bioRxiv directory

1 Improving effect size estimation and statistical power with multi-echo fMRI and its impact on understanding the neural systems supporting mentalizing

D. Sam Schwarzkopf;

10.1101/017327 — Neuroscience — Posted on 2015-03-31

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

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

10.1101/017319 — Microbiology — Posted on 2015-03-31

4 Neanderthal Genomics Suggests a Pleistocene Time Frame for the First Epidemiologic Transition

Charlotte Jane Houldcroft;Simon Underdown;

10.1101/017343 — Genetics — Posted on 2015-03-31

5 Design of a Toolbox of RNA Thermometers

Shaunak Sen;Divyansh Apurva;Rohit Satija;Dan Siegal;Richard M Murray;

10.1101/017269 — Synthetic Biology — Posted on 2015-03-30

6 Developmental and phenotypic plasticity of Arabidopsis thaliana accessions across an ambient temperature range

Carla Ibanez;Yvonne Poeschl;Tom Peterson;Julia Bellstaedt;Kathrin Denk;Andreas Gogol-Doering;Marcel Quint;Carolin Delker;

10.1101/017285 — Plant Biology — Posted on 2015-03-30

7 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 2015-03-30

8 Simple genetic models for autism spectrum disorder

Swagatam Mukhopadhyay;Michael Wigler;Dan Levy;

10.1101/017301 — Genetics — Posted on 2015-03-30

9 Processes driving nocturnal transpiration and implications for estimating land evapotranspiration

Víctor Resco de Dios;Jacques Roy;Juan Pedro Ferrio;Josu Alday;Damien Landais;Alexandru Milcu;Arthur Gessler;

10.1101/017202 — Plant Biology — Posted on 2015-03-30

10 Novel APC-like properties of human NK cells directly regulate T cell activation

Jacob Hanna;Ofer Mandelboim;

10.1101/016816 — Immunology — Posted on 2015-03-30

11 Network analysis of genome-wide selective constraint reveals a gene network active in early fetal brain intolerant of mutation

Jinmyung Choi;Parisa Shooshtari;Kaitlin E Samocha;Mark J Daly;Chris Cotsapas;

10.1101/017277 — Genetics — Posted on 2015-03-29

12 Genetic variability under the seedbank coalescent

Jochen Blath;Bjarki Eldon;Adrian Casanova;Noemi Kurt;Maite Wilke-Berenguer;

10.1101/017244 — Evolutionary Biology — Posted on 2015-03-30

13 Genetic variability under the seedbank coalescent

Jochen Blath;Bjarki Eldon;Adrian Casanova;Noemi Kurt;Maite Wilke-Berenguer;

10.1101/017244 — Evolutionary Biology — Posted on 2015-03-29

14 Disturbance of poised chromatin coincides with increased expression of developmental genes in cancer

Stephan H Bernhart;Helene Kretzmer;Frank Jühling;Peter F Stadler;Steve Hoffmann;

10.1101/017251 — Cancer Biology — Posted on 2015-03-29

15 RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints

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

10.1101/017111 — Bioinformatics — Posted on 2015-03-29

16 Visual cues determine hippocampal directional selectivity

Lavanya Acharya;Zahra M. Aghajan;Cliff Vuong;Jason Moore;Mayank Mehta;

10.1101/017210 — Neuroscience — Posted on 2015-03-28

17 Using targeted re-sequencing for identification of candidate genes and SNPs for a QTL affecting the pH value of chicken muscle

Xidan Li;Xiaodong Liu;Javad Nadaf;Elisabeth Le Bihan-Duval;Cécile Berri;Ian C. Dunn;Richard Talbot;D. J. de Koning;

10.1101/017186 — Genetics — Posted on 2015-03-27

18 Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

Emiliano Trucchi;Benoit Facon;Paolo Gratton;Emiliano Mori;Nils Chr Stenseth;Sissel Jentoft;

10.1101/016493 — Evolutionary Biology — Posted on 2015-03-27

19 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 2015-03-27

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

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

10.1101/017194 — Bioinformatics — Posted on 2015-03-27

21 Accurate Isothermal Amplification Reaction Rate Determination Using High-Frequency Sampling

Thomas Beals;

10.1101/017160 — Molecular Biology — Posted on 2015-03-26

22 How complexity originates: The evolution of animal eyes

Todd H Oakley;Daniel I Speiser;

10.1101/017129 — Evolutionary Biology — Posted on 2015-03-26

23 MMR: A Tool for Read Multi-Mapper Resolution

Andre Kahles;Jonas Behr;Gunnar Rätsch;

10.1101/017103 — Bioinformatics — Posted on 2015-03-26

24 Repellent compound with larger protective zone than DEET identified through activity-screening of Ir40a neurons, does not require Or function

Tom Guda;PInky Kain;Kavita R Sharma;Christine K Pham;Anandasankar Ray;

10.1101/017145 — Neuroscience — Posted on 2015-03-26

25 A large-scale circuit mechanism for hierarchical dynamical processing in the primate cortex

Rishidev Chaudhuri;Kenneth Knoblauch;Marie-Alice Gariel;Henry Kennedy;Xiao-Jing Wang;

10.1101/017137 — Neuroscience — Posted on 2015-03-26

26 Entire genome transcription across evolutionary time exposes non-coding DNA to de novo gene emergence

Rafik Neme;Diethard Tautz;

