bioRxiv directory

Zong Hong Zhang;Dhanisha J. Jhaveri;Vikki M. Marshall;Denis C. Bauer;Janette Edson;Ramesh K. Narayanan;Gregory J. Robinson;Andreas E. Lundberg;Perry F. Bartlett;Naomi R. Wray;Qiongyi Zhao;

10.1101/005611 — Bioinformatics — Posted on 2014-05-28

15 Different profile of transcriptome between wheat Yunong 201 and its high-yield mutant Yunong 3114

Feng Chen;Zhongdong Dong;Ning Zhang;Xiangfen Zhang;Dangqun Cui;

10.1101/005496 — Plant Biology — Posted on 2014-05-27

16 Hip and knee kinematics display complex and time-varying sagittal kinematics during repetitive stepping: Implications for design of a functional fatigue model of the knee extensors and flexors

Corey Scholes;Michael McDonald;Anthony Parker;

10.1101/005538 — Physiology — Posted on 2014-05-26

17 Novel Natural Product Discovery from Marine Sponges and their Obligate Symbiotic Organisms

Regina Monaco;Rena Quinlan;

10.1101/005454 — Pharmacology and Toxicology — Posted on 2014-05-24

18 Reconstructing Austronesian population history in Island Southeast Asia

Mark Lipson;Po-Ru Loh;Nick Patterson;Priya Moorjani;Ying-Chin Ko;Mark Stoneking;Bonnie Berger;David Reich;

10.1101/005603 — Genetics — Posted on 2014-05-27

19 Dynamics of a combined medea-underdominant population transformation system

Chaitanya Gokhale;Richard Guy Reeves;Floyd A Reed;

10.1101/005512 — Evolutionary Biology — Posted on 2014-05-28

20 Dynamics of a combined medea-underdominant population transformation system

Chaitanya Gokhale;Richard Guy Reeves;Floyd A Reed;

10.1101/005512 — Evolutionary Biology — Posted on 2014-05-27

21 Inferring restrictions in the temporal order of mutations during tumor progression: effects of passengers, evolutionary models, and sampling

Ramon Diaz-Uriarte;

10.1101/005587 — Bioinformatics — Posted on 2014-05-27

22 Differential stoichiometry among core ribosomal proteins

Nikolai Slavov;Stefan Semrau;Edoardo Airoldi;Bogdan Budnik;Alexander van Oudenaarden;

10.1101/005553 — Systems Biology — Posted on 2014-05-26

23 Human genomic regions with exceptionally high or low levels of population differentiation identified from 911 whole-genome sequences

Vincenza Colonna;Qasim Ayub;Yuan Chen;Luca Pagani;Pierre Luisi;Marc Pybus;Erik Garrison;Yali Xue;Chris Tyler-Smith;

10.1101/005462 — Genomics — Posted on 2014-05-27

24 Human genomic regions with exceptionally high or low levels of population differentiation identified from 911 whole-genome sequences

Vincenza Colonna;Qasim Ayub;Yuan Chen;Luca Pagani;Pierre Luisi;Marc Pybus;Erik Garrison;Yali Xue;Chris Tyler-Smith;

10.1101/005462 — Genomics — Posted on 2014-05-23

25 Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis

Matteo Carrara;Josephine Lum;Francesca Cordero;Marco Beccuti;Michael Poidinger;Susanna Donatelli;Raffaele A Calogero;Francesca Zolezzi;

10.1101/005546 — Genomics — Posted on 2014-05-26

26 The methylome of the human frontal cortex across development

Andrew E Jaffe;Yuan Gao;Ran Tao;Thomas M Hyde;Daniel R Weinberger;Joel E Kleinman;

10.1101/005504 — Developmental Biology — Posted on 2014-05-27

27 The methylome of the human frontal cortex across development

Andrew E Jaffe;Yuan Gao;Ran Tao;Thomas M Hyde;Daniel R Weinberger;Joel E Kleinman;

