bioRxiv directory

10.1101/020149 — Evolutionary Biology — Posted on 2015-05-31

4 Learning quantitative sequence-function relationships from high-throughput biological data

10.1101/020172 — Bioinformatics — Posted on 2015-05-31

5 Improved Algorithms for Finding Edit Distance Based Motifs

10.1101/020131 — Bioinformatics — Posted on 2015-05-31

6 Expression of E. coli glycogen branching enzyme in an Arabidopsis mutant devoid of endogenous starch branching enzymes induces the synthesis of starch-like polyglucans

Laura Boyer;Xavier Roussel;Adeline Courseaux;Ofilia Mvundza Ndjindji;Christine Lancelon-Pin;Jean-Luc Putaux;Ian Tetlow;Michael Emes;Bruno Pontoire;Christophe D'Hulst;Fabrice Wattebled;

10.1101/019976 — Plant Biology — Posted on 2015-05-29

7 Mixed Models for Meta-Analysis and Sequencing

Brendan Bulik-Sullivan;

10.1101/020115 — Genomics — Posted on 2015-05-29

8 Optimizing error correction of RNAseq reads

Matthew D MacManes;

10.1101/020123 — Bioinformatics — Posted on 2015-05-29

9 Mirror bisulfite sequencing — a method for single-base resolution of hydroxymethylcytosine

Xueguang Sun;Darany Tan;Tzu Hung Chung;Xi-Yu Jia;

10.1101/019943 — Genomics — Posted on 2015-05-29

10 Environmental complexity favors the evolution of learning

Slimane Dridi;Laurent Lehmann;

10.1101/019968 — Evolutionary Biology — Posted on 2015-05-29

11 SAM/BAM format v1.5 extensions for de novo assemblies

Peter J. A. Cock;James K Bonfield;Bastien Chevreux;Heng Li;

10.1101/020024 — Bioinformatics — Posted on 2015-05-29

12 The Moose of Isle Royale: An Unnatural Condition?

Samuel V Scarpino;Rafael F Guerrero;Philip V Scarpino;

10.1101/019984 — Zoology — Posted on 2015-05-29

13 The GL Service: Web Service to Exchange GL String Encoded HLA & KIR Genotypes With Complete and Accurate Allele and Genotype Ambiguity

Robert P Milius;Michael Heuer;Mike George;Jane Pollack;Jill A Hollenbach;Steven J Mack;Martin Maiers;

10.1101/020099 — Bioinformatics — Posted on 2015-05-29

14 Spatial extent of neighboring plants influences the strength of associational effects on mammal herbivory. Insights from a meta-analysis

Emilie Champagne;Jean-Pierre Tremblay;Steeve D Cote;

10.1101/019935 — Ecology — Posted on 2015-05-28

15 Deconvolution of gene expression noise into physical dynamics of cognate promoters

Angel Goñi-Moreno;Ilaria Benedetti;Juhyun Kim;Victor de Lorenzo;

10.1101/019927 — Synthetic Biology — Posted on 2015-05-27

16 Targeted modification of gene function exploiting homology-directed repair of TALEN-mediated double strand breaks in barley

Nagaveni Budhagatapalli;Twan Rutten;Maia Gurushidze;Jochen Kumlehn;Goetz Hensel;

10.1101/019893 — Plant Biology — Posted on 2015-05-28

17 Targeted modification of gene function exploiting homology-directed repair of TALEN-mediated double strand breaks in barley

Nagaveni Budhagatapalli;Twan Rutten;Maia Gurushidze;Jochen Kumlehn;Goetz Hensel;

10.1101/019893 — Plant Biology — Posted on 2015-05-27

18 Origins of major archaeal clades do not correspond to gene acquisitions from bacteria

Mathieu Groussin;Bastien Boussau;Gergely Szöllősi;Laura Eme;Manolo Gouy;Céline Brochier-Armanet;Vincent Daubin;

10.1101/019851 — Evolutionary Biology — Posted on 2015-05-27

19 DYNAMICS OF AN EXPANDING BLACK RHINOCEROS (Diceros bicornis minor) POPULATION

Peter R Law;Brad Fike;Peter C Lent;

10.1101/018523 — Ecology — Posted on 2015-05-27

20 Detection and interpretation of shared genetic influences on 40 human traits

Joseph Pickrell;Tomaz Berisa;Laure Segurel;Joyce Y Tung;David Hinds;

10.1101/019885 — Genomics — Posted on 2015-05-27

21 A simple model-based approach to inferring and visualizing cancer mutation signatures

Yuichi Shiraishi;Georg Tremmel;Satoru Miyano;Matthew Stephens;

10.1101/019901 — Bioinformatics — Posted on 2015-05-27

22 A Unified Architecture of Transcriptional Regulatory Elements

Robin Andersson;Albin Sandelin;Charles G Danko;

10.1101/019844 — Genomics — Posted on 2015-05-26

23 A new idea on the evolution of biodiversity

Roberto Cazzolla Gatti;

10.1101/019828 — Evolutionary Biology — Posted on 2015-05-26

24 General formulation of Luria-Delbrück distribution of the number of mutants

bahram houchmandzadeh;

