Genome Biology | Volume 9 Issue 10

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	Volume 9 Issue 10
	Comment
	Comment Meta-morphosis Gregory A Petsko Genome Biology 2008, 9:111 (3 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Meta-analysis is a popular way to try to get the most out of different studies linking genes and disease. But there are cons as well as pros.
	Review
	Review Large-scale assignment of orthology: back to phylogenetics? Toni Gabaldón Genome Biology 2008, 9:235 (30 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Automated use of phylogenetic trees to deduce orthology relationships in proteins.
	Minireview Condensin goes with the family but not with the flow Marc R Gartenberg, Matthias Merkenschlager Genome Biology 2008, 9:236 (6 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New work on genome-wide condensin binding highlights similarities and differences from cohesin.
	Minireview Bacterial pathogens encode suppressors of RNA-mediated silencing Rebecca A Mosher, David C Baulcombe Genome Biology 2008, 9:237 (17 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Bacterial suppressors of silencing that inhibit multiple steps of plant microRNA biogenesis and function have recently been identified.
	Report
	Meeting report Interdisciplinary bacteria and phages Jeanne M DiChiara, Marlene Belfort Genome Biology 2008, 9:322 (16 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'Molecular Genetics of Bacteria and Phages', Cold Spring Harbor, USA, 20-24 August 2008.
	Meeting report Translation controlled Graham D Pavitt, Mark P Ashe Genome Biology 2008, 9:323 (21 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'Translational Control', Cold Spring Harbor, USA, 3-7 September 2008.
	Meeting report Networks for all Sebastian E Ahnert, Sarah A Teichmann Genome Biology 2008, 9:324 (27 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008.
	Research
	Research Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes Jos Boekhorst, Bas van Breukelen, Albert JR Heck, Berend Snel Genome Biology 2008, 9:R144 (1 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of phosphoproteomics datasets of six eukaryotes shows significant overlap between phosphoproteomes.
	Research Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools Mirana Ramialison, Baubak Bajoghli, Narges Aghaallaei, Laurence Ettwiller, Sylvain Gaudan, Beate Wittbrodt, Thomas Czerny, Joachim Wittbrodt Genome Biology 2008, 9:R145 (1 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel bioinformatics pipeline is used to discover PAX2/5/8 direct downstream targets involved in inner ear development.
	Research A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD⁺biosynthetic gene BNA2 in chromosome end protection Amanda Greenall, Guiyuan Lei, Daniel C Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J Wilkinson, David Lydall Genome Biology 2008, 9:R146 (1 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary NAD+ metabolism may be linked to telomere end protection in yeast.
	Research Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases Monika Ray, Jianhua Ruan, Weixiong Zhang Genome Biology 2008, 9:R148 (8 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of microarray data reveals extensive links between Alzheimer’s disease and cardiovascular diseases.
	Research Identification of CDK2 substrates in human cell lysates Yong Chi, Markus Welcker, Asli A Hizli, Jeffrey J Posakony, Ruedi Aebersold, Bruce E Clurman Genome Biology 2008, 9:R149 (13 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Engineered kinases and thiophosphate enrichment were used to identify many candidate CDK2 substrates in human cell lysates.
	Research Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas Frank Westermann, Daniel Muth, Axel Benner, Tobias Bauer, Kai-Oliver Henrich, André Oberthuer, Benedikt Brors, Tim Beissbarth, Jo Vandesompele, Filip Pattyn, Barbara Hero, Rainer König, Matthias Fischer, Manfred Schwab Genome Biology 2008, 9:R150 (13 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differences in MYCN/c-MYC target gene expression are associated with distinct neuroblastoma subtypes and clinical outcome.
	Research Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations Yutaka Satou, Katsuhiko Mineta, Michio Ogasawara, Yasunori Sasakura, Eiichi Shoguchi, Keisuke Ueno, Lixy Yamada, Jun Matsumoto, Jessica Wasserscheid, Ken Dewar, Graham B Wiley, Simone L Macmil, Bruce A Roe, Robert W Zeller, Kenneth EM Hastings, Patrick Lemaire, Erika Lindquist, Toshinori Endo, Kohji Hotta, Kazuo Inaba Genome Biology 2008, 9:R152 (14 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An improved assembly of the Ciona intestinalis genome reveals that it contains non-canonical introns and that about 20% of Ciona genes reside in operons.
	Research Chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race Alexandra Nunes, Paulo J Nogueira, Maria J Borrego, João P Gomes Genome Biology 2008, 9:R153 (23 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of 15 serovars of Chlamydia trachomatis reveals an evolutionary arms race in pathogen-host interactions.
	Research Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach Julio A Freyre-González, José A Alonso-Pavón, Luis G Treviño-Quintanilla, Julio Collado-Vides Genome Biology 2008, 9:R154 (27 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The E. coli transcriptional regulatory network is shown to have a nonpyramidal architecture of independent modules governed by transcription factors, whose responses are integrated by intermodular genes.
	Research Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome Vicky Tsipouri, Mary G Schueler, Sufen Hu, NISC Comparative Sequencing Program, Amalia Dutra, Evgenia Pak, Harold Riethman, Eric D Green Genome Biology 2008, 9:R155 (28 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative mapping and sequencing was used to characterize the sites of ancestral chromosomal fusions in the Indian muntjac genome.
	Research Changes in protein expression during honey bee larval development Queenie WT Chan, Leonard J Foster Genome Biology 2008, 9:R156 (29 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mass spectrometry-based quantitative proteomics was used to quantify nearly 800 proteins during the honey bee larval development.
	Method A simple, fast, and accurate method of phylogenomic inference Martin Wu, Jonathan A Eisen Genome Biology 2008, 9:R151 (13 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An automated pipeline for phylogenomic analysis (AMPHORA) is presented that overcomes existing limits to large-scale protein phylogenetic inference.
	Method Boolean implication networks derived from large scale, whole genome microarray datasets Debashis Sahoo, David L Dill, Andrew J Gentles, Robert Tibshirani, Sylvia K Plevritis Genome Biology 2008, 9:R157 (30 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for analysis of microarray data is presented that extracts statistically significant Boolean implication relationships between pairs of genes.
	Software Tools for simulating evolution of aligned genomic regions with integrated parameter estimation Avinash Varadarajan, Robert K Bradley, Ian H Holmes Genome Biology 2008, 9:R147 (8 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Three tools for simulating genome evolution are presented: for neutrally evolving DNA, for phylogenetic context-free grammars and for richly structured syntenic blocks of genome sequence.

