Genome Biology | Volume 3 Issue 3

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	Volume 3 Issue 3
	Comment
	Comment The father of us all Gregory A Petsko Genome Biology 2002, 3:comment1004-comment1004.2 (22 February 2002) Full text \| PDF \| PubMed
	Review
	Review Untranslated regions of mRNAs Flavio Mignone, Carmela Gissi, Sabino Liuni, Graziano Pesole Genome Biology 2002, 3:reviews0004-reviews0004.10 (28 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression is finely regulated at the post-transcriptional level. Features of the untranslated regions of mRNAs that control their translation, degradation and localization include stem-loop structures, upstream initiation codons and open reading frames, internal ribosome entry sites and various cis-acting elements that are bound by RNA-binding proteins.
	Protein family review Plant glutathione transferases David P Dixon, Adrian Lapthorn, Robert Edwards Genome Biology 2002, 3:reviews3004-reviews3004.10 (26 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The soluble glutathione transferases (GSTs) are a large, conserved family of proteins that use the tripeptide glutathione as a cosubstrate or coenzyme. They are predominantly expressed in the cytosol and have a range of catalytic and non-catalytic functions, including detoxification of herbicides and protection from oxidative stress, and have been implicated in other cellular processes.
	Minireview Comparative genomics of Arabidopsis and maize: prospects and limitations Volker Brendel, Stefan Kurtz, Virginia Walbot Genome Biology 2002, 3:reviews1005-reviews1005.6 (14 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The completed Arabidopsis genome seems to be of limited value as a model for maize genomics. In addition to the expansion of repetitive sequences in maize and the lack of genomic micro-colinearity, maize-specific or highly-diverged proteins contribute to a predicted maize proteome of about 50,000 proteins, twice the size of that of Arabidopsis.
	Minireview Integration of splicing, transport and translation to achieve mRNA quality control by the nonsense-mediated decay pathway Thomas Schell, Andreas E Kulozik, Matthias W Hentze Genome Biology 2002, 3:reviews1006-reviews1006.6 (26 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Minireview SAGE profiling of the forelimb and hindlimb Malcolm Logan Genome Biology 2002, 3:reviews1007-reviews1007.3 (27 February 2002) Abstract \| Full text \| PDF \| PubMed
	Opinion The gentle art of gene arrangement: the meaning of gene clusters John Trowsdale Genome Biology 2002, 3:comment2002-comment2002.5 (22 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Opinion The model unicellular eukaryote, Schizosaccharomyces pombe Mitsuhiro Yanagida Genome Biology 2002, 3:comment2003-comment2003.4 (22 February 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The fission yeast Schizosaccharomyces pombe has long been a model organism for studies of eukaryotic cells, winning renown especially for studies of the cell cycle. Now that its genome has been sequenced, S. pombe is ready to assume its rightful place in the pantheon of small eukaryotic giants.
	Report
	Web report Software for cell simulation Chaitanya Athale Genome Biology 2002, 3:reports2011 (28 February 2002) Abstract \| Full text
	Paper report Eating less to live longer Nektarios Tavernarakis Genome Biology 2002, 3:reports0012 (15 February 2002) Abstract \| Full text
	Paper report Interfering with RNA interference Nektarios Tavernarakis Genome Biology 2002, 3:reports0013 (15 February 2002) Abstract \| Full text \| Editor’s summary Adenine deamination in double-stranded RNA by specific adenine deaminases efficiently blocks RNA interference in vitro
	Paper report Finding the links within the yeast proteome Reiner Veitia Genome Biology 2002, 3:reports0014 (22 February 2002) Abstract \| Full text
	Paper report Zebrafish embryogenesis genes Wim D'Haeze Genome Biology 2002, 3:reports0015 (22 February 2002) Abstract \| Full text
	Paper report Putting the heat into heat-shock Chris Berrie Genome Biology 2002, 3:reports0016 (28 February 2002) Abstract \| Full text \| Editor’s summary The expression of several heat-shock proteins of nitrogen-fixing bacteria is controlled post-transcriptionally by the thermosensitive secondary structure of the 'ROSE' regulatory sequences in their mRNA
	Paper report Leishmania genes involved in parasitic infection Wim D'Haeze Genome Biology 2002, 3:reports0017 (28 February 2002) Abstract \| Full text \| Editor’s summary Gene-expression studies have identified two new parasite genes potentially involved in the progression of Leishmania infection in mammalian hosts
	Paper report Unraveling antibiotic production Wim D'Haeze Genome Biology 2002, 3:reports0018 (28 February 2002) Abstract \| Full text \| Editor’s summary Large-scale microarray analyses have provided insights into the genetic control of antibiotic production by Streptomyces coelicolor
	Meeting report A hitchhiker's guide to cell biology: exploitation of host-cell functions by intracellular pathogens Susanne M Rafelski, Julie A Theriot Genome Biology 2002, 3:reports4006-reports4006.2 (14 February 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Pathogen-host cell interactions' minisymposium at the 41st Annual Meeting of the American Society for Cell Biology, Washington DC, USA, 8-12 December 2001.
