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Genome Research
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Supplementary material related to the following articles is available online:

From the Current Issue: 18 (7); [Table of Contents]

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. 2008; 18(7): 1180-1189 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Vijay K. Tiwari, Leslie Cope, Kelly M. McGarvey, Joyce E. Ohm, and Stephen B. Baylin

A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations
Genome Res. 2008; 18(7): 1171-1179 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Yao-Ting Huang, Feng-Chi Chen, Chiuan-Jung 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. 2008; 18(7): 1163-1170 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 18(7): 1150-1162 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Wei Chen, Vera Kalscheuer, Andreas Tzschach, Corinna Menzel, Reinhard Ullmann, Marcel Holger 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, Martin Vingron, and H. Hilger Ropers

Mapping translocation breakpoints by next-generation sequencing
Genome Res. 2008; 18(7): 1143-1149 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 18(7): 1133-1142 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Jr-Kai Yu, Daniel Meulemans, Sonja J. McKeown, and Marianne Bronner-Fraser

Insights from the amphioxus genome on the origin of vertebrate neural crest
Genome Res. 2008; 18(7): 1127-1132 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Shengfeng Huang, Shaochun Yuan, Lei Guo, Yanhong Yu, Jun Li, Tao Wu, Tong Liu, Manyi Yang, Kui Wu, Huiling Liu, Jin Ge, Yingcai Yu, Huiqing Huang, Meiling Dong, Cuiling Yu, Shangwu Chen, and Anlong Xu

Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity
Genome Res. 2008; 18(7): 1112-1126 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Linda Z. Holland, Ricard Albalat, Kaoru Azumi, Èlia Benito-Gutiérrez, Matthew J. Blow, Marianne Bronner-Fraser, Frederic Brunet, Thomas Butts, Simona Candiani, Larry J. Dishaw, David E.K. Ferrier, Jordi Garcia-Fernàndez, Jeremy J. Gibson-Brown, Carmela Gissi, Adam Godzik, Finn Hallböök, Dan Hirose, Kazuyoshi Hosomichi, Tetsuro Ikuta, Hidetoshi Inoko, Masanori Kasahara, Jun Kasamatsu, Takeshi Kawashima, Ayuko Kimura, Masaaki Kobayashi, Zbynek Kozmik, Kaoru Kubokawa, Vincent Laudet, Gary W. Litman, Alice C. McHardy, Daniel Meulemans, Masaru Nonaka, Robert P. Olinski, Zeev Pancer, Len A. Pennacchio, Mario Pestarino, Jonathan P. Rast, Isidore Rigoutsos, Marc Robinson-Rechavi, Graeme Roch, Hidetoshi Saiga, Yasunori Sasakura, Masanobu Satake, Yutaka Satou, Michael Schubert, Nancy Sherwood, Takashi Shiina, Naohito Takatori, Javier Tello, Pavel Vopalensky, Shuichi Wada, Anlong Xu, Yuzhen Ye, Keita Yoshida, Fumiko Yoshizaki, Jr-Kai Yu, Qing Zhang, Christian M. Zmasek, Pieter J. de Jong, Kazutoyo Osoegawa, Nicholas H. Putnam, Daniel S. Rokhsar, Noriyuki Satoh, and Peter W.H. Holland

The amphioxus genome illuminates vertebrate origins and cephalochordate biology
Genome Res. 2008; 18(7): 1100-1111 [Abstract] [Full Text]  

Article supplement(s): [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. 2008; 18(7): 1092-1099 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Itay Tirosh and Naama Barkai

Two strategies for gene regulation by promoter nucleosomes
Genome Res. 2008; 18(7): 1084-1091 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Travis N. Mavrich, Ilya P. Ioshikhes, Bryan J. Venters, Cizhong Jiang, Lynn P. Tomsho, Ji Qi, Stephan C. Schuster, Istvan Albert, and B. Franklin Pugh

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
Genome Res. 2008; 18(7): 1073-1083 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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

A high-resolution map of nucleosome positioning on a fission yeast centromere
Genome Res. 2008; 18(7): 1064-1072 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Anton Valouev, Jeffrey Ichikawa, Thaisan Tonthat, Jeremy Stuart, Swati Ranade, Heather Peckham, Kathy Zeng, Joel A. Malek, Gina Costa, Kevin McKernan, Arend Sidow, Andrew Fire, and Steven M. Johnson

