Genome Biology | Volume 3 Issue 9

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 3 Issue 9
	Comment
	Comment Life sentences: Detective Rummage investigates Sydney Brenner Genome Biology 2002, 3:comment1013-comment1013.2 (21 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary It is very ego-warming to be recognized by quotation, but not always easy to find the original source.
	Comment Fish tale Gregory A Petsko Genome Biology 2002, 3:comment1012-comment1012.2 (27 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The draft sequence of the genome of the Japanese pufferfish has just been announced and the temptation to humor is great.
	Review
	Protein family review The retinoblastoma family: twins or distant cousins? Pier Claudio, Tiziana Tonini, Antonio Giordano Genome Biology 2002, 3:reviews3012-reviews3012.9 (28 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The retinoblastoma family consists of the well-studied tumor suppressor pRb/p105 and two recently identified proteins, pRb2/p130 and p107. Members of the family can bind and repress transcription factors and other regulatory proteins and have roles in growth suppression, differentiation and apoptosis.
	Minireview Sushi gets serious: the draft genome sequence of the pufferfish Fugu rubripes Martin S Taylor, Colin AM Semple Genome Biology 2002, 3:reviews1025-reviews1025.6 (28 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The publication of the Fugu rubripes draft genome sequence will take this fish from culinary delicacy to potent tool in deciphering the mysteries of human genome function.
	Minireview Evolutionary origins of the endosperm in flowering plants Célia Baroux, Charles Spillane, Ueli Grossniklaus Genome Biology 2002, 3:reviews1026-reviews1026.5 (30 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recent resurgence of approaches to evolutionary developmental biology combining comparative biology with phylogenetics provides new understanding of endosperm origins.
	Opinion Have microarrays failed to deliver for developmental biology? Rick Livesey Genome Biology 2002, 3:comment2009-comment2009.5 (27 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarrays for some invertebrates and vertebrates have been available for some time, to date there have been few published studies using microarrays to generate novel insights in developmental biology.
	Report
	Paper report Sex determination in fish Jean-Nicolas Volff Genome Biology 2002, 3:reports0052 (27 August 2002) Abstract \| Full text \| Editor’s summary An excellent candidate for the master sex-determining gene on the Y chromosome of the medaka fish is not related to the mammalian SRY gene
	Paper report Human and mouse transriptome databases Chris Berrie Genome Biology 2002, 3:reports0047 (2 September 2002) Abstract \| Full text \| Editor’s summary The specificity of tissue transcriptional activities may be understood via high-throughput gene-expression profiling of a significant fraction of the human and mouse transcriptomes
	Paper report Insights into an extreme lifestyle Wim D'Haeze Genome Biology 2002, 3:reports0048 (2 September 2002) Abstract \| Full text \| Editor’s summary Sequencing Thermoanaerobacter tengcongensis reveals clues as to how this thermophile manages to live an extreme lifestyle
	Paper report Secreting an enterotoxin Wim D'Haeze Genome Biology 2002, 3:reports0049 (2 September 2002) Abstract \| Full text \| Editor’s summary Understanding the secretion of an enterotoxin by enterotoxigenic Escherichia coli strains paves the way to the development of new drugs
	Paper report Anthrax toxin interactions Wim D'Haeze Genome Biology 2002, 3:reports0050 (2 September 2002) Abstract \| Full text \| Editor’s summary Understanding how Bacillus anthracis initiates anthrax in humans
	Paper report Anthrax initiation Wim D'Haeze Genome Biology 2002, 3:reports0051 (2 September 2002) Abstract \| Full text \| Editor’s summary The mechanism by which Bacillus anthracis initiates anthrax in humans involves key protein-protein interactions, the site for which have now been mapped
	Meeting report Legume genomes and discoveries in symbiosis research Michael K Udvardi Genome Biology 2002, 3:reports4028-reports4028.3 (21 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the First International Conference on Legume Genomics and Genetics: Translation to Crop Improvement, Minneapolis-St. Paul, USA, 2-6 June 2002.