	Meeting report Genomics meets nanoscience: probing genes and the cell nucleus at 10^-9 meters Joan Politz, Ana Pombo Genome Biology 2002, 3:reports4007-reports4007.3 (25 February 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Jackson Laboratory 'Genomics meets nanoscience' meeting, Bar Harbor, USA, 9-12 October 2001.
	Deposited research article Using orthologous and paralogous proteins to identify specificity determining residues Leonid A Mirny, Mikhail S Gelfand Genome Biology 2002, 3:preprint0002-preprint0002.20 (19 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Functional specificity of proteins is assumed to be conserved among orthologs and to be different among paralogs. We used this assumption to identify the residues that determine specificity of protein-DNA and protein-ligand recognition and present a method to compute the statistical significance of the predictions.
	Research news Dodo genetics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020301-01 (1 March 2002) Abstract \| Full text \| Editor’s summary Genetic analysis provides insights into the origins of the dodo.
	Research news Good taste Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020301-02 (1 March 2002) Abstract \| Full text \| Editor’s summary G-protein-coupled receptors function as taste sensors of L-amino-acids.
	Research news Shape of a chromodomain Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020304-01 (4 March 2002) Abstract \| Full text \| Editor’s summary The structure of the HP1 chromodomain shows how it recognizes methylated histone tails.
	Research news Chipping away at GATA Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020305-01 (5 March 2002) Abstract \| Full text \| Editor’s summary Researchers have identified additional GATA-1 binding sites in the β-globin locus.
	Research news Cytomegalovirus control Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020306-01 (6 March 2002) Abstract \| Full text \| Editor’s summary Infection by the human cytomegalovirus induces cellular genes that regulate cell cycle progression.
	Research news Shotgun strategies Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020307-01 (7 March 2002) Abstract \| Full text \| Editor’s summary One year after the two human draft genome sequences were published the debate over sequencing strategies continues.
	Research news Proteome purification Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020308-01 (8 March 2002) Abstract \| Full text \| Editor’s summary A high-throughput approach has been applied to purify affinity-tagged human proteins expressed in bacteria.
	Research news Antisense spuds Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020311-01 (11 March 2002) Abstract \| Full text \| Editor’s summary The simultaneous inhibition of three plant enzymes using antisense technology creates improved potato starch.
	Research news Musical protection Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020312-01 (12 March 2002) Abstract \| Full text \| Editor’s summary Copyright protection may be music to the ears of genomics companies.
	Research news Take your PIC Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020313-01 (13 March 2002) Abstract \| Full text \| Editor’s summary Analysis of differentiation-dependent transcription reveals that the pre-initiation complex (PIC) can assemble before chromatin remodelling.
	Research news ATM splicing defect Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020314-01 (14 March 2002) Abstract \| Full text \| Editor’s summary A mutation in the ATM gene can cause aberrant splicing and inclusion of a cryptic exon.
	Research news Embryonic vs somatic mutation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020315-01 (15 March 2002) Abstract \| Full text \| Editor’s summary The mutation frequency of embryonic stem cells is much lower than somatic cells but often involves chromosomal loss and uniparental disomy.
	Research news Where is the proteome? Anna Sharman Genome Biology 2002, 3:spotlight-20020318-01 (18 March 2002) Abstract \| Full text \| Editor’s summary A high-throughput approach to studying the subcellular localization of proteins has provided an overview of yeast protein localization.
	Research news CpG islands Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020319-01 (19 March 2002) Abstract \| Full text \| Editor’s summary Careful analysis of completed human genome sequences defines the properties of CpG islands.
