Genome Biology | Volume 3 Issue 10

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	Volume 3 Issue 10
	Comment
	Comment An Asilomar moment Gregory A Petsko Genome Biology 2002, 3:comment1014-comment1014.3 (25 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As governments in the US and Europe contemplate legislation that would divert funding of some genomics-driven research to Offices of Homeland Security and the like, and that would restrict the freedom of biologists to publish and share some of their data, we of the scientific community are facing a crisis, brought on by fears of bioterrorism, that eerily mirrors the early days of recombinant DNA research.
	Opinion On the importance of being finished Lance E Palmer, W Richard McCombie Genome Biology 2002, 3:comment2010-comment2010.4 (27 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The publication of an increasing number of draft genome sequences presents problems that will only be resolved by improved search tools and by complete finishing of the sequences - and their deposition in publicly accessible databases.
	Review
	Review Are Drosophila telomeres an exception or the rule? Edward J Louis Genome Biology 2002, 3:reviews0007-reviews0007.6 (27 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary At the ends of eukaryotic chromosomes are telomeres, specialized structures with unusual properties. Specific efforts to compare sequences and properties of telomeres across species can reveal the generalities of telomere properties.
	Protein family review Histidine protein kinases: key signal transducers outside the animal kingdom Peter M Wolanin, Peter A Thomason, Jeffry B Stock Genome Biology 2002, 3:reviews3013-reviews3013.8 (25 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Histidine protein kinases (HPKs) are a large family of signal-transduction enzymes that form two-component signaling systems together with their downstream target proteins, the response regulators. The proteins divide into at least 11 subfamilies, only one of which is present in eukaryotes, suggesting that lateral gene transfer gave rise to two-component signaling in these organisms.
	Minireview Large-scale gene-expression studies and the challenge of multiple sclerosis Sergio E Baranzini, Stephen L Hauser Genome Biology 2002, 3:reviews1027-reviews1027.5 (16 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent transcription-profiling studies have found distinct gene-expression patterns in multiple sclerosis; such large-scale studies at different stages of the disease are contributing to understanding multiple sclerosis and developing effective therapy.
	Minireview Variations in abundance: genome-wide responses to genetic variation... and vice versa Bruce A Hamilton Genome Biology 2002, 3:reviews1029-reviews1029.3 (19 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern.
	Minireview A genomic approach to studying cell-size homeostasis in yeast Jonathan BA Millar Genome Biology 2002, 3:reviews1028-reviews1028.4 (20 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study has revealed multiple overlapping pathways that coordinately regulate cell-cycle progression with ribosome biogenesis and translation efficiency, providing new insights into the mechanisms governing cell-size homeostasis in eukaryotes.
	Minireview Ascidian gene-expression profiles William R Jeffery Genome Biology 2002, 3:reviews1030-reviews1030.4 (25 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene-expression profiling will be particularly informative in studies of ascidians, basal chordates whose genomes and embryology are uniquely suited for mapping developmental gene networks.
	Report
	Paper report Autosome inactivation by ectopic XIST in differentiated cells Cathy Holding Genome Biology 2002, 3:reports0053 (30 September 2002) Abstract \| Full text \| Editor’s summary Human XIST, when integrated into autosomes in a fully differentiated adult human tumor cell line, caused localized chromosome inactivation, counter to all previous concepts of a specific narrow window of opportunity for X-inactivation
	Paper report Evolutionary genomics of Salmonella Wim D'Haeze Genome Biology 2002, 3:reports0054 (30 September 2002) Abstract \| Full text \| Editor’s summary Genes acquired by Salmonella enterica during its evolution may have important roles in human infection
	Paper report Acid test for Mycobacterium tuberculosis Wim D'Haeze Genome Biology 2002, 3:reports0055 (30 September 2002) Abstract \| Full text \| Editor’s summary New Mycobacterium tuberculosis genes have been discovered that may have a role in the bacterium's survival in human phagosomes
	Paper report Three-way regulation of cholera toxin production Wim D'Haeze Genome Biology 2002, 3:reports0056 (30 September 2002) Abstract \| Full text \| Editor’s summary A three-component regulatory system involved in cholera toxin production has been characterized
	Paper report The genome of a green sulfur bacterium Wim D'Haeze Genome Biology 2002, 3:reports0057 (30 September 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of the photosynthetic anaerobe Chlorobium tepidum will help us to understand the evolution of photosynthesis
	Paper report Evolution of genomic GC variation Diane P Genereux Genome Biology 2002, 3:reports0058 (25 November 2002) Abstract \| Full text \| Editor’s summary Bioinformatics and classical genetics reveal a positive correlation between recombination rate and GC content at silent sites in coding regions of Saccharomyces cerevisiae
	Meeting report Modeling molecular networks: a systems biology approach to gene function Alessandro Guffanti Genome Biology 2002, 3:reports4031-reports4031.3 (16 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the European Science Foundation Workshop on Modeling of Molecular Networks, Granada, Spain, 11-14 June 2002.