10.1101/017152 — Evolutionary Biology — Posted on 2015-03-26

27 Dilp8 requires the neuronal relaxin receptor Lgr3 to couple growth to developmental timing

Andres Garelli;Fabiana Heredia;Andreia P. Casimiro;Andre Macedo;Catarina Nunes;Marcia Garcez;Angela R. Mantas Dias;Yanel A. Volonte;Takashi Koyama;Alisson M. Gontijo;

10.1101/017053 — Developmental Biology — Posted on 2015-03-25

28 SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data

Andre Kahles;Cheng Soon Ong;Yi Zhong;Gunnar Rätsch;

10.1101/017095 — Bioinformatics — Posted on 2015-03-26

29 Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

Brad Solomon;Carleton Kingsford;

10.1101/017087 — Bioinformatics — Posted on 2015-03-26

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

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

10.1101/016998 — Genomics — Posted on 2015-03-25

31 Threshold trait architecture of Hsp90-buffered variation

Charles C Carey;Kristen F Gorman;Becky Howsmon;Charles Kooperberg;Aaron K Aragaki;Suzannah Rutherford;

10.1101/016980 — Genetics — Posted on 2015-03-25

32 Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

Rohan Maddamsetti;Richard E. Lenski;Jeffrey E. Barrick;

10.1101/017020 — Evolutionary Biology — Posted on 2015-03-25

33 Exploring the effects of high concentration of glucose on soil microbial community: An experimental study using the soil of North Bangalore

Anshuman Swain;

10.1101/017061 — Ecology — Posted on 2015-03-25

34 Interventional Nerve Visualization via the Intrinsic Anisotropic Optical Properties of the Nerves

Kenneth Chin;Andries Meijerink;Patrick Chin;

10.1101/017046 — Biophysics — Posted on 2015-03-25

35 Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence

Elise R Morton;Joshua Lynch;Alain Froment;Sophie Lafosse;Evelyne Heyer;Molly Przeworski;Ran Blekhman;Laure Segurel;

10.1101/016949 — Microbiology — Posted on 2015-03-24

36 Genome-wide Association Study for Number of Vertebrae in an F2 Large White × Minzhu Population of Pigs

Longchao Zhang;Xin Liu;Jing Liang;Kebin Zhao;Hua Yan;Na Li;Lei Pu;Yuebo Zhang;Huibi Shi;Ligang Wang;Lixian Wang;

10.1101/016956 — Genetics — Posted on 2015-03-24

37 Recombining without hotspots: A comprehensive evolutionary portrait of recombination in two closely related species of Drosophila

Caiti Smukowski Heil;Chris Ellison;Matthew Dubin;Mohamed Noor;

10.1101/016972 — Evolutionary Biology — Posted on 2015-03-24

38 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-03-31

39 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-03-27

40 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-03-26

41 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-03-25

42 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-03-24

43 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-03-24

44 Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression

Shensi Shen;Guillermo Rodrigo;Satya Prakash;Eszter Majer;Thomas E Landrain;Boris Kirov;Jose Antonio Daros;Alfonso Jaramillo;

10.1101/016915 — Synthetic Biology — Posted on 2015-03-23

45 The unusual gene order in the Echinoderm Hox cluster is related to the embryo and larva symmetries

Spyros Papageorgiou;

10.1101/016923 — Developmental Biology — Posted on 2015-03-23

46 The advent of genome-wide association studies for bacteria

Peter E Chen;B Jesse Shapiro;

10.1101/016873 — Genomics — Posted on 2015-03-22

47 SumVg: Total heritability explained by all variants in genome-wide association studies based on summary statistics with standard error estimates

Hon-Cheong SO;Pak C. SHAM;

10.1101/016857 — Genomics — Posted on 2015-03-22

48 Exploring functional variation affecting ceRNA regulation in humans

Mulin Jun Li;Jiexing Wu;Peng Jiang;Wei Li;Yun Zhu;Daniel Fernandez;Russell J. H. Ryan;Yiwen Chen;Junwen Wang;Jun S. Liu;X. Shirley Liu;

10.1101/016865 — Genetics — Posted on 2015-03-22

49 Cline coupling and uncoupling in a stickleback hybrid zone

Tim Vines;Anne Dalziel;Arianne Albert;Thor Veen;Patricia Schulte;Dolph Schluter;

10.1101/016832 — Evolutionary Biology — Posted on 2015-03-22

50 Selective strolls: fixation and extinction in diploids are slower for weakly selected mutations than for neutral ones

fabrizio mafessoni;Michael Lachmann;

10.1101/016881 — Evolutionary Biology — Posted on 2015-03-26

51 Selective strolls: fixation and extinction in diploids are slower for weakly selected mutations than for neutral ones

fabrizio mafessoni;Michael Lachmann;

10.1101/016881 — Evolutionary Biology — Posted on 2015-03-23

52 CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinic

Márton Münz;Elise Ruark;Anthony Renwick;Emma Ramsay;Matthew Clarke;Shazia Mahamdallie;Victoria Cloke;Sheila Seal;Ann Strydom;Gerton Lunter;Nazneen Rahman;

10.1101/016808 — Genomics — Posted on 2015-03-21

53 CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinic

Márton Münz;Elise Ruark;Anthony Renwick;Emma Ramsay;Matthew Clarke;Shazia Mahamdallie;Victoria Cloke;Sheila Seal;Ann Strydom;Gerton Lunter;Nazneen Rahman;

