kassaby;

10.1101/026021 — Evolutionary Biology — Posted on 2015-09-04

160 Evolutionary dynamics of roX lncRNA function and genomic occupancy

Jeffrey Jerome Quinn;Qiangfeng C Zhang;Plamen Georgiev;Ibrahim A Ilik;Asifa Akhtar;Howard Y Chang;

10.1101/026013 — Evolutionary Biology — Posted on 2015-09-04

161 Social inheritance can explain the structure of animal social networks

Amiyaal Ilany;Erol Akcay;

10.1101/026120 — Animal Behavior and Cognition — Posted on 2015-09-04

162 Cationic Peptides Facilitate Iron-induced Mutagenesis in Bacteria

Alexandro Rodriguez-Rojas;Olga Makarova;Uta Mueller;Jens Rolff;

10.1101/026112 — Microbiology — Posted on 2015-09-03

163 Small Heat Shock Proteins and Eicosanoid Pathways Modulate Caspase-1 Activity in the Fat Bodies of Antheraea pernyi

Cong fen Zhang;Lei Wang;Guoqing Wei;Cen Qian;Lishang Dai;Yu Sun;Bao jian Zhu;Chao liang Liu;

10.1101/026039 — Immunology — Posted on 2015-09-03

164 Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England

Daniel L Jeffries;Gordon H Copp;Lori-Jayne Lawson Handley;Carl D Sayer;Bernd Hänfling;

10.1101/026088 — Evolutionary Biology — Posted on 2015-09-03

165 A Comparison of Methods: Normalizing High-Throughput RNA Sequencing Data

Rahul Reddy;

10.1101/026062 — Bioinformatics — Posted on 2015-09-03

166 ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

Tarun Mall;John Eckstein;David Norris;Hiral Vora;Nowlan Freese;Ann E. Loraine;

10.1101/025924 — Bioinformatics — Posted on 2015-09-11

167 ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

Tarun Mall;John Eckstein;David Norris;Hiral Vora;Nowlan Freese;Ann E. Loraine;

10.1101/025924 — Bioinformatics — Posted on 2015-09-11

168 ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

Tarun Mall;John Eckstein;David Norris;Hiral Vora;Nowlan Freese;Ann E. Loraine;

10.1101/025924 — Bioinformatics — Posted on 2015-09-03

169 ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

Tarun Mall;John Eckstein;David Norris;Hiral Vora;Nowlan Freese;Ann E. Loraine;

10.1101/025924 — Bioinformatics — Posted on 2015-09-03

170 Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens.

Megan Fritz;Sandra Paa;Jennifer Baltzegar;Fred Gould;

10.1101/025981 — Genomics — Posted on 2015-09-02

171 Comparing RADseq and microsatellites to infer complex phylogeographic patterns, a real data informed perspective in the Crucian carp, Carassius carassius, L.

Daniel L Jeffries;Gordon H Copp;Lori-Jayne Lawson Handley;Håkan Olsén;Carl D Sayer;Bernd Hänfling;

10.1101/025973 — Evolutionary Biology — Posted on 2015-09-02

172 Extreme Mitogenomic Variation Without Cryptic Speciation in Chaetognaths

Ferdinand Marletaz;Yannick Le Parco;Shenglin Liu;Katja Peijnenburg;

10.1101/025957 — Evolutionary Biology — Posted on 2015-09-02

173 Privacy-Preserving Microbiome Analysis Using Secure Computation

Justin Wagner;Joseph N. Paulson;Xiao-Shun Wang;Bobby Bhattacharjee;Hector Corrada Bravo;

10.1101/025999 — Bioinformatics — Posted on 2015-09-03

174 Privacy-Preserving Microbiome Analysis Using Secure Computation

Justin Wagner;Joseph N. Paulson;Xiao-Shun Wang;Bobby Bhattacharjee;Hector Corrada Bravo;

10.1101/025999 — Bioinformatics — Posted on 2015-09-02

175 A Novel Method and Simple On-line Tool for Maximum Likelihood Calibration of Immunoblots and other Measurements that are Quantified in Batches

Steven S Andrews;Suzannah Rutherford;

10.1101/026005 — Biochemistry — Posted on 2015-09-02

176 How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model (TRiPS)

Jostein Starrfelt;Lee Hsiang Liow;

10.1101/025940 — Paleontology — Posted on 2015-09-02

177 Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish

Charlyn Partridge;Matthew MacManes;Rosemary Knapp;Bryan Neff;

10.1101/025916 — Genomics — Posted on 2015-09-02

178 Protein homeostasis imposes a barrier on functional integration of horizontally transferred genes in bacteria

Shimon Bershtein;Adrian Serohijos;Sanchari Bhattacharyya;Michael Manhart;Jeong-Mo Choi;Wangmen Mu;Jingwen Zhou;Eugene Shakhnovich;