	Meeting report Developmental biologists cast a net over sequenced genomes Matthias Gerberding, Nipam H Patel Genome Biology 2002, 3:reports4032-reports4032.3 (24 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the annual meeting of the Society of Developmental Biology, Madison, Wisconsin, USA, 21-24 July 2002.
	Meeting report Viruses in and out Mariam Andrawiss Genome Biology 2002, 3:reports4033-reports4033.4 (24 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the twelfth Congress of Virology, part of 'The world of microbes', the joint meeting of the three divisions of the International Union of Microbiological Societies, Paris, France, 27 July to 1 August 2002
	Meeting report Genomics, proteomics and bioinformatics: all in the same boat Robert B Russell Genome Biology 2002, 3:reports4034-reports4034.2 (24 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Genomics, Proteomics and Bioinformatics for Medicine (GPBM) 2002 meeting, St. Petersburg to Moscow, Russia, 22-30 June 2002.
	Research news Insecticide resistance Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021001-01 (1 October 2002) Abstract \| Full text \| Editor’s summary Overexpression of a Drosophila cytochrome P450 gene is necessary and sufficient for resistance to the insecticide DTT.
	Research news How different are we from chimps? Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021002-01 (2 October 2002) Abstract \| Full text \| Editor’s summary A new comparison of chimpanzee and human genomes suggests the divergence may be as much as five percent.
	Research news The Plasmodium falciparum genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021003-01 (3 October 2002) Abstract \| Full text \| Editor’s summary The parasite genome could pave the way for new drugs and vaccines to fight the disease.
	Research news Malaria genomes 'completed' Pete Moore Genome Biology 2002, 3:spotlight-20021003-03 (3 October 2002) Abstract \| Full text \| Editor’s summary Sequencing the genomes is one thing - but will it really benefit malaria endemic countries?
	Research news Molecular make-up of a malaria mosquito Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021003-02 (3 October 2002) Abstract \| Full text \| Editor’s summary The genome of Anopheles gambiae, the mosquito vector that spreads malaria has been sequenced.
	Research news Plasmodium proteomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021004-01 (4 October 2002) Abstract \| Full text \| Editor’s summary Proteomic analysis of the Plasmodium falciparum parasite may identify novel drug and vaccine targets.
	Research news The dynamics of Drosophila development Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021007-01 (7 October 2002) Abstract \| Full text \| Editor’s summary Microarray analysis of 66 different developmental stages of Drosophila provides an overview of gene expression during the fly life cycle.
	Research news A cheap personal genome? Leslie Pray Genome Biology 2002, 3:spotlight-20021007-02 (7 October 2002) Abstract \| Full text \| Editor’s summary Optimism and doubts expressed at discussion of $1,000 genome.
	Research news The Nobel Prize for Physiology or Medicine 2002 David Bruce Genome Biology 2002, 3:gb-spotlight-20021008-01 (8 October 2002) Abstract \| Full text \| Editor’s summary Sydney Brenner, John Sulston, and Robert Horvitz awarded the 2002 Nobel Prize.
	Research news Adenoviral arrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021008-02 (8 October 2002) Abstract \| Full text \| Editor’s summary Arrays of viral libraries provide a powerful approach to functional gene annotation.
