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Volume 6 Issue 7
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Comment |
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Eighty years ago
Gregory A Petsko Genome Biology 2005, 6:114 (30 June 2005)
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Editor’s summary
The Scopes Monkey Trial was The Trial of the Century; it was evolution, and by extension science itself, that was actually on trial. |
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Review |
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Text-mining and information-retrieval services for molecular biology
Martin Krallinger, Alfonso Valencia Genome Biology 2005, 6:224 (28 June 2005)
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Editor’s summary
A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators. |
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The cyclophilins
Ping Wang, Joseph Heitman Genome Biology 2005, 6:226 (27 June 2005)
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Editor’s summary
Cyclophilins belong to a group of proteins known as immunophilins that have peptidyl-prolyl cis-trans somerase activity. Cyclophilins are found in all cells of all organisms studied. Mammalian cyclophilin A is the major cellular target for, and thus mediates the actions of, the immunosuppressive drug cyclosporin A. |
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The genomics of probiotic intestinal microorganisms
Seppo Salminen, Jussi Nurmi, Miguel Gueimonde Genome Biology 2005, 6:225 (29 June 2005)
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Editor’s summary
The genomic characterization of probiotic bacteria and other commensal intestinal bacteria that is now under way will help to deepen our understanding of their beneficial effects. |
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Conservation anchors in the vertebrate genome
Ronny Aloni, Doron Lancet Genome Biology 2005, 6:115 (29 June 2005)
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Editor’s summary
The frequency of individual ancestral non-coding conserved regions within the genome helps in assessing the probability that they function in transcription regulation or RNA coding. |
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Report |
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Articles selected by Faculty of 1000: transcriptional regulation in parasitic helminths; interspecies expression-profile comparison; rice microRNAs; mRNA localization to the yeast bud tip; compartmental localisation of E. coli proteins
Genome Biology 2005, 6:332 (10 June 2005)
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Editor’s summary
A selection of evaluations from Faculty of 1000 covering transcriptional regulation in parasitic helminths; interspecies expression-profile comparison; rice microRNAs; mRNA localization to the yeast bud tip; compartmental localisation of E. coli proteins. |
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Articles selected by Faculty of 1000: Streptomyces metabolism; diversity of Entamoeba transposons; Arabidopsis polymorphism pattern; miRNA effect on plant transcriptome; energy costs of gene duplications
Genome Biology 2005, 6:333 (24 June 2005)
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Editor’s summary
A selection of evaluations from Faculty of 1000 covering Streptomyces metabolism; diversity of Entamoeba transposons; Arabidopsis polymorphism pattern; miRNA effect on plant transcriptome; energy costs of gene duplications. |
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Molecular helminthology in the Rockies
Mark Blaxter Genome Biology 2005, 6:329 (10 June 2005)
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Editor’s summary
A report on the Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005. |
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Meeting the challenges of drug discovery: a multidisciplinary re-evaluation of current practices
Stephen K Burley, Frances Park Genome Biology 2005, 6:330 (24 June 2005)
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Editor’s summary
A report on the Keystone Symposium 'Meeting the Challenges of Drug Discovery', Vancouver, Canada, 15-19 January 2005. |
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Complex cell behaviors in development: recent progress and emerging challenges
Magdalena Bak-Maier, Ana Stojkovic Genome Biology 2005, 6:331 (29 June 2005)
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Editor’s summary
A report on the British Societies for Cell Biology and Developmental Biology Joint Spring Meeting, University of Warwick, Coventry, UK, 6-9 April 2005. |
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Transcription regulation: no holy grail, but many treasures
Nicola A Hawkes, Patrick Varga-Weisz Genome Biology 2005, 6:334 (29 June 2005)
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Editor’s summary
A report of the Biochemical Society Annual Symposium 'Transcription UK', London, UK, 13-15 April 2005. |
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Migration events play significant role in genetic differentiation: A
microsatellite-based study on Sikkim settlers
Saurav Guha, R Trivedi, V K Kashyap Genome Biology 2005, 6:P9 (3 June 2005)
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Editor’s summary
A study of microsatellite allele frequency data in three populations of Sikkim suggests that they are genetically more akin to the mongoloids of China and distinctly apart from the mongoloids of Northeast India. The findings substantiates that migratory events have played a significant role in the differentiation of mongoloids of India.
