bioRxiv directory

William E Peterman;

10.1101/007575 — Ecology — Posted on 2014-07-29

3 QuASAR: Quantitative Allele Specific Analysis of Reads

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

10.1101/007492 — Bioinformatics — Posted on 2014-07-29

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

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

10.1101/005850 — Genetics — Posted on 2014-07-30

5 Reproductive isolation of hybrid populations driven by genetic incompatibilities

Molly Schumer;Rongfeng Cui;Gil G Rosenthal;Peter Andolfatto;

10.1101/007518 — Evolutionary Biology — Posted on 2014-07-30

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

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

10.1101/007542 — Evolutionary Biology — Posted on 2014-07-29

7 Classification of RNA-Seq Data via Bagging Support Vector Machines

Gokmen Zararsiz;Dincer Goksuluk;Selcuk Korkmaz;Vahap Eldem;Izzet Parug Duru;Ahmet Ozturk;Turgay Unver;

10.1101/007526 — Bioinformatics — Posted on 2014-07-28

8 poRe: an R package for the visualization and analysis of nanopore sequencing data

Mick Watson;Marian Thomson;Judith Risse;Javier Santoyo-Lopez;Richard Talbot;Karim Gharbi;Mark Blaxter;

10.1101/007567 — Bioinformatics — Posted on 2014-07-29

9 Near-optimal decoding of transient stimuli from coupled neuronal subpopulations

James Trousdale;Samuel R. Carroll;Fabrizio Gabbiani;Krešimir Josić;

10.1101/007450 — Neuroscience — Posted on 2014-07-25

10 Burrow architectural types of the Atlantic ghost crab, Ocypode quadrata (Fabricius, 1787) (Brachyura: Ocypodidae), in Brazil

Willian T. A. F. Silva;Tereza C. S. Calado;

10.1101/006098 — Ecology — Posted on 2014-07-25

11 Data mining of Gene expression profiles of Saccharomyces cerevisiae in response to mild heat stress response

Kaiyuan Ji;Wenli Ma;Wenling Zheng;

10.1101/007468 — Bioinformatics — Posted on 2014-07-25

12 Bayesian mixture analysis for metagenomic community profiling.

Sofia Morfopoulou;Vincent Plagnol;

10.1101/007476 — Genomics — Posted on 2014-07-25

13 Long non-coding RNA discovery in Anopheles gambiae using deep RNA sequencing

Adam M Jenkins;Robert M Waterhouse;Alan S Kopin;Marc A.T. Muskavitch;

10.1101/007484 — Genomics — Posted on 2014-07-26

14 MIPSTR: a method for multiplex genotyping of germ-line and somatic STR variation across many individuals

Keisha Dawn Carlson;Peter H Sudmant;Maximilian Oliver Press;Evan E Eichler;Jay Shendure;Christine Queitsch;

10.1101/007500 — Genomics — Posted on 2014-07-28

15 Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research

Àlex Bravo;Janet Piñero;Núria Queralt;Michael Rautschka;Laura I. Furlong;

10.1101/007443 — Bioinformatics — Posted on 2014-07-24

16 Null Models for Community Detection in Spatially-Embedded, Temporal Networks

Marta Sarzynska;Elizabeth A Leicht;Gerardo Chowell;Mason A Porter;

10.1101/007435 — Biophysics — Posted on 2014-07-24

17 Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries

Maria Avila-Arcos;Marcela Sandoval-Velasco;Hannes Schroeder;Meredith L Carpenter;Anna-Sapfo Malaspinas;Nathan Wales;Fernando Peñaloza;Carlos D Bustamante;M. Thomas P Gilbert;

10.1101/007419 — Genomics — Posted on 2014-07-24

18 Butter: High-precision genomic alignment of small RNA-seq data

Michael J Axtell;

10.1101/007427 — Bioinformatics — Posted on 2014-07-23

19 The emergence of network structure, complementarity and convergence from basic ecological and genetic processes

Francisco Encinas-Viso;Carlos J. Melian;Rampal S Etienne;