10.1101/019869 — Evolutionary Biology — Posted on 2015-05-27

25 Stable eusociality via maternal manipulation when resistance is costless

Mauricio González-Forero;

10.1101/019877 — Evolutionary Biology — Posted on 2015-05-27

26 Submerged plants may have substantial growth in shallow water lakes under nitrogen deposition: a theoretical investigation

Ashehad A Ali;

10.1101/019836 — Ecology — Posted on 2015-05-26

27 Deep sequencing of small RNA facilitates tissue and sex specific microRNA discovery in zebrafish

Candida Vaz;Choon Wei Wee;Serene Gek Ping Lee;Philip W Ingham;Vivek Tanavde;Sinnakaruppan Mathavan;

10.1101/019760 — Genomics — Posted on 2015-05-24

28 Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue

Anna Francina Webster;Paul Zumbo;Jennifer Fostel;Jorge Gandara;Susan D Hester;Leslie Recio;Andrew Williams;Chales Wood;Carole Yauk;Christopher E Mason;

10.1101/019794 — Genetics — Posted on 2015-05-24

29 RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

Santiago Herrera;Timothy M. Shank;

10.1101/019745 — Evolutionary Biology — Posted on 2015-05-24

30 Ancestral chromatin configuration constrains chromatin evolution on differentiating sex chromosomes in Drosophila

Qi Zhou;Doris Bachtrog;

10.1101/019786 — Evolutionary Biology — Posted on 2015-05-24

31 Endorsing Darwin – Global biogeography of the epipelagic goose barnacles Lepas spp. (Cirripedia, Lepadomorpha) proves cryptic speciation

Philipp H. Schiffer;Hans-Georg Herbig;

10.1101/019802 — Evolutionary Biology — Posted on 2015-05-24

32 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 2015-05-22

33 Protein degradation in a TX-TL cell-free expression system using ClpXP protease

Zachary Sun;Jongmin Kim;Vipul Singhal;Richard M Murray;

10.1101/019695 — Synthetic Biology — Posted on 2015-05-22

34 Consistent inter-protocol differences in resting-state functional connectomes between normal aging and mild cognitive impairment

Angela Tam;Christian Dansereau;AmanPreet Badhwar;Pierre Orban;Sylvie Belleville;Howard Chertkow;Alain Dagher;Alexandru Hanganu;Oury Monchi;Pedro Rosa-Neto;Amir Shmuel;Seqian Wang;John Breitner;Pierre Bellec;Alzheimer's Disease Neuroimaging Initiative;

10.1101/019646 — Neuroscience — Posted on 2015-05-22

35 Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes

Brenna M. Henn;Laura R Botigue;Stephan Peischl;Isabelle Dupanloup;Mikhail Lipatov;Brian K Maples;Alicia R Martin;Shaila Musharoff;Howard Cann;Michael Snyder;Laurent Excoffier;Jeffrey Kidd;Carlos D Bustamante;

10.1101/019711 — Genomics — Posted on 2015-05-22

36 Determining Exon Connectivity in Complex mRNAs by Nanopore Sequencing

Mohan Bolisetty;Gopinath Rajadinakaran;Brenton Graveley;

10.1101/019752 — Genomics — Posted on 2015-05-22

37 Genomic epidemiology of the current wave of artemisinin resistant malaria

Roberto Amato;Olivo Miotto;Charles Woodrow;Jacob Almagro-Garcia;Ipsita Sinha;Susana Campino;Daniel Mead;Eleanor Drury;Mihir Kekre;Mandy Sanders;Alfred Amambua-Ngwa;Chanaki Amaratunga;Lucas Amenga-Etego;Tim JC Anderson;Voahangy Andrianaranjaka;Tobias Apinjoh;Elizabeth Ashley;Sarah Auburn;Gordon A Awandare;Vito Baraka;Alyssa Barry;Maciej F Boni;Steffen Borrmann;Teun Bousema;Oralee Branch;Peter C Bull;Kesinee Chotivanich;David J Conway;Alister Craig;Nicholas P Day;Abdoulaye Djimdé;Christiane Dolecek;Arjen M Dondorp;Chris Drakeley;Patrick Duffy;Diego F Echeverri-Garcia;Thomas G Egwang;Rick M Fairh

10.1101/019737 — Evolutionary Biology — Posted on 2015-05-24

38 Genomic epidemiology of the current wave of artemisinin resistant malaria

10.1101/019737 — Evolutionary Biology — Posted on 2015-05-22

39 A Perspective on Interaction Tests in Genetic Association Studies

Hugues Aschard;

10.1101/019661 — Genetics — Posted on 2015-05-22

40 Endless forms most beau-toe-ful: evolution of the human hallux

Zach Throckmorton;

10.1101/019653 — Evolutionary Biology — Posted on 2015-05-22

41 A Coalescent Model of a Sweep from a Uniquely Derived Standing Variant

Jeremy J Berg;Graham Coop;

10.1101/019612 — Evolutionary Biology — Posted on 2015-05-22

42 Dynamic effects of extrinsic noise in a simple oscillatory gene network with delayed negative-feedback regulation: an electronic modeling approach

Moisés Santillán;

