Genome Biology | Volume 6 Issue 13

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	Volume 6 Issue 13
	Comment
	Editorial Editorial Genome Biology 2005, 6:123 (3 January 2006) Full text \| PDF
	Comment Foxes and hounds Gregory A Petsko Genome Biology 2005, 6:124 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary With the completion of the dog genome sequence the first step has been taken in understanding one of the most remarkable, and mysterious, phenomena in biology: domestication.
	Review
	Protein family review The AP-2 family of transcription factors Dawid Eckert, Sandra Buhl, Susanne Weber, Richard Jäger, Hubert Schorle Genome Biology 2005, 6:246 (28 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary AP-2 transcription factors are involved in cell-type-specific stimulation of proliferation and the suppression of terminal differentiation during embryonic development. Members of the family are found in mammals (with five different proteins in human and mice), frogs and fish, as well as protochordates, insects and nematodes.
	Minireview New approaches to combating antimicrobial drug resistance Matthew B Avison Genome Biology 2005, 6:243 (23 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent work shows that the inhibition of the SOS stress response in Escherichia coli reduces the development of resistance to the antibiotics ciprofloxacin and rifampicin.
	Minireview Recent developments in membrane-protein structural genomics Fei Gao, Timothy A Cross Genome Biology 2005, 6:244 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work has identified the topology of almost all the inner membrane proteins in Escherichia coli, and advances in nuclear magnetic resonance spectroscopy now allow the determination of α-helical membrane protein structures at high resolution.
	Minireview The regulation of endocytosis by kinases: cell biology meets genomics Zita Balklava, Barth D Grant Genome Biology 2005, 6:245 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new genome-wide analysis of human kinases using RNA interference shows an unexpected depth and complexity to the interactions between signal transduction and vesicular transport.
	Report
	Meeting report New developments in developmental biology David AF Loebel, Samara L Lewis, Renuka S Rao, Leisha D Nolen Genome Biology 2005, 6:364 (23 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 15th International Society of Developmental Biologists Congress, Sydney, Australia, 3-7 September 2005.
	Meeting report From single cells to whole organisms Silke Sperling Genome Biology 2005, 6:365 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the European Science Foundation Conference 'Functional Genomics and Disease', Oslo, Norway, 6-10 September 2005.
	Meeting report Unraveling prion structures and biological functions Michael Ter-Avanesyan, Irina Derkatch, Ilia Baskakov, Vitaly Kushnirov Genome Biology 2005, 6:366 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on a Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on 'Prion Biology', Hinxton, UK, 7-11 September 2005.
	Deposited research article Global analysis of microRNA target gene expression reveals the potential roles of microRNAs in maintaining tissue identity Zhenbao Yu, Zhaofeng Jian, Shi-Hsiang Shen, Enrico Purisima, Edwin Wang Genome Biology 2005, 6:P14 (19 December 2005) Abstract \| Full text \| PDF \| Editor’s summary Microarray analysis revealed that the expression levels of microRNA targets are significantly lower in all mouse and Drosophila tissues than in the embryos.
	Deposited research article Using Topology of the Metabolic Network to Predict Viability of Mutant Strains Zeba Wunderlich, Leonid Mirny Genome Biology 2005, 6:P15 (28 December 2005) Abstract \| Full text \| PDF \| Editor’s summary It is shown that the topology of E. coli's metabolic network is sufficient to predict the viability of knock-out strains with accuracy comparable to flux balance analysis (FBA) on a large, unbiased dataset of mutants.
	Research
	Research Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart Rong Mao, Xiaowen Wang, Edward L Spitznagel, Laurence P Frelin, Jason C Ting, Huashi Ding, Jung-whan Kim, Ingo Ruczinski, Thomas J Downey, Jonathan Pevsner Genome Biology 2005, 6:R107 (16 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis of transcript levels in fetal cerebellum and heart tissues of Down syndrome patients showed a disruption only of chromosome 21 gene expression.
	Research The expression signature of in vitro senescence resembles mouse but not human aging Kristian Wennmalm, Claes Wahlestedt, Ola Larsson Genome Biology 2005, 6:R109 (16 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of several microarray datasets from aging human, mouse and rat and datasets from senescent cells from human and mouse shows a similarity between the expression signatures of cellular senescence and aging in mouse but not in humans.
	Research Molecular processes during fat cell development revealed by gene expression profiling and functional annotation Hubert Hackl, Thomas Burkard, Alexander Sturn, Renee Rubio, Alexander Schleiffer, Sun Tian, John Quackenbush, Frank Eisenhaber, Zlatko Trajanoski Genome Biology 2005, 6:R108 (19 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary In-depth bioinformatics analyses of expressed sequence tags found to be differentially expressed during differentiation of 3T3-L1 pre-adipocyte cells were combined with de novo functional annotation and mapping onto known pathways to generate a molecular atlas of fat-cell development.
