Genome Biology | Volume 3 Issue 6

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	Volume 3 Issue 6
	Comment
	Comment Our own petards Gregory A Petsko Genome Biology 2002, 3:comment1009-comment1009.2 (29 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Several international treaties on chemical and biological weapons expressly prohibit the development, production, stockpiling or acquisition of such weapons. All too often, when troops go into battle, they are attacked by weapons we ourselves conceived and manufactured.
	Review
	Protein family review The T-box family Val Wilson, Frank L Conlon Genome Biology 2002, 3:reviews3008-reviews3008.7 (31 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription factors of the T-box family are found in most animals and are required for early cell-fate decisions, differentiation and organogenesis. They have been implicated in limb patterning and in Holt-Oram, ulnar-mammary and DiGeorge syndromes.
	Minireview Surveying genome replication Stephen Kearsey Genome Biology 2002, 3:reviews1016-reviews1016.4 (24 May 2002) Abstract \| Full text \| PDF \| PubMed
	Minireview Plants and sodium ions: keeping company with the enemy Jose M Pardo, Francisco J Quintero Genome Biology 2002, 3:reviews1017-reviews1017.4 (24 May 2002) Abstract \| Full text \| PDF \| PubMed
	Minireview Insights into cereal genomes from two draft genome sequences of rice Ian Bancroft Genome Biology 2002, 3:reviews1015-reviews1015.3 (28 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Minireview Tracking adaptive evolutionary events in genomic sequences David A Liberles, Marta L Wayne Genome Biology 2002, 3:reviews1018-reviews1018.4 (29 May 2002) Abstract \| Full text \| PDF \| PubMed
	Opinion Focusing on the genetics of hearing: you ain't heard nothin' yet Nick Parkinson, Steve DM Brown Genome Biology 2002, 3:comment2006-comment2006.6 (28 May 2002) Abstract \| Full text \| PDF \| PubMed
	Report
	Web report All about proteins Chang-Su Lim Genome Biology 2002, 3:reports2014 (24 May 2002) Abstract \| Full text
	Paper report Faster DNA sequencing Wim D'Haeze Genome Biology 2002, 3:reports0029 (24 May 2002) Abstract \| Full text \| Editor’s summary A newly developed high-throughput DNA-sequencing method is five times as fast as current commercially available techniques
	Paper report Agrobacterium heat-shock proteome Wim D'Haeze Genome Biology 2002, 3:reports0030 (24 May 2002) Abstract \| Full text \| Editor’s summary A study of the proteins produced by Agrobacterium tumefaciens after heat shock gives clues to how it adapts to environmental stress
	Paper report Inhibiting carotenoids Wim D'Haeze Genome Biology 2002, 3:reports0031 (24 May 2002) Abstract \| Full text \| Editor’s summary A study of carotenoid synthesis was carried out to discover inhibitors that might provide new herbicides
	Paper report Quorum sensing in Vibrio cholerae? Wim D'Haeze Genome Biology 2002, 3:reports0032 (24 May 2002) Abstract \| Full text \| Editor’s summary An investigation of the effects of Vibrio cholerae cell density on virulence
	Meeting report Revealing the intricacies of cancer Anne M Verhagen, Peter Lock Genome Biology 2002, 3:reports4015-reports4015.5 (13 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 14th Lorne Cancer Conference, Lorne, Victoria, Australia, 14-17 February 2002.
	Meeting report Nuclear processes controlled by molecular machines Archa H Fox, Angus I Lamond Genome Biology 2002, 3:reports4016-reports4016.3 (23 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Nuclear Structure and Function' symposium at the joint spring meeting of the British Society for Cell Biology, British Society for Developmental Biology and Genetics Society, York, UK, 20-23 March 2002.
	Meeting report Fission yeast enters a joyful new era Eliana B Gómez, Julie M Bailis, Susan L Forsburg Genome Biology 2002, 3:reports4017-reports4017.3 (23 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Second International Fission Yeast Meeting, Kyoto, Japan, 25-30 March 2002.
