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Taxonomic distribution of large DNA viruses in the sea
Adam Monier, Jean-Michel Claverie, Hiroyuki Ogata
Genome Biology 2008, 9: R106    
(3 July 2008)

Phylogenetic mapping of metagenomics data reveals the taxonomic distribution of large DNA viruses in the sea, including giant viruses of the Mimiviridae family.

[Abstract] [Provisional PDF]

Asymmetric histone modifications between the original and derived loci of human segmental duplications
Deyou Zheng
Genome Biology 2008, 9: R105    
(3 July 2008)

A systematic analysis of histone modifications between human segmental duplications shows that two seemingly identical genomic copies have distinct epigenomic properties.

[Abstract] [Provisional PDF]

Integrating systems biology with clinical research
Rainer Pepperkok, Stefan Wiemann
Genome Biology 2008, 9(7):314   
(1 July 2008)

A report on the conference 'Systems Genomics 2008', Heidelberg, Germany, 2-3 May 2008.

[Abstract] [Full text] [PDF]

Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
Thorsten Schmidt, Dmitrij Frishman
Genome Biology 2008, 9: R104    
(30 June 2008)

A new consensus isochore assignment method and a database of isochore maps for all completely sequenced vertebrate genomes are presented.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Research    
An en masse phenotype and function prediction system for Mus musculus
Murat Taan, Weidong Tian, David P Hill, Francis D Gibbons, Judith A Blake, Frederick P Roth
Genome Biology 2008, 9(Suppl 1):S8 (27 June 2008)
[Full text] [PDF]

Method    
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function
Weidong Tian, Lan V Zhang, Murat Taan, Francis D Gibbons, Oliver D King, Julie Park, Zeba Wunderlich, J Michael Cherry, Frederick P Roth
Genome Biology 2008, 9(Suppl 1):S7 (27 June 2008)
[Full text] [PDF]

Method    
Consistent probabilistic outputs for protein function prediction
Guillaume Obozinski, Gert Lanckriet, Charles Grant, Michael I Jordan, William Stafford Noble
Genome Biology 2008, 9(Suppl 1):S6 (27 June 2008)
[Full text] [PDF]

Method    
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
Wan Kyu Kim, Chase Krumpelman, Edward M Marcotte
Genome Biology 2008, 9(Suppl 1):S5 (27 June 2008)
[Full text] [PDF]

Method    
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
Sara Mostafavi, Debajyoti Ray, David Warde-Farley, Chris Grouios, Quaid Morris
Genome Biology 2008, 9(Suppl 1):S4 (27 June 2008)
[Full text] [PDF]

Research    
Predicting gene function in a hierarchical context with an ensemble of classifiers
Yuanfang Guan, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy, Olga G Troyanskaya
Genome Biology 2008, 9(Suppl 1):S3 (27 June 2008)
[Full text] [PDF]

Research    
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
Lourdes Peña-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning Lin, Gabriel F Berriz, Francis D Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David P Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, Judith A Blake, Minghua Deng, Michael I Jordan, William S Noble, Quaid Morris, Judith Klein-Seetharaman, Ziv Bar-Joseph, Ting Chen, Fengzhu Sun, Olga G Troyanskaya, Edward M Marcotte, Dong Xu, Timothy R Hughes, Frederick P Roth
Genome Biology 2008, 9(Suppl 1):S2 (27 June 2008)
[Full text] [PDF]

Introduction    
A race through the maze of genomic evidence
Timothy R Hughes, Frederick P Roth
Genome Biology 2008, 9(Suppl 1):S1 (27 June 2008)
[Full text] [PDF]

What makes pathogens pathogenic
Garth D Ehrlich, N Luisa Hiller, Fen Ze Hu
Genome Biology 2008, 9(6):225   
(24 June 2008)

A review of the evolution of microbial pathogenicity in the context of the 'symbiome' of microbes and their multicellular hosts.

[Abstract] [Full text] [PDF]

Circular reasoning rather than cyclic expression
Lars Juhl Jensen, Ulrik de Lichtenberg, Thomas Skøt Jensen, Søren Brunak, Peer Bork
Genome Biology 2008, 9(6):403    
(23 June 2008)

A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146.

[Abstract] [Full text] [PDF]

It is alive
Gregory A Petsko
Genome Biology 2008, 9(6):106   
(23 June 2008)

We need to familiarize ourselves with the facts of evolution, so that we can mount a spirited defense against creationism and the forces of ignorance.

[Abstract] [Full text] [PDF] [1 comment]

Genetic analysis of the human infective trypanosome, Trypanosoma brucei gambiense: chromosomal segregation, crossing over and the construction of a genetic map
Anneli Cooper, Andy Tait, Lindsay Sweeney, Alison Tweedie, Liam Morrison, C Michael R Turner, Annette MacLeod
Genome Biology 2008, 9: R103    
(22 June 2008)

A high-resolution genetic linkage map of the STIB 386 strain of Trypanosoma brucei gambiense is presented.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Modified cell cycle status in a mouse model of altered neuronal vulnerability (Wallerian Degeneration Slow; WldS)
Thomas M Wishart, Helen M Pemberton, Sally R James, Chris J McCabe, Thomas H Gillingwater
Genome Biology 2008, 9: R101    
(20 June 2008)

Profiling of gene expression changes in mice harbouring the neurodegenerative Wlds mutation shows a strong correlation between changes in cell cycle pathways and altered vulnerability of terminally differentiated neurons.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

GMODWeb: a web framework for the generic model organism database
Brian D O'Connor, Allen Day, Scott Cain, Olivier Arnaiz, Linda Sperling, Lincoln D Stein
Genome Biology 2008, 9: R102    
(20 June 2008)

GMODWeb is a software framework designed to speed the development of websites for model organism databases.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype
Edward K Lobenhofer, J Todd Auman, Pamela E Blackshear, Gary A Boorman, Pierre R Bushel, Michael L Cunningham, Jennifer M Fostel, Kevin Gerrish, Alexandra N Heinloth, Richard D Irwin, David E Malarkey, B Alex Merrick, Stella O Sieber, Charles J Tucker, Sandra M Ward, Ralph E Wilson, Patrick Hurban, Raymond W Tennant, Richard S Paules
Genome Biology 2008, 9(6):R100    
(20 June 2008)

Histopathology, clinical chemistry, hematology and gene expression data were collected from the rat liver and blood after treatment with eight known hepatotoxins.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

Sequencing the regulatory genome
Stein Aerts, Stefanie Butland
Genome Biology 2008, 9(6):313   
(19 June 2008)

A report on the Cold Spring Harbor Laboratory meeting 'Systems Biology: Global Regulation of Gene Expression', Cold Spring Harbor, USA, 27-30 March 2008.

[Abstract] [Full text] [PDF]

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