10.1101/019638 — Systems Biology — Posted on 2015-05-22

43 Pseudotime estimation: deconfounding single cell time series

John E Reid;Lorenz Wernisch;

10.1101/019588 — Systems Biology — Posted on 2015-05-21

44 Characterizing and Prototyping Genetic Networks with Cell-Free Transcription-Translation Reactions

Melissa K Takahashi;Clarmyra A. Hayes;James Chappell;Zachary Z. Sun;Richard M Murray;Vincent Noireaux;Julius B. Lucks;

10.1101/019620 — Synthetic Biology — Posted on 2015-05-21

45 A flexible, efficient binomial mixed model for identifying differential DNA methylation in bisulfite sequencing data

Amanda J Lea;Jenny Tung;Xiang Zhou;

10.1101/019562 — Genomics — Posted on 2015-05-22

46 A flexible, efficient binomial mixed model for identifying differential DNA methylation in bisulfite sequencing data

Amanda J Lea;Jenny Tung;Xiang Zhou;

10.1101/019562 — Genomics — Posted on 2015-05-21

47 In Vivo Blunt-End Cloning Through CRISPR/Cas9-Facilitated Non-Homologous End-Joining

Jonathan M Geisinger;Sören Turan;Sophia Hernandez;Laura P Spector;Michele P Calos;

10.1101/019570 — Genetics — Posted on 2015-05-27

48 In Vivo Blunt-End Cloning Through CRISPR/Cas9-Facilitated Non-Homologous End-Joining

Jonathan M Geisinger;Sören Turan;Sophia Hernandez;Laura P Spector;Michele P Calos;

10.1101/019570 — Genetics — Posted on 2015-05-21

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

Simon Uribe-Convers;David C Tank;

10.1101/019554 — Evolutionary Biology — Posted on 2015-05-21

50 Engineering Cell Fate: The Roles of iPSC Transcription Factors, Chemicals, Barriers and Enhancing Factors in Reprogramming and Transdifferentiation

Behnam Ebrahimi;

10.1101/019455 — Cell Biology — Posted on 2015-05-21

51 A non-local model for cancer stem cells and the tumor growth paradox

Iacopo Borsi;Antonio Fasano;Mario Primicerio;Thomas Hillen;

10.1101/019604 — Cancer Biology — Posted on 2015-05-21

52 Re-Annotator: Annotation Pipeline for Microarrays

Janine Arloth;Daniel Magnus Bader;Simone Röh;Andre Altmann;

10.1101/019596 — Bioinformatics — Posted on 2015-05-21

53 The Cf-4 receptor-like protein associates with the BAK1 receptor-like kinase to initiate receptor endocytosis and plant immunity

Jelle Postma;Thomas W. H. Liebrand;Guozhi Bi;Alexandre Evrard;Ruby R. Bye;Malick Mbengue;Matthieu H. A. J. Joosten;Silke Robatzek;

10.1101/019471 — Plant Biology — Posted on 2015-05-20

54 The Cf-4 receptor-like protein associates with the BAK1 receptor-like kinase to initiate receptor endocytosis and plant immunity

Jelle Postma;Thomas W. H. Liebrand;Guozhi Bi;Alexandre Evrard;Ruby R. Bye;Malick Mbengue;Matthieu H. A. J. Joosten;Silke Robatzek;

10.1101/019471 — Plant Biology — Posted on 2015-05-19

55 RUST FUNGAL EFFECTORS MIMIC HOST TRANSIT PEPTIDES TO TRANSLOCATE INTO CHLOROPLASTS

Benjamin Petre;Cécile Lorrain;Diane Saunders;Sébastien Duplessis;Sophien Kamoun;

10.1101/019521 — Plant Biology — Posted on 2015-05-23

56 RUST FUNGAL EFFECTORS MIMIC HOST TRANSIT PEPTIDES TO TRANSLOCATE INTO CHLOROPLASTS

Benjamin Petre;Cécile Lorrain;Diane Saunders;Sébastien Duplessis;Sophien Kamoun;

10.1101/019521 — Plant Biology — Posted on 2015-05-19

57 Attention selectively gates afferent signal transmission to area V4

Iris Grothe;David Rotermund;Simon D. Neitzel;Sunita Mandon;Udo A. Ernst;Andreas K. Kreiter;Klaus R. Pawelzik;

10.1101/019547 — Neuroscience — Posted on 2015-05-19

58 Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

Joshua S Bloom;Iulia Kotenko;Meru J Sadhu;Sebastian Treusch;Frank W Albert;Leonid Kruglyak;

10.1101/019513 — Genetics — Posted on 2015-05-19

59 Untangling the roles of parasites in food webs with generative network models

Abigail Z. Jacobs;Jennifer A. Dunne;Cristopher Moore;Aaron Clauset;

10.1101/019497 — Ecology — Posted on 2015-05-19

60 A de novo DNA Sequencing and Variant Calling Algorithm for Nanopores

Tamas Szalay;Jene A Golovchenko;

10.1101/019448 — Bioinformatics — Posted on 2015-05-19

61 Diagnosis of coronary heart diseases using gene expression profiling; stable coronary artery disease, cardiac ischemia with and without myocardial necrosis