	Research news Phage tropism Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020320-01 (20 March 2002) Abstract \| Full text \| Editor’s summary A reverse transcriptase enzyme and genomic repeat sequences coordinate a tropic switch in a bacteriophage
	Research news Ribozyme targeting Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020321-01 (21 March 2002) Abstract \| Full text \| Editor’s summary Cationic liposomes can deliver hammerhead ribozymes, which can be used to prevent tumour growth in vivo.
	Research news Quick to respond Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020322-01 (22 March 2002) Abstract \| Full text \| Editor’s summary Scientists from Celera defend their claim of successful assembly of the human genome using the whole-genome shotgun technique.
	Research news RNAi to RNAi Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020326-01 (26 March 2002) Abstract \| Full text \| Editor’s summary An RNA interference (RNAi) screen has been used to find genes involved in RNA interference.
	Research news Annotating Arabidopsis Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020326-02 (26 March 2002) Abstract \| Full text \| Editor’s summary Japanese researchers have isolated full-length cDNAs covering 60% of the genes in the Arabidopsis genome.
	Research news Tissue transcriptomes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020327-02 (27 March 2002) Abstract \| Full text \| Editor’s summary Extensive analysis of the transcriptomes from mouse and human tissues provides clues about gene function.
	Research news Europe boosts post-genomic research Helen Gavaghan Genome Biology 2002, 3:spotlight-20020327-01 (27 March 2002) Abstract \| Full text \| Editor’s summary The award of almost -40 million to three pan-European post-genomic projects signals a shift in funding of science by the European Union.
	Research news Divine DNA repair Tudor Toma Genome Biology 2002, 3:spotlight-20020328-01 (28 March 2002) Abstract \| Full text \| Editor’s summary The Artemis protein cuts away damaged DNA to allow strands to be rejoined.
	Research news MicroRNAs Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020328-03 (28 March 2002) Abstract \| Full text \| Editor’s summary MicroRNAs in the fly genome are complementary to some 3' untranslated regions.
	Research news Small genomes are still shrinking Tudor Toma Genome Biology 2002, 3:spotlight-20020328-02 (28 March 2002) Abstract \| Full text \| Editor’s summary The small Buchnera genome is still shrinking toward a minimum set of genes necessary for its symbiotic lifestyle.
	Research
	Research Vector algebra in the analysis of genome-wide expression data Finny G Kuruvilla, Peter J Park, Stuart L Schreiber Genome Biology 2002, 3:research0011-research0011.11 (13 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary How best to analyze data from thousands of transcription-profiling experiments remains an important challenge. Using a sample analysis of cells treated with rapamycin, a framework is presented, based on vector algebra for the analysis of transcription profiles, that is geometrically intuitive and computationally efficient.
	Research Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors Lakshminarayan M Iyer, Eugene V Koonin, L Aravind Genome Biology 2002, 3:research0012-research0012.11 (13 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using computational analysis, the amino-terminal module of the D6R/N1R proteins is shown to define a novel, conserved DNA-binding domain (the KilA-N domain) found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. It is suggested to be homologous to the fungal DNA-binding APSES domain; analysis of these domains points to extensive domain shuffling and lineage-specific gene family expansion within DNA virus genomes.
	Research Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA Esperanza Benítez-Bellón, Gabriel Moreno-Hagelsieb, Julio Collado-Vides Genome Biology 2002, 3:research0013-research0013.16 (21 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A collection of 86 sets of co-regulated genes from Escherichia coli were used to evaluate two methods for pattern discovery and pattern searching: dyad analysis/dyad sweeping and multiple alignment analysis. Particular emphasis was placed on minimizing the rate of false positives. With more robust methods, regulatory predictions could help identify the function of unknown genes.
	Research Molecular genetics and structural genomics of the human protein kinase C gene module Kurt Kofler, Martin Erdel, Gerd Utermann, Gottfried Baier Genome Biology 2002, 3:research0014-research0014.10 (27 February 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fine chromosomal mapping of all nine human protein kinase C genes by fluorescence in situ hybridization was carried out, using cosmid and BAC probes. The genes were found to be dispersed throughout the genome; PKC gene structure was also studied.
