Genome Biology | Volume 6 Issue 4

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	Volume 6 Issue 4
	Comment
	Comment Who owns the data? Gregory A Petsko Genome Biology 2005, 6:107 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary About ten years ago, a group of scientists began to argue that it was unfair to ask other scientists to pay to read the results of research that had been publicly funded.
	Review
	Review A non-random walk through the genome Brian Oliver, Tom Misteli Genome Biology 2005, 6:214 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes showing particular expression patterns are not randomly distributed in the genome but are clustered into neighborhoods. This organization may be related to chromatin and the structure of the nucleus.
	Minireview Genomic studies of mood disorders - the brain as a muscle? Alexander B Niculescu Genome Biology 2005, 6:215 (24 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent genomic studies suggest a role for growth factors in mood disorders such as depression.
	Minireview SINEs point to abundant editing in the human genome Joshua DeCerbo, Gordon G Carmichael Genome Biology 2005, 6:216 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent bioinformatic analyses suggest that almost all human transcripts are edited by adenosine deaminases; most of this editing is in Alu elements.
	Minireview Assessing the origin of species in the genomic era Leonie C Moyle Genome Biology 2005, 6:217 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent genomic analyses in Drosophila species suggest that modified olfactory cues are involved in discrimination that is reinforced by natural selection.
	Opinion Anatomical ontologies: names and places in biology Richard Baldock, Albert Burger Genome Biology 2005, 6:108 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recently, ideas from the field of ontology have been picked up by computer scientists as a basis for encoding knowledge and with the hope of achieving interoperability and intelligent system behavior. The use of anatomy ontologies to represent space in biological organisms, specifically mouse and human are reviewed here.
	Report
	Paper report Articles selected by Faculty of 1000: meiosis evolution; picoeukaryote cell-cycle genes; identifying targets of small molecules; rice genome evolution; circadian gene expression cyanobacteria Genome Biology 2005, 6:318 (11 March 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering meiosis evolution; picoeukaryote cell-cycle genes; identifying targets of small molecules; rice genome evolution; circadian gene expression cyanobacteria.
	Paper report Articles selected by Faculty of 1000: heterochromatin correlates with gene silencing; identifying genes for hypertension; protein domain graphs for prokaryotic phylogeny; Drosophila haemocyte function; rice chloroplast-nuclear DNA shuffling Genome Biology 2005, 6:319 (24 March 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering heterochromatin correlation with gene silencing; the identification of genes for hypertension; protein domain graphs for prokaryotic phylogeny; Drosophila haemocyte function; rice chloroplast-nuclear DNA shuffling.
	Meeting report Diverse roles for RNA in gene regulation Nelson C Lau, Eric C Lai Genome Biology 2005, 6:315 (29 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium 'Diverse roles for RNA in gene regulation', Breckenridge, USA, 8-15 January 2005.
	Meeting report Protein degradation, signaling, microRNAs and cancer Peter Gallant Genome Biology 2005, 6:316 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the biannual Swiss Institute for Experimental Cancer Research (ISREC) Symposium on the Cell and Molecular Biology of Cancer, Lausanne, Switzerland, 19-22 January 2005.
	Meeting report Making systems biology work in the 21st century Athel Cornish-Bowden Genome Biology 2005, 6:317 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Biochemical Society meeting 'Systems biology: will it work?', Sheffield, UK, 5 January 2005.
	Deposited research article A novel scheme to assess factors involved in the reproducibility of DNA-microarray data Sacha van Hijum, Anne de Jong, Richard Baerends, Harma A Karsens, Naomi E Kramer, Rasmus Larsen, Chris D den Hengst, Casper J Albers, Jan Kok, Oscar P Kuipers Genome Biology 2005, 6:P4 (3 March 2005) Abstract \| Full text \| PDF \| Editor’s summary In order to provide a quick and robust method for assessing data quality and sources of errors in DNA-microarray experiments a novel and cost-effective validation scheme was devised, implemented, and employed. The method was validated using Lactococcus lactis IL1403 amplicon-based DNA-microarray experiments. It was shown that the validation scheme allows determining conditions that could be improved to yield even higher DNA-microarray data quality.