10.1101/016808 — Genomics — Posted on 2015-03-21

54 CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinic

Márton Münz;Elise Ruark;Anthony Renwick;Emma Ramsay;Matthew Clarke;Shazia Mahamdallie;Victoria Cloke;Sheila Seal;Ann Strydom;Gerton Lunter;Nazneen Rahman;

10.1101/016808 — Genomics — Posted on 2015-03-20

55 Breaking through evolutionary constraint by environmental fluctuations

Marjon GJ de Vos;Alexandre Dawid;Vanda Sunderlikova;Sander J Tans;

10.1101/016790 — Evolutionary Biology — Posted on 2015-03-20

56 Spatial model predicts dispersal and cell turnover cause reduced intra-tumor heterogeneity

Bartlomiej Waclaw;Ivana Bozic;Meredith E Pittman;Ralph H Hruban;Bert Vogelstein;Martin A Nowak;

10.1101/016824 — Cancer Biology — Posted on 2015-03-20

57 Bio4j: a high-performance cloud-enabled graph-based data platform

Pablo Pareja-Tobes;Raquel Tobes;Marina Manrique;Eduardo Pareja;Eduardo Pareja-Tobes;

10.1101/016758 — Bioinformatics — Posted on 2015-03-20

58 Transcriptome Differences between Alternative Sex Determining Genotypes in the House Fly, Musca domestica

Richard P Meisel;Jeffrey G Scott;Andrew G Clark;

10.1101/016774 — Genomics — Posted on 2015-03-20

59 Repeatability of evolution on epistatic landscapes

Benedikt Bauer;Chaitanya S Gokhale;

10.1101/016782 — Evolutionary Biology — Posted on 2015-03-20

60 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;

10.1101/016733 — Biophysics — Posted on 2015-03-19

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

Alexandr N. Tetearing;

10.1101/016691 — Systems Biology — Posted on 2015-03-24

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

Alexandr N. Tetearing;

10.1101/016691 — Systems Biology — Posted on 2015-03-18

63 Self-organization of Computation in Neural Systems

Christian Tetzlaff;Sakyasingha Dasgupta;Tomas Kulvicius;Florentin Wörgötter;

10.1101/016725 — Neuroscience — Posted on 2015-03-19

64 Self-organization of Computation in Neural Systems

Christian Tetzlaff;Sakyasingha Dasgupta;Tomas Kulvicius;Florentin Wörgötter;

10.1101/016725 — Neuroscience — Posted on 2015-03-18

65 Sex chromosome dosage compensation in Heliconius butterflies: global yet still incomplete?

James R Walters;Thomas J Hardcastle;Chris Jiggins;

10.1101/016675 — Genomics — Posted on 2015-03-19

66 Sex chromosome dosage compensation in Heliconius butterflies: global yet still incomplete?

James R Walters;Thomas J Hardcastle;Chris Jiggins;

10.1101/016675 — Genomics — Posted on 2015-03-17

67 The fate of a mutation in a fluctuating environment

Ivana Cvijovic;Benjamin H. Good;Elizabeth R. Jerison;Michael M. Desai;

10.1101/016709 — Evolutionary Biology — Posted on 2015-03-18

68 Distributed Bayesian Networks Reconstruction on the Whole Genome Scale

Alina Frolova;Bartek Wilczyński;

10.1101/016683 — Bioinformatics — Posted on 2015-03-17

69 Dimensionality and the statistical power of multivariate genome-wide association studies

Eladio J. Marquez;David Houle;

10.1101/016592 — Genomics — Posted on 2015-03-17

70 Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

Alicia Schep;Jason D Buenrostro;Sarah K Denny;Katja Schwartz;Gavin Sherlock;William J Greenleaf;

10.1101/016642 — Genomics — Posted on 2015-03-17

71 Two variance component model improves genetic prediction in family data sets

George Tucker;Po-Ru Loh;Iona M MacLeod;Ben J Hayes;Michael E Goddard;Bonnie Berger;Alkes L Price;

10.1101/016618 — Genetics — Posted on 2015-03-17

72 Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection

Mark Christian Harrison;Eamonn B Mallon;Dave Twell;Robert L Hammond;

10.1101/016626 — Evolutionary Biology — Posted on 2015-03-17

73 Introgression obscures and reveals historical relationships among the American live oaks

Deren Eaton;Antonio Gonzalez-Rodriguez;Andrew Hipp;Jeannine Cavender-Bares;

10.1101/016238 — Evolutionary Biology — Posted on 2015-03-17

74 Latent epistatic interaction model identifies loci associated with human working memory

Janos Z Kelemen;Christian Vogler;Angela Beck;Dominique de Quervain;Andreas Papassotiropoulos;Niko Beerenwinkel;

10.1101/016576 — Bioinformatics — Posted on 2015-03-17

75 CIDER: a pipeline for detecting waves of coordinated transcriptional regulation in gene expression time-course data

Marco Mina;Giuseppe Jurman;Cesare Furlanello;

10.1101/012518 — Bioinformatics — Posted on 2015-03-17

76 regionReport: Interactive reports for region-based analyses

Leonardo Collado-Torres;Andrew E Jaffe;Jeffrey T Leek;

10.1101/016659 — Bioinformatics — Posted on 2015-03-17

77 Intersubject information mapping: revealing canonical representations of complex natural stimuli.

Nikolaus Kriegeskorte;