	Meeting report Sequence-based genomics Andrew JG Simpson Genome Biology 2002, 3:reports4029-reports4029.2 (27 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Genome-Based Pathogen Biology meeting, Hinxton, UK, 7-10 July 2002.
	Meeting report When cell biology and neurobiology meet Cristina Pelizon Genome Biology 2002, 3:reports4030-reports4030.3 (27 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the British Society for Cell Biology (BSCB) meetin on 'Cell Biology and Neurobiology: A Meeting for Martin Raff', London, UK, 3-5 July 2002.
	Deposited research article Ranking genes with respect to differential expression Per Broberg Genome Biology 2002, 3:preprint0007-preprint0007.23 (5 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for finding an optimal test statistic for microarrdy data with which to rank genes with respect to differential expression is outlined and tested. At the heart of the method lies an estimate of the false negative and false positive rates. The method outperforms commonly used alternatives.
	Deposited research article Heart Specific Genes Revealed by EST Sampling Karine Mégy, Stéphane Audic, Jean-Michel Claverie Genome Biology 2002, 3:preprint0008-preprint0008.25 (16 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of the expression profiles was preformed to identify genes over-expressed in the human adult heart using the public Expressed Sequence Tags database. The identification of 35 cardiac specific genes significantly over-expressed in the heart is reported. A list of genes expressed in the heart are presented, one of them being a candidate for a bleeding disorder.
	Research news Muscling in on chromosomal clusters Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020902-01 (2 September 2002) Abstract \| Full text \| Editor’s summary Genes expressed in worm muscle are found in clusters throughout the genome.
	Research news Anthrax-induced apoptosis Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020903-01 (3 September 2002) Abstract \| Full text \| Editor’s summary The anthrax-causing bacterium kills activated macrophages by deregulating signalling pathways.
	Research news Stopping hedgehogs Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020904-01 (4 September 2002) Abstract \| Full text \| Editor’s summary Antagonists of the Hedgehog pathway inhibit the growth of medulloblastoma tumors.
	Research news Sweet microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020905-01 (5 September 2002) Abstract \| Full text \| Editor’s summary Oligosaccharide microarrays can be used to detect sugar-protein interactions.
	Research news Seeing the light Theodora Bloom Genome Biology 2002, 3:spotlight-20020906-01 (6 September 2002) Abstract \| Full text \| Editor’s summary The diversity of circadian signalling mechanisms makes it hard to identify the key photopigments of mammalian circadian cycles.
	Research news Shedding light on gene regulation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020906-02 (6 September 2002) Abstract \| Full text \| Editor’s summary A phytochrome photoreceptor from plants has been used to create a gene expression system that can be induced by red light.
	Research news Pheromone phenotypes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020909-01 (9 September 2002) Abstract \| Full text \| Editor’s summary Disruption of a genomic cluster of pheromone receptors results in behavioural and chemosensory dysfunction.
	Research news Sequence of a symbiont Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020910-01 (10 September 2002) Abstract \| Full text \| Editor’s summary The genome of Wigglesworthia glossinidia, the obligate symbiont of the tsetse fly, has been sequenced.
	Research news The aptness of aptamers Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020911-01 (11 September 2002) Abstract \| Full text \| Editor’s summary RNA aptamers can be used to create antidote-controlled anticoagulant agents.
	Research news Rice knockouts Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020912-01 (12 September 2002) Abstract \| Full text \| Editor’s summary Rice genes can be manipulated by homologous recombination.
	Research news Characterizing a stem cell niche Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020913-01 (13 September 2002) Abstract \| Full text \| Editor’s summary A functional genomic approach has been used to investigate a stem-cell supportive stromal cell line.
	Research news High-priority genomes announced Tabitha M Powledge Genome Biology 2002, 3:spotlight-20020913-02 (13 September 2002) Abstract \| Full text \| Editor’s summary The politically popular dog and cow have made the A-list for US genome sequencers.
