Genome Biology | Volume 3 Issue 11

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	Volume 3 Issue 11
	Comment
	Comment The guards themselves Gregory A Petsko Genome Biology 2002, 3:comment1015-comment1015.2 (25 October 2002) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary If we agree that, in the present climate of fear of bioterrorism, some restrictions on the conduct and/or publication of certain types of biological research are likely, it is to our advantage to preempt government action by devising for ourselves restrictions that we can live with, then the inevitable question becomes: how should these restrictions be administered?
	Opinion Breaking barriers through collaboration: the example of the Cell Migration Consortium Alan Horwitz, Nikki Watson, J Parsons Genome Biology 2002, 3:comment2011-comment2011.4 (15 October 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Understanding complex integrated biological processes requires interdisciplinary approaches. The Cell Migration Consortium develops and disseminates new technologies, data, reagents, and shared information, and the development and operation of this Consortium may provide useful insights for those who plan similar approaches.
	Review
	Review Finding signals that regulate alternative splicing in the post-genomic era Andrea N Ladd, Thomas A Cooper Genome Biology 2002, 3:reviews0008-reviews0008.16 (23 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Auxiliary cis elements and trans-acting factors are required for the recognition of constitutive and alternatively spliced exons and their inclusion in pre-mRNA. Genome-wide analyses can aid in the identification of the regulatory elements that direct alternative splicing.
	Protein family review The presenilins Anurag Tandon, Paul Fraser Genome Biology 2002, 3:reviews3014-reviews3014.9 (23 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The presenilins are transmembrane proteins that, as part of a large protein complex, regulate the cleavage of other transmembrane proteins, notably the receptor Notch and the β-amyloid precursor protein. Mutations in presenilin genes increase the production of neurotoxic forms of the amyloid β peptide and contribute to 20-50% of early-onset cases of inherited Alzheimer's disease.
	Minireview Plasmodium falciparum virulence determinants unveiled Brendan S Crabb, Alan F Cowman Genome Biology 2002, 3:reviews1031-reviews1031.4 (25 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human malaria parasite Plasmodium falciparum, has many sequences and genes that play key roles in pathogenesis and immune evasion. We must understand the functions of these elements if the chronicity and unpredictable virulence of Plasmodium is to be explained.
	Minireview The discovery of novel neuropeptides takes flight Ruthann Nichols Genome Biology 2002, 3:reviews1032-reviews1032.2 (28 October 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies have used nanoscale chromatography and mass spectrometry to determine the structures of novel neuropeptides in rat and Drosophila. The results shed light on neuropeptide synthesis and function(s) in both vertebrates and insects.
	Report
	Paper report Differentiation is death Cathy Holding Genome Biology 2002, 3:reports0058 (29 October 2002) Abstract \| Full text \| Editor’s summary The apoptosis signaling molecule caspase 3 is also required for differentiation in myoblasts
	Paper report The compact pufferfish genome Jean-Nicolas Volff Genome Biology 2002, 3:reports0059 (29 October 2002) Abstract \| Full text \| Editor’s summary Comparative genomics using the pufferfish genome will help with identifying and characterizing human genes
	Paper report Brucella strain-specific proteomes Wim D'Haeze Genome Biology 2002, 3:reports0060 (29 October 2002) Abstract \| Full text \| Editor’s summary Experimental analysis of the proteomes of virulent and non-virulent strains of Brucella melitensis reveals differences in the proteins involved in iron metabolism
	Meeting report Mile-high view of plant biology David A Collings Genome Biology 2002, 3:reports4035-reports4035.3 (21 October 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on Plant Biology 2002, the annual meeting of the American Society of Plant Biologists, Denver, USA, 3-7 August 2002.
	Meeting report Understanding biology through intelligent systems Igor Jurisica, Dennis A Wigle Genome Biology 2002, 3:reports4036-reports4036.4 (24 October 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB), Edmonton, Canada, 3-7 August 2002.
	Deposited research article Isochores Merit the Prefix 'Iso' Wentian Li, Pedro Bernaola-Galvan, Pedro Carpena, Jose L Oliver Genome Biology 2002, 3:preprint0009-preprint0009.15 (23 September 2002) Abstract \| Full text \| PDF \| Editor’s summary We propose that analysis of variance (ANOVA) is more suitable than the binomial test to detect isochores and show that human isochores do exist in the human genome.