	Volume 9 Issue 10
	Comment
	Comment Meta-morphosis Gregory A Petsko Genome Biology 2008, 9:111 (3 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Meta-analysis is a popular way to try to get the most out of different studies linking genes and disease. But there are cons as well as pros.
	Review
	Review Large-scale assignment of orthology: back to phylogenetics? Toni Gabaldón Genome Biology 2008, 9:235 (30 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Automated use of phylogenetic trees to deduce orthology relationships in proteins.
	Minireview Condensin goes with the family but not with the flow Marc R Gartenberg, Matthias Merkenschlager Genome Biology 2008, 9:236 (6 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New work on genome-wide condensin binding highlights similarities and differences from cohesin.
	Minireview Bacterial pathogens encode suppressors of RNA-mediated silencing Rebecca A Mosher, David C Baulcombe Genome Biology 2008, 9:237 (17 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Bacterial suppressors of silencing that inhibit multiple steps of plant microRNA biogenesis and function have recently been identified.
	Report
	Meeting report Interdisciplinary bacteria and phages Jeanne M DiChiara, Marlene Belfort Genome Biology 2008, 9:322 (16 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'Molecular Genetics of Bacteria and Phages', Cold Spring Harbor, USA, 20-24 August 2008.
	Meeting report Translation controlled Graham D Pavitt, Mark P Ashe Genome Biology 2008, 9:323 (21 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'Translational Control', Cold Spring Harbor, USA, 3-7 September 2008.
	Meeting report Networks for all Sebastian E Ahnert, Sarah A Teichmann Genome Biology 2008, 9:324 (27 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008.
	Research
	Research Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes Jos Boekhorst, Bas van Breukelen, Albert JR Heck, Berend Snel Genome Biology 2008, 9:R144 (1 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of phosphoproteomics datasets of six eukaryotes shows significant overlap between phosphoproteomes.
	Research Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools Mirana Ramialison, Baubak Bajoghli, Narges Aghaallaei, Laurence Ettwiller, Sylvain Gaudan, Beate Wittbrodt, Thomas Czerny, Joachim Wittbrodt Genome Biology 2008, 9:R145 (1 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel bioinformatics pipeline is used to discover PAX2/5/8 direct downstream targets involved in inner ear development.
	Research A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD⁺biosynthetic gene BNA2 in chromosome end protection Amanda Greenall, Guiyuan Lei, Daniel C Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J Wilkinson, David Lydall Genome Biology 2008, 9:R146 (1 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary NAD+ metabolism may be linked to telomere end protection in yeast.
	Research Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases Monika Ray, Jianhua Ruan, Weixiong Zhang Genome Biology 2008, 9:R148 (8 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of microarray data reveals extensive links between Alzheimer’s disease and cardiovascular diseases.
	Research Identification of CDK2 substrates in human cell lysates Yong Chi, Markus Welcker, Asli A Hizli, Jeffrey J Posakony, Ruedi Aebersold, Bruce E Clurman Genome Biology 2008, 9:R149 (13 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Engineered kinases and thiophosphate enrichment were used to identify many candidate CDK2 substrates in human cell lysates.