10.1101/005504 — Developmental Biology — Posted on 2014-05-26

28 Bio-inspired design of ice-retardant devices based on benthic marine invertebrates: the effect of surface texture

Homayun Mehrabani;Neil Ray;Kyle Tse;Dennis Evangelista;

10.1101/005470 — Biophysics — Posted on 2014-05-24

29 Powerful tests for multi-marker association analysis using ensemble learning

Badri Padhukasahasram;Chandan K Reddy;L. Keoki Williams;

10.1101/005405 — Bioinformatics — Posted on 2014-05-23

30 A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture

Henriette O'Geen;Isabelle M. Henry;Mital S. Bhakta;Joshua F. Meckler;David J. Segal;

10.1101/005413 — Molecular Biology — Posted on 2014-05-22

31 Profiling direct mRNA-microRNA interactions using synthetic biotinylated microRNA-duplexes

Shivangi Wani;Nicole Cloonan;

10.1101/005439 — Genomics — Posted on 2014-05-22

32 Inferring human population size and separation history from multiple genome sequences

Stephan Schiffels;Richard Durbin;

10.1101/005348 — Genetics — Posted on 2014-05-23

33 Inferring human population size and separation history from multiple genome sequences

Stephan Schiffels;Richard Durbin;

10.1101/005348 — Genetics — Posted on 2014-05-21

34 LIMIX: genetic analysis of multiple traits

Christoph Lippert;Francesco Paolo Casale;Barbara Rakitsch;Oliver Stegle;

10.1101/003905 — Genetics — Posted on 2014-05-22

35 LIMIX: genetic analysis of multiple traits

Christoph Lippert;Francesco Paolo Casale;Barbara Rakitsch;Oliver Stegle;

10.1101/003905 — Genetics — Posted on 2014-05-21

36 The distribution of deleterious genetic variation in human populations

Kirk E Lohmueller;

10.1101/005330 — Evolutionary Biology — Posted on 2014-05-21

37 Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

Sebastian Gil Anthony Konietzny;Phillip Byron Pope;Aaron Weimann;Alice Carolyn McHardy;

10.1101/005355 — Bioinformatics — Posted on 2014-05-21

38 IVT-seq reveals extreme bias in RNA-sequencing

Nicholas F Lahens;Ibrahim Halil Kavakli;Ray Zhang;Katharina Hayer;Michael B Black;Hannah Dueck;Angel Pizarro;Junhyong Kim;Rafael A Irizarry;Russell S Thomas;Gregory R Grant;John B Hogenesch;

10.1101/005371 — Genomics — Posted on 2014-05-21

39 Sperm should evolve to make female meiosis fair.

Yaniv Brandvain;Graham Coop;

10.1101/005363 — Evolutionary Biology — Posted on 2014-05-22

40 Sperm should evolve to make female meiosis fair.

Yaniv Brandvain;Graham Coop;

10.1101/005363 — Evolutionary Biology — Posted on 2014-05-21

41 Differences in sensitivity to EGFR inhibitors could be explained by described biochemical differences between oncogenic Ras mutants

Edward C Stites;

10.1101/005397 — Cancer Biology — Posted on 2014-05-21

42 Ultra fast tissue staining with chemical tags

Johannes Kohl;Julian Ng;Sebastian Cachero;Michael-John Dolan;Ben Sutcliffe;Daniel Krüger;Shahar Frechter;Gregory SXE Jefferis;

10.1101/005298 — Neuroscience — Posted on 2014-05-19

43 Phylogenetic confidence intervals for the optimal trait value

Krzysztof Bartoszek;Serik Sagitov;

10.1101/005314 — Evolutionary Biology — Posted on 2014-05-19

44 Adaptation to a novel predator in Drosophila melanogaster: How well are we able to predict evolutionary responses?

Michael DeNieu;William Pitchers;Ian Dworkin;