	Deposited research article The rhomboids: a near ubiquitous family of intramembrane serine proteases evolved via multiple horizontal gene transfers Eugene V Koonin, Kira S Makarova, Laetitia Davidovic, Luca Pellegrini Genome Biology 2002, 3:preprint0010-preprint0010.26 (3 October 2002) Abstract \| Full text \| PDF \| Editor’s summary Results. Phylogenetic tree analysis suggests that, despite the broad distribution in all three kingdoms of life, the rhomboid family was not present in the last universal common ancestor of the extant life forms, but instead evolved in bacteria and has been acquired by archaea and eukaryotes via several independent horizontal gene transfer events. In
	Research news B-lymphocyte lineage genes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021101-01 (1 November 2002) Abstract \| Full text \| Editor’s summary Chromatin immunoprecipitation experiments reveal the genes regulated by the E2A family of transcription factors during early B-cell differentiation.
	Research news Cell-free proteomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021106-01 (6 November 2002) Abstract \| Full text \| Editor’s summary The translation apparatus of wheat seeds has been adapted to create a cell-free system for large-scale protein production.
	Research news Muscle checkpoint Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021106-02 (6 November 2002) Abstract \| Full text \| Editor’s summary Exposure to genotoxic agents triggers a reversible inhibition of myogenic differentiation.
	Research news Muscling in on microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021107-01 (7 November 2002) Abstract \| Full text \| Editor’s summary Expression profiling of skeletal muscle from patients with Duchenne muscular dystrophy has identified a hundred genes associated with the disease pathology.
	Research news numb and numblike in neurogenesis Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021108-01 (8 November 2002) Abstract \| Full text \| Editor’s summary The numb and numblike genes are essential for maintaining neural stem-cell populations during development of the nervous system.
	Research news The need for Nbs1 Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021111-01 (11 November 2002) Abstract \| Full text \| Editor’s summary Experiments with a knockout cell line show that the Nbs1 protein is required for homologous recombination and DNA repair.
	Research news Designer zinc-fingers Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021111-02 (11 November 2002) Abstract \| Full text \| Editor’s summary Transcription factors designed to regulate the vegfa growth factor gene can induce angiogenesis in mouse models.
	Research news Modelling a signalling module Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021112-01 (12 November 2002) Abstract \| Full text \| Editor’s summary A combination of mathematical modelling and experimental validation provides insights into regulation of the NF-κB signalling pathway.
	Research news Chips for viral pathogens Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021113-01 (13 November 2002) Abstract \| Full text \| Editor’s summary A genomic approach can help to detect multiple pathogenic viruses in a single versatile assay.
	Research news Subtle changes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021114-01 (14 November 2002) Abstract \| Full text \| Editor’s summary Analysis of mice with a neuronal deletion of the Mecp2 gene suggests that subtle changes in gene expression may account for the Rett-like mental retardation phenotype.
	Research news Clock control Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021115-01 (15 November 2002) Abstract \| Full text \| Editor’s summary The Drosophila Slimb protein regulates the degradation of phosphorylated clock proteins Period and Timeless.
	Research news Fingers and toes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021118-01 (18 November 2002) Abstract \| Full text \| Editor’s summary Mutational analysis of the mouse Hoxd locus reveals insights into the mechanisms that regulate the Hox genes that define the digits.
	Research news Activation by an HDAC Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021119-01 (19 November 2002) Abstract \| Full text \| Editor’s summary Yeast histone deacetylases can activate gene expression by deacetylating histone tails.
	Research news ISWI with my little eye Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021120-01 (20 November 2002) Abstract \| Full text \| Editor’s summary Chromatin-remodeling complexes are important for opening up chromatin to allow DNA replication.
	Research news JNK and obesity Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021121-01 (21 November 2002) Abstract \| Full text \| Editor’s summary A signaling kinase has been linked to obesity and insulin resistance.
	Research news Chromatin and IP Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021122-01 (22 November 2002) Abstract \| Full text \| Editor’s summary Inositol phosphates regulate chromatin remodeling and transcription.
	Research news Targeted cell ablation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021125-01 (25 November 2002) Abstract \| Full text \| Editor’s summary Controlled hepatocyte ablation using capase-3 creates an inducible model of liver injury.
	Research news Probing photosynthesis Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021126-01 (26 November 2002) Abstract \| Full text \| Editor’s summary Comparative genomic analysis of photosynthetic prokaryotes provides insights into the evolution of photosynthesis.
	Research news Reviving rice Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021127-01 (27 November 2002) Abstract \| Full text \| Editor’s summary An international team has completed high-quality, genomic sequences for two rice chromosomes.