	Research news Methylation and imprinting Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020916-02 (16 September 2002) Abstract \| Full text \| Editor’s summary Deletion of a differentially methylated locus affects the imprinting of nearby genes in mice.
	Research news Some like it hot Tudor P Toma Genome Biology 2002, 3:spotlight-20020916-01 (16 September 2002) Abstract \| Full text \| Editor’s summary An untranslated mRNA acts as a thermosensor controlling the expression of Listeria virulence genes at 37°C.
	Research news Mighty splicing machine Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020917-02 (17 September 2002) Abstract \| Full text \| Editor’s summary Proteomic analysis has identified around 145 proteins that are part of the spliceosome machinery.
	Research news Macaque advocates seek higher status Tabitha M Powledge Genome Biology 2002, 3:spotlight-20020917-01 (17 September 2002) Abstract \| Full text \| Editor’s summary NIH genome priorities misplaced, say miffed monkey researchers.
	Research news "Stemness" Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020918-01 (18 September 2002) Abstract \| Full text \| Editor’s summary Transcriptional analysis has identified sets of genes specifically expressed in stem cells.
	Research news Data access concerns Eugene Russo Genome Biology 2002, 3:spotlight-20020919-02 (19 September 2002) Abstract \| Full text \| Editor’s summary Experts convene at the National Academy of Sciences to discuss restrictions on data access.
	Research news Early introns Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020919-01 (19 September 2002) Abstract \| Full text \| Editor’s summary The discovery of canonical introns in simple eukaryotic organisms challenges ideas about the origins of spliceosomal introns.
	Research news Cutting down Scarecrows Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020920-01 (20 September 2002) Abstract \| Full text \| Editor’s summary A microRNA in Arabidopsis guides the cleavage of mRNAs encoding members of the Scarecrow-like family.
	Research news Forkhead protection Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020923-01 (23 September 2002) Abstract \| Full text \| Editor’s summary The Forkhead transcription factor FOXO3a protects cells from oxidative stress by regulating manganese superoxide dismutase.
	Research news It only takes one bloom Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020924-01 (24 September 2002) Abstract \| Full text \| Editor’s summary Heterozygous mutations of the Blm gene are associated with cancer risk in mice and humans.
	Research news What makes fruit pear-shaped? Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020925-01 (25 September 2002) Abstract \| Full text \| Editor’s summary A novel gene regulates the development of pear-shaped tomatoes.
	Research news Caspase-8 mutations cause autoimmunity Jonathan Weitzman Genome Biology 2002, 3:spotlight-20020927-01 (27 September 2002) Abstract \| Full text \| Editor’s summary Studies of human immunodeficiency patients link caspase-8 to homeostatic regulation of the immune system.
	Research news Testing times ahead Pete Moore Genome Biology 2002, 3:spotlight-20020930-01 (30 September 2002) Abstract \| Full text \| Editor’s summary Talk of the $1000 genome comes as UK's Human Genetics Commission consults on gene testing
	Research news As harlequins grow old Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020930-02 (30 September 2002) Abstract \| Full text \| Editor’s summary The gene underlying underlying progressive neurodegeneration in the harlequin mouse mutant is a mitochondrial oxidorectase involved in cell death.
	Research
	Research NEAT: a domain duplicated in genes near the components of a putative Fe³⁺ siderophore transporter from Gram-positive pathogenic bacteria Miguel A Andrade, Francesca D Ciccarelli, Carolina Perez-Iratxeta, Peer Bork Genome Biology 2002, 3:research0047-research0047.5 (15 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Iron uptake from the host is essential for bacteria that infect animals. A protein domain has been identified that appears in variable copy number in bacterial genes that are usually in the vicinity of a putative Fe³⁺ siderophore transporter. This domain has been denoted NEAT for near transporter.
	Research PRESTA: associating promoter sequences with information on gene expression Václav Mach Genome Biology 2002, 3:research0050-research0050.7 (21 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The software tool PRESTA (PRomoter EST Association) is designed for efficient recovery of characterized and partially verified promoters from GenBank and EMBL libraries. The PRESTA algorithm demonstrates the principle of promoter verification by mapping EST 5' ends.