	Correspondence
	Erratum The trappist's approach to pathfinding: elucidating brain wiring using secretory-trap mutagenesis Andrew J Furley Genome Biology 2002, 3:interactions2001-interactions2001.1 (25 February 2002) Abstract \| Full text \| PDF \| Editor’s summary An erratum to The trappist's approach to pathfinding: elucidating brain wiring using secretory-trap mutagenesis by AJ Furley. Genome Biology 2001, 2:reviews1026.1-1026.5

	Volume 3 Issue 3
	Comment
	Comment The father of us all Gregory A Petsko Genome Biology 2002, 3:comment1004-comment1004.2 (22 February 2002) Full text \| PDF \| PubMed
	Review
	Review Untranslated regions of mRNAs Flavio Mignone, Carmela Gissi, Sabino Liuni, Graziano Pesole Genome Biology 2002, 3:reviews0004-reviews0004.10 (28 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression is finely regulated at the post-transcriptional level. Features of the untranslated regions of mRNAs that control their translation, degradation and localization include stem-loop structures, upstream initiation codons and open reading frames, internal ribosome entry sites and various cis-acting elements that are bound by RNA-binding proteins.
	Protein family review Plant glutathione transferases David P Dixon, Adrian Lapthorn, Robert Edwards Genome Biology 2002, 3:reviews3004-reviews3004.10 (26 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The soluble glutathione transferases (GSTs) are a large, conserved family of proteins that use the tripeptide glutathione as a cosubstrate or coenzyme. They are predominantly expressed in the cytosol and have a range of catalytic and non-catalytic functions, including detoxification of herbicides and protection from oxidative stress, and have been implicated in other cellular processes.
	Minireview Comparative genomics of Arabidopsis and maize: prospects and limitations Volker Brendel, Stefan Kurtz, Virginia Walbot Genome Biology 2002, 3:reviews1005-reviews1005.6 (14 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The completed Arabidopsis genome seems to be of limited value as a model for maize genomics. In addition to the expansion of repetitive sequences in maize and the lack of genomic micro-colinearity, maize-specific or highly-diverged proteins contribute to a predicted maize proteome of about 50,000 proteins, twice the size of that of Arabidopsis.
	Minireview Integration of splicing, transport and translation to achieve mRNA quality control by the nonsense-mediated decay pathway Thomas Schell, Andreas E Kulozik, Matthias W Hentze Genome Biology 2002, 3:reviews1006-reviews1006.6 (26 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Minireview SAGE profiling of the forelimb and hindlimb Malcolm Logan Genome Biology 2002, 3:reviews1007-reviews1007.3 (27 February 2002) Abstract \| Full text \| PDF \| PubMed
	Opinion The gentle art of gene arrangement: the meaning of gene clusters John Trowsdale Genome Biology 2002, 3:comment2002-comment2002.5 (22 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Opinion The model unicellular eukaryote, Schizosaccharomyces pombe Mitsuhiro Yanagida Genome Biology 2002, 3:comment2003-comment2003.4 (22 February 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The fission yeast Schizosaccharomyces pombe has long been a model organism for studies of eukaryotic cells, winning renown especially for studies of the cell cycle. Now that its genome has been sequenced, S. pombe is ready to assume its rightful place in the pantheon of small eukaryotic giants.
	Report
	Web report Software for cell simulation Chaitanya Athale Genome Biology 2002, 3:reports2011 (28 February 2002) Abstract \| Full text
	Paper report Eating less to live longer Nektarios Tavernarakis Genome Biology 2002, 3:reports0012 (15 February 2002) Abstract \| Full text
	Paper report Interfering with RNA interference Nektarios Tavernarakis Genome Biology 2002, 3:reports0013 (15 February 2002) Abstract \| Full text \| Editor’s summary Adenine deamination in double-stranded RNA by specific adenine deaminases efficiently blocks RNA interference in vitro
	Paper report Finding the links within the yeast proteome Reiner Veitia Genome Biology 2002, 3:reports0014 (22 February 2002) Abstract \| Full text
	Paper report Zebrafish embryogenesis genes Wim D'Haeze Genome Biology 2002, 3:reports0015 (22 February 2002) Abstract \| Full text
	Paper report Putting the heat into heat-shock Chris Berrie Genome Biology 2002, 3:reports0016 (28 February 2002) Abstract \| Full text \| Editor’s summary The expression of several heat-shock proteins of nitrogen-fixing bacteria is controlled post-transcriptionally by the thermosensitive secondary structure of the 'ROSE' regulatory sequences in their mRNA
	Paper report Leishmania genes involved in parasitic infection Wim D'Haeze Genome Biology 2002, 3:reports0017 (28 February 2002) Abstract \| Full text \| Editor’s summary Gene-expression studies have identified two new parasite genes potentially involved in the progression of Leishmania infection in mammalian hosts
	Paper report Unraveling antibiotic production Wim D'Haeze Genome Biology 2002, 3:reports0018 (28 February 2002) Abstract \| Full text \| Editor’s summary Large-scale microarray analyses have provided insights into the genetic control of antibiotic production by Streptomyces coelicolor
	Meeting report A hitchhiker's guide to cell biology: exploitation of host-cell functions by intracellular pathogens Susanne M Rafelski, Julie A Theriot Genome Biology 2002, 3:reports4006-reports4006.2 (14 February 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Pathogen-host cell interactions' minisymposium at the 41st Annual Meeting of the American Society for Cell Biology, Washington DC, USA, 8-12 December 2001.