	Research news TRF2 and transcription Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021128-01 (28 November 2002) Abstract \| Full text \| Editor’s summary The Drosophila TRF2 protein acts as a core-promoter recognition factor and directs transcription of a subset of fly genes.
	Research news First Human Proteome Organisation congress Laura Spinney Genome Biology 2002, 3:gb-spotlight-20021129-01 (29 November 2002) Abstract \| Full text \| Editor’s summary Success of proteomics venture rests on improving tools and resolving bioinformatics and intellectual property issues.
	Research news CA-repeat enhancer Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021129-02 (29 November 2002) Abstract \| Full text \| Editor’s summary An intronic CA repeat is a splicing enhancer for the human endothelial nitric oxide synthase gene.
	Research
	Research Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering Audrey P Gasch, Michael B Eisen Genome Biology 2002, 3:research0059-research0059.22 (10 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A heuristically modified version of fuzzy k-means clustering has been used to identify overlapping clusters of yeast genes based on published gene-expression data following the response of yeast cells to environmental changes. A prevalent theme in the regulation of yeast gene expression seems to be the condition-specific coregulation of overlapping sets of genes.
	Research Genomic functional annotation using co-evolution profiles of gene clusters Yu Zheng, Richard J Roberts, Simon Kasif Genome Biology 2002, 3:research0060-research0060.9 (10 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The current speed of sequencing already exceeds the capability of annotation. A new method for functional annotation is proposed using the conservation patterns of gene clusters and has been applied to the genome of Escherichia coli and established functional relationships among 176 gene clusters, comprising 738 genes.
	Research The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism Vivek Anantharaman, L Aravind Genome Biology 2002, 3:research0061-research0061.9 (14 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The PRC-H β-barrel domain, a distinct cytoplasmic β-barrel domain whose fold has no close structural relationship to any other well known β-barrel domain, is the prototype of a novel superfamily of protein domains approximately 80 residues long. This domian is a widespread, ancient domain that appears to have been recruited to a variety of biological systems, ranging from RNA processing to photosynthesis.
	Research Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands Patrick Joost, Axel Methner Genome Biology 2002, 3:research0063-research0063.16 (17 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary G-protein-coupled receptors (GPCRs) are the largest and most diverse family of transmembrane receptors. A pylogenetic analysis shows the overall relationship of 277 human GPCRs. An emphasis on receptors with no identified natural ligand may prove valuable for identification of the ligands of 'orphan' receptors.
	Research Within the fold: assessing differential expression measures and reproducibility in microarray assays Ivana V Yang, Emily Chen, Jeremy P Hasseman, Wei Liang, Bryan C Frank, Shuibang Wang, Vasily Sharov, Alexander I Saeed, Joseph White, Jerry Li, Norman H Lee, Timothy J Yeatman, John Quackenbush Genome Biology 2002, 3:research0062-research0062.12 (24 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed. More accurate measures are required to identify high-confidence sets of genes with biologically meaningful changes in transcription. A general procedure for analyzing cDNA microarray data is proposed and validated. It is shown that pooled reference samples should be based not only on the expression of individual genes in each cell line but also on the expression levels of genes within cell lines.
	Research The society of genes: networks of functional links between genes from comparative genomics Itai Yanai, Charles DeLisi Genome Biology 2002, 3:research0064-research0064.12 (25 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics provides at least three methods for identifying functional links between genes: examination of phylogenetic distributions, analysis of conserved proximity and observations of fusions of genes into a multidomain gene in another organism. We show that the functional networks obtained by applying these methods have different topologies and that the information they provide is largely additive. In particular, the combined networks of functional links contain an average of 57% of an organism's complete genetic complement, uncover substantial portions of known pathways, and suggest the function of previously unannotated genes. In addition, the combined networks are qualitatively different from the networks obtained using individual methods.
	Research Improved analytical methods for microarray-based genome-composition analysis Charles C Kim, Elizabeth A Joyce, Kaman Chan, Stanley Falkow Genome Biology 2002, 3:research0065-research0065.17 (29 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-composition analysis using microarrays can be used to categorize genes into 'present' and 'divergent' categories. This involves selecting a signal value that is used as a cutoff to discriminate present and divergent genes, but this can result in the misclassification of many genes. A method is described that depends on the shape of the signal-ratio distribution and does not require empirical determination of a cutoff. Many genes previously classified as present using static methods are in fact divergent on the basis of microarray signal; this is corrected by our algorithm.