10.1101/016436 — Neuroscience — Posted on 2015-03-14

78 Efficient strategies for calculating blockwise likelihoods under the coalescent

Konrad Lohse;Martin Chmelik;Simon Henry Martin;Nick H Barton;

10.1101/016469 — Genetics — Posted on 2015-03-13

79 Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis

Po-Ru Loh;Gaurav Bhatia;Alexander Gusev;Hilary K Finucane;Brendan K Bulik-Sullivan;Samuela J Pollack;Schizophrenia Working Group Psychiatric Genomics Consortium;Teresa R de Candia;Sang Hong Lee;Naomi R Wray;Kenneth S Kendler;Michael C O'Donovan;Benjamin M Neale;Nick Patterson;Alkes L Price;

10.1101/016527 — Genetics — Posted on 2015-03-14

80 Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome

Amy Goldberg;Noah A Rosenberg;

10.1101/016543 — Genetics — Posted on 2015-03-14

81 Eight thousand years of natural selection in Europe

Iain Mathieson;Iosif Lazaridis;Nadin Rohland;Swapan Mallick;Nick Patterson;Songul Alpaslan Roodenberg;Eadaoin Harney;Kristin Stewardson;Daniel Fernandes;Mario Novak;Kendra Sirak;Cristina Gamba;Eppie R. Jones;Bastien Llamas;Stanislav Dryomov;Joseph Pickrell;Juan Luis Arsuaga;Jose Maria Bermudez de Castro;Eudald Carbonell;Fokke Gerritsen;Aleksandr Khokhlov;Pavel Kuznetsov;Marina Lozano;Harald Meller;Oleg Mochalov;Vayacheslav Moiseyev;Manuel A. Rojo Guerra;Jacob Roodenberg;Josep Maria Verges;Johannes Krause;Alan Cooper;Kurt W. Alt;Dorcas Brown;David Anthony;Carles Lalueza-Fox;Wolfgang Haak;Ron Pi

10.1101/016477 — Genetics — Posted on 2015-03-14

82 Calculating the Human Mutation Rate by Using a NUMT from the Early Oligocene

Ian Logan;

10.1101/016428 — Genetics — Posted on 2015-03-14

83 The Spatial Mixing of Genomes in Secondary Contact Zones

Alisa Sedghifar;Yaniv Brandvain;Peter L. Ralph;Graham Coop;

10.1101/016337 — Evolutionary Biology — Posted on 2015-03-14

84 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 2015-03-14

85 The structure of probabilistic networks

Timothée Poisot;Alyssa Cirtwill;Kévin Cazelles;Dominique Gravel;Marie-Josée Fortin;Daniel Stouffer;

10.1101/016485 — Ecology — Posted on 2015-03-14

86 Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

Michael A. Cianfrocco;Andres E. Leschziner;

10.1101/016451 — Biophysics — Posted on 2015-03-14

87 LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads

Rene L Warren;Benjamin P Vandervalk;Steven JM Jones;Inanc Birol;

10.1101/016519 — Bioinformatics — Posted on 2015-03-20

88 LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads

Rene L Warren;Benjamin P Vandervalk;Steven JM Jones;Inanc Birol;

10.1101/016519 — Bioinformatics — Posted on 2015-03-17

89 LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads

Rene L Warren;Benjamin P Vandervalk;Steven JM Jones;Inanc Birol;

10.1101/016519 — Bioinformatics — Posted on 2015-03-14

90 Cryptic haplotypes of "Candidatus Liberibacter africanus"

Warrick Nelson;Sandrine Eveillard;Marie-Pierre Dubrana;Joseph Bové;

10.1101/016410 — Microbiology — Posted on 2015-03-12

91 Cryptic haplotypes of "Candidatus Liberibacter africanus"

Warrick Nelson;Sandrine Eveillard;Marie-Pierre Dubrana;Joseph Bové;

10.1101/016410 — Microbiology — Posted on 2015-03-11

92 PoMo: An Allele Frequency-based Approach for Species Tree Estimation

Nicola De Maio;Dominik Schrempf;Carolin Kosiol;

10.1101/016360 — Evolutionary Biology — Posted on 2015-03-11

93 Measuring forces and stresses in situ in living tissues

Forces-in-tissue workshop participants;

10.1101/016394 — Developmental Biology — Posted on 2015-03-11

94 Hippocampal Spine Head Sizes are Highly Precise

Thomas M Bartol;Cailey Bromer;Justin P Kinney;Michael A Chirillo;Jennifer N Bourne;Kristen M Harris;Terrence J Sejnowski;

10.1101/016329 — Neuroscience — Posted on 2015-03-11

95 Proteomic analysis of Dhh1 complexes reveals a role for Hsp40 chaperone Ydj1 in yeast P-body assembly

Gregory A. Cary;Dani B.N. Vinh;Patrick May;Rolf Kuestner;Aimee M. Dudley;

10.1101/016402 — Molecular Biology — Posted on 2015-03-11

96 A Branching Process to Characterize the Dynamics of Stem Cell Differentiation

david miguez;

10.1101/016295 — Developmental Biology — Posted on 2015-03-11

97 Dynamics of miRNA driven feed-forward loop depends upon miRNA action mechanisms

Maria Duk;Maria Samsonova;Alexander Samsonov;