	Deposited research article A non-parametric approach for identifying differentially expressed genes in factorial microarray experiments Qihua Tan, Jesper Dahlgaard, Werner Vach, Basem M Abdallah, Moustapha Kassem, Torben A Kruse Genome Biology 2005, 6:P5 (10 March 2005) Abstract \| Full text \| PDF \| Editor’s summary A non-parametric approach is prsented that uses bootstrap-assisted correspondence analysis to identify and validate genes that are differentially expressed in factorial microarray experiments which are characterized by simultaneous measurement of the effects of multiple experiment factors.
	Deposited research article Sequence complementarity of U2 snRNA and U2A' intron predicts intron function Maria Lundin Genome Biology 2005, 6:P6 (29 March 2005) Abstract \| Full text \| PDF \| Editor’s summary This paper exemplifies a putative function of an intron RNA (i5e6i6) of the U2 small nuclear ribonucleoprotein particle (U2 snRNP) A' specific protein (U2A') pre mRNA. A possible RNA-RNA structure formed by complementary sequences in U2A'i5e6i6 and U2 snRNA is conserved in vertebrates, suggesting a role of U2A'i5e6i6 in the 3'end processing of U2 snRNA primary transcript.
	Research news Zinc finger nucleases correct genes Graciela Flores Genome Biology 2005, 6:spotlight-20050404-01 (4 April 2005) Abstract \| Full text \| Editor’s summary Technique used successfully for IL2R-gamma receptor, mutated in X-linked SCID
	Research news Improving adenovirus vaccines Don Monroe Genome Biology 2005, 6:spotlight-20050405-01 (5 April 2005) Abstract \| Full text \| Editor’s summary Including the target in the viral capsid allows immune boost against Pseudomonas
	Research news Mouse, fly wound repair linked Charles Q Choi Genome Biology 2005, 6:spotlight-20050415-01 (15 April 2005) Abstract \| Full text \| Editor’s summary Reports suggest common control factors for the healing of mammal skin and insect cuticle
	Research news New model of leukocyte arrest Graciela Flores Genome Biology 2005, 6:spotlight-20050418-01 (18 April 2005) Abstract \| Full text \| Editor’s summary Paper suggests chemokines stop lymphocytes in a fraction of a second, faster than previously thought
	Research news Human RNA silences viral DNA Charles Q Choi Genome Biology 2005, 6:spotlight-20050422-01 (22 April 2005) Abstract \| Full text \| Editor’s summary MicroRNA plays an unexpected role in the process, researchers report in Science
	Research news Same-sex fungi can mate Charles Q Choi Genome Biology 2005, 6:spotlight-20050426-01 (26 April 2005) Abstract \| Full text \| Editor’s summary C. neoformans' sexual cycle could shed light on the evolution from asexuality to sex
	Research news A primitive energy pathway in fungus Charles Q Choi Genome Biology 2005, 6:spotlight-20050429-02 (29 April 2005) Abstract \| Full text \| Editor’s summary Energy-generating proton pump previously seen only in prokaryotes is identified in L. maculans
	Research news Gene may regulate need for sleep Harvey Black Genome Biology 2005, 6:spotlight-20050429-01 (29 April 2005) Abstract \| Full text \| Editor’s summary In Drosophila, a point mutation in Shaker results in flies that snooze much less than wildtype
	Research
	Research Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana Xiu-Jie Wang, Terry Gaasterland, Nam-Hai Chua Genome Biology 2005, 6:R30 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A new computational method for predicting cis-encoded natural antisense transcripts (NATs) in Arabidopsis identified 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed, and analysis of MPSS data suggested that for most pairs one of the two transcripts is predominantly expressed in a tissue-specific manner.