10.1101/007393 — Evolutionary Biology — Posted on 2014-07-23

20 Poretools: a toolkit for analyzing nanopore sequence data

Nicholas Loman;Aaron Quinlan;

10.1101/007401 — Bioinformatics — Posted on 2014-07-23

21 Characterization of the Peer Review Network at the Center for Scientific Review, National Institutes of Health

Kevin Boyack;Mei-Ching Chen;George Chacko;

10.1101/007377 — Scientific Communication and Education — Posted on 2014-07-26

22 Characterization of the Peer Review Network at the Center for Scientific Review, National Institutes of Health

Kevin Boyack;Mei-Ching Chen;George Chacko;

10.1101/007377 — Scientific Communication and Education — Posted on 2014-07-23

23 Efficient site-specific editing of the C. elegans genome

Donglei Zhang;Michael Glotzer;

10.1101/007344 — Genetics — Posted on 2014-07-31

24 Efficient site-specific editing of the C. elegans genome

Donglei Zhang;Michael Glotzer;

10.1101/007344 — Genetics — Posted on 2014-07-21

25 Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes

Todd J. Treangen;Brian D. Ondov;Sergey Koren;Adam M. Phillippy;

10.1101/007351 — Bioinformatics — Posted on 2014-07-22

26 Comparative analysis of principal components can be misleading

Josef C Uyeda;Daniel S. Caetano;Matthew W Pennell;

10.1101/007369 — Evolutionary Biology — Posted on 2014-07-22

27 Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics

Shaunak Sen;Richard M Murray;

10.1101/007385 — Systems Biology — Posted on 2014-07-22

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

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

10.1101/007310 — Synthetic Biology — Posted on 2014-07-21

29 A New Perspective on HIV Cure

Florian Hladik;

10.1101/007294 — Microbiology — Posted on 2014-07-21

30 Non-respiratory functions of Saccharomyces cerevisiae mitochondria are required for optimal attractiveness to Drosophila melanogaster

Kelly M Schiabor;Allison S Quan;Michael Eisen;

10.1101/007336 — Genetics — Posted on 2014-07-21

31 Aligning sequence from molecular inversion probes

Brent S Pedersen;

10.1101/007260 — Bioinformatics — Posted on 2014-07-19

32 Exaggerated estrous swellings and male mate choice in primates: testing the reliable indicator hypothesis in the Amboseli baboons.

Courtney L Fitzpatrick;Jeanne Altmann;Susan C Alberts;

10.1101/007278 — Animal Behavior and Cognition — Posted on 2014-07-21

33 Rewiring of genetic networks in response to modification of genetic background

Djordje Bajic;Clara Moreno;Juan F Poyatos;

10.1101/007229 — Systems Biology — Posted on 2014-07-17

34 Expression noise facilitates the evolution of gene regulation

Luise Wolf;Olin K Silander;Erik J van Nimwegen;

10.1101/007237 — Systems Biology — Posted on 2014-07-18

35 Concerning RNA-Guided Gene Drives for the Alteration of Wild Populations

Kevin M Esvelt;Andrea L Smidler;Flaminia Catteruccia;George M Church;

10.1101/007203 — Synthetic Biology — Posted on 2014-07-17

36 No evidence that sex and transposable elements drive genome size variation in evening primroses

J Arvid Agren;Stephan Greiner;Marc TJ Johnson;Stephen I Wright;

10.1101/007161 — Evolutionary Biology — Posted on 2014-07-16

37 Assessing allele specific expression across multiple tissues from RNA-seq read data

Matti Pirinen;Tuuli Lappalainen;Noah A Zaitlen;GTEx Consortium;Emmanouil T Dermitzakis;Peter Donnelly;Mark I McCarthy;Manuel A Rivas;

10.1101/007211 — Bioinformatics — Posted on 2014-07-17

38 Conservation of expression regulation throughout the animal kingdom

Michael Kuhn;Andreas Beyer;

10.1101/007252 — Bioinformatics — Posted on 2014-07-18

39 A plea for evidence in ecosystem service science: a framework and its application

Anne-Christine Mupepele;Carsten F. Dormann;