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
Genome Res. 2008; 18(7): 1051-1063 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Elizabeth A. Grice, Heidi H. Kong, Gabriel Renaud, Alice C. Young, NISC Comparative Sequencing Program, Gerard G. Bouffard, Robert W. Blakesley, Tyra G. Wolfsberg, Maria L. Turner, and Julia A. Segre

A diversity profile of the human skin microbiota
Genome Res. 2008; 18(7): 1043-1050 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Stefan Kirsch, Claudia Münch, 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. 2008; 18(7): 1030-1042 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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 sequences from multiple individuals
Genome Res. 2008; 18(7): 1020-1029 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

From Past Issues:

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. 2008; 0(2008): gr.078576.108v2 [Abstract]  

Article supplement(s): [Supplemental Research Data]

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

DupMasker: A tool for annotating primate segmental duplications
Genome Res. 2008; 0(2008): gr.078477.108v2 [Abstract]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 0(2008): gr.077115.108v2 [Abstract]  

Article supplement(s): [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. 2008; 0(2008): gr.076661.108v2 [Abstract]  

Article supplement(s): [Supplemental Research Data]

Paz Polak and Peter F. Arndt

Transcription induces strand-specific mutations at the 5' end of human genes
Genome Res. 2008; 0(2008): gr.076570.108v2 [Abstract]  

Article supplement(s): [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. 2008; 0(2008): gr.076091.108v2 [Abstract]  

Article supplement(s): [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. 2008; 0(2008): gr.075713.107v2 [Abstract]  

Article supplement(s): [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. 2008; 0(2008): gr.075630.107v2 [Abstract]  

Article supplement(s): [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. 2008; 0(2008): gr.073155.107v2 [Abstract]  

Article supplement(s): [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. 2008; 0(2008): gr.073080.107v2 [Abstract]  

Article supplement(s): [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. 2008; 0(2008): gr.072769.107v2 [Abstract]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 0(2008): gr.072090.107v2 [Abstract]  

Article supplement(s): [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. 2008; 0(2008): gr.067181.107v1 [Abstract]  

Article supplement(s): [Supplemental Research Data]

Alexander Stark, Pouya Kheradpour, Sushmita Roy, and Manolis Kellis

Reliable prediction of regulator targets using 12 Drosophila genomes
Genome Res. 2007; 0(2007): gr.7090407v1 [Abstract]  

Article supplement(s): [Correction] [Drosophila 12 Genomes] [Supplemental Research Data]

Martin Beye, Irene Gattermeier, Martin Hasselmann, Tanja Gempe, Morten Schioett, John F. Baines, David Schlipalius, Florence Mougel, Christine Emore, Olav Rueppell, Anu Sirviö, Ernesto Guzmán-Novoa, Greg Hunt, Michel Solignac, and Robert E. Page Jr.

Exceptionally high levels of recombination across the honey bee genome
Genome Res. 2006; 0(2006): gr.5680406v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Christine G. Elsik, Kim C. Worley, Lan Zhang, Natalia V. Milshina, Huaiyang Jiang, Justin T. Reese, Kevin L. Childs, Anand Venkatraman, C. Michael Dickens, George M. Weinstock, and Richard A. Gibbs

Community annotation: Procedures, protocols, and supporting tools
Genome Res. 2006; 0(2006): gr.5580606v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Joël Savard, Diethard Tautz, Stephen Richards, George M. Weinstock, Richard A. Gibbs, John H. Werren, Hervé Tettelin, and Martin J. Lercher

Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects
Genome Res. 2006; 0(2006): gr.5204306v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Peter K. Dearden, Megan J. Wilson, Lisha Sablan, Peter W. Osborne, Melanie Havler, Euan McNaughton, Kiyoshi Kimura, Natalia V. Milshina, Martin Hasselmann, Tanja Gempe, Morten Schioett, Susan J. Brown, Christine G. Elsik, Peter W.H. Holland, Tatsuhiko Kadowaki, and Martin Beye

Patterns of conservation and change in honey bee developmental genes
Genome Res. 2006; 0(2006): gr.5108606v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Elad B. Rubin, Yair Shemesh, Mira Cohen, Sharona Elgavish, Hugh M. Robertson, and Guy Bloch

Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock
Genome Res. 2006; 0(2006): gr.5094806v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Hugh M. Robertson and Karl H.J. Gordon

Canonical TTAGG-repeat telomeres and telomerase in the honey bee Apis mellifera
Genome Res. 2006; 0(2006): gr.5085606v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Sylvain Forêt and Ryszard Maleszka

Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera)
Genome Res. 2006; 0(2006): gr.5075706v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Hugh M. Robertson and Kevin W. Wanner

The chemoreceptor superfamily in the honey bee Apis mellifera: Expansion of the odorant, but not gustatory, receptor family
Genome Res. 2006; 0(2006): gr.5057506v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Tara D. Sutherland, Peter M. Campbell, Sarah Weisman, Holly E. Trueman, Alagacone Sriskantha, Wolfgang J. Wanjura, and Victoria S. Haritos

A highly divergent gene cluster in honey bees encodes a novel silk family
Genome Res. 2006; 0(2006): gr.5052606v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Mark David Drapeau, Stefan Albert, Robert Kucharski, Carsten Prusko, and Ryszard Maleszka

Evolution of the Yellow/Major Royal Jelly Protein family and the emergence of social behaviorin honey bees
Genome Res. 2006; 0(2006): gr.5012006v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Noam Kaplan and Michal Linial

ProtoBee: Hierarchical classification and annotation of the honey bee proteome
Genome Res. 2006; 0(2006): gr.4916306v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus]

Soochin Cho, Zachary Y. Huang, Daniel R. Green, Deborah R. Smith, and Jianzhi Zhang

Evolution of the complementary sex-determination gene of honey bees: Balancing selectionand trans-species polymorphisms
Genome Res. 2006; 0(2006): gr.4695306v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplementary Research Data]

Andrew K. Jones, Valerie Raymond-Delpech, Steeve H. Thany, Monique Gauthier, and David B. Sattelle

The nicotinic acetylcholine receptor gene family of the honey bee, Apis mellifera
Genome Res. 2006; 0(2006): gr.4549206v1 [Abstract]  

Article supplement(s): [Honey Bee Genome Focus] [Supplemental Research Data]

Astrid Lægreid, Torgeir R. Hvidsten, Herman Midelfart, Jan Komorowski, and Arne K. Sandvik

Predicting Gene Ontology Biological Process From Temporal Gene Expression Patterns
Genome Res. 2003; 0(2003): GR-11445Rv1 [Abstract]  

Article supplement(s): [Supplemental Research Data] [Supplemental Research Data]

James W. Thomas, Mary G. Schueler, Tyrone J. Summers, Robert W. Blakesley, Jennifer C. McDowell, Pamela J. Thomas, Jacquelyn R. Idol, Valerie V.B. Maduro, Shih-Queen Lee-Lin, Jeffrey W. Touchman, Gerard G. Bouffard, Stephen M. Beckstrom-Sternberg, NISC Comparative Sequencing Program, and Eric D. Green

Pericentromeric Duplications in the Laboratory Mouse
Genome Res. 2002; 0(2002): GR-7914Rv1 [Abstract]  

Article supplement(s): [Supplemental Research Data]

Pavel Pevzner and Glenn Tesler

Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes
Genome Res. 2002; 0(2002): GR-7575Rv1 [Abstract]  

Article supplement(s): [Supplemental Research Data]

John E. Collins, Melanie E. Goward, Charlotte G. Cole, Luc J. Smink, Elizabeth J. Huckle, Sarah Knowles, Jacqueline M. Bye, David M. Beare, and Ian Dunham

Reevaluating Human Gene Annotation: A Second-Generation Analysis of Chromosome 22
Genome Res. 2002; 0(2002): GR-6957Rv1 [Abstract]  

Article supplement(s): [Supplemental Research Data]

Maido Remm and Erik Sonnhammer

Classification of Transmembrane Protein Families in the Caenorhabditis elegans Genome and Identification of Human Orthologs
Genome Res. 2000; 0(2000): GR-1491Rv1-99999 [Abstract] [Full Text]  

Article supplement(s): [ Supplemental Research Data]

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. 2008; 18(6): 1005-1010 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 18(6): 995-1004 [Abstract] [Full Text]  

Article supplement(s): [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. 2008; 18(6): 986-994 [Abstract] [Full Text]  

Article supplement(s): [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. 2008; 18(6): 974-985 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Evgeny A. Glazov, Pauline A. Cottee, Wesley C. Barris, Robert J. Moore, Brian P. Dalrymple, and Mark L. Tizard

A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
Genome Res. 2008; 18(6): 957-964 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Qingwu Yang and Sing-Hoi Sze

Large-scale analysis of gene clustering in bacteria
Genome Res. 2008; 18(6): 949-956 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 18(6): 939-948 [Abstract] [Full Text]  