	Research news OptIPuter boots up Karen Heyman Genome Biology 2002, 3:gb-spotlight-20021008-03 (8 October 2002) Abstract \| Full text \| Editor’s summary High-capacity optical network promises easier data sharing for collaborations.
	Research news Linking replication and transcription Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021009-01 (9 October 2002) Abstract \| Full text \| Editor’s summary Researchers have used microarray experiments to explore the interplay between replication timing and gene transcription in Drosophila.
	Research news Journal trio embraces MIAME Laura DeFrancesco Genome Biology 2002, 3:gb-spotlight-20021010-01 (10 October 2002) Abstract \| Full text \| Editor’s summary Nature, Cell, Lancet will require researchers to comply with microarray standard
	Research news Anchoring nuclei to the cytoskeleton Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021011-01 (11 October 2002) Abstract \| Full text \| Editor’s summary The ANC-1 protein in worms binds to the nuclear envelope and the actin cytoskeleton so as to position nuclei in syncytial cells.
	Research news Biotech claims comprehensive SNP map Laura DeFrancesco Genome Biology 2002, 3:spotlight-20021014-01 (14 October 2002) Abstract \| Full text \| Editor’s summary Perlegen amasses 1.7 million human SNPs with high-density arrays.
	Research news A genome for bioremediation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021014-02 (14 October 2002) Abstract \| Full text \| Editor’s summary Genome sequencing has been completed for Shewanella oneidensis, a metal-ion-reducing bacterium important for bioremediation and reducing environmental pollutants.
	Research news Regulating large chromatin domains Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021015-01 (15 October 2002) Abstract \| Full text \| Editor’s summary Analysis of chromatin-remodelling complexes demonstrates the targeting role of the SATB1 protein in thymocytes.
	Research news A second HP1 Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021016-01 (16 October 2002) Abstract \| Full text \| Editor’s summary A two-hybrid protein-protein interaction screen has identified an HP1-interacting protein that is also involved in heterochromatin formation and gene silencing.
	Research news Polycomb in the prostate Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021017-01 (17 October 2002) Abstract \| Full text \| Editor’s summary Gene-expression profiling of prostate cancer cells reveals a link between a polycomb-group protein and metastasis or poor prognosis.
	Research news Bitter taste Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021017-02 (17 October 2002) Abstract \| Full text \| Editor’s summary A human receptor activated by bitter tastes has been identified.
	Research news Rb and telomeres Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021018-01 (18 October 2002) Abstract \| Full text \| Editor’s summary Members of the retinoblastoma (Rb) protein family regulate telomere length in mouse fibroblasts
	Research news Tetraspanins in flies Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021021-01 (21 October 2002) Abstract \| Full text \| Editor’s summary Genetic analysis reveals functions for tetraspanin proteins in synapse formation in Drosophila.
	Research news Site-specific integration Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021022-01 (22 October 2002) Abstract \| Full text \| Editor’s summary A phage integrase has been used to achieve targeted integration of the human Factor IX gene in the mouse genome.
	Research news An example of a 'riboswitch' Tudor P Toma Genome Biology 2002, 3:spotlight-20021022-02 (22 October 2002) Abstract \| Full text \| Editor’s summary Messenger RNAs regulate thiamine biosynthesis in E. coli without the need for protein cofactors.
	Research news Automated analysis of tissue microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021023-01 (23 October 2002) Abstract \| Full text \| Editor’s summary Algorithms that allow the automated quantitation of protein levels improve the use of tissue microarrays.
	Research news Retina enrichment Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021024-01 (24 October 2002) Abstract \| Full text \| Editor’s summary Data-mining of EST databases has identified genes specifically expressed in the retina that are candidates for retinopathy genes.
	Research news A green cell-cycle transcriptome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021025-01 (25 October 2002) Abstract \| Full text \| Editor’s summary Transcriptome analysis of tobacco Bright Yellow-2 cells reveals a large set of genes that are modulated during the cell cycle in plants.
	Research news Strength in numbers Diane Martindale Genome Biology 2002, 3:spotlight-20021028-01 (28 October 2002) Abstract \| Full text \| Editor’s summary Canada is pursuing international genomics partnerships to make the most of national resources.