10.1101/005322 — Evolutionary Biology — Posted on 2014-05-19

45 Automation and Evaluation of the SOWH Test with SOWHAT

Samuel H. Church;Joseph F. Ryan;Casey W. Dunn;

10.1101/005264 — Bioinformatics — Posted on 2014-05-19

46 A putative antiviral role of plant cytidine deaminases

Susana Martín;José M. Cuevas;Ana Grande-Pérez;Santiago F. Elena;

10.1101/005256 — Microbiology — Posted on 2014-05-16

47 Strategic Social Learning and the Population Dynamics of Human Behavior: The Game of Go

Bret A Beheim;Calvin Thigpen;Richard McElreath;

10.1101/005223 — Evolutionary Biology — Posted on 2014-05-19

48 Strategic Social Learning and the Population Dynamics of Human Behavior: The Game of Go

Bret A Beheim;Calvin Thigpen;Richard McElreath;

10.1101/005223 — Evolutionary Biology — Posted on 2014-05-16

49 SraTailor: GUI software for visualizing high-throughput sequence read archives

Shinya Oki;Kazumitsu Maehara;Yasuyuki Ohkawa;Chikara Meno;

10.1101/005231 — Bioinformatics — Posted on 2014-05-16

50 Locus architecture affects mRNA expression levels in Drosophila embryos

Tara Lydiard-Martin;Meghan Bragdon;Kelly B Eckenrode;Zeba Wunderlich;Angela H DePace;

10.1101/005173 — Systems Biology — Posted on 2014-05-14

51 Collecting reward to defend homeostasis: A homeostatic reinforcement learning theory

Mehdi Keramati;Boris Gutkin;

10.1101/005140 — Neuroscience — Posted on 2014-05-14

52 Generation of Aggregates of Mouse ES Cells that Show Symmetry Breaking, Polarisation and Emergent Collective Behaviour in vitro.

Peter Baillie-Johnson;Susanne C van den Brink;Tina Balayo;David A Turner;Alfonso Martinez Arias;

10.1101/005215 — Developmental Biology — Posted on 2014-05-19

53 Generation of Aggregates of Mouse ES Cells that Show Symmetry Breaking, Polarisation and Emergent Collective Behaviour in vitro.

Peter Baillie-Johnson;Susanne C van den Brink;Tina Balayo;David A Turner;Alfonso Martinez Arias;

10.1101/005215 — Developmental Biology — Posted on 2014-05-15

54 RNA-seq gene profiling - a systematic empirical comparison

Nuno A Fonseca;John A Marioni;Alvis Brazma;

10.1101/005207 — Bioinformatics — Posted on 2014-05-29

55 RNA-seq gene profiling - a systematic empirical comparison

Nuno A Fonseca;John A Marioni;Alvis Brazma;

10.1101/005207 — Bioinformatics — Posted on 2014-05-14

56 qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

Stephen D. Turner;

10.1101/005165 — Bioinformatics — Posted on 2014-05-14

57 A new insight for the screening of potential β-lactamase inhibitors

Vijai Singh;Dharmendra Kumar Chaudhary;

10.1101/005181 — Bioinformatics — Posted on 2014-05-15

58 A new insight for the screening of potential β-lactamase inhibitors

Vijai Singh;Dharmendra Kumar Chaudhary;

10.1101/005181 — Bioinformatics — Posted on 2014-05-14

59 When genomes collide: multiple modes of germline misregulation in a dysgenic syndrome of Drosophila virilis

Mauricio A. Galdos;Alexandra A. Erwin;Michelle L. Wickersheim;Chris C. Harrison;Kendra D. Marr;Justin Blumenstiel;

10.1101/005124 — Genetics — Posted on 2014-05-13

60 Cosi2 : An efficient simulator of exact and approximate coalescent with selection

Ilya Shlyakhter;Pardis C. Sabeti;Stephen F. Schaffner;