Article supplement(s): [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. 2008; 18(6): 930-938 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 18(6): 918-929 [Abstract] [Full Text]  

Article supplement(s): [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. 2008; 18(6): 900-910 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 18(6): 888-899 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Mikael Brandström and Hans Ellegren

Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
Genome Res. 2008; 18(6): 881-887 [Abstract] [Full Text]  

Article supplement(s): [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. 2008; 18(6): 869-880 [Abstract] [Full Text]  

Article supplement(s): [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. 2008; 18(6): 859-868 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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. 2008; 18(6): 847-858 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Tatiana M. Karafet, Fernando L. Mendez, Monica B. Meilerman, Peter A. Underhill, Stephen L. Zegura, and Michael F. Hammer

New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
Genome Res. 2008; 18(5): 830-838 [Abstract] [Full Text]  

Article supplement(s): [Y-Chromosome Phylogenetic Tree Poster] [Supplemental Research Data]

Daniel R. Zerbino and Ewan Birney

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Genome Res. 2008; 18(5): 821-829 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Jonathan Butler, Iain MacCallum, Michael Kleber, Ilya A. Shlyakhter, Matthew K. Belmonte, Eric S. Lander, Chad Nusbaum, and David B. Jaffe

ALLPATHS: De novo assembly of whole-genome shotgun microreads
Genome Res. 2008; 18(5): 810-820 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

David Hernandez, Patrice François, Laurent Farinelli, Magne Østerås, and Jacques Schrenzel

De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
Genome Res. 2008; 18(5): 802-809 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Yih-Jyh Shann, Ching Cheng, Chun-Hui Chiao, Dow-Tien Chen, Pei-Hsin Li, and Ming-Ta Hsu

Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines
Genome Res. 2008; 18(5): 791-801 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Rafael A. Irizarry, Christine Ladd-Acosta, Benilton Carvalho, Hao Wu, Sheri A. Brandenburg, Jeffrey A. Jeddeloh, Bo Wen, and Andrew P. Feinberg

Comprehensive high-throughput arrays for relative methylation (CHARM)
Genome Res. 2008; 18(5): 780-790 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Hans T. Bjornsson, Thomas J. Albert, Christine M. Ladd-Acosta, Roland D. Green, Michael A. Rongione, Christina M. Middle, Rafael A. Irizarry, Karl W. Broman, and Andrew P. Feinberg

SNP-specific array-based allele-specific expression analysis
Genome Res. 2008; 18(5): 771-779 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

William Brockman, Pablo Alvarez, Sarah Young, Manuel Garber, Georgia Giannoukos, William L. Lee, Carsten Russ, Eric S. Lander, Chad Nusbaum, and David B. Jaffe

Quality scores and SNP detection in sequencing-by-synthesis systems
Genome Res. 2008; 18(5): 763-770 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Jun Chen, Yeong C. Kim, Yong-Chul Jung, Zhenyu Xuan, Geoff Dworkin, Yanming Zhang, Michael Q. Zhang, and San Ming Wang

Scanning the human genome at kilobase resolution
Genome Res. 2008; 18(5): 751-762 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Bernard La Scola, Khalid Elkarkouri, Wenjun Li, Tara Wahab, Ghislain Fournous, Jean-Marc Rolain, Silpak Biswas, Michel Drancourt, Catherine Robert, Stéphane Audic, Sven Löfdahl, and Didier Raoult

Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm
Genome Res. 2008; 18(5): 742-750 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Timothy P. Stinear, Torsten Seemann, Paul F. Harrison, Grant A. Jenkin, John K. Davies, Paul D.R. Johnson, Zahra Abdellah, Claire Arrowsmith, Tracey Chillingworth, Carol Churcher, Kay Clarke, Ann Cronin, Paul Davis, Ian Goodhead, Nancy Holroyd, Kay Jagels, Angela Lord, Sharon Moule, Karen Mungall, Halina Norbertczak, Michael A. Quail, Ester Rabbinowitsch, Danielle Walker, Brian White, Sally Whitehead, Pamela L.C. Small, Roland Brosch, Lalita Ramakrishnan, Michael A. Fischbach, Julian Parkhill, and Stewart T. Cole

Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis
Genome Res. 2008; 18(5): 729-741 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

David A. Ray, Cedric Feschotte, Heidi J.T. Pagan, Jeremy D. Smith, Ellen J. Pritham, Peter Arensburger, Peter W. Atkinson, and Nancy L. Craig

Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus
Genome Res. 2008; 18(5): 717-728 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

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Issue supplement(s): [This issue is sponsored by Roche Applied Science] [Y-Chromosome Phylogenetic Tree Poster]

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David Ribet, Francis Harper, Anne Dupressoir, Marie Dewannieux, Gérard Pierron, and Thierry Heidmann

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Kevin Bullaughey, Molly Przeworski, and Graham Coop

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Shengdong Ke, Xiang H.-F. Zhang, and Lawrence A. Chasin

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Julie E. Horvath, David W. Weisrock, Stephanie L. Embry, Isabella Fiorentino, James P. Balhoff, Peter Kappeler, Gregory A. Wray, Huntington F. Willard, and Anne D. Yoder

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Saurabh Sinha, Adam S. Adler, Yair Field, Howard Y. Chang, and Eran Segal

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Malay Kumar Basu, Liran Carmel, Igor B. Rogozin, and Eugene V. Koonin

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Zhongmin Tian, Andrew S. Greene, Jennifer L. Pietrusz, Isaac R. Matus, and Mingyu Liang

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Xiang Gao, Yi Hou, Hirotaka Ebina, Henry L. Levin, and Daniel F. Voytas

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Victor Kunin, Shaomei He, Falk Warnecke, S. Brook Peterson, Hector Garcia Martin, Matthew Haynes, Natalia Ivanova, Linda L. Blackall, Mya Breitbart, Forest Rohwer, Katherine D. McMahon, and Philip Hugenholtz

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Tobias Mourier, Celine Carret, Sue Kyes, Zoe Christodoulou, Paul P. Gardner, Daniel C. Jeffares, Robert Pinches, Bart Barrell, Matt Berriman, Sam Griffiths-Jones, Alasdair Ivens, Chris Newbold, and Arnab Pain

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Naruo Nikoh, Kohjiro Tanaka, Fukashi Shibata, Natsuko Kondo, Masahiro Hizume, Masakazu Shimada, and Takema Fukatsu

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Heiko Schober, Véronique Kalck, Miguel A. Vega-Palas, Griet Van Houwe, Daniel Sage, Michael Unser, Marc R. Gartenberg, and Susan M. Gasser

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David M. McGaughey, Ryan M. Vinton, Jimmy Huynh, Amr Al-Saif, Michael A. Beer, and Andrew S. McCallion

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Elfar Torarinsson, Zizhen Yao, Eric D. Wiklund, Jesper B. Bramsen, Claus Hansen, Jørgen Kjems, Niels Tommerup, Walter L. Ruzzo, and Jan Gorodkin

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Zhuo Du, Yiqiang Zhao, and Ning Li

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Anuphap Prachumwat and Wen-Hsiung Li

Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes
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Amir Goren, Eddo Kim, Maayan Amit, Ron Bochner, Galit Lev-Maor, Nadav Ahituv, and Gil Ast

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Lixia Yao and Andrey Rzhetsky

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Article supplement(s): [Supplemental Research Data] [Podcast]

Brandi L. Cantarel, Ian Korf, Sofia M.C. Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Alejandro Sánchez Alvarado, and Mark Yandell

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Nacho Molina and Erik van Nimwegen

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Devin R. Scannell and Kenneth H. Wolfe

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Jian Chen, Xiaoying Shi, Ranjani Padmanabhan, Qiong Wang, Zhidan Wu, Susan C. Stevenson, Marc Hild, Dan Garza, and Hao Li

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Guo-Qing Tang and E. Stuart Maxwell

Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation
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Schraga Schwartz, João Silva, David Burstein, Tal Pupko, Eduardo Eyras, and Gil Ast

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Xavier Roca, Andrew J. Olson, Atmakuri R. Rao, Espen Enerly, Vessela N. Kristensen, Anne-Lise Børresen-Dale, Brage S. Andresen, Adrian R. Krainer, and Ravi Sachidanandam

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Katherine C. Teeter, Bret A. Payseur, Leslie W. Harris, Margaret A. Bakewell, Lisa M. Thibodeau, Janelle E. O’Brien, James G. Krenz, Maria A. Sans-Fuentes, Michael W. Nachman, and Priscilla K. Tucker

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Leah O. Barrera, Zirong Li, Andrew D. Smith, Karen C. Arden, Webster K. Cavenee, Michael Q. Zhang, Roland D. Green, and Bing Ren