	Research news Moth mating Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021028-02 (28 October 2002) Abstract \| Full text \| Editor’s summary Size is important when it comes to the mating preferences of female moths.
	Research news Networks in the yeast genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021029-01 (29 October 2002) Abstract \| Full text \| Editor’s summary Defining the binding sites for all transcriptional regulators on a genome-wide scale can generate models of complex regulatory networks.
	Research news The specificity of synthetic siRNAs Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021030-01 (30 October 2002) Abstract \| Full text \| Editor’s summary Short interfering RNAs can distinguish between mutant and wild-type p53, suggesting therapeutic applications that restore wild-type function.
	Research news Forensic genomics Steve Nadis Genome Biology 2002, 3:spotlight-20021031-01 (31 October 2002) Abstract \| Full text \| Editor’s summary A technique to track bioterrorists or the deadliest human pathogens.
	Research
	Research Long terminal repeat retrotransposons of Oryza sativa Eugene M McCarthy, Jingdong Liu, Gao Lizhi, John F McDonald Genome Biology 2002, 3:research0053-research0053.11 (13 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new data-mining program, LTR_STRUC, was used to mine the GenBank rice (Oryza sativa) database as well as the more extensive Monsanto rice dataset for long terminal repeat retrotransposons. Each of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred.
	Research Mining microarray expression data by literature profiling Damien Chaussabel, Alan Sher Genome Biology 2002, 3:research0055-research0055.16 (13 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The lack of efficient techniques for assessing the biological implications of microarray gene-expression data remains an important obstacle in exploiting this information. To address this need, a mining technique has been developed based on the analysis of literature profiles generated by extracting the frequencies of certain terms from thousands of abstracts stored in the Medline literature database.
	Research Molecular archeology of L1 insertions in the human genome Suzanne T Szak, Oxana K Pickeral, Wojciech Makalowski, Mark S Boguski, David Landsman, Jef D Boeke Genome Biology 2002, 3:research0052-research0052.18 (19 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed analysis of the anatomy and distribution of L1 elements in the human genome was carried out using a new computer program, TSDfinder, designed to identify transposon boundaries precisely. Conclusions: The sequence data give no indication that the creation of L1 structural variants depends on characteristics of the insertion locus.
	Research Genomic analysis of membrane protein families: abundance and conserved motifs Yang Liu, Donald M Engelman, Mark Gerstein Genome Biology 2002, 3:research0054-research0054.12 (19 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide analysis was carried out on patterns of the classified polytopic membrane protein families, and the distribution of conserved amino acids and motifs in the transmembrane helix regions in these families was also analyzed.
	Research Analysis of EF-hand-containing proteins in Arabidopsis Irene S Day, Vaka S Reddy, Gul Shad Ali, ASN Reddy Genome Biology 2002, 3:research0056-research0056.24 (23 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three out of the four classes of Ca²⁺-binding proteins in plants contain Ca ²⁺ -binding EF-hand motif(s). A maximum of 250 proteins possibly having EF-hands were identified. Diverse proteins, including enzymes, proteins involved in transcription and translation, protein- and nucleic-acid-binding proteins and a large number of unknown proteins, have one or more putative EF-hands.
	Research Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes DB Guiliano, N Hall, SJM Jones, LN Clark, CH Corton, BG Barrell, ML Blaxter Genome Biology 2002, 3:research0057-research0057.14 (26 September 2002) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary To assess whether the pattern of high rates of genome rearrangement, with a bias towards within-chromosome events is true of nematodes in general, genome sequence was used to compare the model Caenorhabditis elegans and the filarial parasite Brugia malayi. It is suggested that intrachromosomal rearrangement is a major force driving chromosomal organization in nematodes.
	Research Asymmetric directional mutation pressures in bacteria Jean R Lobry, Noboru Sueoka Genome Biology 2002, 3:research0058-research0058.14 (26 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary When there are no strand-specific biases in mutation and selection rates between the two strands of DNA, the average nucleotide composition is theoretically expected to be A = T and G = C within each strand. By focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced bacterial chromosomes, asymmetric directional mutation pressures have been detected.

