Genome Biology | Volume 5 Issue 4

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	Volume 5 Issue 4
	Comment
	Comment Doctor Dunsel Gregory A Petsko Genome Biology 2004, 5:104 (29 March 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Repressingly, a robot scientist can generate functional genomic hypothesis and carry out experiments, increasing the working scientist's feelings of redundancy.
	Review
	Review Structural genomics of membrane proteins Peter Walian, Timothy A Cross, Bing K Jap Genome Biology 2004, 5:215 (15 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Improvements in membrane-protein molecular biology and biochemistry, technical advances in structural data collection and processing, and the availability of numerous sequenced genomes have paved the way for membrane-protein structural genomics efforts.
	Protein family review The annexins Stephen E Moss, Reg O Morgan Genome Biology 2004, 5:219 (31 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. More than a thousand proteins of the annexin superfamily have been identified in major eukaryotic phyla, but annexins are absent from yeasts and prokaryotes.
	Minireview Drosophila as an emerging model to study metastasis Madhuri Kango-Singh, Georg Halder Genome Biology 2004, 5:216 (25 March 2004) Abstract \| Full text \| PDF \| Editor’s summary Two recent studies describe a system for testing how multiple genetic events synergize to promote neoplastic growth and metastasis in Drosophila.
	Minireview Global orchestration of gene expression by the biological clock of cyanobacteria Carl Johnson Genome Biology 2004, 5:217 (29 March 2004) Abstract \| Full text \| PDF \| Editor’s summary Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks.
	Minireview Nonsense-mediated mRNA decay: from vacuum cleaner to Swiss army knife Gabriele Neu-Yilik, Niels H Gehring, Matthias W Hentze, Andreas E Kulozik Genome Biology 2004, 5:218 (30 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Two new approaches have identified physiological nonsense-mediated mRNA decay (NMD) substrates, and suggest that NMD functions as a multipurpose tool in the modulation of gene expression.
	Opinion The mammalian transcriptome and the function of non-coding DNA sequences Svetlana A Shabalina, Nikolay A Spiridonov Genome Biology 2004, 5:105 (25 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Many non-coding sequences transcribed from the mammalian genome are proving to have important regulatory roles, but the functions of the majority remain mysterious.
	Report
	Paper report Articles selected by Faculty of 1000: human and chimp methylation patterns; activity-based protein profiling; transcriptional activator targets identified by FRET; onion ESTs; gene organization and mutation rates Genome Biology 2004, 5:320 (18 March 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering human and chimp methylation patterns, activity-based protein profiling, transcriptional activator targets identified by FRET, a set of onion ESTs and gene organization and mutation rates.
	Paper report Articles selected by Faculty of 1000: proteomics of PH domains; machine-learning prediction of RNA-binding proteins; coated vesicle proteomics; classifying protein domain combinations; amino acid usage within proteomes Genome Biology 2004, 5:321 (24 March 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the proteomics of PH domains; machine-learning prediction of RNA-binding proteins; coated vesicle proteomics; classifying protein domain combinations; amino acid usage within proteomes.
	Meeting report The nature, pattern and function of human sequence variation Evan E Eichler, Kelly A Frazer Genome Biology 2004, 5:318 (12 March 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the 2004 Keystone Symposium 'Human Genome Sequence Variation and the Inherited Basis of Common Disease', Breckenridge, USA, 8-13 January 2004.
	Meeting report Molecular approaches to malaria: on the way to integration Zbynek Bozdech Genome Biology 2004, 5:319 (26 March 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Molecular Approaches to Malaria meeting, Lorne, Australia, 4-8 February 2004.
	Deposited research article Characterization of Indian cattle breeds, Ongole and Deoni (Bos indicus) using microsatellite markers Muralidhar Metta, Sriramana Kanginakudru, Narasimharao Gudiseva, Javaregowda Nagaraju Genome Biology 2004, 5:P8 (4 March 2004) Abstract \| Full text \| PDF \| Editor’s summary Two Indian cattle breeds, Ongole and Deoni, were characterized using microsatellite markers, revealing six Ongole and three Deoni specific alleles.