	Meeting report Genomics meets nanoscience: probing genes and the cell nucleus at 10^-9 meters Joan Politz, Ana Pombo Genome Biology 2002, 3:reports4007-reports4007.3 (25 February 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Jackson Laboratory 'Genomics meets nanoscience' meeting, Bar Harbor, USA, 9-12 October 2001.
	Deposited research article Using orthologous and paralogous proteins to identify specificity determining residues Leonid A Mirny, Mikhail S Gelfand Genome Biology 2002, 3:preprint0002-preprint0002.20 (19 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Functional specificity of proteins is assumed to be conserved among orthologs and to be different among paralogs. We used this assumption to identify the residues that determine specificity of protein-DNA and protein-ligand recognition and present a method to compute the statistical significance of the predictions.
	Research news Dodo genetics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020301-01 (1 March 2002) Abstract \| Full text \| Editor’s summary Genetic analysis provides insights into the origins of the dodo.
	Research news Good taste Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020301-02 (1 March 2002) Abstract \| Full text \| Editor’s summary G-protein-coupled receptors function as taste sensors of L-amino-acids.
	Research news Shape of a chromodomain Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020304-01 (4 March 2002) Abstract \| Full text \| Editor’s summary The structure of the HP1 chromodomain shows how it recognizes methylated histone tails.
	Research news Chipping away at GATA Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020305-01 (5 March 2002) Abstract \| Full text \| Editor’s summary Researchers have identified additional GATA-1 binding sites in the β-globin locus.
	Research news Cytomegalovirus control Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020306-01 (6 March 2002) Abstract \| Full text \| Editor’s summary Infection by the human cytomegalovirus induces cellular genes that regulate cell cycle progression.
	Research news Shotgun strategies Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020307-01 (7 March 2002) Abstract \| Full text \| Editor’s summary One year after the two human draft genome sequences were published the debate over sequencing strategies continues.
	Research news Proteome purification Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020308-01 (8 March 2002) Abstract \| Full text \| Editor’s summary A high-throughput approach has been applied to purify affinity-tagged human proteins expressed in bacteria.
	Research news Antisense spuds Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020311-01 (11 March 2002) Abstract \| Full text \| Editor’s summary The simultaneous inhibition of three plant enzymes using antisense technology creates improved potato starch.
	Research news Musical protection Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020312-01 (12 March 2002) Abstract \| Full text \| Editor’s summary Copyright protection may be music to the ears of genomics companies.
	Research news Take your PIC Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020313-01 (13 March 2002) Abstract \| Full text \| Editor’s summary Analysis of differentiation-dependent transcription reveals that the pre-initiation complex (PIC) can assemble before chromatin remodelling.
	Research news ATM splicing defect Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020314-01 (14 March 2002) Abstract \| Full text \| Editor’s summary A mutation in the ATM gene can cause aberrant splicing and inclusion of a cryptic exon.
	Research news Embryonic vs somatic mutation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020315-01 (15 March 2002) Abstract \| Full text \| Editor’s summary The mutation frequency of embryonic stem cells is much lower than somatic cells but often involves chromosomal loss and uniparental disomy.
	Research news Where is the proteome? Anna Sharman Genome Biology 2002, 3:spotlight-20020318-01 (18 March 2002) Abstract \| Full text \| Editor’s summary A high-throughput approach to studying the subcellular localization of proteins has provided an overview of yeast protein localization.
	Research news CpG islands Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020319-01 (19 March 2002) Abstract \| Full text \| Editor’s summary Careful analysis of completed human genome sequences defines the properties of CpG islands.
	Research news Phage tropism Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020320-01 (20 March 2002) Abstract \| Full text \| Editor’s summary A reverse transcriptase enzyme and genomic repeat sequences coordinate a tropic switch in a bacteriophage
	Research news Ribozyme targeting Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020321-01 (21 March 2002) Abstract \| Full text \| Editor’s summary Cationic liposomes can deliver hammerhead ribozymes, which can be used to prevent tumour growth in vivo.