	Volume 3 Issue 10
	Comment
	Comment An Asilomar moment Gregory A Petsko Genome Biology 2002, 3:comment1014-comment1014.3 (25 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As governments in the US and Europe contemplate legislation that would divert funding of some genomics-driven research to Offices of Homeland Security and the like, and that would restrict the freedom of biologists to publish and share some of their data, we of the scientific community are facing a crisis, brought on by fears of bioterrorism, that eerily mirrors the early days of recombinant DNA research.
	Opinion On the importance of being finished Lance E Palmer, W Richard McCombie Genome Biology 2002, 3:comment2010-comment2010.4 (27 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The publication of an increasing number of draft genome sequences presents problems that will only be resolved by improved search tools and by complete finishing of the sequences - and their deposition in publicly accessible databases.
	Review
	Review Are Drosophila telomeres an exception or the rule? Edward J Louis Genome Biology 2002, 3:reviews0007-reviews0007.6 (27 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary At the ends of eukaryotic chromosomes are telomeres, specialized structures with unusual properties. Specific efforts to compare sequences and properties of telomeres across species can reveal the generalities of telomere properties.
	Protein family review Histidine protein kinases: key signal transducers outside the animal kingdom Peter M Wolanin, Peter A Thomason, Jeffry B Stock Genome Biology 2002, 3:reviews3013-reviews3013.8 (25 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Histidine protein kinases (HPKs) are a large family of signal-transduction enzymes that form two-component signaling systems together with their downstream target proteins, the response regulators. The proteins divide into at least 11 subfamilies, only one of which is present in eukaryotes, suggesting that lateral gene transfer gave rise to two-component signaling in these organisms.
	Minireview Large-scale gene-expression studies and the challenge of multiple sclerosis Sergio E Baranzini, Stephen L Hauser Genome Biology 2002, 3:reviews1027-reviews1027.5 (16 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent transcription-profiling studies have found distinct gene-expression patterns in multiple sclerosis; such large-scale studies at different stages of the disease are contributing to understanding multiple sclerosis and developing effective therapy.
	Minireview Variations in abundance: genome-wide responses to genetic variation... and vice versa Bruce A Hamilton Genome Biology 2002, 3:reviews1029-reviews1029.3 (19 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern.
	Minireview A genomic approach to studying cell-size homeostasis in yeast Jonathan BA Millar Genome Biology 2002, 3:reviews1028-reviews1028.4 (20 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study has revealed multiple overlapping pathways that coordinately regulate cell-cycle progression with ribosome biogenesis and translation efficiency, providing new insights into the mechanisms governing cell-size homeostasis in eukaryotes.
	Minireview Ascidian gene-expression profiles William R Jeffery Genome Biology 2002, 3:reviews1030-reviews1030.4 (25 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene-expression profiling will be particularly informative in studies of ascidians, basal chordates whose genomes and embryology are uniquely suited for mapping developmental gene networks.
	Report
	Paper report Autosome inactivation by ectopic XIST in differentiated cells Cathy Holding Genome Biology 2002, 3:reports0053 (30 September 2002) Abstract \| Full text \| Editor’s summary Human XIST, when integrated into autosomes in a fully differentiated adult human tumor cell line, caused localized chromosome inactivation, counter to all previous concepts of a specific narrow window of opportunity for X-inactivation
	Paper report Evolutionary genomics of Salmonella Wim D'Haeze Genome Biology 2002, 3:reports0054 (30 September 2002) Abstract \| Full text \| Editor’s summary Genes acquired by Salmonella enterica during its evolution may have important roles in human infection
	Paper report Acid test for Mycobacterium tuberculosis Wim D'Haeze Genome Biology 2002, 3:reports0055 (30 September 2002) Abstract \| Full text \| Editor’s summary New Mycobacterium tuberculosis genes have been discovered that may have a role in the bacterium's survival in human phagosomes
	Paper report Three-way regulation of cholera toxin production Wim D'Haeze Genome Biology 2002, 3:reports0056 (30 September 2002) Abstract \| Full text \| Editor’s summary A three-component regulatory system involved in cholera toxin production has been characterized
	Paper report The genome of a green sulfur bacterium Wim D'Haeze Genome Biology 2002, 3:reports0057 (30 September 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of the photosynthetic anaerobe Chlorobium tepidum will help us to understand the evolution of photosynthesis
	Paper report Evolution of genomic GC variation Diane P Genereux Genome Biology 2002, 3:reports0058 (25 November 2002) Abstract \| Full text \| Editor’s summary Bioinformatics and classical genetics reveal a positive correlation between recombination rate and GC content at silent sites in coding regions of Saccharomyces cerevisiae
	Meeting report Modeling molecular networks: a systems biology approach to gene function Alessandro Guffanti Genome Biology 2002, 3:reports4031-reports4031.3 (16 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the European Science Foundation Workshop on Modeling of Molecular Networks, Granada, Spain, 11-14 June 2002.