	Deposited research article Gene expression profiles of peripheral blood cells in type 2 diabetes and nephropathy in Asian Indians Paturi V Rao, Xinfang Lu, Patrick Pattee, Mark Turner, Nandgaonkar Suguna, Srinivasa R Nagalla Genome Biology 2004, 5:P9 (9 March 2004) Abstract \| Full text \| PDF \| Editor’s summary This study explores the global gene expression changes in peripheral blood cells in diabetes and diabetic nephropathy identifies potential candidate genes and molecular networks regulated in diabetes and nephropathy.
	Research
	Research Prediction of Saccharomyces cerevisiae replication origins Adam M Breier, Sourav Chatterji, Nicholas R Cozzarelli Genome Biology 2004, 5:R22 (4 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study presents the first algorithm, Oriscan, to predict eukaryotic replication origins and examines the structure of the origins and evolutionary conservation of origin sequences at the nucleotide level in several Saccharomyces species.
	Research Hotspots of mammalian chromosomal evolution Jeffrey A Bailey, Robert Baertsch, W Kent, David Haussler, Evan E Eichler Genome Biology 2004, 5:R23 (8 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study reports an abundance of primate-specific segmental duplications at the breakpoints of syntenic blocks in the human genome. Segmental duplications are associated with syntenic rearrangements but do not necessarily cause them.
	Research A transcriptional timetable of autumn senescence Anders Andersson, Johanna Keskitalo, Andreas Sjödin, Rupali Bhalerao, Fredrik Sterky, Kirsten Wissel, Karolina Tandre, Henrik Aspeborg, Richard Moyle, Yasunori Ohmiya, Rishikesh Bhalerao, Amy Brunner, Petter Gustafsson, Jan Karlsson, Joakim Lundeberg, Ove Nilsson, Göran Sandberg, Steven Strauss, Björn Sundberg, Mathias Uhlen, Stefan Jansson, Peter Nilsson Genome Biology 2004, 5:R24 (10 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary A microarray has been created from 36,354 ESTs from Populus species and used to study autumn senescence in the leaves of the aspen tree Populus tremula.
	Research The regulatory content of intergenic DNA shapes genome architecture Craig E Nelson, Bradley M Hersh, Sean B Carroll Genome Biology 2004, 5:R25 (15 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The relationship between regulatory complexity and gene spacing was examined in Caenorhabditis elegans and Drosophila melanogaster. Intergenic distance, and hence genome architecture, is shaped by regulatory information contained in noncoding DNA.
	Research Comparative genomics of gene-family size in closely related bacteria Ravindra Pushker, Alex Mira, Francisco Rodríguez-Valera Genome Biology 2004, 5:R27 (18 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary The size of a given gene family is remarkably similar in strains of the same species and in closely related species, suggesting that homologous gene families are vertically transmitted and depend little on horizontal gene transfer.
	Research Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae Justin C Fay, Heather L McCullough, Paul D Sniegowski, Michael B Eisen Genome Biology 2004, 5:R26 (24 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown in the presence or absence of copper sulfate. Insights were gained into the molecular basis of naturally occurring traits.
	Method Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements Heping Zhou, Kerri Bouwman, Mark Schotanus, Cornelius Verweij, Jorge A Marrero, Deborah Dillon, Jose Costa, Paul Lizardi, Brian B Haab Genome Biology 2004, 5:R28 (30 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Two-color rolling-circle amplification on antibody microarrays produces a 30-fold higher fluorescence than direct-labeling and indirect-detection methods, allowing acquisition of expression profiles from a great diversity of proteins.
	Method Enriching for direct regulatory targets in perturbed gene-expression profiles Susannah G Tringe, Andreas Wagner, Stephanie W Ruby Genome Biology 2004, 5:R29 (30 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study presents an algorithm to infer direct regulatory relationships using gene expression profiles from cells in which individual genes are deleted or overexpressed.