	Volume 3 Issue 11
	Comment
	Comment The guards themselves Gregory A Petsko Genome Biology 2002, 3:comment1015-comment1015.2 (25 October 2002) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary If we agree that, in the present climate of fear of bioterrorism, some restrictions on the conduct and/or publication of certain types of biological research are likely, it is to our advantage to preempt government action by devising for ourselves restrictions that we can live with, then the inevitable question becomes: how should these restrictions be administered?
	Opinion Breaking barriers through collaboration: the example of the Cell Migration Consortium Alan Horwitz, Nikki Watson, J Parsons Genome Biology 2002, 3:comment2011-comment2011.4 (15 October 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Understanding complex integrated biological processes requires interdisciplinary approaches. The Cell Migration Consortium develops and disseminates new technologies, data, reagents, and shared information, and the development and operation of this Consortium may provide useful insights for those who plan similar approaches.
	Review
	Review Finding signals that regulate alternative splicing in the post-genomic era Andrea N Ladd, Thomas A Cooper Genome Biology 2002, 3:reviews0008-reviews0008.16 (23 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Auxiliary cis elements and trans-acting factors are required for the recognition of constitutive and alternatively spliced exons and their inclusion in pre-mRNA. Genome-wide analyses can aid in the identification of the regulatory elements that direct alternative splicing.
	Protein family review The presenilins Anurag Tandon, Paul Fraser Genome Biology 2002, 3:reviews3014-reviews3014.9 (23 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The presenilins are transmembrane proteins that, as part of a large protein complex, regulate the cleavage of other transmembrane proteins, notably the receptor Notch and the β-amyloid precursor protein. Mutations in presenilin genes increase the production of neurotoxic forms of the amyloid β peptide and contribute to 20-50% of early-onset cases of inherited Alzheimer's disease.
	Minireview Plasmodium falciparum virulence determinants unveiled Brendan S Crabb, Alan F Cowman Genome Biology 2002, 3:reviews1031-reviews1031.4 (25 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human malaria parasite Plasmodium falciparum, has many sequences and genes that play key roles in pathogenesis and immune evasion. We must understand the functions of these elements if the chronicity and unpredictable virulence of Plasmodium is to be explained.
	Minireview The discovery of novel neuropeptides takes flight Ruthann Nichols Genome Biology 2002, 3:reviews1032-reviews1032.2 (28 October 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies have used nanoscale chromatography and mass spectrometry to determine the structures of novel neuropeptides in rat and Drosophila. The results shed light on neuropeptide synthesis and function(s) in both vertebrates and insects.
	Report
	Paper report Differentiation is death Cathy Holding Genome Biology 2002, 3:reports0058 (29 October 2002) Abstract \| Full text \| Editor’s summary The apoptosis signaling molecule caspase 3 is also required for differentiation in myoblasts
	Paper report The compact pufferfish genome Jean-Nicolas Volff Genome Biology 2002, 3:reports0059 (29 October 2002) Abstract \| Full text \| Editor’s summary Comparative genomics using the pufferfish genome will help with identifying and characterizing human genes
	Paper report Brucella strain-specific proteomes Wim D'Haeze Genome Biology 2002, 3:reports0060 (29 October 2002) Abstract \| Full text \| Editor’s summary Experimental analysis of the proteomes of virulent and non-virulent strains of Brucella melitensis reveals differences in the proteins involved in iron metabolism
	Meeting report Mile-high view of plant biology David A Collings Genome Biology 2002, 3:reports4035-reports4035.3 (21 October 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on Plant Biology 2002, the annual meeting of the American Society of Plant Biologists, Denver, USA, 3-7 August 2002.
	Meeting report Understanding biology through intelligent systems Igor Jurisica, Dennis A Wigle Genome Biology 2002, 3:reports4036-reports4036.4 (24 October 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB), Edmonton, Canada, 3-7 August 2002.
	Deposited research article Isochores Merit the Prefix 'Iso' Wentian Li, Pedro Bernaola-Galvan, Pedro Carpena, Jose L Oliver Genome Biology 2002, 3:preprint0009-preprint0009.15 (23 September 2002) Abstract \| Full text \| PDF \| Editor’s summary We propose that analysis of variance (ANOVA) is more suitable than the binomial test to detect isochores and show that human isochores do exist in the human genome.