	Deposited research article Identification of attenuation and antitermination regulation in prokaryotes Warren C Lathe, Mikita Suyama, Peer Bork Genome Biology 2002, 3:preprint0003-preprint0003.60 (30 April 2002) Abstract \| Full text \| PDF \| Editor’s summary The prediction of genes with attenuation or antitermination regulation is reported. The method is based on known characteristics of upstream sequences of regulated genes. We analyzed 26 complete genomes and are thus able to give a more complete picture of attenuation regulation in prokaryotes.
	Research news Offspring from infertile parents? Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020605-01 (5 June 2002) Abstract \| Full text \| Editor’s summary Lentiviruses can be used to deliver genes to the testes and rescue infertility in sterile mice.
	Research news Calibrating chips Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020606-01 (6 June 2002) Abstract \| Full text \| Editor’s summary The use of calibrated reference samples should help with the interpretation and comparison of microarray data.
	Research news Geotaxis genes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020607-01 (7 June 2002) Abstract \| Full text \| Editor’s summary A combination of genetics and genomic approaches has identified Drosophila genes involved in complex behavior
	Research news Interfering with HIV Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020610-01 (10 June 2002) Abstract \| Full text \| Editor’s summary Short interfering RNAs targeted at either host or viral genes may prevent HIV infection.
	Research news Kinase mutations in cancer Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020611-01 (11 June 2002) Abstract \| Full text \| Editor’s summary A systematic screen has identified oncogenic mutations in the BRAF kinase in human cancers.
	Research news Universal bioinformatics system Paula Park Genome Biology 2002, 3:spotlight-20020612-01 (12 June 2002) Abstract \| Full text \| Editor’s summary I3C hopes to make identifying and tracking genes and proteins easier, and to encourage open-source software in bioinformatics.
	Research news Processing ribosomal RNA Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020612-02 (12 June 2002) Abstract \| Full text \| Editor’s summary A large complex of proteins containing U3 snoRNA and 28 functionally associated proteins has been purified and characterized.
	Research news Annotating Anopheles Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020613-01 (13 June 2002) Abstract \| Full text \| Editor’s summary A large section of sequence from the mosquito genome has been annotated and compared with Drosophila.
	Research news BRCA2 loss in Fanconi Anemia Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020614-01 (14 June 2002) Abstract \| Full text \| Editor’s summary Analysis of Fanconi Anemia cell lines reveals deletions in the breast cancer susceptibility gene BRCA2.
	Research news Comparing Enterococcus genomes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020617-01 (17 June 2002) Abstract \| Full text \| Editor’s summary Analysis of the genomes from different Enterococcus strains led to the discovery of a pathogenicity island important in antibiotic resistance.
	Research news Somatic hypermutation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020618-01 (18 June 2002) Abstract \| Full text \| Editor’s summary Experiments in fibroblasts have identified an enzyme that induces hypermutation resembling the hypermutator of immunoglobulin genes in lymphocytes.
	Research news A better map of the human genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020619-01 (19 June 2002) Abstract \| Full text \| Editor’s summary A new map of the human genome has five times higher resolution than previous maps.
	Research news Transcription groupies David Bruce Genome Biology 2002, 3:spotlight-20020619-02 (19 June 2002) Abstract \| Full text \| Editor’s summary Microarray analysis suggests that the Drosophila genome contains many large groups of adjacent genes that are expressed similarly but are not functionally related.
	Research news Operons in worms Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020620-01 (20 June 2002) Abstract \| Full text \| Editor’s summary There seem to be a large number of operons in the Caenorhabditis elegans genome.
	Research news Masters of the mitochondria Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020621-01 (21 June 2002) Abstract \| Full text \| Editor’s summary Two mitochondrial proteins have been found to control transcription of mitochondrial DNA.