Nabila Kazmi;Tom Gaunt;

10.1101/019505 — Bioinformatics — Posted on 2015-05-19

62 GenoWAP: Post-GWAS Prioritization Through Integrated Analysis of Genomic Functional Annotation

Qiongshi Lu;Xinwei Yao;Yiming Hu;Hongyu Zhao;

10.1101/019539 — Bioinformatics — Posted on 2015-05-20

63 An accurate genetic clock

David H Hamilton;

10.1101/019414 — Genetics — Posted on 2015-05-20

64 An accurate genetic clock

David H Hamilton;

10.1101/019414 — Genetics — Posted on 2015-05-18

65 Stochastic models of evidence accumulation in changing environments

Alan Veliz-Cuba;Zachary P Kilpatrick;Kresimir Josic;

10.1101/019398 — Neuroscience — Posted on 2015-05-16

66 Character trees from transcriptome data: origin and individuation of morphological characters and the so-called “species signal”

Jacob Musser;Gunter Wagner;

10.1101/019380 — Genomics — Posted on 2015-05-29

67 Character trees from transcriptome data: origin and individuation of morphological characters and the so-called “species signal”

Jacob Musser;Gunter Wagner;

10.1101/019380 — Genomics — Posted on 2015-05-16

68 svclassify: a method to establish benchmark structural variant calls

Hemang Parikh;Marghoob Mohiyuddin;Hugo Y. K. Lam;Hariharan Iyer;Desu Chen;Mark Pratt;Gabor Bartha;Noah Spies;Wolfgang Losert;Justin M. Zook;Marc L. Salit;

10.1101/019372 — Genomics — Posted on 2015-05-22

69 svclassify: a method to establish benchmark structural variant calls

Hemang Parikh;Marghoob Mohiyuddin;Hugo Y. K. Lam;Hariharan Iyer;Desu Chen;Mark Pratt;Gabor Bartha;Noah Spies;Wolfgang Losert;Justin M. Zook;Marc L. Salit;

10.1101/019372 — Genomics — Posted on 2015-05-16

70 Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori

Valeria Montano;Xavier Didelot;Matthieu Foll;Bodo Linz;Richard Reinhardt;Sebastian Suerbaum;Yoshan Moodley;Jeffrey David Jensen;

10.1101/019430 — Evolutionary Biology — Posted on 2015-05-18

71 miR-551a and miR-551b target GLIPR2 and promote tumor growth in High-Risk Head and Neck Cancer by modulating autophagy

Narasimha Kumar Karanam;Michael D Story;Liang-Hao Ding;Tae Hyun Hwang;Hao Tang;

10.1101/019406 — Cancer Biology — Posted on 2015-05-17

72 miR-551a and miR-551b target GLIPR2 and promote tumor growth in High-Risk Head and Neck Cancer by modulating autophagy

Narasimha Kumar Karanam;Michael D Story;Liang-Hao Ding;Tae Hyun Hwang;Hao Tang;

10.1101/019406 — Cancer Biology — Posted on 2015-05-16

73 ReproPhylo: An Environment for Reproducible Phylogenomics

Amir Szitenberg;Max John;Mark L Blaxter;David H Lunt;

10.1101/019349 — Bioinformatics — Posted on 2015-05-18

74 ReproPhylo: An Environment for Reproducible Phylogenomics

Amir Szitenberg;Max John;Mark L Blaxter;David H Lunt;

10.1101/019349 — Bioinformatics — Posted on 2015-05-15

75 Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing

Minh Duc Cao;Devika Ganesamoorthy;Alysha Elliott;Huihui Zhang;Matthew Cooper;Lachlan Coin;

10.1101/019356 — Bioinformatics — Posted on 2015-05-20

76 Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing

Minh Duc Cao;Devika Ganesamoorthy;Alysha Elliott;Huihui Zhang;Matthew Cooper;Lachlan Coin;

10.1101/019356 — Bioinformatics — Posted on 2015-05-15

77 The case for absolute ligand discrimination : modeling information processing and decision by immune T cells

Paul François;Grégoire Altan-Bonnet;

10.1101/019273 — Biophysics — Posted on 2015-05-14

78 Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION

John M Urban;Jacob Bliss;Charles E Lawrence;Susan A Gerbi;

10.1101/019281 — Genomics — Posted on 2015-05-20

79 Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION

John M Urban;Jacob Bliss;Charles E Lawrence;Susan A Gerbi;

10.1101/019281 — Genomics — Posted on 2015-05-13

80 FIQT: a simple, powerful method to accurately estimate effect sizes in genome scans

Tim B Bigdeli;Donghyung Lee;Brien P Riley;Vladimir I Vladimirov;Ayman H Fanous;Kenneth S Kendler;Silviu-Alin Bacanu;

10.1101/019299 — Genetics — Posted on 2015-05-13

81 The Multi-allelic Genetic Architecture of a Variance-heterogeneity Locus for Molybdenum Accumulation Acts as a Source of Unexplained Additive Genetic Variance

Simon K G Forsberg;Matthew E Andreatta;Xin-Yuan Huang;John Danku;David E Salt;Örjan Carlborg;