	Research Human members of the eukaryotic protein kinase family Mitch Kostich, Jessie English, Vincent Madison, Ferdous Gheyas, Luquan Wang, Ping Qiu, Jonathan Greene, Thomas M Laz Genome Biology 2002, 3:research0043-research0043.12 (22 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Publicly available genetic sequence data were searched for human sequences that potentially represent protein kinases, important players in virtually every signaling pathway. After removal of duplicates, splice variants and pseudogenes, this search yielded 510 sequences with recognizable similarity to eukaryotic protein kinases.
	Research Computational discovery of sense-antisense transcription in the human and mouse genomes Jay Shendure, George M Church Genome Biology 2002, 3:research0044-research0044.14 (22 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Overlapping but oppositely oriented transcripts have the potential to form sense-antisense perfect double-stranded (ds) RNA duplexes. A bioinformatics approach has identified over 217 candidate overlapping transcriptional units, bringing the total number of predicted and validated examples of overlapping but oppositely oriented transcripts to over 300.
	Research Design and implementation of microarray gene expression markup language (MAGE-ML) Paul T Spellman, Michael Miller, Jason Stewart, Charles Troup, Ugis Sarkans, Steve Chervitz, Derek Bernhart, Gavin Sherlock, Catherine Ball, Marc Lepage, Marcin Swiatek, WL Marks, Jason Goncalves, Scott Markel, Daniel Iordan, Mohammadreza Shojatalab, Angel Pizarro, Joe White, Robert Hubley, Eric Deutsch, Martin Senger, Bruce J Aronow, Alan Robinson, Doug Bassett, Christian J Stoeckert, Alvis Brazma Genome Biology 2002, 3:research0046-research0046.9 (23 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.
	Research Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus KwangChul Oh, Kristine Hardeman, Maria G Ivanchenko, Mary Ellard-Ivey, Andreas Nebenführ, TJ White, Terri L Lomax Genome Biology 2002, 3:research0049-research0049.11 (28 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Arabidopsis thaliana genome sequence provides a catalog of reference genes applicable to comparative microsynteny analysis of other species, facilitating map-based cloning in economically important crops. Such an analysis was applied to the tomato expressed sequence tag (EST) database to expedite high-resolution mapping of the Diageotropica gene within the distal end of chromosome 1 in tomato.
	Research Gene-expression profile comparisons distinguish seven organs of maize Yangrae Cho, John Fernandes, Soo-Hwan Kim, Virginia Walbot Genome Biology 2002, 3:research0045-research0045.16 (29 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Relative mRNA levels from maize organs have been quantified by hybridization to maize arrays fabricated with 5,376 unique expressed sequence tag clones. mRNAs from embryos, three vegetative organs (leaf blades, leaf sheaths and roots), husk leaves and two types of floral organs (immature ears and silks) reveal that a majority of genes expressed in diverse organs with little difference in transcript levels.
	Research Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture Gary Xie, Carol A Bonner, Roy A Jensen Genome Biology 2002, 3:research0051-research0051.17 (29 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The factors that accommodate the transition of different chlamydial species to the persistent state of pathogenesis include marked differences in the strategied deplyed to obtain tryptophan from host resources. Chlamydia psittaci appears to have a novel mechanism for intercepting an early intermediate of tryptophan catabolism and recycling it back to tryptophan.
	Research A new non-linear normalization method for reducing variability in DNA microarray experiments Christopher Workman, Lars Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Nielser, Hans-Henrik Saxild, Claus Nielsen, Søren Brunak, Steen Knudsen Genome Biology 2002, 3:research0048-research0048.16 (30 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A simple and robust non-linear method is presented for normalization using array signal distribution analysis and cubic splines. Both the regression and spline-based methods described performed better than existing linear methods when assessed on the variability of replicate arrays

	Volume 3 Issue 9
	Comment
	Comment Life sentences: Detective Rummage investigates Sydney Brenner Genome Biology 2002, 3:comment1013-comment1013.2 (21 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary It is very ego-warming to be recognized by quotation, but not always easy to find the original source.