	Research news Dealing with damage Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020624-01 (24 June 2002) Abstract \| Full text \| Editor’s summary Genes induced by DNA-damaging agents appear not to be those required for survival.
	Research news Mosquito microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020625-01 (25 June 2002) Abstract \| Full text \| Editor’s summary Microarrays experiments reveal changes in the mosquito transcriptome in response to infection and stress.
	Research news Responding to loss Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020626-01 (26 June 2002) Abstract \| Full text \| Editor’s summary Microarray analysis defines the 'telomerase deletion response' in the absence of telomere maintenance.
	Research news Mining myelination Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020627-01 (27 June 2002) Abstract \| Full text \| Editor’s summary Expression-profile analysis in Schwann cells identifies genes involved in myelination.
	Research news Short, but sweet Tudor Toma Genome Biology 2002, 3:spotlight-20020628-02 (28 June 2002) Abstract \| Full text \| Editor’s summary Short interfering RNAs can inhibit HIV-1 replication and confer intracellular antiviral immunity against poliovirus.
	Research news Placental imprinting Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020628-03 (28 June 2002) Abstract \| Full text \| Editor’s summary The paternally imprinted Igf2 gene plays a critical role in regulating placental growth.
	Research news Kyoto Prize 2002 David Bruce Genome Biology 2002, 3:spotlight-20020628-01 (28 June 2002) Abstract \| Full text \| Editor’s summary Leroy Hood has been recognized for his contribution to the development of the technology that enabled rapid genome sequencing.
	Research
	Research Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays Johann Y Lin, Jonathan R Pollack, Fan-Li Chou, Christian A Rees, Allen T Christian, Joel S Bedford, Patrick O Brown, Mark H Ginsberg Genome Biology 2002, 3:research0026-research0026.7 (14 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To fulfill the need for more efficient gene mapping in somatic cell mutants, a new DNA microarray comparative genomic hybridization method has been devloped that can rapidly and efficiently map the physical location of genes complementing somatic cell mutants to a small candidate genomic region.
	Research ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins Lars Hjelmqvist, Miquel Tuson, Gemma Marfany, Enric Herrero, Susana Balcells, Roser Gonzàlez-Duarte Genome Biology 2002, 3:research0027-research0027.16 (14 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary While characterizing genes from the retinitis pigmentosa locus RP26, a new gene, ORMDL, has been identified. It belongs to a novel gene family comprising three genes in humans, with homologs in yeast, microsporidia, plants, Drosophila, urochordates and vertebrates. These genes encode transmembrane proteins anchored in the endoplasmic reticulum (ER).
	Research Estimation of genetic distances from human and mouse introns Jose Castresana Genome Biology 2002, 3:research0028-research0028.7 (14 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genetic distances between 504 human introns and their orthologous mouse counterparts were calculated from a set of 63 pairs of human and mouse genes, using a method that can extract reliably aligned regions from the introns in an objective manner. A significant correlation was found between the genetic distance measured in the conserved intron segments and the synonymous and nonsynonymous distances measured in the corresponding coding exons.
	Research Full-length messenger RNA sequences greatly improve genome annotation Brian J Haas, Natalia Volfovsky, Christopher D Town, Maxim Troukhan, Nickolai Alexandrov, Kenneth A Feldmann, Richard B Flavell, Owen White, Steven L Salzberg Genome Biology 2002, 3:research0029-research0029.12 (30 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an effort to create a set of very high-quality gene models, the sequence of 5,000 full-length gene transcripts from Arabidopsis was used to re-annotate its genome. These transcripts were mapped to their exact chromosomal locations and gene models that provide a reference set for this organism were created. Approximately 35% of the transcripts indicated that previously annotated genes needed modification, and 5% of the transcripts represented newly discovered genes.