10.1101/019323 — Genetics — Posted on 2015-05-14

82 Molecular Fossils from Microorganisms Preserved in Glacial Ice

P. Buford Price;J. Jeffrey Morris;Ryan C. Bay;Ajeeth Adhikari;Stephen J. Giovannoni;Kevin L. Vergin;

10.1101/019240 — Evolutionary Biology — Posted on 2015-05-13

83 NADH as a cancer medicine

Michael D Forrest;

10.1101/019307 — Cancer Biology — Posted on 2015-05-13

84 Roary: Rapid large-scale prokaryote pan genome analysis

Andrew J Page;Carla A Cummins;Martin Hunt;Vanessa K Wong;Sandra Reuter;Matthew T. G. Holden;Maria Fookes;Jacqueline A Keane;Julian Parkhill;

10.1101/019315 — Bioinformatics — Posted on 2015-05-13

85 GenOO: A Modern Perl Framework for High Throughput Sequencing analysis

Manolis Maragkakis;Panagiotis Alexiou;Zissimos Mourelatos;

10.1101/019265 — Bioinformatics — Posted on 2015-05-13

86 Layering genetic circuits to build a single cell, bacterial half adder

Adison Wong;Huijuan Wang;Chueh Loo Poh;Richard Kitney;

10.1101/019257 — Synthetic Biology — Posted on 2015-05-30

87 Layering genetic circuits to build a single cell, bacterial half adder

Adison Wong;Huijuan Wang;Chueh Loo Poh;Richard Kitney;

10.1101/019257 — Synthetic Biology — Posted on 2015-05-12

88 Stretch Induced Hyperexcitability of Mice Callosal Pathway

Anthony Fan;Kevin Stebbings;Daniel Llano;Taher Saif;

10.1101/019190 — Neuroscience — Posted on 2015-05-11

89 Cortical microcircuit determination through global perturbation and sparse sampling in grid cells

John Widloski;Ila R Fiete;

10.1101/019224 — Neuroscience — Posted on 2015-05-18

90 Cortical microcircuit determination through global perturbation and sparse sampling in grid cells

John Widloski;Ila R Fiete;

10.1101/019224 — Neuroscience — Posted on 2015-05-13

91 Cortical microcircuit determination through global perturbation and sparse sampling in grid cells

John Widloski;Ila R Fiete;

10.1101/019224 — Neuroscience — Posted on 2015-05-12

92 Ecological and evolutionary adaptations shape the gut microbiome of BaAka African rainforest hunter-gatherers

Andres Gomez;Klara Petrzelkova;Carl J Yeoman;Micahel B Burns;Katherine R Amato;Klara Vlckova;David Modry;Angelique Todd;Carolyn A Jost Robbinson;Melissa Remis;Manolito Torralba;Karen E Nelson;Franck Carbonero;H Rex Gaskins;Brenda A Wilson;Rebecca M Stumpf;Bryan A White;Steven R Leigh;Ran Blekhman;

10.1101/019232 — Microbiology — Posted on 2015-05-12

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

Adam P Levine;Anthony W Segal;

10.1101/019174 — Immunology — Posted on 2015-05-11

94 Whole genome analysis of an extended pedigree with Prader–Willi Syndrome, hereditary hemochromatosis, and dysautonomia-like symptoms

Han Fang;Yiyang Wu;Margaret Yoon;Laura T. Jiménez-Barrón;Jason A. O'Rawe;Gareth Highnam;David Mittelman;Gholson Lyon;

10.1101/019182 — Genetics — Posted on 2015-05-11

95 Genome Wide Variant Analysis of Simplex Autism Families with an Integrative Clinical-Bioinformatics Pipeline

Laura T Jiménez-Barrón;Jason A O'Rawe;Yiyang Wu;Margaret Yoon;Han Fang;Ivan Iossifov;Gholson Lyon;

10.1101/019208 — Genetics — Posted on 2015-05-11

96 Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies

Julia A Palacios;John Wakeley;Sohini Ramachandran;

10.1101/019216 — Genetics — Posted on 2015-05-11

97 Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies

Julia A Palacios;John Wakeley;Sohini Ramachandran;

10.1101/019216 — Genetics — Posted on 2015-05-11

98 Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals.

Xun Lan;Jonathan K Pritchard;

10.1101/019166 — Evolutionary Biology — Posted on 2015-05-10

99 Coalescent times and patterns of genetic diversity in species with facultative sex: effects of gene conversion, population structure and heterogeneity

Matthew Hartfield;Stephen I. Wright;Aneil F. Agrawal;

10.1101/019158 — Evolutionary Biology — Posted on 2015-05-10

100 Open science resources for the discovery and analysis of Tara Oceans Data

Stéphane Pesant;Fabrice Not;Marc Picheral;Stefanie Kandels-Lewis;Noan Le Bescot;Gabriel Gorsky;Daniele Iudicone;Eric Karsenti;Sabrina Speich;Romain Troublé;Celine Dimier;Sarah Searson;Tara Oceans Consortium Coordinators;

10.1101/019117 — Systems Biology — Posted on 2015-05-08

101 Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition

Nadia Shakoor;Greg Ziegler;Brian P Dilkes;Zachary Brenton;Richard Boyles;Erin L Connolly;Stephen Kresovich;Ivan Baxter;