	Comment Fish tale Gregory A Petsko Genome Biology 2002, 3:comment1012-comment1012.2 (27 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The draft sequence of the genome of the Japanese pufferfish has just been announced and the temptation to humor is great.
	Review
	Protein family review The retinoblastoma family: twins or distant cousins? Pier Claudio, Tiziana Tonini, Antonio Giordano Genome Biology 2002, 3:reviews3012-reviews3012.9 (28 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The retinoblastoma family consists of the well-studied tumor suppressor pRb/p105 and two recently identified proteins, pRb2/p130 and p107. Members of the family can bind and repress transcription factors and other regulatory proteins and have roles in growth suppression, differentiation and apoptosis.
	Minireview Sushi gets serious: the draft genome sequence of the pufferfish Fugu rubripes Martin S Taylor, Colin AM Semple Genome Biology 2002, 3:reviews1025-reviews1025.6 (28 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The publication of the Fugu rubripes draft genome sequence will take this fish from culinary delicacy to potent tool in deciphering the mysteries of human genome function.
	Minireview Evolutionary origins of the endosperm in flowering plants Célia Baroux, Charles Spillane, Ueli Grossniklaus Genome Biology 2002, 3:reviews1026-reviews1026.5 (30 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recent resurgence of approaches to evolutionary developmental biology combining comparative biology with phylogenetics provides new understanding of endosperm origins.
	Opinion Have microarrays failed to deliver for developmental biology? Rick Livesey Genome Biology 2002, 3:comment2009-comment2009.5 (27 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarrays for some invertebrates and vertebrates have been available for some time, to date there have been few published studies using microarrays to generate novel insights in developmental biology.
	Report
	Paper report Sex determination in fish Jean-Nicolas Volff Genome Biology 2002, 3:reports0052 (27 August 2002) Abstract \| Full text \| Editor’s summary An excellent candidate for the master sex-determining gene on the Y chromosome of the medaka fish is not related to the mammalian SRY gene
	Paper report Human and mouse transriptome databases Chris Berrie Genome Biology 2002, 3:reports0047 (2 September 2002) Abstract \| Full text \| Editor’s summary The specificity of tissue transcriptional activities may be understood via high-throughput gene-expression profiling of a significant fraction of the human and mouse transcriptomes
	Paper report Insights into an extreme lifestyle Wim D'Haeze Genome Biology 2002, 3:reports0048 (2 September 2002) Abstract \| Full text \| Editor’s summary Sequencing Thermoanaerobacter tengcongensis reveals clues as to how this thermophile manages to live an extreme lifestyle
	Paper report Secreting an enterotoxin Wim D'Haeze Genome Biology 2002, 3:reports0049 (2 September 2002) Abstract \| Full text \| Editor’s summary Understanding the secretion of an enterotoxin by enterotoxigenic Escherichia coli strains paves the way to the development of new drugs
	Paper report Anthrax toxin interactions Wim D'Haeze Genome Biology 2002, 3:reports0050 (2 September 2002) Abstract \| Full text \| Editor’s summary Understanding how Bacillus anthracis initiates anthrax in humans
	Paper report Anthrax initiation Wim D'Haeze Genome Biology 2002, 3:reports0051 (2 September 2002) Abstract \| Full text \| Editor’s summary The mechanism by which Bacillus anthracis initiates anthrax in humans involves key protein-protein interactions, the site for which have now been mapped
	Meeting report Legume genomes and discoveries in symbiosis research Michael K Udvardi Genome Biology 2002, 3:reports4028-reports4028.3 (21 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the First International Conference on Legume Genomics and Genetics: Translation to Crop Improvement, Minneapolis-St. Paul, USA, 2-6 June 2002.