	Research Contribution of transcriptional regulation to natural variations in Arabidopsis Wenqiong J Chen, Sherman H Chang, Matthew E Hudson, Wai-King Kwan, Jingqiu Li, Bram Estes, Daniel Knoll, Liang Shi, Tong Zhu Genome Biology 2005, 6:R32 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Among five accessions 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis, identifying 60 genes that were differentially expressed in different accession backgrounds in an organ-dependent manner. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession.
	Research Conservation of tandem stop codons in yeasts Han Liang, Andre RO Cavalcanti, Laura F Landweber Genome Biology 2005, 6:R31 (16 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This study shows that a statistical excess of stop codons has evolved at the third codon downstream of the real stop codon UAA in yeasts. Comparative analysis indicates that stop codons at this location are considerably more conserved than sense codons, suggesting that these tandem stop codons are maintained by selection.
	Research A genomic approach to investigate developmental cell death in woody tissues of Populus trees Charleen Moreau, Nikolay Aksenov, Maribel Lorenzo, Bo Segerman, Christiane Funk, Peter Nilsson, Stefan Jansson, Hannele Tuominen Genome Biology 2005, 6:R34 (22 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Populus EST dataset was used for in silico transcript profiling of the programmed death of the xylem fibres in woody tissues of Populus stem. The analysis suggests the involvement of two novel extracellular serine proteases, nodulin-like proteins and an AtOST1 (Arabidopsis thaliana OPEN STOMATA 1) homolog in signaling fiber-cell death.
	Research An evolutionary and functional assessment of regulatory network motifs Aurélien Mazurie, Samuel Bottani, Massimo Vergassola Genome Biology 2005, 6:R35 (24 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Cross-species comparison and functional analysis of over-abundant motifs in an integrated network of yeast transcriptional and protein-protein interaction data showed that the over-abundance of the network motifs does not have any immediate functional or evolutive counterpart.
	Research Quantitative genomics of starvation stress resistance in Drosophila Susan T Harbison, Sherman Chang, Kim P Kamdar, Trudy FC Mackay Genome Biology 2005, 6:R36 (24 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The efficacy of transcriptional profiling for identifying networks of pleiotropic genes regulating complex traits was assessed. The transcriptional response to starvation stress in males and females of the Oregon-R and 2b Drosophila strains, as well as four recombinant inbred lines derived from them, was shown to be different between the sexes and to involve approximately 25% of the genome.
	Research Promoter features related to tissue specificity as measured by Shannon entropy Jonathan Schug, Winfried-Paul Schuller, Claudia Kappen, J Michael Salbaum, Maja Bucan, Christian J Stoeckert Genome Biology 2005, 6:R33 (29 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide analysis of promoters was carried out in the context of gene expression patterns in tissue surveys using human microarray and EST-based expression data. The study revealed that most genes show statistically significant tissue-dependent variations of expression level and identified components of promoters that distinguish tissue-specific from ubiquitous genes.
	Research The microbial selenoproteome of the Sargasso Sea Yan Zhang, Dmitri E Fomenko, Vadim N Gladyshev Genome Biology 2005, 6:R37 (29 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the selenoproteome of the largest microbial sequence dataset, the Sargasso Sea environmental genome sequences, identified 310 selenoprotein genes that clustered into 25 families. This included 101 new selenoprotein genes that belonged to 15 families, doubling the number of prokaryotic selenoprotein families.
	Method Pilot Anopheles gambiae full-length cDNA study: sequencing and initial characterization of 35,575 clones Shawn M Gomez, Karin Eiglmeier, Beatrice Segurens, Pierre Dehoux, Arnaud Couloux, Claude Scarpelli, Patrick Wincker, Jean Weissenbach, Paul T Brey, Charles W Roth Genome Biology 2005, 6:R39 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A preliminary analysis of over 35,000 clones from a full-length enriched cDNA library from the malaria mosquito vector Anopheles gambiae identifies nearly 3,700 genes, including a large number of genes that had not been annotated previously.