10.1101/019083 — Genetics — Posted on 2015-05-08

102 Mitochondria, mutations and sex: a new hypothesis for the evolution of sex based on mitochondrial mutational erosion

Justin Havird;Matthew D Hall;Damian Dowling;

10.1101/019125 — Evolutionary Biology — Posted on 2015-05-08

103 ZIFA: Dimensionality reduction for zero-inflated single cell gene expression analysis

Christopher Yau;Emma Pierson;

10.1101/019141 — Bioinformatics — Posted on 2015-05-08

104 Improving the Power of Structural Variation Detection by Augmenting the Reference

Jan Schroeder;Santhosh Girirajan;Anthony T Papenfuss;Paul Medvedev;

10.1101/019109 — Bioinformatics — Posted on 2015-05-08

105 Sharing and specificity of co-expression networks across 35 human tissues

Emma Pierson;GTEx Consortium;Daphne Koller;Alexis Battle;Sara Mostafavi;

10.1101/010843 — Bioinformatics — Posted on 2015-05-08

106 Two-Dimensional Mapping of 3D Data from Confocal Microscopy

Anthony Fan;Justin Cassidy;Richard W. Carthew;Sascha Hilgenfeldt;

10.1101/019133 — Bioengineering — Posted on 2015-05-08

107 Bayesian Inference of Divergence Times and Feeding Evolution in Grey Mullets (Mugilidae)

Francesco Santini;Michael R. May;Giorgio Carnevale;Brian R. Moore;

10.1101/019075 — Evolutionary Biology — Posted on 2015-05-07

108 Diverse Early Life-History Strategies in Migratory Amazonian Catfish: Implications for Conservation and Management

Jens C Hegg;Tommaso Giarrizzo;Brian P Kennedy;

10.1101/018671 — Ecology — Posted on 2015-05-09

109 Diverse Early Life-History Strategies in Migratory Amazonian Catfish: Implications for Conservation and Management

Jens C Hegg;Tommaso Giarrizzo;Brian P Kennedy;

10.1101/018671 — Ecology — Posted on 2015-05-07

110 Perspectives on Quorum sensing in Fungi

Sarangam Majumdar;Subhoshmita Mondal;

10.1101/019034 — Biophysics — Posted on 2015-05-07

111 Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data

Jovana Maksimovic;Johann A Gagnon-Bartsch;Terence P Speed;Alicia Oshlack;

10.1101/019042 — Bioinformatics — Posted on 2015-05-07

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

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

10.1101/019067 — Bioinformatics — Posted on 2015-05-07

113 A vision for ubiquitous sequencing

Yaniv Erlich;

10.1101/019018 — Genomics — Posted on 2015-05-07

114 Comparison Between Non-Catheterized And Catheter Associated Urinary Tract Infections Caused By Extended Spectrum Β-Lactamase Producing Escherichia Coli And Klebsiella Pneumoniae

Fouzia Ashraf;Shagufta Shagufta Iram;Gul-e-zar Riaz;Farhan Rasheed;Mahmood Shaukat;

10.1101/019026 — Microbiology — Posted on 2015-05-06

115 Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

Jean-Philippe Fortin;Kasper D Hansen;

10.1101/019000 — Genomics — Posted on 2015-05-06

116 Negative Niche Construction Favors the Evolution of Cooperation

Brian D Connelly;Katherine J Dickinson;Sarah P Hammarlund;Benjamin Kerr;

10.1101/018994 — Evolutionary Biology — Posted on 2015-05-06

117 Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome

María Muñoz-Amatriaín;Stefano Lonardi;MingCheng Luo;Kavitha Madishetty;Jan Svensson;Matthew Moscou;Steve Wanamaker;Tao Jiang;Andris Kleinhofs;Gary Muehlbauer;Roger Wise;Nils Stein;Yaqin Ma;Edmundo Rodriguez;Dave Kudrna;Prasanna R Bhat;Shiaoman Chao;Pascal Condamine;Shane Heinen;Josh Resnik;Rod Wing;Heather N Witt;Matthew Alpert;Marco Beccuti;Serdar Bozdag;Francesca Cordero;Hamid Mirebrahim;Rachid Ounit;Yonghui Wu;Frank You;Jie Zheng;Hana Šimková;Jaroslav Doležel;Jane Grimwood;Jeremy Schmutz;Denisa Duma;Lothar Altschmied;Tom Blake;Phil Bregitzer;Laurel Cooper;Muharrem Dilbirligi;Anders Falk;Lei

10.1101/018978 — Genomics — Posted on 2015-05-05

118 A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years

Hang Zhou;Sile Hu;Rostislav Matveev;Qianhui Yu;Jing Li;Philipp Khaitovich;Li Jin;Michael Lachmann;Mark Stoneking;Qiaomei Fu;Kun Tang;

10.1101/018929 — Evolutionary Biology — Posted on 2015-05-26

119 A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years

Hang Zhou;Sile Hu;Rostislav Matveev;Qianhui Yu;Jing Li;Philipp Khaitovich;Li Jin;Michael Lachmann;Mark Stoneking;Qiaomei Fu;Kun Tang;