10.1101/025841 — Systems Biology — Posted on 2015-09-01

179 Sampling the conformational space of the catalytic subunit of human γ-secretase

Xiao-chen Bai;Eeson Rajendra;Guanghui Yang;Yigong Shi;Sjors Scheres;

10.1101/025890 — Molecular Biology — Posted on 2015-09-01

180 Allele-specific expression reveals interactions between genetic variation and environment

David A Knowles;Joe R Davis;Anil Raj;Xiaowei Zhu;James B Potash;Myrna M Weissman;Jianxin Shi;Douglas F Levinson;Sara Mostafavi;Stephen B Montgomery;Alexis Battle;

10.1101/025874 — Genomics — Posted on 2015-09-13

181 Allele-specific expression reveals interactions between genetic variation and environment

David A Knowles;Joe R Davis;Anil Raj;Xiaowei Zhu;James B Potash;Myrna M Weissman;Jianxin Shi;Douglas F Levinson;Sara Mostafavi;Stephen B Montgomery;Alexis Battle;

10.1101/025874 — Genomics — Posted on 2015-09-01

182 Incomplete domestication of South American grain amaranth (Amaranthus caudatus) from its wild relatives

Markus G Stetter;Thomas Müller;Karl Schmid;

10.1101/025866 — Evolutionary Biology — Posted on 2015-09-01

183 Sampling networks of ecological interactions

Pedro Jordano;

10.1101/025734 — Ecology — Posted on 2015-09-06

184 Sampling networks of ecological interactions

Pedro Jordano;

10.1101/025734 — Ecology — Posted on 2015-09-03

185 Sampling networks of ecological interactions

Pedro Jordano;

10.1101/025734 — Ecology — Posted on 2015-09-01

186 Species Tailoured Contribution of Volumetric Growth and Tissue Convergence to Posterior Body Elongation in Vertebrates

Benjamin Steventon;Fernando Duarte;Ronan Lagadec;Sylvie Mazan;Jean-François Nicolas;Estelle Hirsinger;

10.1101/025882 — Developmental Biology — Posted on 2015-09-01

187 The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression

Yasin Senbabaoglu;Andrew G Winer;Ron S Gejman;Ming Liu;Augustin Luna;Irina Ostrovnaya;Nils Weinhold;William Lee;Samuel D Kaffenberger;Ying Bei Chen;Martin H Voss;Jonathan A Coleman;Paul Russo;Victor E Reuter;Timothy A Chan;Emily H Cheng;David A Scheinberg;Ming O Li;James J Hsieh;Chris Sander;Ari Hakimi;

10.1101/025908 — Cancer Biology — Posted on 2015-09-01

188 Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

Moritz Smolka;Philipp Rescheneder;Michael C Schatz;Arndt von Haeseler;Fritz J Sedlazeck;

10.1101/025858 — Bioinformatics — Posted on 2015-09-01

189 How can we study the evolution of animal minds?

Maxime Cauchoix;Alexis Chaine;

10.1101/024422 — Animal Behavior and Cognition — Posted on 2015-09-01

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

Chris J. Topping;Lars Dalby;Flemming Skov;

10.1101/025833 — Systems Biology — Posted on 2015-09-21

191 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 2015-09-10

192 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 2015-09-04

193 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 2015-09-14

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

Hervé Tricoire;Michael Rera;

10.1101/025411 — Bioinformatics — Posted on 2015-09-01

195 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 2015-09-07

196 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 2015-09-08

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

See Hong Chiu;Lei Xie;

10.1101/024513 — Bioinformatics — Posted on 2015-09-24

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

G Sampath;

10.1101/024158 — Bioengineering — Posted on 2015-09-08

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

G Sampath;

10.1101/024158 — Bioengineering — Posted on 2015-09-07

200 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 2015-09-07

201 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 2015-09-06

202 Estimating directed connectivity from cortical recordings and reconstructed sources

Margarita Papadopoulou;Karl J Friston;Daniele Marinazzo;

10.1101/023523 — Neuroscience — Posted on 2015-09-01

203 GOTHiC, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C data

Borbala Mifsud;Inigo Martincorena;Elodie Darbo;Robert Sugar;Stefan Schoenfelder;Peter Fraser;Nicholas Luscombe;

10.1101/023317 — Genomics — Posted on 2015-09-23

204 Cancer classification in the genomic era: five contemporary problems

Qingxuan Song;Sofia D Merajver;Jun Z Li;

10.1101/023127 — Genomics — Posted on 2015-09-28

205 Accelerating Scientific Publication in Biology

Ronald D Vale;