10.1101/016162 — Systems Biology — Posted on 2015-03-10

98 Fables and foibles: a critical analysis of the Palaeoflora database and the Coexistence approach for palaeoclimate reconstruction

Guido Grimm;Thomas Denk;Johannes Martin Bouchal;Alastair John Potts;

10.1101/016378 — Paleontology — Posted on 2015-03-10

99 Metassembler: Merging and optimizing de novo genome assemblies

Alejandro Hernandez Wences;Michael Schatz;

10.1101/016352 — Bioinformatics — Posted on 2015-03-10

100 ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data

Jane Hawkey;Mohammad Hamidian;Ryan R Wick;David J Edwards;Helen Billman-Jacobe;Ruth M Hall;Kathryn E Holt;

10.1101/016345 — Bioinformatics — Posted on 2015-03-10

101 No association between plant mating system & geographic range overlap

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

10.1101/016261 — Evolutionary Biology — Posted on 2015-03-09

102 Phylogeography by Diffusion on a Sphere

Remco Bouckaert;

10.1101/016311 — Evolutionary Biology — Posted on 2015-03-09

103 Tissue dynamics of the forebrain neural plate

Stephen Young;Joel N Jennings;Guy B Blanchard;Alexandre J Kabla;Richard Adams;

10.1101/016303 — Developmental Biology — Posted on 2015-03-09

104 Revisiting the Structure/Function Relationships of H/ACA(-like) RNAs: A Unified Model for Euryarchaea and Crenarchaea

Claire Toffano-Nioche;Daniel Gautheret;Fabrice Leclerc;

10.1101/016246 — Bioinformatics — Posted on 2015-03-10

105 Revisiting the Structure/Function Relationships of H/ACA(-like) RNAs: A Unified Model for Euryarchaea and Crenarchaea

Claire Toffano-Nioche;Daniel Gautheret;Fabrice Leclerc;

10.1101/016246 — Bioinformatics — Posted on 2015-03-09

106 Different Coupling Modes Mediate Cortical Cross-Frequency Interactions

Randolph F Helfrich;Christoph S Herrmann;Andreas K Engel;Till R Schneider;

10.1101/016212 — Neuroscience — Posted on 2015-03-07

107 Intragenomic homogeneity on Liberibacter 16S rDNA confirms phylogeny and explains ecological strategy

Warrick R Nelson;Nelson A Wulff;Joseph M Bové;

10.1101/016188 — Microbiology — Posted on 2015-03-08

108 Pathway based factor analysis of gene expression data produces highly heritable phenotypes that associate with age

Andrew Anand Brown;Zhihao Ding;Ana Viñuela;Dan Glass;Leopold Parts;Timothy Spector;John Winn;Richard Durbin;

10.1101/016154 — Genomics — Posted on 2015-03-06

109 Mutational oncogenic signatures on structurally resolved protein interacting interfaces

Luz Garcia-Alonso;Joaquin Dopazo;

10.1101/016204 — Genomics — Posted on 2015-03-07

110 svviz: a read viewer for validating structural variants

Noah Spies;Justin M Zook;Marc Salit;Arend Sidow;

10.1101/016063 — Genomics — Posted on 2015-03-07

111 Mbd3/NuRD is a Key Inhibitory Module During the Induction and Maintenance of Naïve Pluripotency

Asaf Zviran;Yoach Rais;Nofar Mor;Noa Novershtern;Jacob H Hanna;

10.1101/013961 — Developmental Biology — Posted on 2015-03-06

112 Efficient APC/C substrate degradation in cells undergoing mitotic exit depends on K11 ubiquitin linkages

Mingwei Min;Tycho Mevissen;Maria De Luca;David Komander;Catherine Lindon;

10.1101/016139 — Cell Biology — Posted on 2015-03-06

113 Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads

Hung-I Harry Chen;Yuanhang Liu;Yi Zou;Zhao Lai;Devanand Sarkar;Yufei Huang;Yidong Chen;

10.1101/016196 — Bioinformatics — Posted on 2015-03-07

114 Tools and best practices for allelic expression analysis

Stephane E Castel;Ami Levy-Moonshine;Pejman Mohammadi;Eric Banks;Tuuli Lappalainen;

10.1101/016097 — Genomics — Posted on 2015-03-06

115 A Comparison of Methods to Measure Fitness in Escherichia coli

Michael J Wiser;Richard E Lenski;

10.1101/016121 — Evolutionary Biology — Posted on 2015-03-06

116 Detecting Signals of Seasonal Influenza Severity through Age Dynamics

Elizabeth C Lee;Cécile Viboud;Lone Simonsen;Farid Khan;Shweta Bansal;

10.1101/016105 — Ecology — Posted on 2015-03-06

117 Nitric oxide regulates growth coordination during regeneration

Jacob S. Jaszczak;Jacob B. Wolpe;Anh Q. Dao;Adrian Halme;

10.1101/016030 — Developmental Biology — Posted on 2015-03-06

Yusei Kobori;Satoshi Mizuta;

10.1101/016089 — Bioinformatics — Posted on 2015-03-06

119 Complexity of dendritic SER increases at enlarging synapses during LTP

Michael Chirillo;Jennifer Bourne;Laurence Lindsey;Kristen Harris;