10.1101/018929 — Evolutionary Biology — Posted on 2015-05-05

120 Theoretical consequences of the Mutagenic Chain Reaction for manipulating natural populations

Robert Unckless;Philipp Messer;Andrew Clark;

10.1101/018986 — Evolutionary Biology — Posted on 2015-05-05

121 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 2015-05-05

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

Ignasi Bartomeus;Jochen Fründ;Neal M. Williams;

10.1101/018952 — Ecology — Posted on 2015-05-05

123 Obstructions in Vascular Networks. Critical vs Non-critical Topological Sites for Blood Supply

Aimee Torres Rojas;Alejandro Meza Romero;Ignacio Pagonabarraga;Rui Travasso;Eugenia Corvera Poiré;

10.1101/018960 — Biophysics — Posted on 2015-05-05

124 Surface-driven registration method for the structure-informed segmentation of diffusion MR images

Oscar Esteban;Dominique Zosso;Alessandro Daducci;Meritxell Bach-Cuadra;Maria J. Ledesma-Carbayo;Jean-Philippe Thiran;Andres Santos;

10.1101/018945 — Bioengineering — Posted on 2015-05-05

125 Genome analysis leads to discovery of Quorum Sensing Genes in Cedecea neteri

Kian-Hin Tan;Kok-Gan Chan;Chan;

10.1101/018887 — Microbiology — Posted on 2015-05-03

126 Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for HIV-1

Daniel I S Rosenbloom;Oliver Elliott;Alison L Hill;Timothy J Henrich;Janet M Siliciano;Robert F Siliciano;

10.1101/018911 — Microbiology — Posted on 2015-05-03

127 Tropical Soil Metagenome Library Reveals Complex Microbial Assemblage

Kok Gan Chan;Zahidah Ismail;

10.1101/018895 — Microbiology — Posted on 2015-05-03

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

David J. Harris;

10.1101/018861 — Ecology — Posted on 2015-05-26

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

David J. Harris;

10.1101/018861 — Ecology — Posted on 2015-05-01

130 Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

Daniel A Keedy;James Fraser;Henry van den Bedem;

10.1101/018879 — Biophysics — Posted on 2015-05-04

131 Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution

Prashanti Manda;James P Balhoff;Hilmar Lapp;Paula Mabee;Todd Vision;

10.1101/018853 — Bioinformatics — Posted on 2015-05-01

132 Replication is Recursion; or, Lambda: the Biological Imperative

Scott Federhen;

10.1101/018804 — Bioinformatics — Posted on 2015-05-01

133 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 2015-05-01

134 GO-PCA: An Unsupervised Method to Explore Biological Heterogeneity Based on Gene Expression and Prior Knowledge

Florian Wagner;

10.1101/018705 — Bioinformatics — Posted on 2015-05-05

135 Evaluating different passive optical clearing protocols for two-photon deep tissue imaging in adult intact visceral and neuronal organs

R.C Vlieg;C Gillespie;W M Steve Lee;

10.1101/018622 — Bioengineering — Posted on 2015-05-11

136 Acute and chronic gregarisation are associated with distinct DNA methylation fingerprints in desert locusts

Eamonn B Mallon;Harindra E Amarasinghe;Swidbert R Ott;

10.1101/018499 — Zoology — Posted on 2015-05-05

137 On the structure of population activity under fluctuations in attentional state

Alexander S Ecker;George H Denfield;Matthias Bethge;Andreas S Tolias;

10.1101/018226 — Neuroscience — Posted on 2015-05-22

138 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 2015-05-30

139 Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

Ben Busby;Allissa Dillman;Claire L. Simpson;Ian Fingerman;Sijung Yun;David M. Kristensen;Lisa Federer;Naisha Shah;Matthew C. LaFave;Laura Jimenez-Barron;Manusha Pande;Wen Luo;Brendan Miller;Cem Mayden;Dhruva Chandramohan;Kipper Fletez-Brant;Paul W. Bible;Sergej Nowoshilow;Alfred Chan;Eric JC Galvez;Jeremy Chignell;Joseph N. Paulson;Manoj Kandpal;Suhyeon Yoon;Esther Asaki;Abhinav Nellore;Adam Stine;Robert Sanders;Jesse Becker;Matt Lesko;Mordechai Abzug;Eugene Yaschenko;

10.1101/018085 — Genomics — Posted on 2015-05-05

140 An evaluation of the accuracy and speed of metagenome analysis tools

Stinus Lindgreen;Karen L Adair;Paul Gardner;

10.1101/017830 — Bioinformatics — Posted on 2015-05-15

141 Testing for ancient selection using cross-population allele frequency differentiation

Fernando Racimo;

10.1101/017566 — Evolutionary Biology — Posted on 2015-05-12

142 Testing for ancient selection using cross-population allele frequency differentiation

Fernando Racimo;

10.1101/017566 — Evolutionary Biology — Posted on 2015-05-12

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

Michael V. Lombardo;Bonnie Auyeung;Rosemary J Holt;Jack Waldman;Amber N. V. Ruigrok;Natasha Mooney;Edward T Bullmore;Simon Baron-Cohen;Prantik Kundu;

