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Volume 9 Issue 5

Comment

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The new Manichaeans

Gregory A Petsko Genome Biology 2008, 9:105 (29 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

It doesn't serve science well to drift towards a Manichaean view by calling religion 'nonsense'. People of faith may be the natural allies of biologists when it comes to matters of conservation and climate protection.

Review

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RNA polymerase II stalling: loading at the start prepares genes for a sprint

Jia Wu, Michael Snyder Genome Biology 2008, 9:220 (2 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Promoter-proximal polymerase II stalling prepares genes for prompt expression when signals are received.

Protein family review   Free

Glypicans

Jorge Filmus, Mariana Capurro, Jonathan Rast Genome Biology 2008, 9:224 (22 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The glypican family of cell-surface heparan sulfate proteoglycans modulate the actions of many developmentally important signal proteins.

Minireview   Free

A role for Numb in p53 stabilization

Stephanie Carter, Karen H Vousden Genome Biology 2008, 9:221 (9 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Loss of Numb could enable breast cancer cells to bypass the p53 tumor suppressor response

Minireview   Free

The genome sequence of Podospora anserina, a classic model fungus

Mathieu Paoletti, Sven J Saupe Genome Biology 2008, 9:223 (15 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The genome sequence of the coprophilous fungus Podospora anserina shows both typical ascomycete features and how this species is adapted to its specialized environment.

Minireview   Free

Porin new light onto chromatin and nuclear organization

Lee E Finlan, Wendy A Bickmore Genome Biology 2008, 9:222 (16 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The capture of associations between chromatin and nuclear pore complexes throws new light on chromosome organization in the nucleus.

Report

Meeting report   Free

A rational approach to cancer therapy

Kylie L Gorringe, Ian G Campbell Genome Biology 2008, 9:306 (7 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A report on the 20th Annual Lorne Cancer Conference, Lorne, Australia, 14-16 February 2008.

Meeting report   Free

Epigenomes under scrutiny

Jacqueline E Mermoud Genome Biology 2008, 9:308 (14 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A report on the 3rd UK Stem Cell Meeting 'Epigenetics & Differentiation', London, UK, 11 March 2008.

Meeting report   Free

All systems are go

Claire E Eyers, Onrapak Reamtong Genome Biology 2008, 9:307 (15 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A report on 'Genomes to Systems', the Fourth Conference of the Consortium for Post-Genome Science, Manchester, UK, 17-19 March 2008.

Meeting report   Free

Probing the cancer genome

Heidi Greulich Genome Biology 2008, 9:309 (15 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A report on the Keystone Symposium 'Cancer Genomics and Epigenomics', Taos, USA, 19-24 February 2008.

Research

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The genome sequence of the model ascomycete fungus Podospora anserina

Eric Espagne, Olivier Lespinet, Fabienne Malagnac, Corinne Da Silva, Olivier Jaillon, Betina M Porcel, Arnaud Couloux, Jean-Marc Aury, Béatrice Ségurens, Julie Poulain, Véronique Anthouard, Sandrine Grossetete, Hamid Khalili, Evelyne Coppin, Michelle Déquard-Chablat, Marguerite Picard, Véronique Contamine, Sylvie Arnaise, Anne Bourdais, Véronique Berteaux-Lecellier, Daniel Gautheret, Ronald P de Vries, Evy Battaglia, Pedro M Coutinho, Etienne GJ Danchin, Bernard Henrissat, Riyad EL Khoury, Annie Sainsard-Chanet, Antoine Boivin, Bérangère Pinan-Lucarré, Carole H Sellem, Robert Debuchy, Patrick Wincker, Jean Weissenbach, Philippe Silar et al. Genome Biology 2008, 9:R77 (6 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A 10X draft sequence of Podospora anserina genome shows highly dynamic evolution since its divergence from Neurospora crassa.

Research   Open Access

Finishing the finished human chromosome 22 sequence

Charlotte G Cole, Owen T McCann, John E Collins, Karen Oliver, David Willey, Susan M Gribble, Fengtang Yang, Karen McLaren, Jane Rogers, Zemin Ning, David M Beare, Ian Dunham Genome Biology 2008, 9:R78 (13 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A combination of approaches was used to close 8 of the 11 gaps in the original sequence of human chromosome 22, and to generate a total 1.018 Mb of new sequence.

Research   Open Access Highly Accessed

CpG island density and its correlations with genomic features in mammalian genomes

Leng Han, Bing Su, Wen-Hsiung Li, Zhongming Zhao Genome Biology 2008, 9:R79 (13 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A systematic analysis of CpG islands in ten mammalian genomes suggests that an increase in chromosome number elevates GC content and prevents loss of CpG islands.

Research   Open Access Highly Accessed

Estrogen, not intrinsic aging, is the major regulator of delayed human wound healing in the elderly

Matthew J Hardman, Gillian S Ashcroft Genome Biology 2008, 9:R80 (13 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Analysis of gene expression in male elderly and young human wounds suggests that estrogen has a more profound influence on aging than previously thought.