	Research A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks John S Reece-Hoyes, Bart Deplancke, Jane Shingles, Christian A Grove, Ian A Hope, Albertha JM Walhout Genome Biology 2005, 6:R110 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A compendium of 934 transcription factor genes in C. elegans and identified by computational searches and extensive manual
	Research Systematic analysis of gene expression in human brains before and after death Henriette Franz, Claudia Ullmann, Albert Becker, Margaret Ryan, Sabine Bahn, Thomas Arendt, Matthias Simon, Svante Pääbo, Philipp Khaitovich Genome Biology 2005, 6:R112 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene expression profiles of pre- and post-mortem human brains suggests that post-mortem human brain samples are suitable for investigating general gene-expression patterns.
	Research The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders G Lynn Law, Kellie S Bickel, Vivian L MacKay, David R Morris Genome Biology 2005, 6:R111 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Eight per cent of yeast transcripts, mostly involved in responses to stress or external stimuli, were found to be under-loaded with ribosomes, and most of them exhibited structural changes in their 5’ transcript leaders in response to the environmental signal.
	Method Discovery of biological networks from diverse functional genomic data Chad L Myers, Drew Robson, Adam Wible, Matthew A Hibbs, Camelia Chiriac, Chandra L Theesfeld, Kara Dolinski, Olga G Troyanskaya Genome Biology 2005, 6:R114 (19 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BioPIXIE is a probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data.
	Method A novel approach to identifying regulatory motifs in distantly related genomes Ruth Van Hellemont, Pieter Monsieurs, Gert Thijs, Bart De Moor, Yves Van de Peer, Kathleen Marchal Genome Biology 2005, 6:R113 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A two-step procedure for identifying regulatory motifs in distantly related organisms is described that combines the advantages of sequence alignment and motif detection approaches.
	Software iVici: Interrelational Visualization and Correlation Interface Kirill Tarassov, Stephen W Michnick Genome Biology 2005, 6:R115 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary iVici, a new tool for the simultaneous visualization and correlation of multiple datasets, allows the analysis and comparison of different types of networks.
	Correspondence
	Correction Correction: Multiclass classification of microarray data with repeated measurements: application to cancer Ka Yeung, Roger E Bumgarner Genome Biology 2005, 6:405 (3 January 2006) Full text \| PDF

	Volume 6 Issue 13
	Comment
	Editorial Editorial Genome Biology 2005, 6:123 (3 January 2006) Full text \| PDF
	Comment Foxes and hounds Gregory A Petsko Genome Biology 2005, 6:124 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary With the completion of the dog genome sequence the first step has been taken in understanding one of the most remarkable, and mysterious, phenomena in biology: domestication.
	Review
	Protein family review The AP-2 family of transcription factors Dawid Eckert, Sandra Buhl, Susanne Weber, Richard Jäger, Hubert Schorle Genome Biology 2005, 6:246 (28 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary AP-2 transcription factors are involved in cell-type-specific stimulation of proliferation and the suppression of terminal differentiation during embryonic development. Members of the family are found in mammals (with five different proteins in human and mice), frogs and fish, as well as protochordates, insects and nematodes.
	Minireview New approaches to combating antimicrobial drug resistance Matthew B Avison Genome Biology 2005, 6:243 (23 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent work shows that the inhibition of the SOS stress response in Escherichia coli reduces the development of resistance to the antibiotics ciprofloxacin and rifampicin.
	Minireview Recent developments in membrane-protein structural genomics Fei Gao, Timothy A Cross Genome Biology 2005, 6:244 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work has identified the topology of almost all the inner membrane proteins in Escherichia coli, and advances in nuclear magnetic resonance spectroscopy now allow the determination of α-helical membrane protein structures at high resolution.
	Minireview The regulation of endocytosis by kinases: cell biology meets genomics Zita Balklava, Barth D Grant Genome Biology 2005, 6:245 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new genome-wide analysis of human kinases using RNA interference shows an unexpected depth and complexity to the interactions between signal transduction and vesicular transport.
	Report
	Meeting report New developments in developmental biology David AF Loebel, Samara L Lewis, Renuka S Rao, Leisha D Nolen Genome Biology 2005, 6:364 (23 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 15th International Society of Developmental Biologists Congress, Sydney, Australia, 3-7 September 2005.
	Meeting report From single cells to whole organisms Silke Sperling Genome Biology 2005, 6:365 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the European Science Foundation Conference 'Functional Genomics and Disease', Oslo, Norway, 6-10 September 2005.
	Meeting report Unraveling prion structures and biological functions Michael Ter-Avanesyan, Irina Derkatch, Ilia Baskakov, Vitaly Kushnirov Genome Biology 2005, 6:366 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on a Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on 'Prion Biology', Hinxton, UK, 7-11 September 2005.
