8 May 2008

Qingwu Yang and Sing-Hoi Sze

Large-scale analysis of gene clustering in bacteria
Genome Res. Published May 8, 2008, 10.1101/gr.072322.107 [Abstract] [PDF] [Supplemental Research Data]  

7 May 2008

Marijke Bauters, Hilde Van Esch, Michael J. Friez, Odile Boespflug-Tanguy, Martin Zenker, Angela M. Vianna-Morgante, Carla Rosenberg, Jaakko Ignatius, Martine Raynaud, Karen Hollanders, Karen Govaerts, Kris Vandenreijt, Florence Niel, Pierre Blanc, Roger E. Stevenson, Jean-Pierre Fryns, Peter Marynen, Charles E. Schwartz, and Guy Froyen

Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair
Genome Res. Published May 7, 2008, 10.1101/gr.075903.107 [Abstract] [PDF] [Supplemental Research Data]  

Keiko Akagi, Jingfeng Li, Robert M. Stephens, Natalia Volfovsky, and David E. Symer

Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
Genome Res. Published May 7, 2008, 10.1101/gr.075770.107 [Abstract] [PDF] [Supplemental Research Data]  

Byung-Kwan Cho, Eric M. Knight, Christian L. Barrett, and Bernhard Ø. Palsson

Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
Genome Res. Published May 7, 2008, 10.1101/gr.070276.107 [Abstract] [PDF] [Supplemental Research Data]  

Gabriel Musso, Michael Costanzo, ManQin Huangfu, Andrew M. Smith, Jadine Paw, Bryan-Joseph San Luis, Charles Boone, Guri Giaever, Corey Nislow, Andrew Emili, and Zhaolei Zhang

The extensive and condition-dependent nature of epistasis among whole-genome-duplicates in yeast
Genome Res. Published May 7, 2008, 10.1101/gr.076174.108 [Abstract] [PDF] ACCEPTED PREPRINT  

Georg Zeller, Richard M. Clark, Korbinian Schneeberger, Anja Bohlen, Detlef Weigel, and Gunnar Rätsch

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
Genome Res. Published May 7, 2008, 10.1101/gr.070169.107 [Abstract] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Pontus Larsson, Andrea Hinas, David H. Ardell, Leif A. Kirsebom, Anders Virtanen, and Fredrik Söderbom

De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring
Genome Res. Published May 7, 2008, 10.1101/gr.069104.107 [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 May 7, 2008, 10.1101/gr.076570.108 [Abstract] [PDF] ACCEPTED PREPRINT  

Frédéric Veyrunes, Paul D. Waters, Pat Miethke, Willem Rens, Daniel McMillan, Amber E. Alsop, Frank Grützner, Janine E. Deakin, Camilla M. Whittington, Kyriena Schatzkamer, Colin L. Kremitzki, Tina Graves, Malcolm A. Ferguson-Smith, Wes Warren, and Jennifer A. Marshall Graves

Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes
Genome Res. Published May 7, 2008, 10.1101/gr.7101908 [Abstract] [PDF]  

Allan F. McRae, Enda M. Byrne, Zhen Zhen Zhao, Grant W. Montgomery, and Peter M. Visscher

Power and SNP tagging in whole mitochondrial genome association studies
Genome Res. Published May 7, 2008, 10.1101/gr.074872.107 [Abstract] [PDF]  

Jürgen Schmitz, Anja Zemann, Gennady Churakov, Heiner Kuhl, Frank Grützner, Richard Reinhardt, and Jürgen Brosius

Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs
Genome Res. Published May 7, 2008, 10.1101/gr.7177908 [Abstract] [PDF] [Supplemental Research Data]  

Camilla M. Whittington, Anthony T. Papenfuss, Paramjit Bansal, Allan M. Torres, Emily S.W. Wong, Janine E. Deakin, Tina Graves, Amber Alsop, Kyriena Schatzkamer, Colin Kremitzki, Chris P. Ponting, Peter Temple-Smith, Wesley C. Warren, Philip W. Kuchel, and Katherine Belov

Defensins and the convergent evolution of platypus and reptile venom genes
Genome Res. Published May 7, 2008, 10.1101/gr.7149808 [Abstract] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Elizabeth P. Murchison, Pouya Kheradpour, Ravi Sachidanandam, Carly Smith, Emily Hodges, Zhenyu Xuan, Manolis Kellis, Frank Grützner, Alexander Stark, and Gregory J. Hannon

Conservation of small RNA pathways in platypus
Genome Res. Published May 7, 2008, 10.1101/gr.073056.107 [Abstract] [PDF] [Supplemental Research Data]  

Jae-Il Park, Jenia Semyonov, Chia Lin Chang, Wei Yi, Wesley Warren, and Sheau Yu Teddy Hsu

Origin of INSL3-mediated testicular descent in therian mammals
Genome Res. Published May 7, 2008, 10.1101/gr.7119108 [Abstract] [PDF] [Supplemental Research Data]  

2 May 2008

Isabel Aznarez, Yoseph Barash, Ofer Shai, David He, Julian Zielenski, Lap-Chee Tsui, John Parkinson, Brendan Frey, Johanna M Rommens, and Benjamin 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 May 2, 2008, 10.1101/gr.073155.107 [Abstract] [PDF] ACCEPTED PREPRINT  