10.1101/022368 — Scientific Communication and Education — Posted on 2015-09-12

206 High Frequency Haplotypes are Expected Events, not Historical Figures

Elsa G Guillot;Murray P Cox;

10.1101/022160 — Genetics — Posted on 2015-09-17

207 Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Tutku Aykanat;Susan E Johnston;Panu Orell;Eero Niemelä;Jaakko Erkinaro;Craig R Primmer;

10.1101/022178 — Evolutionary Biology — Posted on 2015-09-07

208 Livestock market data for modeling disease spread among US cattle

Ian T. Carroll;Shweta Bansal;

10.1101/021980 — Bioinformatics — Posted on 2015-09-25

209 Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

Paul D Blischak;Laura S Kubatko;Andrea D Wolfe;

10.1101/021907 — Evolutionary Biology — Posted on 2015-09-23

210 SARTools: a DESeq2- and edgeR-based R pipeline for comprehensive differential analysis of RNA-Seq data

Hugo Varet;Jean-Yves Coppée;Marie-Agnès Dillies;

10.1101/021741 — Bioinformatics — Posted on 2015-09-26

211 Discovery of methylation loci and analyses of differential methylation from replicated high-throughput sequencing data

Thomas J Hardcastle;

10.1101/021436 — Bioinformatics — Posted on 2015-09-25

212 Striatal dynamics explain duration judgments

Thiago S. Gouvêa;Tiago Monteiro;Asma Motiwala;Sofia Soares;Christian K. Machens;Joseph J. Paton;

10.1101/020883 — Neuroscience — Posted on 2015-09-10

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 2015-09-25

214 Approximately independent linkage disequilibrium blocks in human populations

Tomaz Berisa;Joseph K. Pickrell;

10.1101/020255 — Genomics — Posted on 2015-09-16

215 Pyvolve: a flexible Python module for simulating sequences along phylogenies

Stephanie J Spielman;Claus O Wilke;

10.1101/020214 — Bioinformatics — Posted on 2015-09-10

216 The effects of time-varying temperature on delays in genetic networks

Marcella M Gomez;Richard M Murray;Matthew R Bennett;

10.1101/019687 — Systems Biology — Posted on 2015-09-24

217 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 2015-09-15

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 2015-09-08

219 A novel SOD1-dependent mechanism for the iron-induced production of toxic SOD1 and oxidative stress that initiates ALS

Liang Zhong Lim;Jianxing Song;

10.1101/018846 — Biochemistry — Posted on 2015-09-06

220 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 2015-09-14

221 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 2015-09-16

222 Development of social behaviour in young zebrafish.

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

10.1101/017863 — Neuroscience — Posted on 2015-09-21

223 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 2015-09-02

224 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 2015-09-09

225 Using heterogeneity in the population structure of U.S. swine farms to compare transmission models for porcine epidemic diarrhoea

Eamon B O'Dea;Harry Snelson;Shweta Bansal;

10.1101/017178 — Ecology — Posted on 2015-09-26

226 Detecting hidden diversification shifts in models of trait-dependent speciation and extinction

Jeremy M Beaulieu;Brian C O'Meara;

10.1101/016386 — Evolutionary Biology — Posted on 2015-09-21

227 Association mapping reveals the role of mutation-selection balance in the maintenance of genomic variation for gene expression.

Emily B. Josephs;Young Wha Lee;John R. Stinchcombe;Stephen I. Wright;

10.1101/015743 — Evolutionary Biology — Posted on 2015-09-21

228 Exome Sequencing and Prediction of Long-Term Kidney Allograft Function

Laurent Mesnard;Thangamani Muthukumar;Maren Burbach;Carol Li;Huimin Shang;Darshana Dadhania;John R Lee;Vijay K Sharma;Jenny Xiang;Caroline Suberbielle;Maryvonnick Carmagnat;Nacera Ouali;Eric Rondeau;John Friedewald;Michael Abecassis;Manikkam Suthanthiran;Fabien Campagne;

10.1101/015651 — Genomics — Posted on 2015-09-27

229 Minimum Information for Reporting Next Generation Sequence Genotyping (MIRING): Guidelines for Reporting HLA and KIR Genotyping via Next Generation Sequencing

Steven J. Mack;Robert P Milius;Benjamin D Gifford;Jürgen Sauter;Jan Hofmann;Kazutoyo Osoegawa;James Robinson;Mathjis Groeneweg;Gregory S Turenchalk;Alex Adai;Cherie Holcomb;Erik H Rozemuller;Maarten T Penning;Michael L Heuer;Chunlin Wang;Marc L Salit;Alexander H Schmidt;Peter R Parham;Carlheinz Müller;Tim Hague;Gottfried Fischer;Marcelo Fernandez-Viňa;Jill A Hollenbach;Paul J Norman;Martin Maiers;