	Meeting report Sequence-based genomics Andrew JG Simpson Genome Biology 2002, 3:reports4029-reports4029.2 (27 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Genome-Based Pathogen Biology meeting, Hinxton, UK, 7-10 July 2002.
	Meeting report When cell biology and neurobiology meet Cristina Pelizon Genome Biology 2002, 3:reports4030-reports4030.3 (27 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the British Society for Cell Biology (BSCB) meetin on 'Cell Biology and Neurobiology: A Meeting for Martin Raff', London, UK, 3-5 July 2002.
	Deposited research article Ranking genes with respect to differential expression Per Broberg Genome Biology 2002, 3:preprint0007-preprint0007.23 (5 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for finding an optimal test statistic for microarrdy data with which to rank genes with respect to differential expression is outlined and tested. At the heart of the method lies an estimate of the false negative and false positive rates. The method outperforms commonly used alternatives.
	Deposited research article Heart Specific Genes Revealed by EST Sampling Karine Mégy, Stéphane Audic, Jean-Michel Claverie Genome Biology 2002, 3:preprint0008-preprint0008.25 (16 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of the expression profiles was preformed to identify genes over-expressed in the human adult heart using the public Expressed Sequence Tags database. The identification of 35 cardiac specific genes significantly over-expressed in the heart is reported. A list of genes expressed in the heart are presented, one of them being a candidate for a bleeding disorder.
	Research news Muscling in on chromosomal clusters Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020902-01 (2 September 2002) Abstract \| Full text \| Editor’s summary Genes expressed in worm muscle are found in clusters throughout the genome.
	Research news Anthrax-induced apoptosis Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020903-01 (3 September 2002) Abstract \| Full text \| Editor’s summary The anthrax-causing bacterium kills activated macrophages by deregulating signalling pathways.
	Research news Stopping hedgehogs Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020904-01 (4 September 2002) Abstract \| Full text \| Editor’s summary Antagonists of the Hedgehog pathway inhibit the growth of medulloblastoma tumors.
	Research news Sweet microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020905-01 (5 September 2002) Abstract \| Full text \| Editor’s summary Oligosaccharide microarrays can be used to detect sugar-protein interactions.
	Research news Seeing the light Theodora Bloom Genome Biology 2002, 3:spotlight-20020906-01 (6 September 2002) Abstract \| Full text \| Editor’s summary The diversity of circadian signalling mechanisms makes it hard to identify the key photopigments of mammalian circadian cycles.
	Research news Shedding light on gene regulation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020906-02 (6 September 2002) Abstract \| Full text \| Editor’s summary A phytochrome photoreceptor from plants has been used to create a gene expression system that can be induced by red light.
	Research news Pheromone phenotypes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020909-01 (9 September 2002) Abstract \| Full text \| Editor’s summary Disruption of a genomic cluster of pheromone receptors results in behavioural and chemosensory dysfunction.
	Research news Sequence of a symbiont Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020910-01 (10 September 2002) Abstract \| Full text \| Editor’s summary The genome of Wigglesworthia glossinidia, the obligate symbiont of the tsetse fly, has been sequenced.
	Research news The aptness of aptamers Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020911-01 (11 September 2002) Abstract \| Full text \| Editor’s summary RNA aptamers can be used to create antidote-controlled anticoagulant agents.
	Research news Rice knockouts Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020912-01 (12 September 2002) Abstract \| Full text \| Editor’s summary Rice genes can be manipulated by homologous recombination.
	Research news Characterizing a stem cell niche Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020913-01 (13 September 2002) Abstract \| Full text \| Editor’s summary A functional genomic approach has been used to investigate a stem-cell supportive stromal cell line.
	Research news High-priority genomes announced Tabitha M Powledge Genome Biology 2002, 3:spotlight-20020913-02 (13 September 2002) Abstract \| Full text \| Editor’s summary The politically popular dog and cow have made the A-list for US genome sequencers.
	Research news Methylation and imprinting Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020916-02 (16 September 2002) Abstract \| Full text \| Editor’s summary Deletion of a differentially methylated locus affects the imprinting of nearby genes in mice.