	Meeting report Developmental biologists cast a net over sequenced genomes Matthias Gerberding, Nipam H Patel Genome Biology 2002, 3:reports4032-reports4032.3 (24 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the annual meeting of the Society of Developmental Biology, Madison, Wisconsin, USA, 21-24 July 2002.
	Meeting report Viruses in and out Mariam Andrawiss Genome Biology 2002, 3:reports4033-reports4033.4 (24 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the twelfth Congress of Virology, part of 'The world of microbes', the joint meeting of the three divisions of the International Union of Microbiological Societies, Paris, France, 27 July to 1 August 2002
	Meeting report Genomics, proteomics and bioinformatics: all in the same boat Robert B Russell Genome Biology 2002, 3:reports4034-reports4034.2 (24 September 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Genomics, Proteomics and Bioinformatics for Medicine (GPBM) 2002 meeting, St. Petersburg to Moscow, Russia, 22-30 June 2002.
	Research news Insecticide resistance Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021001-01 (1 October 2002) Abstract \| Full text \| Editor’s summary Overexpression of a Drosophila cytochrome P450 gene is necessary and sufficient for resistance to the insecticide DTT.
	Research news How different are we from chimps? Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021002-01 (2 October 2002) Abstract \| Full text \| Editor’s summary A new comparison of chimpanzee and human genomes suggests the divergence may be as much as five percent.
	Research news The Plasmodium falciparum genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021003-01 (3 October 2002) Abstract \| Full text \| Editor’s summary The parasite genome could pave the way for new drugs and vaccines to fight the disease.
	Research news Malaria genomes 'completed' Pete Moore Genome Biology 2002, 3:spotlight-20021003-03 (3 October 2002) Abstract \| Full text \| Editor’s summary Sequencing the genomes is one thing - but will it really benefit malaria endemic countries?
	Research news Molecular make-up of a malaria mosquito Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021003-02 (3 October 2002) Abstract \| Full text \| Editor’s summary The genome of Anopheles gambiae, the mosquito vector that spreads malaria has been sequenced.
	Research news Plasmodium proteomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021004-01 (4 October 2002) Abstract \| Full text \| Editor’s summary Proteomic analysis of the Plasmodium falciparum parasite may identify novel drug and vaccine targets.
	Research news The dynamics of Drosophila development Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021007-01 (7 October 2002) Abstract \| Full text \| Editor’s summary Microarray analysis of 66 different developmental stages of Drosophila provides an overview of gene expression during the fly life cycle.
	Research news A cheap personal genome? Leslie Pray Genome Biology 2002, 3:spotlight-20021007-02 (7 October 2002) Abstract \| Full text \| Editor’s summary Optimism and doubts expressed at discussion of $1,000 genome.
	Research news The Nobel Prize for Physiology or Medicine 2002 David Bruce Genome Biology 2002, 3:gb-spotlight-20021008-01 (8 October 2002) Abstract \| Full text \| Editor’s summary Sydney Brenner, John Sulston, and Robert Horvitz awarded the 2002 Nobel Prize.
	Research news Adenoviral arrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021008-02 (8 October 2002) Abstract \| Full text \| Editor’s summary Arrays of viral libraries provide a powerful approach to functional gene annotation.
