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Volume 9(11);  2008
Comment
The wisdom, and madness, of crowds
Gregory A Petsko
Genome Biol. 2008; 9(11): 112. Published online 2008 December 1. doi: 10.1186/gb-2008-9-11-112.
PMCID: PMC2614482
| PubLink |
Minireviews
Network-based approaches for linking metabolism with environment
Sarath Chandra Janga and M Madan Babu
Genome Biol. 2008; 9(11): 239. Published online 2008 November 24. doi: 10.1186/gb-2008-9-11-239.
PMCID: PMC2614483
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Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis
Robert P Zinzen and Eileen EM Furlong
Genome Biol. 2008; 9(11): 240. Published online 2008 November 4. doi: 10.1186/gb-2008-9-11-240.
PMCID: PMC2614484
| PubLink |
Protein Family Review
The Hedgehog protein family
Thomas R Bürglin
Genome Biol. 2008; 9(11): 241. Published online 2008 November 19. doi: 10.1186/gb-2008-9-11-241.
PMCID: PMC2614485
| PubLink |
Meeting Reports
A new era for proteomics research?
Mathias Uhlen
Genome Biol. 2008; 9(11): 325. Published online 2008 November 4. doi: 10.1186/gb-2008-9-11-325.
PMCID: PMC2614486
| PubLink |
From sequence to structure to networks
Nir Yosef and Lukas Käll
Genome Biol. 2008; 9(11): 326. Published online 2008 November 4. doi: 10.1186/gb-2008-9-11-326.
PMCID: PMC2614487
| PubLink |
Bacterial networking
Kathleen Marchal and Sigrid CJ De Keersmaecker
Genome Biol. 2008; 9(11): 327. Published online 2008 November 12. doi: 10.1186/gb-2008-9-11-327.
PMCID: PMC2614488
| PubLink |
Method
Whole genome transcriptome polymorphisms in Arabidopsis thaliana
Xu Zhang, Jake K Byrnes, Thomas S Gal, Wen-Hsiung Li, and Justin O Borevitz
Genome Biol. 2008; 9(11): R165. Published online 2008 November 24. doi: 10.1186/gb-2008-9-11-r165.
PMCID: PMC2614497
Software
ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets
Patrick J Killion and Vishwanath R Iyer
Genome Biol. 2008; 9(11): R159. Published online 2008 November 12. doi: 10.1186/gb-2008-9-11-r159.
PMCID: PMC2614491
Correspondence
Do we use the appropriate controls for the identification of informative methylation markers for early cancer detection?
Yasser Riazalhosseini and Jörg D Hoheisel
Genome Biol. 2008; 9(11): 405. Published online 2008 November 26. doi: 10.1186/gb-2008-9-11-405.
PMCID: PMC2614489
Research
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
Mircea Podar, Iain Anderson, Kira S Makarova, James G Elkins, Natalia Ivanova, Mark A Wall, Athanasios Lykidis, Kostantinos Mavromatis, Hui Sun, Matthew E Hudson, Wenqiong Chen, Cosmin Deciu, Don Hutchison, Jonathan R Eads, Abraham Anderson, Fillipe Fernandes, Ernest Szeto, Alla Lapidus, Nikos C Kyrpides, Milton H Saier, Jr, Paul M Richardson, Reinhard Rachel, Harald Huber, Jonathan A Eisen, Eugene V Koonin, Martin Keller, and Karl O Stetter
Genome Biol. 2008; 9(11): R158. Published online 2008 November 10. doi: 10.1186/gb-2008-9-11-r158.
PMCID: PMC2614490
Characterization of the differentially methylated region of the Impact gene that exhibits Glires-specific imprinting
Kohji Okamura, Richard F Wintle, and Stephen W Scherer
Genome Biol. 2008; 9(11): R160. Published online 2008 November 13. doi: 10.1186/gb-2008-9-11-r160.
PMCID: PMC2614492
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
Jimmy H Saw, Bruce W Mountain, Lu Feng, Marina V Omelchenko, Shaobin Hou, Jennifer A Saito, Matthew B Stott, Dan Li, Guang Zhao, Junli Wu, Michael Y Galperin, Eugene V Koonin, Kira S Makarova, Yuri I Wolf, Daniel J Rigden, Peter F Dunfield, Lei Wang, and Maqsudul Alam
Genome Biol. 2008; 9(11): R161. Published online 2008 November 17. doi: 10.1186/gb-2008-9-11-r161.
PMCID: PMC2614493
Proteomics studies confirm the presence of alternative protein isoforms on a large scale
Michael L Tress, Bernd Bodenmiller, Ruedi Aebersold, and Alfonso Valencia
Genome Biol. 2008; 9(11): R162. Published online 2008 November 18. doi: 10.1186/gb-2008-9-11-r162.
PMCID: PMC2614494
Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases
Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki, and Ichizo Kobayashi
Genome Biol. 2008; 9(11): R163. Published online 2008 November 21. doi: 10.1186/gb-2008-9-11-r163.
PMCID: PMC2614495
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata
Gaëlle Lelandais, Véronique Tanty, Colette Geneix, Catherine Etchebest, Claude Jacq, and Frédéric Devaux
Genome Biol. 2008; 9(11): R164. Published online 2008 November 24. doi: 10.1186/gb-2008-9-11-r164.
PMCID: PMC2614496
Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip
Shilpi Arora, Yipeng Wang, Zhenyu Jia, Saynur Vardar-Sengul, Ayla Munawar, Kutbuddin S Doctor, Michael Birrer, Michael McClelland, Eileen Adamson, and Dan Mercola
Genome Biol. 2008; 9(11): R166. Published online 2008 November 25. doi: 10.1186/gb-2008-9-11-r166.
PMCID: PMC2614498
Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
Anna Shevchenko, Assen Roguev, Daniel Schaft, Luke Buchanan, Bianca Habermann, Cagri Sakalar, Henrik Thomas, Nevan J Krogan, Andrej Shevchenko, and A Francis Stewart
Genome Biol. 2008; 9(11): R167. Published online 2008 November 28. doi: 10.1186/gb-2008-9-11-r167.
PMCID: PMC2614481
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