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Yogeshwar D. Kelkar, Svitlana Tyekucheva, Francesca Chiaromonte, and Kateryna D. Makova

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Dawn M. Stults, Michael W. Killen, Heather H. Pierce, and Andrew J. Pierce

Genomic architecture and inheritance of human ribosomal RNA gene clusters
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Martin C. Frith, Eivind Valen, Anders Krogh, Yoshihide Hayashizaki, Piero Carninci, and Albin Sandelin

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Pouya Kheradpour, Alexander Stark, Sushmita Roy, and Manolis Kellis

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Alfredo Villasante, José P. Abad, Rosario Planelló, María Méndez-Lago, Susan E. Celniker, and Beatriz de Pablos

Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase
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Article supplement(s): [Supplemental Research Data]

Juliane C. Dohm, Claudio Lottaz, Tatiana Borodina, and Heinz Himmelbauer

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
Genome Res. 2007; 17(11): 1697-1706 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Robert Lyle, Paola Prandini, Kazutoyo Osoegawa, Boudewijn ten Hallers, Sean Humphray, Baoli Zhu, Eduardo Eyras, Robert Castelo, Christine P. Bird, Sarantos Gagos, Carol Scott, Antony Cox, Samuel Deutsch, Catherine Ucla, Marc Cruts, Sophie Dahoun, Xinwei She, Frederique Bena, Sheng-Yue Wang, Christine Van Broeckhoven, Evan E. Eichler, Roderic Guigo, Jane Rogers, Pieter J. de Jong, Alexandre Reymond, and Stylianos E. Antonarakis

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21
Genome Res. 2007; 17(11): 1690-1696 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Joan U. Pontius, James C. Mullikin, Douglas R. Smith, Agencourt Sequencing Team, Kerstin Lindblad-Toh, Sante Gnerre, Michele Clamp, Jean Chang, Robert Stephens, Beena Neelam, Natalia Volfovsky, Alejandro A. Schäffer, Richa Agarwala, Kristina Narfström, William J. Murphy, Urs Giger, Alfred L. Roca, Agostinho Antunes, Marilyn Menotti-Raymond, Naoya Yuhki, Jill Pecon-Slattery, Warren E. Johnson, Guillaume Bourque, Glenn Tesler, NISC Comparative Sequencing Program, and Stephen J. O’Brien

Initial sequence and comparative analysis of the cat genome
Genome Res. 2007; 17(11): 1675-1689 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Kai Wang, Mingyao Li, Dexter Hadley, Rui Liu, Joseph Glessner, Struan F.A. Grant, Hakon Hakonarson, and Maja Bucan

PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
Genome Res. 2007; 17(11): 1665-1674 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Guillaume Blanc, Hiroyuki Ogata, Catherine Robert, Stéphane Audic, Jean-Michel Claverie, and Didier Raoult

Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome
Genome Res. 2007; 17(11): 1657-1664 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Thierry Wirth, Giovanna Morelli, Barica Kusecek, Alex van Belkum, Cindy van der Schee, Axel Meyer, and Mark Achtman

The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis
Genome Res. 2007; 17(11): 1647-1656 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Marius K. Lemberg and Matthew Freeman

Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases
Genome Res. 2007; 17(11): 1634-1646 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Tomer Shlomi, Markus Herrgard, Vasiliy Portnoy, Efrat Naim, Bernhard Ø. Palsson, Roded Sharan, and Eytan Ruppin

Systematic condition-dependent annotation of metabolic genes
Genome Res. 2007; 17(11): 1626-1633 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Shisong Ma, Qingqiu Gong, and Hans J. Bohnert

An Arabidopsis gene network based on the graphical Gaussian model
Genome Res. 2007; 17(11): 1614-1625 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Laurie Gordon, Shan Yang, Mary Tran-Gyamfi, Dan Baggott, Mari Christensen, Aaron Hamilton, Richard Crooijmans, Martien Groenen, Susan Lucas, Ivan Ovcharenko, and Lisa Stubbs

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
Genome Res. 2007; 17(11): 1603-1613 [Abstract] [Full Text]  

Article supplement(s): [Supplemental Research Data]

Chris Wallace, Richard J. Dobson, Patricia B. Munroe, and Mark J. Caulfield

Information capture using SNPs from HapMap and whole-genome chips differs in a sample of inflammatory and cardiovascular gene-centric regions from genome-wide estimates
Genome Res. 2007; 17(11): 1596-1602