	Research news OptIPuter boots up Karen Heyman Genome Biology 2002, 3:gb-spotlight-20021008-03 (8 October 2002) Abstract \| Full text \| Editor’s summary High-capacity optical network promises easier data sharing for collaborations.
	Research news Linking replication and transcription Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021009-01 (9 October 2002) Abstract \| Full text \| Editor’s summary Researchers have used microarray experiments to explore the interplay between replication timing and gene transcription in Drosophila.
	Research news Journal trio embraces MIAME Laura DeFrancesco Genome Biology 2002, 3:gb-spotlight-20021010-01 (10 October 2002) Abstract \| Full text \| Editor’s summary Nature, Cell, Lancet will require researchers to comply with microarray standard
	Research news Anchoring nuclei to the cytoskeleton Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021011-01 (11 October 2002) Abstract \| Full text \| Editor’s summary The ANC-1 protein in worms binds to the nuclear envelope and the actin cytoskeleton so as to position nuclei in syncytial cells.
	Research news Biotech claims comprehensive SNP map Laura DeFrancesco Genome Biology 2002, 3:spotlight-20021014-01 (14 October 2002) Abstract \| Full text \| Editor’s summary Perlegen amasses 1.7 million human SNPs with high-density arrays.
	Research news A genome for bioremediation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021014-02 (14 October 2002) Abstract \| Full text \| Editor’s summary Genome sequencing has been completed for Shewanella oneidensis, a metal-ion-reducing bacterium important for bioremediation and reducing environmental pollutants.
	Research news Regulating large chromatin domains Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021015-01 (15 October 2002) Abstract \| Full text \| Editor’s summary Analysis of chromatin-remodelling complexes demonstrates the targeting role of the SATB1 protein in thymocytes.
	Research news A second HP1 Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021016-01 (16 October 2002) Abstract \| Full text \| Editor’s summary A two-hybrid protein-protein interaction screen has identified an HP1-interacting protein that is also involved in heterochromatin formation and gene silencing.
	Research news Polycomb in the prostate Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021017-01 (17 October 2002) Abstract \| Full text \| Editor’s summary Gene-expression profiling of prostate cancer cells reveals a link between a polycomb-group protein and metastasis or poor prognosis.
	Research news Bitter taste Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021017-02 (17 October 2002) Abstract \| Full text \| Editor’s summary A human receptor activated by bitter tastes has been identified.
	Research news Rb and telomeres Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021018-01 (18 October 2002) Abstract \| Full text \| Editor’s summary Members of the retinoblastoma (Rb) protein family regulate telomere length in mouse fibroblasts
	Research news Tetraspanins in flies Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021021-01 (21 October 2002) Abstract \| Full text \| Editor’s summary Genetic analysis reveals functions for tetraspanin proteins in synapse formation in Drosophila.
	Research news Site-specific integration Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021022-01 (22 October 2002) Abstract \| Full text \| Editor’s summary A phage integrase has been used to achieve targeted integration of the human Factor IX gene in the mouse genome.
	Research news An example of a 'riboswitch' Tudor P Toma Genome Biology 2002, 3:spotlight-20021022-02 (22 October 2002) Abstract \| Full text \| Editor’s summary Messenger RNAs regulate thiamine biosynthesis in E. coli without the need for protein cofactors.
	Research news Automated analysis of tissue microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021023-01 (23 October 2002) Abstract \| Full text \| Editor’s summary Algorithms that allow the automated quantitation of protein levels improve the use of tissue microarrays.
	Research news Retina enrichment Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021024-01 (24 October 2002) Abstract \| Full text \| Editor’s summary Data-mining of EST databases has identified genes specifically expressed in the retina that are candidates for retinopathy genes.
	Research news A green cell-cycle transcriptome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021025-01 (25 October 2002) Abstract \| Full text \| Editor’s summary Transcriptome analysis of tobacco Bright Yellow-2 cells reveals a large set of genes that are modulated during the cell cycle in plants.
	Research news Strength in numbers Diane Martindale Genome Biology 2002, 3:spotlight-20021028-01 (28 October 2002) Abstract \| Full text \| Editor’s summary Canada is pursuing international genomics partnerships to make the most of national resources.