	Research news Some like it hot Tudor P Toma Genome Biology 2002, 3:spotlight-20020916-01 (16 September 2002) Abstract \| Full text \| Editor’s summary An untranslated mRNA acts as a thermosensor controlling the expression of Listeria virulence genes at 37°C.
	Research news Mighty splicing machine Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020917-02 (17 September 2002) Abstract \| Full text \| Editor’s summary Proteomic analysis has identified around 145 proteins that are part of the spliceosome machinery.
	Research news Macaque advocates seek higher status Tabitha M Powledge Genome Biology 2002, 3:spotlight-20020917-01 (17 September 2002) Abstract \| Full text \| Editor’s summary NIH genome priorities misplaced, say miffed monkey researchers.
	Research news "Stemness" Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020918-01 (18 September 2002) Abstract \| Full text \| Editor’s summary Transcriptional analysis has identified sets of genes specifically expressed in stem cells.
	Research news Data access concerns Eugene Russo Genome Biology 2002, 3:spotlight-20020919-02 (19 September 2002) Abstract \| Full text \| Editor’s summary Experts convene at the National Academy of Sciences to discuss restrictions on data access.
	Research news Early introns Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020919-01 (19 September 2002) Abstract \| Full text \| Editor’s summary The discovery of canonical introns in simple eukaryotic organisms challenges ideas about the origins of spliceosomal introns.
	Research news Cutting down Scarecrows Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020920-01 (20 September 2002) Abstract \| Full text \| Editor’s summary A microRNA in Arabidopsis guides the cleavage of mRNAs encoding members of the Scarecrow-like family.
	Research news Forkhead protection Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020923-01 (23 September 2002) Abstract \| Full text \| Editor’s summary The Forkhead transcription factor FOXO3a protects cells from oxidative stress by regulating manganese superoxide dismutase.
	Research news It only takes one bloom Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020924-01 (24 September 2002) Abstract \| Full text \| Editor’s summary Heterozygous mutations of the Blm gene are associated with cancer risk in mice and humans.
	Research news What makes fruit pear-shaped? Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020925-01 (25 September 2002) Abstract \| Full text \| Editor’s summary A novel gene regulates the development of pear-shaped tomatoes.
	Research news Caspase-8 mutations cause autoimmunity Jonathan Weitzman Genome Biology 2002, 3:spotlight-20020927-01 (27 September 2002) Abstract \| Full text \| Editor’s summary Studies of human immunodeficiency patients link caspase-8 to homeostatic regulation of the immune system.
	Research news Testing times ahead Pete Moore Genome Biology 2002, 3:spotlight-20020930-01 (30 September 2002) Abstract \| Full text \| Editor’s summary Talk of the $1000 genome comes as UK's Human Genetics Commission consults on gene testing
	Research news As harlequins grow old Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020930-02 (30 September 2002) Abstract \| Full text \| Editor’s summary The gene underlying underlying progressive neurodegeneration in the harlequin mouse mutant is a mitochondrial oxidorectase involved in cell death.
	Research
	Research NEAT: a domain duplicated in genes near the components of a putative Fe³⁺ siderophore transporter from Gram-positive pathogenic bacteria Miguel A Andrade, Francesca D Ciccarelli, Carolina Perez-Iratxeta, Peer Bork Genome Biology 2002, 3:research0047-research0047.5 (15 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Iron uptake from the host is essential for bacteria that infect animals. A protein domain has been identified that appears in variable copy number in bacterial genes that are usually in the vicinity of a putative Fe³⁺ siderophore transporter. This domain has been denoted NEAT for near transporter.
	Research PRESTA: associating promoter sequences with information on gene expression Václav Mach Genome Biology 2002, 3:research0050-research0050.7 (21 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The software tool PRESTA (PRomoter EST Association) is designed for efficient recovery of characterized and partially verified promoters from GenBank and EMBL libraries. The PRESTA algorithm demonstrates the principle of promoter verification by mapping EST 5' ends.