10.1101/007021 — Scientific Communication and Education — Posted on 2014-07-11

40 Reagent contamination can critically impact sequence-based microbiome analyses

Susannah Salter;Michael J Cox;Elena M Turek;Szymon T Calus;William O Cookson;Miriam F Moffatt;Paul Turner;Julian Parkhill;Nick Loman;Alan W Walker;

10.1101/007187 — Molecular Biology — Posted on 2014-07-16

41 THE GENETIC LANDSCAPE OF TRANSCRIPTIONAL NETWORKS IN A COMBINED HAPLOID/DIPLOID PLANT SYSTEM

Jukka-Pekka Verta;Christian R Landry;John J MacKay;

10.1101/007153 — Genomics — Posted on 2014-07-15

42 Massively calcified endosomal death (MCED) of endothelial cells

Larry Weisenthal;

10.1101/007112 — Cell Biology — Posted on 2014-07-15

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

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

10.1101/007120 — Bioinformatics — Posted on 2014-07-15

44 Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI’s RNA-seq archive

Anthony O Olarerin-George;John B Hogenesch;

10.1101/007054 — Genomics — Posted on 2014-07-11

45 Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood

Fan Gao;Kai Wang;

10.1101/007062 — Genomics — Posted on 2014-07-11

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

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

10.1101/007047 — Evolutionary Biology — Posted on 2014-07-11

47 Stress-Induced Mutagenesis and Complex Adaptation

Yoav Ram;Lilach Hadany;

10.1101/007096 — Evolutionary Biology — Posted on 2014-07-21

48 Stress-Induced Mutagenesis and Complex Adaptation

Yoav Ram;Lilach Hadany;

10.1101/007096 — Evolutionary Biology — Posted on 2014-07-14

49 Benchmark Analysis of Algorithms for Determining and Quantifying Full-length mRNA Splice Forms from RNA-Seq Data

Katharina Hayer;Angel Pizzaro;Nicholas L Lahens;John B Hogenesch;Gregory R Grant;

10.1101/007088 — Bioinformatics — Posted on 2014-07-14

50 A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

Mathieu Larocque;Thierry Chénard;Rafael Najmanovich;

10.1101/006932 — Systems Biology — Posted on 2014-07-25

51 A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

Mathieu Larocque;Thierry Chénard;Rafael Najmanovich;

10.1101/006932 — Systems Biology — Posted on 2014-07-09

52 Stable heteroplasmy at the single cell level is facilitated by inter-cellular exchange of mtDNA

Anitha D Jayaprakash;Erica Benson;Swapna Gone;Raymond Liang;Jaehee Shim;Luca Lambertini;Masoud M Toloue;Mike Wigler;Stuart Aaronson;Ravi Sachidanandam;

10.1101/007005 — Genetics — Posted on 2014-07-23

53 Stable heteroplasmy at the single cell level is facilitated by inter-cellular exchange of mtDNA

Anitha D Jayaprakash;Erica Benson;Swapna Gone;Raymond Liang;Jaehee Shim;Luca Lambertini;Masoud M Toloue;Mike Wigler;Stuart Aaronson;Ravi Sachidanandam;

10.1101/007005 — Genetics — Posted on 2014-07-11

54 Stable heteroplasmy at the single cell level is facilitated by inter-cellular exchange of mtDNA

Anitha D Jayaprakash;Erica Benson;Swapna Gone;Raymond Liang;Jaehee Shim;Luca Lambertini;Masoud M Toloue;Mike Wigler;Stuart Aaronson;Ravi Sachidanandam;

10.1101/007005 — Genetics — Posted on 2014-07-10

55 Extraordinarily wide genomic impact of a selective sweep associated with the evolution of sex ratio distorter suppression

Emily A Hornett;Bruce Moran;Louise A Reynolds;Sylvain Charlat;Samuel Tazzyman;Nina Wedell;Chris D Jiggins;Gregory Hurst;

10.1101/006981 — Evolutionary Biology — Posted on 2014-07-09

56 Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

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

10.1101/007039 — Evolutionary Biology — Posted on 2014-07-11

57 Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

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

10.1101/007039 — Evolutionary Biology — Posted on 2014-07-11

58 Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

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

10.1101/007039 — Evolutionary Biology — Posted on 2014-07-10

59 Extracting robust trends in species’ distributions from unstructured opportunistic data: a comparison of methods

Nick JB Isaac;Arco J van Strien;Tom A August;Marnix P de Zeeuw;David B Roy;