10.1101/015974 — Neuroscience — Posted on 2015-03-04

120 Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells

Alain Pacis;Ludovic Tailleux;John Lambourne;Vania Yotova;Anne Dumaine;Anne Danckaert;Francesca Luca;Jean-Christophe Grenier;Kasper Hansen;Brigitte Gicquel;Miao Yu;Athma Pai;Jenny Tung;Chuan He;Tomi Pastinen;Roger Pique-Regi;Yoav Gilad;Luis Barreiro;

10.1101/016022 — Genomics — Posted on 2015-03-04

121 Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat

Ben P Williams;Daniela Pignatta;Steven Henikoff;Mary Gehring;

10.1101/015941 — Genetics — Posted on 2015-03-04

122 The origins of a novel butterfly wing patterning gene from within a family of conserved cell cycle regulators

Nicola Nadeau;Carolina Pardo-Diaz;Annabel Whibley;Megan Ann Supple;Richard Wallbank;Grace C. Wu;Luana Maroja;Laura Ferguson;Heather Hines;Camilo Salazar;Richard ffrench-Constant;Mathieu Joron;William Owen McMillan;Chris Jiggins;

10.1101/016006 — Evolutionary Biology — Posted on 2015-03-24

123 The origins of a novel butterfly wing patterning gene from within a family of conserved cell cycle regulators

10.1101/016006 — Evolutionary Biology — Posted on 2015-03-05

124 The interplay between DNA methylation and sequence divergence in recent human evolution

Irene Hernando-Herraez;Holger Heyn;Marcos Fernandez-Callejo;Enrique Vidal;Hugo Fernandez-Bellon;Javier Prado-Martinez;Andrew J Sharp;Manel Esteller;Tomas Marques-Bonet;

10.1101/015966 — Evolutionary Biology — Posted on 2015-03-03

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

Shriprakash Sinha;

10.1101/015834 — Systems Biology — Posted on 2015-03-21

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

Shriprakash Sinha;

10.1101/015834 — Systems Biology — Posted on 2015-03-18

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

Shriprakash Sinha;

10.1101/015834 — Systems Biology — Posted on 2015-03-03

128 A matter of attention: Crossmodal congruence enhances and impairs performance in a novel trimodal matching paradigm

Jonas Misselhorn;Jonathan Daume;Andreas K. Engel;Uwe Friese;

10.1101/015958 — Neuroscience — Posted on 2015-03-03

129 Phase i trials in melanoma: A framework to translate preclinical findings to the clinic

Eunjung Kim;Vito W. Rebecca;Keiran S.M. Smalley;Alexander R.A. Anderson;

10.1101/015925 — Cancer Biology — Posted on 2015-03-26

130 Phase i trials in melanoma: A framework to translate preclinical findings to the clinic

Eunjung Kim;Vito W. Rebecca;Keiran S.M. Smalley;Alexander R.A. Anderson;

10.1101/015925 — Cancer Biology — Posted on 2015-03-03

131 Identification of novel transcriptional regulators of PKA subunits in Saccharomyces cerevisiae by Quantitative Promoter–Reporter Screening

Constanza Maria Pautasso;Katherine Chatfield-Reed;Gordon Chua;Vanina Zaremberg;Silvia Rossi;

10.1101/015891 — Molecular Biology — Posted on 2015-03-02

132 Distinctive Features of a Saudi Genome

Ibrahim B. Alabdulkareem;Anthony J. Robertson;Sami Al Garawi;Mohammed Aljumah;Saeed Al-Turki;Mohammed A Al Balwi;

10.1101/015909 — Genomics — Posted on 2015-03-02

133 Selection and explosive growth may hamper the performance of rare variant association tests

Lawrence H. Uricchio;John S. Witte;Ryan D. Hernandez;

10.1101/015917 — Evolutionary Biology — Posted on 2015-03-02

134 A Pan-cancer catalogue of driver protein interaction interfaces

Eduard Porta-Pardo;Thomas Hrabe;Adam Godzik;

10.1101/015883 — Cancer Biology — Posted on 2015-03-02

135 A Pan-cancer catalogue of driver protein interaction interfaces

Eduard Porta-Pardo;Thomas Hrabe;Adam Godzik;

10.1101/015883 — Cancer Biology — Posted on 2015-03-02

136 BamHash: a checksum program for verifying the integrity of sequence data

Arna Óskarsdóttir;Gísli Másson;Páll Melsted;

10.1101/015867 — Bioinformatics — Posted on 2015-03-03

137 BamHash: a checksum program for verifying the integrity of sequence data

Arna Óskarsdóttir;Gísli Másson;Páll Melsted;

10.1101/015867 — Bioinformatics — Posted on 2015-03-02

138 Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

Bjarni Vilhjalmsson;Jian Yang;Hilary Kiyo Finucane;Alexander Gusev;Sara Lindstrom;Stephan Ripke;Giulio Genovese;Po-Ru Loh;Gaurav Bhatia;Ron Do;Tristian Hayeck;Hong-Hee Won;Schizophrenia Working Group of the Psychiatric Genomics Consortium;the Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) study;Sekar Kathiresan;Michele Pato;Carlos Pato;Rulla Tamimi;Eli Stahl;Noah Zaitlen;Bogdan Pasaniuc;Mikkel Schierup;Phillip De Jager;Nikolaos Patsopoulos;Steven A McCarroll;Mark Daly;Shaun Purcell;Daniel Chasman;Benjamin Neale;Mike Goddard;Peter M Visscher;Peter Kraft;Nick J Patte