	Research Phylogenetic analysis of the human basic helix-loop-helix proteins Valérie Ledent, Odier Paquet, Michel Vervoort Genome Biology 2002, 3:research0030-research0030.18 (30 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The basic helix-loop-helix (bHLH) proteins are a large and complex multigene family of transcription factors with important roles in animal development. This article identifies 39 bHLH genes in Caenorhabditis elegans, 58 in Drosophila melanogaster and 125 in human, in 44 orthologous families in total. Genes from these families seem to have been present in the last common ancestor of worm, fly and human.
	Research Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries Cheryl Jenkins, Vishram Kedar, John A Fuerst Genome Biology 2002, 3:research0031-research0031.11 (30 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The random-sequence-tag approach applied here to Gemmata obscuriglobus and Pirellula Marina, provides the first report of gene recovery and analysis from members of the planctomycetes using genome-based methods. Gene homologs identified were predominantly similar to genes of Bacteria, but some matches to genes from Eukarya suggest that lateral gene transfer events may have involved this division during evolution.
	Software Software and methods for oligonucleotide and cDNA array data analysis Matthew A Zapala, Daniel J Lockhart, Daniel G Pankratz, Anthony J Garcia, Carrolee Barlow, David J Lockhart Genome Biology 2002, 3:software0001-software0001.9 (23 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two HTML-based programs were developed to analyze and filter gene-expression data. A background subtraction and normalization program for cDNA arrays was also built that provides an informative summary report with data-quality assessments. These programs are freeware.
	Correspondence
	Correspondence Ontologies for programs, not people Lawrence Hunter Genome Biology 2002, 3:interactions1002-interactions1002.2 (31 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to Life sentences: Ontology recapitulates philology by Sydney Brenner, Genome Biology 2002, 3:comment1006.1-1006.2.
	Correspondence Smelling of roses? Sue Povey, Hester Wain Genome Biology 2002, 3:interactions1003-interactions1003.2 (31 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to What's in a name? By Gregory Petsko, Genome Biology 2002, 3:comment 1005.1-1005.2.

	Volume 3 Issue 6
	Comment
	Comment Our own petards Gregory A Petsko Genome Biology 2002, 3:comment1009-comment1009.2 (29 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Several international treaties on chemical and biological weapons expressly prohibit the development, production, stockpiling or acquisition of such weapons. All too often, when troops go into battle, they are attacked by weapons we ourselves conceived and manufactured.
	Review
	Protein family review The T-box family Val Wilson, Frank L Conlon Genome Biology 2002, 3:reviews3008-reviews3008.7 (31 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription factors of the T-box family are found in most animals and are required for early cell-fate decisions, differentiation and organogenesis. They have been implicated in limb patterning and in Holt-Oram, ulnar-mammary and DiGeorge syndromes.
	Minireview Surveying genome replication Stephen Kearsey Genome Biology 2002, 3:reviews1016-reviews1016.4 (24 May 2002) Abstract \| Full text \| PDF \| PubMed
	Minireview Plants and sodium ions: keeping company with the enemy Jose M Pardo, Francisco J Quintero Genome Biology 2002, 3:reviews1017-reviews1017.4 (24 May 2002) Abstract \| Full text \| PDF \| PubMed
	Minireview Insights into cereal genomes from two draft genome sequences of rice Ian Bancroft Genome Biology 2002, 3:reviews1015-reviews1015.3 (28 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Minireview Tracking adaptive evolutionary events in genomic sequences David A Liberles, Marta L Wayne Genome Biology 2002, 3:reviews1018-reviews1018.4 (29 May 2002) Abstract \| Full text \| PDF \| PubMed
	Opinion Focusing on the genetics of hearing: you ain't heard nothin' yet Nick Parkinson, Steve DM Brown Genome Biology 2002, 3:comment2006-comment2006.6 (28 May 2002) Abstract \| Full text \| PDF \| PubMed