10.1101/005090 — Genetics — Posted on 2014-05-14

61 Evidences of a cytotoxic activity of S-adenosylmethionine on OCI-AML3 cells

Kathrin Aprile von Hohenstaufen;Irina Puoti;Marisa Meloni;Barbara De Servi;

10.1101/004978 — Pharmacology and Toxicology — Posted on 2014-05-08

62 Independent Theta Phase Coding Accounts for CA1 Population Sequences and Enables Flexible Remapping

Angus Chadwick;Mark C. W. van Rossum;Matthew F. Nolan;

10.1101/005066 — Neuroscience — Posted on 2014-05-12

63 The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

Bargavi Thyagarajan;Jesse D Bloom;

10.1101/005041 — Microbiology — Posted on 2014-05-12

64 Diversity and evolution of centromere repeats in the maize genome

Paul Bilinski;Kevin Distor;Jose Gutierrez-Lopez;Gabriela Mendoza Mendoza;Jinghua Shi;R. Kelly Dawe;Jeffrey Ross-Ibarra;

10.1101/005058 — Genomics — Posted on 2014-05-12

65 CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes

John Aach;Prashant Mali;George M Church;

10.1101/005074 — Genomics — Posted on 2014-05-12

66 bíogo: a simple high-performance bioinformatics toolkit for the Go language

R Daniel Kortschak;David L Adelson;

10.1101/005033 — Bioinformatics — Posted on 2014-05-12

67 diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals

Paula Tataru;Jasmine A. Nirody;Yun S. Song;

10.1101/005082 — Bioinformatics — Posted on 2014-05-13

68 diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals

Paula Tataru;Jasmine A. Nirody;Yun S. Song;

10.1101/005082 — Bioinformatics — Posted on 2014-05-12

69 Mycoplasma stress response: adaptive regulation or broken brakes?

Pavel V Mazin;Gleb Y Fisunov;Alexey Y Gorbachev;Ilya A Altukhov;Tatiana A Semashko;Dmitry G Alexeev;Vadim M Govorun;

10.1101/004960 — Systems Biology — Posted on 2014-05-09

70 Module organizational principles and dynamics in biological networks

Chun-Yu Lin;Tsai-ling Lee;Yi-Wei Lin;Yu-Shu Lo;Chih-Ta Lin;Jinn-Moon Yang;

10.1101/005025 — Systems Biology — Posted on 2014-05-11

71 Background selection as baseline for nucleotide variation across the Drosophila genome

Josep M Comeron;

10.1101/005017 — Evolutionary Biology — Posted on 2014-05-09

72 An appraisal of the classic forest succession paradigm with the shade tolerance index

Jean F Lienard;Ionut Florescu;Nikolay Strigul;

10.1101/004994 — Ecology — Posted on 2014-05-10

73 Data-intensive modeling of forest dynamics

Jean F Lienard;Dominique Gravel;Nikolay Strigul;

10.1101/005009 — Ecology — Posted on 2014-05-10

74 Spatial variation in water loss predicts terrestrial salamander distribution and population dynamics

William Peterman;Raymond D Semlitsch;

10.1101/004986 — Ecology — Posted on 2014-05-09

75 Differential relationships between habitat fragmentation and within-population genetic diversity of three forest-dwelling birds

Benjamin Zuckerberg;Matt Carling;Roi Dor;Elise Ferree;Garth Spellman;Andrea Townsend;

10.1101/004903 — Genetics — Posted on 2014-05-08

76 Application of Global Transcriptome Data in Gene Ontology Classification and Construction of a Gene Ontology Interaction Network

Mario Fruzangohar;Esmaeil Ebrahimie;David L Adelson;

10.1101/004911 — Bioinformatics — Posted on 2014-05-14

77 Application of Global Transcriptome Data in Gene Ontology Classification and Construction of a Gene Ontology Interaction Network

Mario Fruzangohar;Esmaeil Ebrahimie;David L Adelson;