	Deposited research article The rhomboids: a near ubiquitous family of intramembrane serine proteases evolved via multiple horizontal gene transfers Eugene V Koonin, Kira S Makarova, Laetitia Davidovic, Luca Pellegrini Genome Biology 2002, 3:preprint0010-preprint0010.26 (3 October 2002) Abstract \| Full text \| PDF \| Editor’s summary Results. Phylogenetic tree analysis suggests that, despite the broad distribution in all three kingdoms of life, the rhomboid family was not present in the last universal common ancestor of the extant life forms, but instead evolved in bacteria and has been acquired by archaea and eukaryotes via several independent horizontal gene transfer events. In
	Research news B-lymphocyte lineage genes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021101-01 (1 November 2002) Abstract \| Full text \| Editor’s summary Chromatin immunoprecipitation experiments reveal the genes regulated by the E2A family of transcription factors during early B-cell differentiation.
	Research news Cell-free proteomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021106-01 (6 November 2002) Abstract \| Full text \| Editor’s summary The translation apparatus of wheat seeds has been adapted to create a cell-free system for large-scale protein production.
	Research news Muscle checkpoint Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021106-02 (6 November 2002) Abstract \| Full text \| Editor’s summary Exposure to genotoxic agents triggers a reversible inhibition of myogenic differentiation.
	Research news Muscling in on microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021107-01 (7 November 2002) Abstract \| Full text \| Editor’s summary Expression profiling of skeletal muscle from patients with Duchenne muscular dystrophy has identified a hundred genes associated with the disease pathology.
	Research news numb and numblike in neurogenesis Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021108-01 (8 November 2002) Abstract \| Full text \| Editor’s summary The numb and numblike genes are essential for maintaining neural stem-cell populations during development of the nervous system.
	Research news The need for Nbs1 Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021111-01 (11 November 2002) Abstract \| Full text \| Editor’s summary Experiments with a knockout cell line show that the Nbs1 protein is required for homologous recombination and DNA repair.
	Research news Designer zinc-fingers Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021111-02 (11 November 2002) Abstract \| Full text \| Editor’s summary Transcription factors designed to regulate the vegfa growth factor gene can induce angiogenesis in mouse models.
	Research news Modelling a signalling module Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021112-01 (12 November 2002) Abstract \| Full text \| Editor’s summary A combination of mathematical modelling and experimental validation provides insights into regulation of the NF-κB signalling pathway.
	Research news Chips for viral pathogens Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021113-01 (13 November 2002) Abstract \| Full text \| Editor’s summary A genomic approach can help to detect multiple pathogenic viruses in a single versatile assay.
	Research news Subtle changes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021114-01 (14 November 2002) Abstract \| Full text \| Editor’s summary Analysis of mice with a neuronal deletion of the Mecp2 gene suggests that subtle changes in gene expression may account for the Rett-like mental retardation phenotype.
	Research news Clock control Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021115-01 (15 November 2002) Abstract \| Full text \| Editor’s summary The Drosophila Slimb protein regulates the degradation of phosphorylated clock proteins Period and Timeless.
	Research news Fingers and toes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021118-01 (18 November 2002) Abstract \| Full text \| Editor’s summary Mutational analysis of the mouse Hoxd locus reveals insights into the mechanisms that regulate the Hox genes that define the digits.
	Research news Activation by an HDAC Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021119-01 (19 November 2002) Abstract \| Full text \| Editor’s summary Yeast histone deacetylases can activate gene expression by deacetylating histone tails.
	Research news ISWI with my little eye Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021120-01 (20 November 2002) Abstract \| Full text \| Editor’s summary Chromatin-remodeling complexes are important for opening up chromatin to allow DNA replication.
	Research news JNK and obesity Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021121-01 (21 November 2002) Abstract \| Full text \| Editor’s summary A signaling kinase has been linked to obesity and insulin resistance.
	Research news Chromatin and IP Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021122-01 (22 November 2002) Abstract \| Full text \| Editor’s summary Inositol phosphates regulate chromatin remodeling and transcription.
	Research news Targeted cell ablation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021125-01 (25 November 2002) Abstract \| Full text \| Editor’s summary Controlled hepatocyte ablation using capase-3 creates an inducible model of liver injury.
	Research news Probing photosynthesis Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021126-01 (26 November 2002) Abstract \| Full text \| Editor’s summary Comparative genomic analysis of photosynthetic prokaryotes provides insights into the evolution of photosynthesis.
	Research news Reviving rice Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021127-01 (27 November 2002) Abstract \| Full text \| Editor’s summary An international team has completed high-quality, genomic sequences for two rice chromosomes.