	Report
	Web report All about proteins Chang-Su Lim Genome Biology 2002, 3:reports2014 (24 May 2002) Abstract \| Full text
	Paper report Faster DNA sequencing Wim D'Haeze Genome Biology 2002, 3:reports0029 (24 May 2002) Abstract \| Full text \| Editor’s summary A newly developed high-throughput DNA-sequencing method is five times as fast as current commercially available techniques
	Paper report Agrobacterium heat-shock proteome Wim D'Haeze Genome Biology 2002, 3:reports0030 (24 May 2002) Abstract \| Full text \| Editor’s summary A study of the proteins produced by Agrobacterium tumefaciens after heat shock gives clues to how it adapts to environmental stress
	Paper report Inhibiting carotenoids Wim D'Haeze Genome Biology 2002, 3:reports0031 (24 May 2002) Abstract \| Full text \| Editor’s summary A study of carotenoid synthesis was carried out to discover inhibitors that might provide new herbicides
	Paper report Quorum sensing in Vibrio cholerae? Wim D'Haeze Genome Biology 2002, 3:reports0032 (24 May 2002) Abstract \| Full text \| Editor’s summary An investigation of the effects of Vibrio cholerae cell density on virulence
	Meeting report Revealing the intricacies of cancer Anne M Verhagen, Peter Lock Genome Biology 2002, 3:reports4015-reports4015.5 (13 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 14th Lorne Cancer Conference, Lorne, Victoria, Australia, 14-17 February 2002.
	Meeting report Nuclear processes controlled by molecular machines Archa H Fox, Angus I Lamond Genome Biology 2002, 3:reports4016-reports4016.3 (23 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Nuclear Structure and Function' symposium at the joint spring meeting of the British Society for Cell Biology, British Society for Developmental Biology and Genetics Society, York, UK, 20-23 March 2002.
	Meeting report Fission yeast enters a joyful new era Eliana B Gómez, Julie M Bailis, Susan L Forsburg Genome Biology 2002, 3:reports4017-reports4017.3 (23 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Second International Fission Yeast Meeting, Kyoto, Japan, 25-30 March 2002.
	Deposited research article Identification of attenuation and antitermination regulation in prokaryotes Warren C Lathe, Mikita Suyama, Peer Bork Genome Biology 2002, 3:preprint0003-preprint0003.60 (30 April 2002) Abstract \| Full text \| PDF \| Editor’s summary The prediction of genes with attenuation or antitermination regulation is reported. The method is based on known characteristics of upstream sequences of regulated genes. We analyzed 26 complete genomes and are thus able to give a more complete picture of attenuation regulation in prokaryotes.
	Research news Offspring from infertile parents? Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020605-01 (5 June 2002) Abstract \| Full text \| Editor’s summary Lentiviruses can be used to deliver genes to the testes and rescue infertility in sterile mice.
	Research news Calibrating chips Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020606-01 (6 June 2002) Abstract \| Full text \| Editor’s summary The use of calibrated reference samples should help with the interpretation and comparison of microarray data.
	Research news Geotaxis genes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020607-01 (7 June 2002) Abstract \| Full text \| Editor’s summary A combination of genetics and genomic approaches has identified Drosophila genes involved in complex behavior
	Research news Interfering with HIV Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020610-01 (10 June 2002) Abstract \| Full text \| Editor’s summary Short interfering RNAs targeted at either host or viral genes may prevent HIV infection.
	Research news Kinase mutations in cancer Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020611-01 (11 June 2002) Abstract \| Full text \| Editor’s summary A systematic screen has identified oncogenic mutations in the BRAF kinase in human cancers.
	Research news Universal bioinformatics system Paula Park Genome Biology 2002, 3:spotlight-20020612-01 (12 June 2002) Abstract \| Full text \| Editor’s summary I3C hopes to make identifying and tracking genes and proteins easier, and to encourage open-source software in bioinformatics.