	Research Human members of the eukaryotic protein kinase family Mitch Kostich, Jessie English, Vincent Madison, Ferdous Gheyas, Luquan Wang, Ping Qiu, Jonathan Greene, Thomas M Laz Genome Biology 2002, 3:research0043-research0043.12 (22 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Publicly available genetic sequence data were searched for human sequences that potentially represent protein kinases, important players in virtually every signaling pathway. After removal of duplicates, splice variants and pseudogenes, this search yielded 510 sequences with recognizable similarity to eukaryotic protein kinases.
	Research Computational discovery of sense-antisense transcription in the human and mouse genomes Jay Shendure, George M Church Genome Biology 2002, 3:research0044-research0044.14 (22 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Overlapping but oppositely oriented transcripts have the potential to form sense-antisense perfect double-stranded (ds) RNA duplexes. A bioinformatics approach has identified over 217 candidate overlapping transcriptional units, bringing the total number of predicted and validated examples of overlapping but oppositely oriented transcripts to over 300.
	Research Design and implementation of microarray gene expression markup language (MAGE-ML) Paul T Spellman, Michael Miller, Jason Stewart, Charles Troup, Ugis Sarkans, Steve Chervitz, Derek Bernhart, Gavin Sherlock, Catherine Ball, Marc Lepage, Marcin Swiatek, WL Marks, Jason Goncalves, Scott Markel, Daniel Iordan, Mohammadreza Shojatalab, Angel Pizarro, Joe White, Robert Hubley, Eric Deutsch, Martin Senger, Bruce J Aronow, Alan Robinson, Doug Bassett, Christian J Stoeckert, Alvis Brazma Genome Biology 2002, 3:research0046-research0046.9 (23 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.
	Research Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus KwangChul Oh, Kristine Hardeman, Maria G Ivanchenko, Mary Ellard-Ivey, Andreas Nebenführ, TJ White, Terri L Lomax Genome Biology 2002, 3:research0049-research0049.11 (28 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Arabidopsis thaliana genome sequence provides a catalog of reference genes applicable to comparative microsynteny analysis of other species, facilitating map-based cloning in economically important crops. Such an analysis was applied to the tomato expressed sequence tag (EST) database to expedite high-resolution mapping of the Diageotropica gene within the distal end of chromosome 1 in tomato.
	Research Gene-expression profile comparisons distinguish seven organs of maize Yangrae Cho, John Fernandes, Soo-Hwan Kim, Virginia Walbot Genome Biology 2002, 3:research0045-research0045.16 (29 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Relative mRNA levels from maize organs have been quantified by hybridization to maize arrays fabricated with 5,376 unique expressed sequence tag clones. mRNAs from embryos, three vegetative organs (leaf blades, leaf sheaths and roots), husk leaves and two types of floral organs (immature ears and silks) reveal that a majority of genes expressed in diverse organs with little difference in transcript levels.
	Research Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture Gary Xie, Carol A Bonner, Roy A Jensen Genome Biology 2002, 3:research0051-research0051.17 (29 August 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The factors that accommodate the transition of different chlamydial species to the persistent state of pathogenesis include marked differences in the strategied deplyed to obtain tryptophan from host resources. Chlamydia psittaci appears to have a novel mechanism for intercepting an early intermediate of tryptophan catabolism and recycling it back to tryptophan.
	Research A new non-linear normalization method for reducing variability in DNA microarray experiments Christopher Workman, Lars Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Nielser, Hans-Henrik Saxild, Claus Nielsen, Søren Brunak, Steen Knudsen Genome Biology 2002, 3:research0048-research0048.16 (30 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A simple and robust non-linear method is presented for normalization using array signal distribution analysis and cubic splines. Both the regression and spline-based methods described performed better than existing linear methods when assessed on the variability of replicate arrays

Explore Genome Biology

Articles

Volume 3 Issue 9

Comment

Review

Report

Research