10.1101/015859 — Bioinformatics — Posted on 2015-03-04

139 Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

10.1101/015859 — Bioinformatics — Posted on 2015-03-02

140 Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China

Zhuo Zhao;Hua Wang;Jie Zhang;Zhi-Peng Liu;Ming Liu;Yuan Zhang;Li Sun;Hui Zhang;

10.1101/015875 — Genetics — Posted on 2015-03-01

141 Speciation in Heliconius Butterflies: Minimal Contact Followed by Millions of Generations of Hybridisation

Simon Henry Martin;Anders Eriksson;Krzysztof M. Kozak;Andrea Manica;Chris D. Jiggins;

10.1101/015800 — Evolutionary Biology — Posted on 2015-03-02

142 Speciation in Heliconius Butterflies: Minimal Contact Followed by Millions of Generations of Hybridisation

Simon Henry Martin;Anders Eriksson;Krzysztof M. Kozak;Andrea Manica;Chris D. Jiggins;

10.1101/015800 — Evolutionary Biology — Posted on 2015-03-01

143 Recent evolution in Rattus norvegicus is shaped by declining effective population size

Eva E Deinum;Daniel L Halligan;Rob W Ness;Yao-Hua Zhang;Lin Cong;Jian-Xu Zhang;Peter D Keightley;

10.1101/015818 — Evolutionary Biology — Posted on 2015-03-01

144 Chemical integration of proteins in signaling and development

Jeffrey M. Dick;

10.1101/015826 — Biochemistry — Posted on 2015-03-01

145 A complete bacterial genome assembled de novo using only nanopore sequencing data

Nicholas James Loman;Joshua Quick;Jared T Simpson;

10.1101/015552 — Bioinformatics — Posted on 2015-03-11

146 Natural Variants of ELF3 Affect Thermomorphogenesis by Transcriptionally Modulating PIF4-Dependent Auxin Response Genes

Anja Raschke;Carla Ibañez;Kristian Karsten Ullrich;Muhammad Usman Anwer;Sebastian Becker;Annemarie Glöckner;Jana Trenner;Kathrin Denk;Bernhard Saal;Xiaodong Sun;Min Ni;Seth Jon Davis;Carolin Delker;Marcel Quint;

10.1101/015305 — Plant Biology — Posted on 2015-03-19

147 Natural Variants of ELF3 Affect Thermomorphogenesis by Transcriptionally Modulating PIF4-Dependent Auxin Response Genes

10.1101/015305 — Plant Biology — Posted on 2015-03-18

148 Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel

David Houle;Eladio J. Márquez;

10.1101/014936 — Genetics — Posted on 2015-03-05

149 Epistasis and Entropy

Kristina Crona;

10.1101/014829 — Evolutionary Biology — Posted on 2015-03-03

150 Crossmodal integration improves sensory detection thresholds in the ferret

Karl Jonas Hollensteiner;Florian Pieper;Gerhard Engler;Peter König;Andreas Karl Engel;

10.1101/014407 — Neuroscience — Posted on 2015-03-09

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

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

10.1101/014092 — Neuroscience — Posted on 2015-03-09

152 RNA-guided gene drives can efficiently and reversibly bias inheritance in wild yeast

James E DiCarlo;Alejandro Chavez;Sven L Dietz;Kevin M Esvelt;George M Church;

10.1101/013896 — Synthetic Biology — Posted on 2015-03-19

153 The Ecological Forecast Horizon, and examples of its uses and determinants

Owen L Petchey;Mikael Pontarp;Thomas M Massie;Sonia Kéfi;Arpat Ozgul;Maja Weilenmann;Gian Marco Palamara;Florian Altermatt;Blake J Matthews;Jonathan M Levine;Dylan Z Childs;Brian J McGill;Michael E Schaepman;Bernhard Schmid;Piet Spaak;Andrew P Beckerman;Frank Pennekamp;Ian S Pearse;

10.1101/013441 — Ecology — Posted on 2015-03-29

154 Software for the analysis and visualization of deep mutational scanning data

Jesse D Bloom;

10.1101/013623 — Bioinformatics — Posted on 2015-03-25

155 Dynamic reorganization of brain functional networks during cognition

Michał Bola;Bernhard Sabel;

10.1101/012922 — Neuroscience — Posted on 2015-03-26

156 Indication of family-specific DNA methylation patterns in developing oysters

Claire E. Olson;Steven B. Roberts;

10.1101/012831 — Genetics — Posted on 2015-03-13

157 Fitness costs in spatially structured environments

Florence Debarre;

10.1101/012740 — Evolutionary Biology — Posted on 2015-03-04

158 Limits to adaptation along environmental gradients

Jitka Polechová;Nick Barton;

10.1101/012690 — Evolutionary Biology — Posted on 2015-03-14

159 Limits to adaptation along environmental gradients

Jitka Polechová;Nick Barton;

10.1101/012690 — Evolutionary Biology — Posted on 2015-03-14

160 Limits to adaptation along environmental gradients

Jitka Polechová;Nick Barton;

10.1101/012690 — Evolutionary Biology — Posted on 2015-03-13

161 Limits to adaptation along environmental gradients

Jitka Polechová;Nick Barton;

10.1101/012690 — Evolutionary Biology — Posted on 2015-03-12

162 Testing for genetic associations in arbitrarily structured populations

Minsun Song;Wei Hao;John D. Storey;