	Research news Processing ribosomal RNA Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020612-02 (12 June 2002) Abstract \| Full text \| Editor’s summary A large complex of proteins containing U3 snoRNA and 28 functionally associated proteins has been purified and characterized.
	Research news Annotating Anopheles Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020613-01 (13 June 2002) Abstract \| Full text \| Editor’s summary A large section of sequence from the mosquito genome has been annotated and compared with Drosophila.
	Research news BRCA2 loss in Fanconi Anemia Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020614-01 (14 June 2002) Abstract \| Full text \| Editor’s summary Analysis of Fanconi Anemia cell lines reveals deletions in the breast cancer susceptibility gene BRCA2.
	Research news Comparing Enterococcus genomes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020617-01 (17 June 2002) Abstract \| Full text \| Editor’s summary Analysis of the genomes from different Enterococcus strains led to the discovery of a pathogenicity island important in antibiotic resistance.
	Research news Somatic hypermutation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020618-01 (18 June 2002) Abstract \| Full text \| Editor’s summary Experiments in fibroblasts have identified an enzyme that induces hypermutation resembling the hypermutator of immunoglobulin genes in lymphocytes.
	Research news A better map of the human genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020619-01 (19 June 2002) Abstract \| Full text \| Editor’s summary A new map of the human genome has five times higher resolution than previous maps.
	Research news Transcription groupies David Bruce Genome Biology 2002, 3:spotlight-20020619-02 (19 June 2002) Abstract \| Full text \| Editor’s summary Microarray analysis suggests that the Drosophila genome contains many large groups of adjacent genes that are expressed similarly but are not functionally related.
	Research news Operons in worms Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020620-01 (20 June 2002) Abstract \| Full text \| Editor’s summary There seem to be a large number of operons in the Caenorhabditis elegans genome.
	Research news Masters of the mitochondria Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020621-01 (21 June 2002) Abstract \| Full text \| Editor’s summary Two mitochondrial proteins have been found to control transcription of mitochondrial DNA.
	Research news Dealing with damage Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020624-01 (24 June 2002) Abstract \| Full text \| Editor’s summary Genes induced by DNA-damaging agents appear not to be those required for survival.
	Research news Mosquito microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020625-01 (25 June 2002) Abstract \| Full text \| Editor’s summary Microarrays experiments reveal changes in the mosquito transcriptome in response to infection and stress.
	Research news Responding to loss Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020626-01 (26 June 2002) Abstract \| Full text \| Editor’s summary Microarray analysis defines the 'telomerase deletion response' in the absence of telomere maintenance.
	Research news Mining myelination Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020627-01 (27 June 2002) Abstract \| Full text \| Editor’s summary Expression-profile analysis in Schwann cells identifies genes involved in myelination.
	Research news Short, but sweet Tudor Toma Genome Biology 2002, 3:spotlight-20020628-02 (28 June 2002) Abstract \| Full text \| Editor’s summary Short interfering RNAs can inhibit HIV-1 replication and confer intracellular antiviral immunity against poliovirus.
	Research news Placental imprinting Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020628-03 (28 June 2002) Abstract \| Full text \| Editor’s summary The paternally imprinted Igf2 gene plays a critical role in regulating placental growth.
	Research news Kyoto Prize 2002 David Bruce Genome Biology 2002, 3:spotlight-20020628-01 (28 June 2002) Abstract \| Full text \| Editor’s summary Leroy Hood has been recognized for his contribution to the development of the technology that enabled rapid genome sequencing.
	Research
	Research Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays Johann Y Lin, Jonathan R Pollack, Fan-Li Chou, Christian A Rees, Allen T Christian, Joel S Bedford, Patrick O Brown, Mark H Ginsberg Genome Biology 2002, 3:research0026-research0026.7 (14 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To fulfill the need for more efficient gene mapping in somatic cell mutants, a new DNA microarray comparative genomic hybridization method has been devloped that can rapidly and efficiently map the physical location of genes complementing somatic cell mutants to a small candidate genomic region.