	Research Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas Frank Westermann, Daniel Muth, Axel Benner, Tobias Bauer, Kai-Oliver Henrich, André Oberthuer, Benedikt Brors, Tim Beissbarth, Jo Vandesompele, Filip Pattyn, Barbara Hero, Rainer König, Matthias Fischer, Manfred Schwab Genome Biology 2008, 9:R150 (13 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differences in MYCN/c-MYC target gene expression are associated with distinct neuroblastoma subtypes and clinical outcome.
	Research Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations Yutaka Satou, Katsuhiko Mineta, Michio Ogasawara, Yasunori Sasakura, Eiichi Shoguchi, Keisuke Ueno, Lixy Yamada, Jun Matsumoto, Jessica Wasserscheid, Ken Dewar, Graham B Wiley, Simone L Macmil, Bruce A Roe, Robert W Zeller, Kenneth EM Hastings, Patrick Lemaire, Erika Lindquist, Toshinori Endo, Kohji Hotta, Kazuo Inaba Genome Biology 2008, 9:R152 (14 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An improved assembly of the Ciona intestinalis genome reveals that it contains non-canonical introns and that about 20% of Ciona genes reside in operons.
	Research Chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race Alexandra Nunes, Paulo J Nogueira, Maria J Borrego, João P Gomes Genome Biology 2008, 9:R153 (23 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of 15 serovars of Chlamydia trachomatis reveals an evolutionary arms race in pathogen-host interactions.
	Research Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach Julio A Freyre-González, José A Alonso-Pavón, Luis G Treviño-Quintanilla, Julio Collado-Vides Genome Biology 2008, 9:R154 (27 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The E. coli transcriptional regulatory network is shown to have a nonpyramidal architecture of independent modules governed by transcription factors, whose responses are integrated by intermodular genes.
	Research Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome Vicky Tsipouri, Mary G Schueler, Sufen Hu, NISC Comparative Sequencing Program, Amalia Dutra, Evgenia Pak, Harold Riethman, Eric D Green Genome Biology 2008, 9:R155 (28 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative mapping and sequencing was used to characterize the sites of ancestral chromosomal fusions in the Indian muntjac genome.
	Research Changes in protein expression during honey bee larval development Queenie WT Chan, Leonard J Foster Genome Biology 2008, 9:R156 (29 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mass spectrometry-based quantitative proteomics was used to quantify nearly 800 proteins during the honey bee larval development.
	Method A simple, fast, and accurate method of phylogenomic inference Martin Wu, Jonathan A Eisen Genome Biology 2008, 9:R151 (13 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An automated pipeline for phylogenomic analysis (AMPHORA) is presented that overcomes existing limits to large-scale protein phylogenetic inference.
	Method Boolean implication networks derived from large scale, whole genome microarray datasets Debashis Sahoo, David L Dill, Andrew J Gentles, Robert Tibshirani, Sylvia K Plevritis Genome Biology 2008, 9:R157 (30 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for analysis of microarray data is presented that extracts statistically significant Boolean implication relationships between pairs of genes.
	Software Tools for simulating evolution of aligned genomic regions with integrated parameter estimation Avinash Varadarajan, Robert K Bradley, Ian H Holmes Genome Biology 2008, 9:R147 (8 October 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Three tools for simulating genome evolution are presented: for neutrally evolving DNA, for phylogenetic context-free grammars and for richly structured syntenic blocks of genome sequence.

Explore Genome Biology

Articles

Volume 9 Issue 10

Comment

Review

Report

Research