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Research |
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Creation and disruption of protein features by alternative splicing - a novel mechanism to modulate function
Michael Hiller, Klaus Huse, Matthias Platzer, Rolf Backofen Genome Biology 2005, 6:R58 (22 June 2005)
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Editor’s summary
A new mechanism of alternative splicing is proposed which creates a protein feature by putting together two non-consecutive exons and destroys a feature by inserting an exon in its body. Evidence for this rare mechanism is provided by a genome-wide search with four specific protein features. |
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Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins
Shiri Freilich, Tim Massingham, Sumit Bhattacharyya, Hannes Ponstingl, Paul A Lyons, Tom C Freeman, Janet M Thornton Genome Biology 2005, 6:R56 (29 June 2005)
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Editor’s summary
A microaaray analysis of mouse gene expression combined with the proteins functional and phyletic classification suggests that phyletic age (and not function) is the dominant factor shaping the expression profle of a protein. |
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Functional analysis of human and chimpanzee promoters
Florian Heissig, Johannes Krause, Jaroslaw Bryk, Philipp Khaitovich, Wolfgang Enard, Svante Pääbo Genome Biology 2005, 6:R57 (1 July 2005)
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Editor’s summary
Twelve promoters of genes differentially expressed between humans and chimpanzees were tested for expression activity in culture cells. Seven promoters showed a significant difference in expression level between the human and chimpanzee promoter, but only three were in the same direction as the tissues, indicating that relevant expression differences between humans and chimpanzees will be difficult to predict from cell culture experiments or DNA sequences |
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Genomic analysis of metabolic pathway gene expression in mice
Anatole Ghazalpour, Sudheer Doss, Sonal S Sheth, Leslie A Ingram-Drake, Eric E Schadt, Aldons J Lusis, Thomas A Drake Genome Biology 2005, 6:R59 (1 July 2005)
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Editor’s summary
In order to evaluate metabolic pathways associated with obesity, global gene-expression data were integrated with phenotypic and genetic segregation analyses, identifying 13 metabolic pathways the genes of which are coordinately regulated in association with obesity. Four genomic regions were found to control the coordinated expression of these pathways and novel genes potentially associated with the identified pathways were identified. |
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Genomic analysis of heat-shock factor targets in Drosophila
Ian Birch-Machin, Shan Gao, David Huen, Richard McGirr, Robert AH White, Steven Russell Genome Biology 2005, 6:R63 (10 June 2005)
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Editor’s summary
A ChIP-assay approach is used for the whole-genome transcription factor target mapping in vivo using an intact whole organism. Using this ChIP-array 141 genes are identified in a genomic search for Hsf targets in Drosophila. |
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Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human
Charles L Magness, P Campion Fellin, Matthew J Thomas, Marcus J Korth, Michael B Agy, Sean C Proll, Matthew Fitzgibbon, Christina A Scherer, Douglas G Miner, Michael G Katze, Shawn P Iadonato Genome Biology 2005, 6:R60 (30 June 2005)
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Editor’s summary
Putative Macaca mulata orthologs for over 6,000 human genes have been sequenced from eleven tissues and three species of macaque. Macaque inter- and intraspecific nucleotide diversity is also reported. |
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Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray
Mark G Carter, Alexei A Sharov, Vincent VanBuren, Dawood B Dudekula, Condie E Carmack, Charlie Nelson, Minoru SH Ko Genome Biology 2005, 6:R61 (30 June 2005)
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Editor’s summary
An in-situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes is presented. Exogenous RNA controls derived from yeast allow quantitative estimation of absolute endogenous transcript abundance |
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Validation and refinement of gene-regulatory pathways on a network of physical interactions
Chen-Hsiang Yeang, H Craig Mak, Scott McCuine, Christopher Workman, Tommi Jaakkola, Trey Ideker Genome Biology 2005, 6:R62 (1 July 2005)
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Editor’s summary
A new automated procedure for prioritizing genetic perturbations was used to evaluate 38 candidate regulatory networks in yeast. Further analysis of four high-priority gene knockout experiments provided new insights into two regulatory pathways |
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Correspondence |
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New names for old strains? Wolbachia wSim is actually wRi
Iñaki Iturbe-Ormaetxe, Markus Riegler, Scott L O'Neill Genome Biology 2005, 6:401 (24 June 2005)
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Editor’s summary
A response to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology 2005, 6:R23 |
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Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Steven L Salzberg, Julie Dunning Hotopp, Arthur L Delcher, Mihai Pop, Douglas R Smith, Michael B Eisen, William C Nelson Genome Biology 2005, 6:402 (24 June 2005)
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Editor’s summary
A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology 2005, 6:R23 |
