14 July 2008

Andrew L Hufton, Detlef Groth, Martin Vingron, Hans Lehrach, Albert J Poustka, and Georgia Panopoulou

Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement
Genome Res. Published July 14, 2008, 10.1101/gr.080119.108 [Abstract] [PDF] ACCEPTED PREPRINT  

11 July 2008

Zhaoshi Jiang, Robert Hubley, Arian Smit, and Evan E. Eichler

DupMasker: A tool for annotating primate segmental duplications
Genome Res. Published July 11, 2008, 10.1101/gr.078477.108 [Abstract] [PDF] [Supplemental Research Data]  

Matthew J. Blow, Tao Zhang, Tanja Woyke, Camilla F. Speller, Andrei Krivoshapkin, Dongya Y. Yang, Anatoly Derevianko, and Edward M. Rubin

Identification of ancient remains through genomic sequencing
Genome Res. Published July 11, 2008, 10.1101/gr.076091.108 [Abstract] [PDF] [Supplemental Research Data]  

Hanna M. Petrykowska, Christopher M. Vockley, and Laura Elnitski

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus
Genome Res. Published July 11, 2008, 10.1101/gr.073817.107 [Abstract] [PDF]  

Belinda J Norris and Vicki A Whan

A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep
Genome Res. Published July 11, 2008, 10.1101/gr.072090.107 [Abstract] [PDF] [Supplemental Research Data]  

10 July 2008

Matthew M. Hill, Karl W. Broman, Elia Stupka, William C. Smith, Di Jiang, and Arend Sidow

The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution
Genome Res. Published July 10, 2008, 10.1101/gr.078576.108 [Abstract] [PDF] [Supplemental Research Data]  

Zheng Lian, Alexander Karpikov, Jin Lian, Milind C. Mahajan, Stephen Hartman, Mark Gerstein, Michael Snyder, and Sherman M. Weissman

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation
Genome Res. Published July 10, 2008, 10.1101/gr.075804.107 [Abstract] [PDF]  

David Monk, Alexandre Wagschal, Philippe Arnaud, Pari Sima-Muller, Layla Parker-Katiraee, Déborah Bourc’his, Stephen W. Scherer, Robert Feil, Philip Stanier, and Gudrun E. Moore

Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing
Genome Res. Published July 10, 2008, 10.1101/gr.077115.108 [Abstract] [PDF] [Supplemental Research Data]  

Qian-Ru Li, Anne-Ruxandra Carvunis, Haiyuan Yu, Jing-Dong J. Han, Quan Zhong, Nicolas Simonis, Stanley Tam, Tong Hao, Niels J. Klitgord, Denis Dupuy, Danny Mou, Ilan Wapinski, Aviv Regev, David E. Hill, Michael E. Cusick, and Marc Vidal

Revisiting the Saccharomyces cerevisiae predicted ORFeome
Genome Res. Published July 10, 2008, 10.1101/gr.076661.108 [Abstract] [PDF] [Supplemental Research Data]  

Brian P. Chadwick

DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts
Genome Res. Published July 10, 2008, 10.1101/gr.075713.107 [Abstract] [PDF] [Supplemental Research Data]  

Dan Xie, Jun Cai, Na-Yu Chia, Huck H. Ng, and Sheng Zhong

Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells
Genome Res. Published July 10, 2008, 10.1101/gr.072769.107 [Abstract] [PDF] [Supplemental Research Data]  

Paz Polak and Peter F. Arndt

Transcription induces strand-specific mutations at the 5' end of human genes
Genome Res. Published July 10, 2008, 10.1101/gr.076570.108 [Abstract] [PDF] [Supplemental Research Data]  

Jeffrey D. Wall, Murray P. Cox, Fernando L. Mendez, August Woerner, Tesa Severson, and Michael F. Hammer

A novel DNA sequence database for analyzing human demographic history
Genome Res. Published July 10, 2008, 10.1101/gr.075630.107 [Abstract] [PDF] [Supplemental Research Data]  

Paul F. O’Reilly, Ewan Birney, and David J. Balding

Confounding between recombination and selection, and the Ped/Pop method for detecting selection
Genome Res. Published July 10, 2008, 10.1101/gr.067181.107 [Abstract] [PDF] [Supplemental Research Data]  

Isabel Aznarez, Yoseph Barash, Ofer Shai, David He, Julian Zielenski, Lap-Chee Tsui, John Parkinson, Brendan J. Frey, Johanna M. Rommens, and Benjamin J. Blencowe

A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation
Genome Res. Published July 10, 2008, 10.1101/gr.073155.107 [Abstract] [PDF] [Supplemental Research Data]  

Hong Yu, Shanshan Zhu, Bing Zhou, Huiling Xue, and Jing-Dong J. Han

Inferring causal relationships among different histone modifications and gene expression
Genome Res. Published July 10, 2008, 10.1101/gr.073080.107 [Abstract] [PDF] [Supplemental Research Data]  

9 July 2008

Jeffrey G. Reid, Francis C. Lynn, Ankur K. Nagaraja, Rafal B. Drabek, Donna M. Muzny, Chad A. Shaw, Michelle K. Weiss, Arash O. Naghavi, Mahjabeen F. Khan, Huifeng Zhu, Gemunu H. Gunaratne, David B. Corry, Jonathan N. Miller, Michael S. German, Richard A. Gibbs, Martin M. Matzuk, and Preethi H Gunaratne

Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes
Genome Res. Published July 9, 2008, 10.1101/gr.078246.108 [Abstract] [PDF] ACCEPTED PREPRINT  