10.1101/017350 — Neuroscience — Posted on 2015-05-09

144 Genetic variability under the seedbank coalescent

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

10.1101/017244 — Evolutionary Biology — Posted on 2015-05-06

145 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-05-24

146 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-05-03

147 A general theory of individuated multicellularity

Felipe A. Veloso;

10.1101/016840 — Developmental Biology — Posted on 2015-05-03

148 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 2015-05-06

149 Measuring forces and stresses in situ in living tissues

Forces-in-tissue workshop participants;

10.1101/016394 — Developmental Biology — Posted on 2015-05-22

150 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 2015-05-25

151 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 2015-05-16

152 Using Mixtures of Biological Samples as Process Controls for RNA-sequencing experiments

Jerod Parsons;Sarah Munro;P. Scott Pine;Jennifer McDaniel;Michele Mehaffey;Marc Salit;

10.1101/015107 — Bioinformatics — Posted on 2015-05-15

153 Discovery and characterization of Alu repeat sequences via precise local read assembly

Julia H Wildschutte;Alayna A Baron;Nicolette M Diroff;Jeffrey M Kidd;

10.1101/014977 — Genomics — Posted on 2015-05-21

154 Fleas (Siphonaptera) are Cretaceous, and Evolved with Theria

Qiyun Zhu;Michael W Hastriter;Michael F Whiting;Katharina Dittmar;

10.1101/014308 — Evolutionary Biology — Posted on 2015-05-07

155 NCBI BLAST+ integrated into Galaxy

Peter J. A. Cock;John M. Chilton;Björn Grüning;James E. Johnson;Nicola Soranzo;

10.1101/014043 — Bioinformatics — Posted on 2015-05-04

156 Scaling probabilistic models of genetic variation to millions of humans

Prem Gopalan;Wei Hao;David M. Blei;John D. Storey;

10.1101/013227 — Genetics — Posted on 2015-05-28

157 The rate and molecular spectrum of spontaneous mutations in the GC-rich multi-chromosome genome of Burkholderia cenocepacia

Marcus M Dillon;Way Sung;Michael Lynch;Vaughn S Cooper;

10.1101/011841 — Evolutionary Biology — Posted on 2015-05-09

158 SubClonal Hierarchy Inference from Somatic Mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing

Noushin Niknafs;Violeta Beleva Guthrie;Daniel Q Naiman;Rachel Karchin;

10.1101/011833 — Bioinformatics — Posted on 2015-05-11

159 Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence

Julien Y Dutheil;Kasper Munch;Kiwoong Nam;Thomas Mailund;Mikkel Schierup;

10.1101/011601 — Evolutionary Biology — Posted on 2015-05-11

160 Comprehensive comparison of large-scale tissue expression datasets

Alberto Santos;Kalliopi Tsafou;Christian Stolte;Sune Frankild;Seán O'Donoghue;Lars Juhl Jensen;

10.1101/010975 — Systems Biology — Posted on 2015-05-13

161 HiFive: a tool suite for easy and efficient HiC and 5C data analysis

Michael EG Sauria;Jennifer E Phillips-Cremins;Victor G Corces;James Taylor;

10.1101/009951 — Bioinformatics — Posted on 2015-05-08

162 FourCSeq: Analysis of 4C sequencing data

Felix A. Klein;Tibor Pakozdi;Simon Anders;Yad Ghavi-Helm;Eileen E. M. Furlong;Wolfgang Huber;

10.1101/009548 — Bioinformatics — Posted on 2015-05-12

163 Pinwheel-dipole configuration in cat early visual cortex

Jérôme Ribot;Alberto Romagnoni;Chantal Milleret;Daniel Bennequin;Jonathan D. Touboul;

10.1101/009308 — Neuroscience — Posted on 2015-05-09

164 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 2015-05-30

165 Sources of PCR-induced distortions in high-throughput sequencing datasets

Justus M Kebschull;Anthony M Zador;

10.1101/008375 — Genomics — Posted on 2015-05-21

166 CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional Data

Daniele Ramazzotti;Giulio Caravagna;Loes Olde Loohuis;Alex Graudenzi;Ilya Korsunsky;Giancarlo Mauri;Marco Antoniotti;Bud Mishra;

10.1101/008110 — Bioinformatics — Posted on 2015-05-07

167 Automation and Evaluation of the SOWH Test with SOWHAT

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

10.1101/005264 — Bioinformatics — Posted on 2015-05-07

168 Data-intensive modeling of forest dynamics

Jean F Lienard;Dominique Gravel;Nikolay Strigul;

10.1101/005009 — Ecology — Posted on 2015-05-02

169 Large-scale non-targeted metabolomic profiling in three human population-based studies

Andrea Ganna;Tove Fall;Samira Salihovic;Woojoo Lee;Corey D Broeckling;Jitender Kumar;Sara Hägg;Markus Stenemo;Patrik K.E. Magnusson;Jessica Prenni;Lars Lind;Yudi Pawitan;Erik Ingelsson;

10.1101/002782 — Bioinformatics — Posted on 2015-05-28

Archive, 2015-05