Research   Open Access Highly Accessed

Loss of genes implicated in gastric function during platypus evolution

Gonzalo R Ordoñez, LaDeana W Hillier, Wesley C Warren, Frank Grützner, Carlos López-Otín, Xose S Puente Genome Biology 2008, 9:R81 (15 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Several genes implicated in food digestion have been deleted or inactivated in platypus. This loss perhaps explains the anatomical and physiological differences in the gastrointestinal tract between monotremes and other vertebrates and provides insights into platypus genome evolution.

Research   Open Access Highly Accessed

Individual mRNA expression profiles reveal the effects of specific microRNAs

Amit Arora, David AC Simpson Genome Biology 2008, 9:R82 (16 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The effect of a microRNA on the levels of its target mRNAs can be measured within a single gene expression profile

Research   Open Access Highly Accessed

Gene expression profiling of human prostate cancer stem cells reveals a pro-inflammatory phenotype and the importance of extracellular matrix interactions

Richard Birnie, Steven D Bryce, Claire Roome, Vincent Dussupt, Alastair Droop, Shona H Lang, Paul A Berry, Catherine F Hyde, John L Lewis, Michael J Stower, Norman J Maitland, Anne T Collins Genome Biology 2008, 9:R83 (20 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

An expression signature of human prostate cancer stem cells identifies 581 differentially expressed genes and suggests that the JAK-STAT pathway and focal adhesion signaling are important.

Research   Open Access

Organization of the pronephric kidney revealed by large-scale gene expression mapping

Daniela Raciti, Luca Reggiani, Lars Geffers, Qiuhong Jiang, Francesca Bacchion, Astrid E Subrizi, Dave Clements, Christopher Tindal, Duncan R Davidson, Brigitte Kaissling, André W Brändli Genome Biology 2008, 9:R84 (20 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Gene expression mapping reveals 8 functionally distinct domains in the Xenopus pronephros. Interestingly, no structure equivalent to the mammalian collecting duct is identified.

Research   Open Access

Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae

Yeonyee Oh, Nicole Donofrio, Huaqin Pan, Sean Coughlan, Douglas E Brown, Shaowu Meng, Thomas Mitchell, Ralph A Dean Genome Biology 2008, 9:R85 (20 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Analysis of genome-wide gene-expression changes during spore germination and appressorium formation in Magnaporthe oryzae revealed that protein degradation and amino-acid metabolism are essential for appressorium formation and subsequent infection.

Research   Open Access

A computational model of gene expression reveals early transcriptional events at the subtelomeric regions of the malaria parasite, Plasmodium falciparum

Matthias Scholz, Martin J Fraunholz Genome Biology 2008, 9:R88 (27 May 2008)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A mathematical model of the intraerythrocytic developmental cycle identifies a delay between subtelomeric and central chromosomal gene activities in the malaria parasite, Plasmodium falciparum.

Research   Open Access Highly Accessed

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria

Alexis Dufresne, Martin Ostrowski, David J Scanlan, Laurence Garczarek, Sophie Mazard, Brian P Palenik, Ian T Paulsen, Nicole de Marsac, Patrick Wincker, Carole Dossat, Steve Ferriera, Justin Johnson, Anton F Post, Wolfgang R Hess, Frédéric Partensky Genome Biology 2008, 9:R90 (28 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Local niche occupancy of marine Synechococcus lineages is facilitated by lateral gene transfers. Genomic islands act as repositories for these transferred genes.

Research   Open Access

Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice

Jonathan M Mudge, Stuart D Armstrong, Karen McLaren, Robert J Beynon, Jane L Hurst, Christine Nicholson, Duncan H Robertson, Laurens G Wilming, Jennifer L Harrow Genome Biology 2008, 9:R91 (28 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Targeted sequencing, manual genome annotation, phylogenetic analysis and mass spectrometry were used to characterise major urinary proteins (MUPs) and the Mup clusters of two strains of inbred mice.

Method   Open Access

GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

Heidi Lyng, Malin Lando, Runar S Brøvig, Debbie H Svendsrud, Morten Johansen, Eivind Galteland, Odd T Brustugun, Leonardo A Meza-Zepeda, Ola Myklebost, Gunnar B Kristensen, Eivind Hovig, Trond Stokke Genome Biology 2008, 9:R86 (23 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

GeneCount is a new method for exploring gene dosages and intratumor copy number heterogeneity in cancers from clinical array comparative genomic hybridization data.

Method   Open Access Highly Accessed

Sequence-based prediction of protein-protein interactions by means of codon usage

Hamed Najafabadi, Reza Salavati Genome Biology 2008, 9:R87 (23 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A new approach based on similarity in codon usage is used to predict protein-protein interactions.

Software   Open Access Highly Accessed

Calling on a million minds for community annotation in WikiProteins

Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert-Jan van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Jimmy Wales, Gerard Meijssen, Erik Moeller, Peter Roes, Katy Borner, Amos Bairoch Genome Biology 2008, 9:R89 (28 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

WikiProteins is a novel tool that allows community annotation in an open access, wiki-based system.


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