3 July 2008

Jeff Elhai, Michiko Kato, Sarah Cousins, Peter Lindblad, and Jose Luis Costa

Very small mobile repeated elements in cyanobacterial genomes
Genome Res. Published July 3, 2008, 10.1101/gr.074336.107 [Abstract] [PDF] ACCEPTED PREPRINT  

1 July 2008

Wenli Zhang, Xiue Wang, Qingyi Yu, Ray Ming, and Jiming Jiang

DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya
Genome Res. Published July 1, 2008, 10.1101/gr.078808.108 [Abstract] [PDF] ACCEPTED PREPRINT  

26 June 2008

Alisha Holloway, David Begun, Adam Siepel, and Katherine Pollard

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
Genome Res. Published June 26, 2008, 10.1101/gr.077131.108 [Abstract] [PDF] ACCEPTED PREPRINT OPEN ACCESS ARTICLE  

Nicholas R. Thomson, Debra J. Clayton, Daniel Windhorst, George Vernikos, Susanne Davidson, Carol Churcher, Michael A. Quail, Mark Stevens, Michael A. Jones, Michael Watson, Andy Barron, Abigail Layton, Derek Pickard, Robert A. Kingsley, Alex Bignell, Louise Clark, Barbara Harris, Doug Ormond, Zahra Abdellah, Karen Brooks, Inna Cherevach, Tracey Chillingworth, John Woodward, Halina Norberczak, Angela Lord, Claire Arrowsmith, Kay Jagels, Sharon Moule, Karen Mungall, Mandy Saunders, Sally Whitehead, Jose A. Chabalgoity, Duncan Maskell, Tom Humphreys, Mark Roberts, Paul A. Barrow, Gordon Dougan, and Julian Parkhill

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
Genome Res. Published June 26, 2008, 10.1101/gr.077404.108 [Abstract] [PDF] ACCEPTED PREPRINT  

24 June 2008

Vardhman Rakyan, Thomas Down, Natalie Thorne, Paul Flicek, Eugene Kulesha, Stefan Graf, Eleni Tomazou, Liselotte Backdahl, Nathan Johnson, Marils Herberth, Kevin Howe, David Jackson, Marcos Miretti, Heike Fiegler, John Marioni, Ewan Birney, Tim Hubbard, Nigel Carter, Simon Tavare, and Stephan Beck

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
Genome Res. Published June 24, 2008, 10.1101/gr.077479.108 [Abstract] [PDF] ACCEPTED PREPRINT OPEN ACCESS ARTICLE  

18 June 2008

Marcel E Dinger, Paulo P Amaral, Tim R Mercer, Ken C Pang, Stephen J Bruce, Brooke B Gardiner, Marjan E Askarian-Amiri, Kelin Ru, Giulia Solda, Cas Simons, Susan M Sunkin, Mark L Crowe, Sean M Grimmond, Andrew C Perkins, and John S. Mattick

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
Genome Res. Published June 18, 2008, 10.1101/gr.078378.108 [Abstract] [PDF] ACCEPTED PREPRINT  

Romain Studer, Laurent Duret, Simon Penel, and Marc Robinson-Rechavi

Pervasive positive selection on duplicated and non duplicated vertebrate protein coding genes
Genome Res. Published June 18, 2008, 10.1101/gr.076992.108 [Abstract] [PDF] ACCEPTED PREPRINT OPEN ACCESS ARTICLE  

13 June 2008

Doriana Misceo, Oronzo Capozzi, Roberta Roberto, Maria Pia Dell'Oglio, Mariano Rocchi, Roscoe Stanyon, and Nicoletta Archidiacono

Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution, punctuated synteny mapping
Genome Res. Published June 13, 2008, 10.1101/gr.078295.108 [Abstract] [PDF] ACCEPTED PREPRINT  

11 June 2008

John Marioni, Christopher Mason, Shrikant Mane, Matthew Stephens, and Yoav Gilad

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Genome Res. Published June 11, 2008, 10.1101/gr.079558.108 [Abstract] [PDF] ACCEPTED PREPRINT OPEN ACCESS ARTICLE  

Weichun Huang and Gabor T Marth

EagleView: a genome assembly viewer for next-generation sequencing technologies
Genome Res. Published June 11, 2008, 10.1101/gr.076067.108 [Abstract] [PDF] ACCEPTED PREPRINT  

Jean-Claude Walser, Loic Ponger, and Anthony V. Furano

CpG Dinucleotides and the Mutation Rate of Non-CpG DNA
Genome Res. Published June 11, 2008, 10.1101/gr.076455.108 [Abstract] [PDF] ACCEPTED PREPRINT  

Qi Zhou, Guo-jie Zhang, Yue Zhang, Shi-yu Xu, Ruo-ping Zhao, Zubing Zhan, Xin Li, Yun Ding, Shuang Yang, and Wen Wang

On the origin of new genes in Drosophila
Genome Res. Published June 11, 2008, 10.1101/gr.076588.108 [Abstract] [PDF] ACCEPTED PREPRINT  

19 May 2008

Claire Amadou, Geraldine Pascal, Sophie Mangenot, Michelle Glew, Cyril Bontemps, Delphine Capela, Sebastien Carrere, Stephane Cruveiller, Carole Dossat, Aurelie Lajus, Marta Marchetti, Verena Poinsot, Zoe Rouy, Bertrand Servin, Maged Saad, Chantal Schenowitz, Valerie Barbe, Jacques Batut, Claudine Medigue, and Catherine Masson-Boivin

Genome sequence of the β-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia
Genome Res. Published May 19, 2008, 10.1101/gr.076448.108 [Abstract] [PDF] ACCEPTED PREPRINT  

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