	Deposited research article Global analysis of microRNA target gene expression reveals the potential roles of microRNAs in maintaining tissue identity Zhenbao Yu, Zhaofeng Jian, Shi-Hsiang Shen, Enrico Purisima, Edwin Wang Genome Biology 2005, 6:P14 (19 December 2005) Abstract \| Full text \| PDF \| Editor’s summary Microarray analysis revealed that the expression levels of microRNA targets are significantly lower in all mouse and Drosophila tissues than in the embryos.
	Deposited research article Using Topology of the Metabolic Network to Predict Viability of Mutant Strains Zeba Wunderlich, Leonid Mirny Genome Biology 2005, 6:P15 (28 December 2005) Abstract \| Full text \| PDF \| Editor’s summary It is shown that the topology of E. coli's metabolic network is sufficient to predict the viability of knock-out strains with accuracy comparable to flux balance analysis (FBA) on a large, unbiased dataset of mutants.
	Research
	Research Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart Rong Mao, Xiaowen Wang, Edward L Spitznagel, Laurence P Frelin, Jason C Ting, Huashi Ding, Jung-whan Kim, Ingo Ruczinski, Thomas J Downey, Jonathan Pevsner Genome Biology 2005, 6:R107 (16 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis of transcript levels in fetal cerebellum and heart tissues of Down syndrome patients showed a disruption only of chromosome 21 gene expression.
	Research The expression signature of in vitro senescence resembles mouse but not human aging Kristian Wennmalm, Claes Wahlestedt, Ola Larsson Genome Biology 2005, 6:R109 (16 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of several microarray datasets from aging human, mouse and rat and datasets from senescent cells from human and mouse shows a similarity between the expression signatures of cellular senescence and aging in mouse but not in humans.
	Research Molecular processes during fat cell development revealed by gene expression profiling and functional annotation Hubert Hackl, Thomas Burkard, Alexander Sturn, Renee Rubio, Alexander Schleiffer, Sun Tian, John Quackenbush, Frank Eisenhaber, Zlatko Trajanoski Genome Biology 2005, 6:R108 (19 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary In-depth bioinformatics analyses of expressed sequence tags found to be differentially expressed during differentiation of 3T3-L1 pre-adipocyte cells were combined with de novo functional annotation and mapping onto known pathways to generate a molecular atlas of fat-cell development.
	Research A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks John S Reece-Hoyes, Bart Deplancke, Jane Shingles, Christian A Grove, Ian A Hope, Albertha JM Walhout Genome Biology 2005, 6:R110 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A compendium of 934 transcription factor genes in C. elegans and identified by computational searches and extensive manual
	Research Systematic analysis of gene expression in human brains before and after death Henriette Franz, Claudia Ullmann, Albert Becker, Margaret Ryan, Sabine Bahn, Thomas Arendt, Matthias Simon, Svante Pääbo, Philipp Khaitovich Genome Biology 2005, 6:R112 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene expression profiles of pre- and post-mortem human brains suggests that post-mortem human brain samples are suitable for investigating general gene-expression patterns.
	Research The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders G Lynn Law, Kellie S Bickel, Vivian L MacKay, David R Morris Genome Biology 2005, 6:R111 (3 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Eight per cent of yeast transcripts, mostly involved in responses to stress or external stimuli, were found to be under-loaded with ribosomes, and most of them exhibited structural changes in their 5’ transcript leaders in response to the environmental signal.
	Method Discovery of biological networks from diverse functional genomic data Chad L Myers, Drew Robson, Adam Wible, Matthew A Hibbs, Camelia Chiriac, Chandra L Theesfeld, Kara Dolinski, Olga G Troyanskaya Genome Biology 2005, 6:R114 (19 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BioPIXIE is a probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data.
	Method A novel approach to identifying regulatory motifs in distantly related genomes Ruth Van Hellemont, Pieter Monsieurs, Gert Thijs, Bart De Moor, Yves Van de Peer, Kathleen Marchal Genome Biology 2005, 6:R113 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A two-step procedure for identifying regulatory motifs in distantly related organisms is described that combines the advantages of sequence alignment and motif detection approaches.
	Software iVici: Interrelational Visualization and Correlation Interface Kirill Tarassov, Stephen W Michnick Genome Biology 2005, 6:R115 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary iVici, a new tool for the simultaneous visualization and correlation of multiple datasets, allows the analysis and comparison of different types of networks.
	Correspondence
	Correction Correction: Multiclass classification of microarray data with repeated measurements: application to cancer Ka Yeung, Roger E Bumgarner Genome Biology 2005, 6:405 (3 January 2006) Full text \| PDF

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Volume 6 Issue 13

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