	Research ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins Lars Hjelmqvist, Miquel Tuson, Gemma Marfany, Enric Herrero, Susana Balcells, Roser Gonzàlez-Duarte Genome Biology 2002, 3:research0027-research0027.16 (14 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary While characterizing genes from the retinitis pigmentosa locus RP26, a new gene, ORMDL, has been identified. It belongs to a novel gene family comprising three genes in humans, with homologs in yeast, microsporidia, plants, Drosophila, urochordates and vertebrates. These genes encode transmembrane proteins anchored in the endoplasmic reticulum (ER).
	Research Estimation of genetic distances from human and mouse introns Jose Castresana Genome Biology 2002, 3:research0028-research0028.7 (14 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genetic distances between 504 human introns and their orthologous mouse counterparts were calculated from a set of 63 pairs of human and mouse genes, using a method that can extract reliably aligned regions from the introns in an objective manner. A significant correlation was found between the genetic distance measured in the conserved intron segments and the synonymous and nonsynonymous distances measured in the corresponding coding exons.
	Research Full-length messenger RNA sequences greatly improve genome annotation Brian J Haas, Natalia Volfovsky, Christopher D Town, Maxim Troukhan, Nickolai Alexandrov, Kenneth A Feldmann, Richard B Flavell, Owen White, Steven L Salzberg Genome Biology 2002, 3:research0029-research0029.12 (30 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an effort to create a set of very high-quality gene models, the sequence of 5,000 full-length gene transcripts from Arabidopsis was used to re-annotate its genome. These transcripts were mapped to their exact chromosomal locations and gene models that provide a reference set for this organism were created. Approximately 35% of the transcripts indicated that previously annotated genes needed modification, and 5% of the transcripts represented newly discovered genes.
	Research Phylogenetic analysis of the human basic helix-loop-helix proteins Valérie Ledent, Odier Paquet, Michel Vervoort Genome Biology 2002, 3:research0030-research0030.18 (30 May 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The basic helix-loop-helix (bHLH) proteins are a large and complex multigene family of transcription factors with important roles in animal development. This article identifies 39 bHLH genes in Caenorhabditis elegans, 58 in Drosophila melanogaster and 125 in human, in 44 orthologous families in total. Genes from these families seem to have been present in the last common ancestor of worm, fly and human.
	Research Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries Cheryl Jenkins, Vishram Kedar, John A Fuerst Genome Biology 2002, 3:research0031-research0031.11 (30 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The random-sequence-tag approach applied here to Gemmata obscuriglobus and Pirellula Marina, provides the first report of gene recovery and analysis from members of the planctomycetes using genome-based methods. Gene homologs identified were predominantly similar to genes of Bacteria, but some matches to genes from Eukarya suggest that lateral gene transfer events may have involved this division during evolution.
	Software Software and methods for oligonucleotide and cDNA array data analysis Matthew A Zapala, Daniel J Lockhart, Daniel G Pankratz, Anthony J Garcia, Carrolee Barlow, David J Lockhart Genome Biology 2002, 3:software0001-software0001.9 (23 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two HTML-based programs were developed to analyze and filter gene-expression data. A background subtraction and normalization program for cDNA arrays was also built that provides an informative summary report with data-quality assessments. These programs are freeware.
	Correspondence
	Correspondence Ontologies for programs, not people Lawrence Hunter Genome Biology 2002, 3:interactions1002-interactions1002.2 (31 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to Life sentences: Ontology recapitulates philology by Sydney Brenner, Genome Biology 2002, 3:comment1006.1-1006.2.
	Correspondence Smelling of roses? Sue Povey, Hester Wain Genome Biology 2002, 3:interactions1003-interactions1003.2 (31 May 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to What's in a name? By Gregory Petsko, Genome Biology 2002, 3:comment 1005.1-1005.2.

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Volume 3 Issue 6

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