	Volume 5 Issue 4
	Comment
	Comment Doctor Dunsel Gregory A Petsko Genome Biology 2004, 5:104 (29 March 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Repressingly, a robot scientist can generate functional genomic hypothesis and carry out experiments, increasing the working scientist's feelings of redundancy.
	Review
	Review Structural genomics of membrane proteins Peter Walian, Timothy A Cross, Bing K Jap Genome Biology 2004, 5:215 (15 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Improvements in membrane-protein molecular biology and biochemistry, technical advances in structural data collection and processing, and the availability of numerous sequenced genomes have paved the way for membrane-protein structural genomics efforts.
	Protein family review The annexins Stephen E Moss, Reg O Morgan Genome Biology 2004, 5:219 (31 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. More than a thousand proteins of the annexin superfamily have been identified in major eukaryotic phyla, but annexins are absent from yeasts and prokaryotes.
	Minireview Drosophila as an emerging model to study metastasis Madhuri Kango-Singh, Georg Halder Genome Biology 2004, 5:216 (25 March 2004) Abstract \| Full text \| PDF \| Editor’s summary Two recent studies describe a system for testing how multiple genetic events synergize to promote neoplastic growth and metastasis in Drosophila.
	Minireview Global orchestration of gene expression by the biological clock of cyanobacteria Carl Johnson Genome Biology 2004, 5:217 (29 March 2004) Abstract \| Full text \| PDF \| Editor’s summary Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks.
	Minireview Nonsense-mediated mRNA decay: from vacuum cleaner to Swiss army knife Gabriele Neu-Yilik, Niels H Gehring, Matthias W Hentze, Andreas E Kulozik Genome Biology 2004, 5:218 (30 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Two new approaches have identified physiological nonsense-mediated mRNA decay (NMD) substrates, and suggest that NMD functions as a multipurpose tool in the modulation of gene expression.
	Opinion The mammalian transcriptome and the function of non-coding DNA sequences Svetlana A Shabalina, Nikolay A Spiridonov Genome Biology 2004, 5:105 (25 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Many non-coding sequences transcribed from the mammalian genome are proving to have important regulatory roles, but the functions of the majority remain mysterious.
	Report
	Paper report Articles selected by Faculty of 1000: human and chimp methylation patterns; activity-based protein profiling; transcriptional activator targets identified by FRET; onion ESTs; gene organization and mutation rates Genome Biology 2004, 5:320 (18 March 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering human and chimp methylation patterns, activity-based protein profiling, transcriptional activator targets identified by FRET, a set of onion ESTs and gene organization and mutation rates.
	Paper report Articles selected by Faculty of 1000: proteomics of PH domains; machine-learning prediction of RNA-binding proteins; coated vesicle proteomics; classifying protein domain combinations; amino acid usage within proteomes Genome Biology 2004, 5:321 (24 March 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the proteomics of PH domains; machine-learning prediction of RNA-binding proteins; coated vesicle proteomics; classifying protein domain combinations; amino acid usage within proteomes.
	Meeting report The nature, pattern and function of human sequence variation Evan E Eichler, Kelly A Frazer Genome Biology 2004, 5:318 (12 March 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the 2004 Keystone Symposium 'Human Genome Sequence Variation and the Inherited Basis of Common Disease', Breckenridge, USA, 8-13 January 2004.
	Meeting report Molecular approaches to malaria: on the way to integration Zbynek Bozdech Genome Biology 2004, 5:319 (26 March 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Molecular Approaches to Malaria meeting, Lorne, Australia, 4-8 February 2004.
	Deposited research article Characterization of Indian cattle breeds, Ongole and Deoni (Bos indicus) using microsatellite markers Muralidhar Metta, Sriramana Kanginakudru, Narasimharao Gudiseva, Javaregowda Nagaraju Genome Biology 2004, 5:P8 (4 March 2004) Abstract \| Full text \| PDF \| Editor’s summary Two Indian cattle breeds, Ongole and Deoni, were characterized using microsatellite markers, revealing six Ongole and three Deoni specific alleles.