10.1101/006999 — Ecology — Posted on 2014-07-10

60 The whole diagram of the discovered host immunological pathways

Wanchung Hu;

10.1101/006965 — Immunology — Posted on 2014-07-08

61 V genes in primates from whole genome shotgun data

David N Olivieri;Francisco Gambon-Deza;

10.1101/006924 — Immunology — Posted on 2014-07-08

62 Improved genome inference in the MHC using a population reference graph

Alexander Dilthey;Charles J Cox;Zamin Iqbal;Matthew R Nelson;Gil McVean;

10.1101/006973 — Genomics — Posted on 2014-07-08

63 Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

Gavin Douglas;Gesseca Gos;Kim Steige;Adriana Salcedo;Karl Holm;J. Arvid Ågren;Khaled Hazzouri;Wei Wang;Adrian E. Platts;Emily B. Josephs;Robert J. Williamson;Barbara Neuffer;Martin Lascoux;Tanja Slotte;Stephen Wright;

10.1101/006783 — Evolutionary Biology — Posted on 2014-07-04

64 Convergent Evolution During Local Adaptation to Patchy Landscapes

Peter L. Ralph;Graham Coop;

10.1101/006940 — Evolutionary Biology — Posted on 2014-07-08

65 Recurrent alternative splicing isoform switches in tumor samples provide novel signatures of cancer

Endre Sebestyén;Michał Zawisza;Eduardo Eyras;

10.1101/006908 — Bioinformatics — Posted on 2014-07-07

66 Recurrent alternative splicing isoform switches in tumor samples provide novel signatures of cancer

Endre Sebestyén;Michał Zawisza;Eduardo Eyras;

10.1101/006908 — Bioinformatics — Posted on 2014-07-04

67 Modeling Cellular Information Processing Using a Dynamical Approximation of Cellular mRNA

Bradly Alicea;

10.1101/006775 — Systems Biology — Posted on 2014-07-02

68 Bonsai: An event-based framework for processing and controlling data streams

Gonçalo Lopes;Niccolò Bonacchi;João Frazão;Joana P. Neto;Bassam V. Atallah;Sofia Soares;Luís Moreira;Sara Matias;Pavel M. Itskov;Patrícia A. Correia;Roberto E. Medina;Lorenza Calcaterra;Elena Dreosti;Joseph J. Paton;Adam R. Kampff;

10.1101/006791 — Neuroscience — Posted on 2014-07-02

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

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

10.1101/006825 — Genomics — Posted on 2014-07-02

70 Nuclear stability and transcriptional directionality separate functionally distinct RNA species

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

10.1101/005447 — Genomics — Posted on 2014-07-02

71 Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity

Corey T Watson;Karyn Meltz Steinberg;Tina A Graves-Lindsay;Rene L Warren;Maika Malig;Jacqueline E Schein;Richard K Wilson;Rob Holt;Evan Eichler;Felix Breden;

10.1101/006866 — Genomics — Posted on 2014-07-03

72 Single haplotype assembly of the human genome from a hydatidiform mole

Karyn Meltz Steinberg;Valerie K Schneider;Tina A Graves-Lindsay;Robert S Fulton;Richa Agarwala;John Huddleston;Sergey A Shiryayev;Aleksandr Morgulis;Urvashi Surti;Wesley C Warren;Deanna M Church;Evan E Eichler;Richard K Wilson;

10.1101/006841 — Genomics — Posted on 2014-07-03

73 Products of the Parkinson’s-disease related glyoxalase DJ-1, D-lactate and glycolate, support mitochondrial membrane potential and neuronal survival

Yusuke Toyoda;Cihan Erkut;Francisco Pan-Montojo;Sebastian Boland;Martin P. Stewart;Daniel J. M?ller;Wolfgang Wurst;Anthony A. Hyman;Teymuras V. Kurzchalia;