Mikael Brandström and Hans Ellegren

Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
Genome Res. Published May 2, 2008, 10.1101/gr.075242.107 [Abstract] [PDF] [Supplemental Research Data]  

Ei-suke Saito, Vincent W. Keng, Junji Takeda, and Kyoji Horie

Translation from nonautonomous type IAP retrotransposon is a critical determinant of transposition activity: Implication for retrotransposon-mediated genome evolution
Genome Res. Published May 2, 2008, 10.1101/gr.069310.107 [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 anti-sense transcripts
Genome Res. Published May 2, 2008, 10.1101/gr.075713.107 [Abstract] [PDF] ACCEPTED PREPRINT  

30 April 2008

Itay Tirosh and Naama Barkai

Two strategies for gene regulation by promoter nucleosomes
Genome Res. Published April 30, 2008, 10.1101/gr.076059.108 [Abstract] [PDF] ACCEPTED PREPRINT  

29 April 2008

Stefan Kirsch, Claudia Munch, Zhaoshi Jiang, Ze Cheng, Lin Chen, Christiane Batz, Evan E. Eichler, and Werner Schempp

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
Genome Res. Published April 29, 2008, 10.1101/gr.076711.108 [Abstract] [PDF] ACCEPTED PREPRINT  

25 April 2008

Giusy Della Gatta, Mukesh Bansal, Alberto Ambesi-Impiombato, Dario Antonini, Caterina Missero, and Diego di Bernardo

Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
Genome Res. Published April 25, 2008, 10.1101/gr.073601.107 [Abstract] [PDF] [Supplemental Research Data]  

Mahesh Yaragatti, Claudio Basilico, and Lisa Dailey

Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions
Genome Res. Published April 25, 2008, 10.1101/gr.073460.107 [Abstract] [PDF] [Supplemental Research Data]  

24 April 2008

Hanna Petrykowska, Christopher Vockley, and Laura Elnitski

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus
Genome Res. Published April 24, 2008, 10.1101/gr.073817.107 [Abstract] [PDF] ACCEPTED PREPRINT  

21 April 2008

Nitin Gupta, Jamal Benhamida, Vipul Bhargava, Daniel Goodman, Elisabeth Kain, Ian Kerman, Ngan Nguyen, Noah Ollikainen, Jesse Rodriguez, Jian Wang, Mary S Lipton, Margaret Romine, Vineet Bafna, Richard D Smith, and Pavel A Pevzner

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
Genome Res. Published April 21, 2008, 10.1101/gr.074344.107 [Abstract] [PDF] ACCEPTED PREPRINT  

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

Identification of the source of ancient remains through genomic sequencing
Genome Res. Published April 21, 2008, 10.1101/gr.076091.108 [Abstract] [PDF] ACCEPTED PREPRINT  

16 April 2008

Ivan Iossifov, Tian Zheng, Miron Baron, T. Conrad Gilliam, and Andrey Rzhetsky

Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
Genome Res. Published April 16, 2008, 10.1101/gr.075622.107 [Abstract] [PDF] ACCEPTED PREPRINT OPEN ACCESS ARTICLE  

14 April 2008

Jun S. Song, Xingkun Liu, Xiaole Shirley Liu, and Xiangwei He

A high-resolution map of nucleosome positioning on a fission yeast centromere
Genome Res. Published April 14, 2008, 10.1101/gr.075374.107 [Abstract] [PDF] ACCEPTED PREPRINT  

Chaim Linhart, Yonit Halperin, and Ron Shamir

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
Genome Res. Published April 14, 2008, 10.1101/gr.076117.108 [Abstract] [PDF] ACCEPTED PREPRINT  

Ines Hellmann, Yuan Mang, Zhiping Gu, Peter Li, Francisco M De La Vega, Andrew G. Clark, and Rasmus Nielsen

Population genetic analysis of shotgun assemblies of genomic sequence from multiple individuals
Genome Res. Published April 14, 2008, 10.1101/gr.074187.107 [Abstract] [PDF] ACCEPTED PREPRINT  

27 March 2008

Yao-Ting Huang, Feng-Chi Chen, Hsin-Liang Chen, and Trees-Juen Chuang

Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
Genome Res. Published March 27, 2008, 10.1101/gr.075556.107 [Abstract] [PDF] ACCEPTED PREPRINT OPEN ACCESS ARTICLE  

7 March 2008

Wei Chen, Vera Kalscheu, Andreas Tzschach, Corinna Menzel, Reinhard Ullmann, Marcel Schulz, Fikret Erdogan, Na Li, Zofia Kijas, Ger Arkesteijn, Isidora Lopez Pajares, Margret Goetz-Sothmann, Uwe Heinrich, Imma Rost, Andreas Dufke, Ute Grasshoff, Birgitta Glaeser Glaeser, Martin Vingron, and Hans Hilger Ropers

Mapping translocation breakpoints by next-generation sequencing
Genome Res. Published March 7, 2008, 10.1101/gr.076166.108 [Abstract] [PDF] ACCEPTED PREPRINT  

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