	Research news TRF2 and transcription Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021128-01 (28 November 2002) Abstract \| Full text \| Editor’s summary The Drosophila TRF2 protein acts as a core-promoter recognition factor and directs transcription of a subset of fly genes.
	Research news First Human Proteome Organisation congress Laura Spinney Genome Biology 2002, 3:gb-spotlight-20021129-01 (29 November 2002) Abstract \| Full text \| Editor’s summary Success of proteomics venture rests on improving tools and resolving bioinformatics and intellectual property issues.
	Research news CA-repeat enhancer Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021129-02 (29 November 2002) Abstract \| Full text \| Editor’s summary An intronic CA repeat is a splicing enhancer for the human endothelial nitric oxide synthase gene.
	Research
	Research Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering Audrey P Gasch, Michael B Eisen Genome Biology 2002, 3:research0059-research0059.22 (10 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A heuristically modified version of fuzzy k-means clustering has been used to identify overlapping clusters of yeast genes based on published gene-expression data following the response of yeast cells to environmental changes. A prevalent theme in the regulation of yeast gene expression seems to be the condition-specific coregulation of overlapping sets of genes.
	Research Genomic functional annotation using co-evolution profiles of gene clusters Yu Zheng, Richard J Roberts, Simon Kasif Genome Biology 2002, 3:research0060-research0060.9 (10 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The current speed of sequencing already exceeds the capability of annotation. A new method for functional annotation is proposed using the conservation patterns of gene clusters and has been applied to the genome of Escherichia coli and established functional relationships among 176 gene clusters, comprising 738 genes.
	Research The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism Vivek Anantharaman, L Aravind Genome Biology 2002, 3:research0061-research0061.9 (14 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The PRC-H β-barrel domain, a distinct cytoplasmic β-barrel domain whose fold has no close structural relationship to any other well known β-barrel domain, is the prototype of a novel superfamily of protein domains approximately 80 residues long. This domian is a widespread, ancient domain that appears to have been recruited to a variety of biological systems, ranging from RNA processing to photosynthesis.
	Research Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands Patrick Joost, Axel Methner Genome Biology 2002, 3:research0063-research0063.16 (17 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary G-protein-coupled receptors (GPCRs) are the largest and most diverse family of transmembrane receptors. A pylogenetic analysis shows the overall relationship of 277 human GPCRs. An emphasis on receptors with no identified natural ligand may prove valuable for identification of the ligands of 'orphan' receptors.
	Research Within the fold: assessing differential expression measures and reproducibility in microarray assays Ivana V Yang, Emily Chen, Jeremy P Hasseman, Wei Liang, Bryan C Frank, Shuibang Wang, Vasily Sharov, Alexander I Saeed, Joseph White, Jerry Li, Norman H Lee, Timothy J Yeatman, John Quackenbush Genome Biology 2002, 3:research0062-research0062.12 (24 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed. More accurate measures are required to identify high-confidence sets of genes with biologically meaningful changes in transcription. A general procedure for analyzing cDNA microarray data is proposed and validated. It is shown that pooled reference samples should be based not only on the expression of individual genes in each cell line but also on the expression levels of genes within cell lines.
	Research The society of genes: networks of functional links between genes from comparative genomics Itai Yanai, Charles DeLisi Genome Biology 2002, 3:research0064-research0064.12 (25 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics provides at least three methods for identifying functional links between genes: examination of phylogenetic distributions, analysis of conserved proximity and observations of fusions of genes into a multidomain gene in another organism. We show that the functional networks obtained by applying these methods have different topologies and that the information they provide is largely additive. In particular, the combined networks of functional links contain an average of 57% of an organism's complete genetic complement, uncover substantial portions of known pathways, and suggest the function of previously unannotated genes. In addition, the combined networks are qualitatively different from the networks obtained using individual methods.
	Research Improved analytical methods for microarray-based genome-composition analysis Charles C Kim, Elizabeth A Joyce, Kaman Chan, Stanley Falkow Genome Biology 2002, 3:research0065-research0065.17 (29 October 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-composition analysis using microarrays can be used to categorize genes into 'present' and 'divergent' categories. This involves selecting a signal value that is used as a cutoff to discriminate present and divergent genes, but this can result in the misclassification of many genes. A method is described that depends on the shape of the signal-ratio distribution and does not require empirical determination of a cutoff. Many genes previously classified as present using static methods are in fact divergent on the basis of microarray signal; this is corrected by our algorithm.

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Volume 3 Issue 11

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