10.1101/012682 — Genetics — Posted on 2015-03-04

163 Evolutionary dynamics of collective action in spatially structured populations

Jorge Peña;Georg Nöldeke;Laurent Lehmann;

10.1101/012229 — Evolutionary Biology — Posted on 2015-03-24

164 Independent Co-option of a Tailed Bacteriophage into a Killing Complex in Pseudomonas

Kevin L Hockett;Tanya Renner;David A Baltrus;

10.1101/011486 — Microbiology — Posted on 2015-03-27

165 Interactive analysis and quality assessment of single-cell copy-number variations

Tyler Garvin;Robert Aboukhalil;Jude Kendall;Timour Baslan;Gurinder S Atwal;James Hicks;Michael Wigler;Michael Schatz;

10.1101/011346 — Bioinformatics — Posted on 2015-03-06

166 Distinct behavioral effects of prefrontal and parietal cortex inactivations on an accumulation of evidence task in the rat

Jeffrey C Erlich;Bingni W Brunton;Chunyu A Duan;Timothy D Hanks;Carlos D Brody;

10.1101/011031 — Neuroscience — Posted on 2015-03-21

167 Distinct behavioral effects of prefrontal and parietal cortex inactivations on an accumulation of evidence task in the rat

Jeffrey C Erlich;Bingni W Brunton;Chunyu A Duan;Timothy D Hanks;Carlos D Brody;

10.1101/011031 — Neuroscience — Posted on 2015-03-21

168 SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants

Julian S. Gehring;Bernd Fischer;Michael Lawrence;Wolfgang Huber;

10.1101/010686 — Bioinformatics — Posted on 2015-03-16

169 Social evolution and genetic interactions in the short and long term

Jeremy Van Cleve;

10.1101/010371 — Evolutionary Biology — Posted on 2015-03-29

170 NeuroVault.org: A web-based repository for collecting and sharing unthresholded statistical maps of the human brain

Krzysztof Jacek Gorgolewski;Gael Varoquaux;Gabriel Rivera;Yannick Schwartz;Satrajit S. Ghosh;Camille Maumet;Vanessa Sochat;Thomas E. Nichols;Russell A. Poldrack;Jean-Baptiste Poline;Tal Yarkoni;Daniel S. Margulies;

10.1101/010348 — Neuroscience — Posted on 2015-03-16

171 NeuroVault.org: A web-based repository for collecting and sharing unthresholded statistical maps of the human brain

10.1101/010348 — Neuroscience — Posted on 2015-03-12

172 Species delimitation and phylogeny estimation under the multispecies coalescent

Graham R Jones;

10.1101/010199 — Evolutionary Biology — Posted on 2015-03-22

173 An evidence assessment tool for ecosystem services and conservation studies

Anne-Christine Mupepele;Jessica C. Walsh;William J. Sutherland;Carsten F. Dormann;

10.1101/010140 — Scientific Communication and Education — Posted on 2015-03-09

174 Viscous deformation of relaxing ventricle and pulsatile blood propelling (numerical model)

Yuri Kamnev;

10.1101/009522 — Physiology — Posted on 2015-03-12

175 Scaling properties of evolutionary paths in a biophysical model of protein adaptation

Michael Manhart;Alexandre V. Morozov;

10.1101/010082 — Evolutionary Biology — Posted on 2015-03-14

176 largeQvalue: A program for calculating FDR estimates with large datasets

Andrew Anand Brown;

10.1101/010074 — Bioinformatics — Posted on 2015-03-18

177 An analytical approach to bistable biological circuit discrimination using real algebraic geometry

Dan Siegal-Gaskins;Elisa Franco;Tiffany Zhou;Richard M Murray;

10.1101/008581 — Systems Biology — Posted on 2015-03-30

178 An analytical approach to bistable biological circuit discrimination using real algebraic geometry

Dan Siegal-Gaskins;Elisa Franco;Tiffany Zhou;Richard M Murray;

10.1101/008581 — Systems Biology — Posted on 2015-03-01

179 The downward spiral: eco-evolutionary feedback loops lead to the emergence of ‘elastic’ ranges

Alexander Kubisch;Anna-Marie Winter;Emanuel A. Fronhofer;

10.1101/008458 — Ecology — Posted on 2015-03-03

180 Mesoscale analyses of fungal networks as an approach for quantifying phenotypic traits

Sang Hoon Lee;Mark D Fricker;Mason A Porter;

10.1101/006544 — Plant Biology — Posted on 2015-03-24

181 Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses

Benjamin Schwessinger;Ofir Bahar;Thomas Nicolas;Nicolas Holton;Vladimir Nekrasov;Randy Ruan;Patrick Canlas;Arsalan Daudi;Christopher Petzold;Vasanth Singan;Rita Kuo;Mansi Chovatia;Chris Daum;Joshua Heazlewood;Cyril Zipfel;Pamela Ronald;

10.1101/006155 — Plant Biology — Posted on 2015-03-10

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

R Daniel Kortschak;David L Adelson;

10.1101/005033 — Bioinformatics — Posted on 2015-03-27

183 Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones

Stefan Siebert;Freya E. Goetz;Samuel H. Church;Pathikrit Bhattacharyya;Felipe Zapata;Steven H.D. Haddock;Casey W. Dunn;

10.1101/001685 — Developmental Biology — Posted on 2015-03-16

Archive, 2015-03