	Deposited research article Gene expression profiles of peripheral blood cells in type 2 diabetes and nephropathy in Asian Indians Paturi V Rao, Xinfang Lu, Patrick Pattee, Mark Turner, Nandgaonkar Suguna, Srinivasa R Nagalla Genome Biology 2004, 5:P9 (9 March 2004) Abstract \| Full text \| PDF \| Editor’s summary This study explores the global gene expression changes in peripheral blood cells in diabetes and diabetic nephropathy identifies potential candidate genes and molecular networks regulated in diabetes and nephropathy.
	Research
	Research Prediction of Saccharomyces cerevisiae replication origins Adam M Breier, Sourav Chatterji, Nicholas R Cozzarelli Genome Biology 2004, 5:R22 (4 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study presents the first algorithm, Oriscan, to predict eukaryotic replication origins and examines the structure of the origins and evolutionary conservation of origin sequences at the nucleotide level in several Saccharomyces species.
	Research Hotspots of mammalian chromosomal evolution Jeffrey A Bailey, Robert Baertsch, W Kent, David Haussler, Evan E Eichler Genome Biology 2004, 5:R23 (8 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study reports an abundance of primate-specific segmental duplications at the breakpoints of syntenic blocks in the human genome. Segmental duplications are associated with syntenic rearrangements but do not necessarily cause them.
	Research A transcriptional timetable of autumn senescence Anders Andersson, Johanna Keskitalo, Andreas Sjödin, Rupali Bhalerao, Fredrik Sterky, Kirsten Wissel, Karolina Tandre, Henrik Aspeborg, Richard Moyle, Yasunori Ohmiya, Rishikesh Bhalerao, Amy Brunner, Petter Gustafsson, Jan Karlsson, Joakim Lundeberg, Ove Nilsson, Göran Sandberg, Steven Strauss, Björn Sundberg, Mathias Uhlen, Stefan Jansson, Peter Nilsson Genome Biology 2004, 5:R24 (10 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary A microarray has been created from 36,354 ESTs from Populus species and used to study autumn senescence in the leaves of the aspen tree Populus tremula.
	Research The regulatory content of intergenic DNA shapes genome architecture Craig E Nelson, Bradley M Hersh, Sean B Carroll Genome Biology 2004, 5:R25 (15 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The relationship between regulatory complexity and gene spacing was examined in Caenorhabditis elegans and Drosophila melanogaster. Intergenic distance, and hence genome architecture, is shaped by regulatory information contained in noncoding DNA.
	Research Comparative genomics of gene-family size in closely related bacteria Ravindra Pushker, Alex Mira, Francisco Rodríguez-Valera Genome Biology 2004, 5:R27 (18 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary The size of a given gene family is remarkably similar in strains of the same species and in closely related species, suggesting that homologous gene families are vertically transmitted and depend little on horizontal gene transfer.
	Research Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae Justin C Fay, Heather L McCullough, Paul D Sniegowski, Michael B Eisen Genome Biology 2004, 5:R26 (24 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown in the presence or absence of copper sulfate. Insights were gained into the molecular basis of naturally occurring traits.
	Method Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements Heping Zhou, Kerri Bouwman, Mark Schotanus, Cornelius Verweij, Jorge A Marrero, Deborah Dillon, Jose Costa, Paul Lizardi, Brian B Haab Genome Biology 2004, 5:R28 (30 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Two-color rolling-circle amplification on antibody microarrays produces a 30-fold higher fluorescence than direct-labeling and indirect-detection methods, allowing acquisition of expression profiles from a great diversity of proteins.
	Method Enriching for direct regulatory targets in perturbed gene-expression profiles Susannah G Tringe, Andreas Wagner, Stephanie W Ruby Genome Biology 2004, 5:R29 (30 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study presents an algorithm to infer direct regulatory relationships using gene expression profiles from cells in which individual genes are deleted or overexpressed.

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Volume 5 Issue 4

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