	Research news Quick to respond Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020322-01 (22 March 2002) Abstract \| Full text \| Editor’s summary Scientists from Celera defend their claim of successful assembly of the human genome using the whole-genome shotgun technique.
	Research news RNAi to RNAi Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020326-01 (26 March 2002) Abstract \| Full text \| Editor’s summary An RNA interference (RNAi) screen has been used to find genes involved in RNA interference.
	Research news Annotating Arabidopsis Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020326-02 (26 March 2002) Abstract \| Full text \| Editor’s summary Japanese researchers have isolated full-length cDNAs covering 60% of the genes in the Arabidopsis genome.
	Research news Tissue transcriptomes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020327-02 (27 March 2002) Abstract \| Full text \| Editor’s summary Extensive analysis of the transcriptomes from mouse and human tissues provides clues about gene function.
	Research news Europe boosts post-genomic research Helen Gavaghan Genome Biology 2002, 3:spotlight-20020327-01 (27 March 2002) Abstract \| Full text \| Editor’s summary The award of almost -40 million to three pan-European post-genomic projects signals a shift in funding of science by the European Union.
	Research news Divine DNA repair Tudor Toma Genome Biology 2002, 3:spotlight-20020328-01 (28 March 2002) Abstract \| Full text \| Editor’s summary The Artemis protein cuts away damaged DNA to allow strands to be rejoined.
	Research news MicroRNAs Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020328-03 (28 March 2002) Abstract \| Full text \| Editor’s summary MicroRNAs in the fly genome are complementary to some 3' untranslated regions.
	Research news Small genomes are still shrinking Tudor Toma Genome Biology 2002, 3:spotlight-20020328-02 (28 March 2002) Abstract \| Full text \| Editor’s summary The small Buchnera genome is still shrinking toward a minimum set of genes necessary for its symbiotic lifestyle.
	Research
	Research Vector algebra in the analysis of genome-wide expression data Finny G Kuruvilla, Peter J Park, Stuart L Schreiber Genome Biology 2002, 3:research0011-research0011.11 (13 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary How best to analyze data from thousands of transcription-profiling experiments remains an important challenge. Using a sample analysis of cells treated with rapamycin, a framework is presented, based on vector algebra for the analysis of transcription profiles, that is geometrically intuitive and computationally efficient.
	Research Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors Lakshminarayan M Iyer, Eugene V Koonin, L Aravind Genome Biology 2002, 3:research0012-research0012.11 (13 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using computational analysis, the amino-terminal module of the D6R/N1R proteins is shown to define a novel, conserved DNA-binding domain (the KilA-N domain) found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. It is suggested to be homologous to the fungal DNA-binding APSES domain; analysis of these domains points to extensive domain shuffling and lineage-specific gene family expansion within DNA virus genomes.
	Research Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA Esperanza Benítez-Bellón, Gabriel Moreno-Hagelsieb, Julio Collado-Vides Genome Biology 2002, 3:research0013-research0013.16 (21 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A collection of 86 sets of co-regulated genes from Escherichia coli were used to evaluate two methods for pattern discovery and pattern searching: dyad analysis/dyad sweeping and multiple alignment analysis. Particular emphasis was placed on minimizing the rate of false positives. With more robust methods, regulatory predictions could help identify the function of unknown genes.
	Research Molecular genetics and structural genomics of the human protein kinase C gene module Kurt Kofler, Martin Erdel, Gerd Utermann, Gottfried Baier Genome Biology 2002, 3:research0014-research0014.10 (27 February 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fine chromosomal mapping of all nine human protein kinase C genes by fluorescence in situ hybridization was carried out, using cosmid and BAC probes. The genes were found to be dispersed throughout the genome; PKC gene structure was also studied.
	Correspondence
	Erratum The trappist's approach to pathfinding: elucidating brain wiring using secretory-trap mutagenesis Andrew J Furley Genome Biology 2002, 3:interactions2001-interactions2001.1 (25 February 2002) Abstract \| Full text \| PDF \| Editor’s summary An erratum to The trappist's approach to pathfinding: elucidating brain wiring using secretory-trap mutagenesis by AJ Furley. Genome Biology 2001, 2:reviews1026.1-1026.5

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Volume 3 Issue 3

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