10.1101/004911 — Bioinformatics — Posted on 2014-05-08

78 Pushed beyond the brink: Allee effects, environmental stochasticity, and extinction

Gregory Roth;Sebastian Schreiber;

10.1101/004887 — Ecology — Posted on 2014-05-07

79 Genetic dissection of MAPK-mediated complex traits across S. cerevisiae

Sebastian Treusch;Frank W Albert;Joshua S Bloom;Iulia E Kotenko;Leonid Kruglyak;

10.1101/004895 — Genetics — Posted on 2014-05-07

80 A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate

Max V Staller;Charless C Fowlkes;Meghan D.J. Bragdon;Zeba B. Wunderlich;Angela DePace;

10.1101/004788 — Systems Biology — Posted on 2014-05-06

81 Visual areas exert feedforward and feedback influences through distinct frequency channels

Andre M Bastos;Julien Vezoli;Conrado A Bosman;Jan-Mathijs Schoffelen;Robert Oostenveld;Jarrod R Dowdall;Peter De Weerd;Henry Kennedy;Pascal Fries;

10.1101/004804 — Neuroscience — Posted on 2014-05-06

82 Missing kinaesthesia challenges precise naturalistic cortical prosthetic control

Ferran Galán;Mark R Baker;Kai Alter;Stuart N Baker;

10.1101/004861 — Neuroscience — Posted on 2014-05-06

83 MOSAIC EPIGENETIC DYSREGULATION OF ECTODERMAL CELLS IN AUTISM SPECTRUM DISORDER

Esther R. Berko;Masako Suzuki;Faygel Beren;Christophe Lemetre;Christine M. Alaimo;R. Brent Calder;Karen Ballaban-Gil;Batya Gounder;Kaylee Kampf;Jill Kirschen;Shahina B. Maqbool;Zeineen Momin;David M. Reynolds;Natalie Russo;Lisa Shulman;Edyta Stasiek;Jessica Tozour;Maria Valicenti-McDermott;Shenglong Wang;Brett S. Abrahams;Joseph Hargitai;Dov Inbar;Zhengdong Zhang;Joseph D. Buxbaum;Sophie Molholm;John J. Foxe;Robert W. Marion;Adam Auton;John Greally;

10.1101/004853 — Genomics — Posted on 2014-05-06

84 Some plants dont play games: An ideal free distribution explains the root production of plants that do not engage in a tragedy of the commons game.

Gordon McNickle;Joel S Brown;

10.1101/004820 — Ecology — Posted on 2014-05-07

85 Some plants dont play games: An ideal free distribution explains the root production of plants that do not engage in a tragedy of the commons game.

Gordon McNickle;Joel S Brown;

10.1101/004820 — Ecology — Posted on 2014-05-06

86 Cooperation between Noncanonical Ras Network Mutations in Cancer

Edward C Stites;Paul C Trampont;Lisa B Haney;Scott F Walk;Kodi S Ravichandran;

10.1101/004846 — Cancer Biology — Posted on 2014-05-06

87 N-BLR, a primate-specific non-coding transcript, modulates the epithelial-to-mesenchymal transition and leads to colorectal cancer invasion and migration

Isidore Rigoutsos;Sang Kil Lee;Su Youn Nam;Tina Catela Ivkovic;Martin Pichler;Simona Rossi;Peter Clark;Jing Yi;Hui Ling;Masayoshi Shimizu;Roxana Simona Redis;Maitri Yogen Shah;Xinna Zhang;Eun Jung Jung;Aristotelis Tsirigos;Li Huang;Jana Ferdin;Roberta Gafa;Riccardo Spizzo;Milena Nicoloso;Maryam Shariati;Aida Tiron;Jen Jen Yeh;Raul Teruel;Sonia Melo;Lianchun Xiao;Elsa Renee Flores;Massimo Negrini;Menashe Bar Eli;Sendurai Mani;Chang-Gong Liu;Ioana Berindan-Neagoe;Manel Esteller;Michael Keating;Giovanni Lanza;George Calin;