	Research news Moth mating Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021028-02 (28 October 2002) Abstract \| Full text \| Editor’s summary Size is important when it comes to the mating preferences of female moths.
	Research news Networks in the yeast genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021029-01 (29 October 2002) Abstract \| Full text \| Editor’s summary Defining the binding sites for all transcriptional regulators on a genome-wide scale can generate models of complex regulatory networks.
	Research news The specificity of synthetic siRNAs Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021030-01 (30 October 2002) Abstract \| Full text \| Editor’s summary Short interfering RNAs can distinguish between mutant and wild-type p53, suggesting therapeutic applications that restore wild-type function.
	Research news Forensic genomics Steve Nadis Genome Biology 2002, 3:spotlight-20021031-01 (31 October 2002) Abstract \| Full text \| Editor’s summary A technique to track bioterrorists or the deadliest human pathogens.
	Research
	Research Long terminal repeat retrotransposons of Oryza sativa Eugene M McCarthy, Jingdong Liu, Gao Lizhi, John F McDonald Genome Biology 2002, 3:research0053-research0053.11 (13 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new data-mining program, LTR_STRUC, was used to mine the GenBank rice (Oryza sativa) database as well as the more extensive Monsanto rice dataset for long terminal repeat retrotransposons. Each of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred.
	Research Mining microarray expression data by literature profiling Damien Chaussabel, Alan Sher Genome Biology 2002, 3:research0055-research0055.16 (13 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The lack of efficient techniques for assessing the biological implications of microarray gene-expression data remains an important obstacle in exploiting this information. To address this need, a mining technique has been developed based on the analysis of literature profiles generated by extracting the frequencies of certain terms from thousands of abstracts stored in the Medline literature database.
	Research Molecular archeology of L1 insertions in the human genome Suzanne T Szak, Oxana K Pickeral, Wojciech Makalowski, Mark S Boguski, David Landsman, Jef D Boeke Genome Biology 2002, 3:research0052-research0052.18 (19 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed analysis of the anatomy and distribution of L1 elements in the human genome was carried out using a new computer program, TSDfinder, designed to identify transposon boundaries precisely. Conclusions: The sequence data give no indication that the creation of L1 structural variants depends on characteristics of the insertion locus.
	Research Genomic analysis of membrane protein families: abundance and conserved motifs Yang Liu, Donald M Engelman, Mark Gerstein Genome Biology 2002, 3:research0054-research0054.12 (19 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide analysis was carried out on patterns of the classified polytopic membrane protein families, and the distribution of conserved amino acids and motifs in the transmembrane helix regions in these families was also analyzed.
	Research Analysis of EF-hand-containing proteins in Arabidopsis Irene S Day, Vaka S Reddy, Gul Shad Ali, ASN Reddy Genome Biology 2002, 3:research0056-research0056.24 (23 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three out of the four classes of Ca²⁺-binding proteins in plants contain Ca ²⁺ -binding EF-hand motif(s). A maximum of 250 proteins possibly having EF-hands were identified. Diverse proteins, including enzymes, proteins involved in transcription and translation, protein- and nucleic-acid-binding proteins and a large number of unknown proteins, have one or more putative EF-hands.
	Research Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes DB Guiliano, N Hall, SJM Jones, LN Clark, CH Corton, BG Barrell, ML Blaxter Genome Biology 2002, 3:research0057-research0057.14 (26 September 2002) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary To assess whether the pattern of high rates of genome rearrangement, with a bias towards within-chromosome events is true of nematodes in general, genome sequence was used to compare the model Caenorhabditis elegans and the filarial parasite Brugia malayi. It is suggested that intrachromosomal rearrangement is a major force driving chromosomal organization in nematodes.
	Research Asymmetric directional mutation pressures in bacteria Jean R Lobry, Noboru Sueoka Genome Biology 2002, 3:research0058-research0058.14 (26 September 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary When there are no strand-specific biases in mutation and selection rates between the two strands of DNA, the average nucleotide composition is theoretically expected to be A = T and G = C within each strand. By focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced bacterial chromosomes, asymmetric directional mutation pressures have been detected.

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