	Method Derivation of genetic interaction networks from quantitative phenotype data Becky L Drees, Vesteinn Thorsson, Gregory W Carter, Alexander W Rives, Marisa Z Raymond, Iliana Avila-Campillo, Paul Shannon, Timothy Galitski Genome Biology 2005, 6:R38 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic interaction networks were derived from quantitative phenotype data by analyzing agar-invasion phenotypes of mutant yeast strains, which showed specific modes of genetic interaction with specific biological processes.

	Volume 6 Issue 4
	Comment
	Comment Who owns the data? Gregory A Petsko Genome Biology 2005, 6:107 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary About ten years ago, a group of scientists began to argue that it was unfair to ask other scientists to pay to read the results of research that had been publicly funded.
	Review
	Review A non-random walk through the genome Brian Oliver, Tom Misteli Genome Biology 2005, 6:214 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes showing particular expression patterns are not randomly distributed in the genome but are clustered into neighborhoods. This organization may be related to chromatin and the structure of the nucleus.
	Minireview Genomic studies of mood disorders - the brain as a muscle? Alexander B Niculescu Genome Biology 2005, 6:215 (24 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent genomic studies suggest a role for growth factors in mood disorders such as depression.
	Minireview SINEs point to abundant editing in the human genome Joshua DeCerbo, Gordon G Carmichael Genome Biology 2005, 6:216 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent bioinformatic analyses suggest that almost all human transcripts are edited by adenosine deaminases; most of this editing is in Alu elements.
	Minireview Assessing the origin of species in the genomic era Leonie C Moyle Genome Biology 2005, 6:217 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent genomic analyses in Drosophila species suggest that modified olfactory cues are involved in discrimination that is reinforced by natural selection.
	Opinion Anatomical ontologies: names and places in biology Richard Baldock, Albert Burger Genome Biology 2005, 6:108 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recently, ideas from the field of ontology have been picked up by computer scientists as a basis for encoding knowledge and with the hope of achieving interoperability and intelligent system behavior. The use of anatomy ontologies to represent space in biological organisms, specifically mouse and human are reviewed here.
	Report
	Paper report Articles selected by Faculty of 1000: meiosis evolution; picoeukaryote cell-cycle genes; identifying targets of small molecules; rice genome evolution; circadian gene expression cyanobacteria Genome Biology 2005, 6:318 (11 March 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering meiosis evolution; picoeukaryote cell-cycle genes; identifying targets of small molecules; rice genome evolution; circadian gene expression cyanobacteria.
	Paper report Articles selected by Faculty of 1000: heterochromatin correlates with gene silencing; identifying genes for hypertension; protein domain graphs for prokaryotic phylogeny; Drosophila haemocyte function; rice chloroplast-nuclear DNA shuffling Genome Biology 2005, 6:319 (24 March 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering heterochromatin correlation with gene silencing; the identification of genes for hypertension; protein domain graphs for prokaryotic phylogeny; Drosophila haemocyte function; rice chloroplast-nuclear DNA shuffling.
	Meeting report Diverse roles for RNA in gene regulation Nelson C Lau, Eric C Lai Genome Biology 2005, 6:315 (29 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium 'Diverse roles for RNA in gene regulation', Breckenridge, USA, 8-15 January 2005.
	Meeting report Protein degradation, signaling, microRNAs and cancer Peter Gallant Genome Biology 2005, 6:316 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the biannual Swiss Institute for Experimental Cancer Research (ISREC) Symposium on the Cell and Molecular Biology of Cancer, Lausanne, Switzerland, 19-22 January 2005.
	Meeting report Making systems biology work in the 21st century Athel Cornish-Bowden Genome Biology 2005, 6:317 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Biochemical Society meeting 'Systems biology: will it work?', Sheffield, UK, 5 January 2005.
	Deposited research article A novel scheme to assess factors involved in the reproducibility of DNA-microarray data Sacha van Hijum, Anne de Jong, Richard Baerends, Harma A Karsens, Naomi E Kramer, Rasmus Larsen, Chris D den Hengst, Casper J Albers, Jan Kok, Oscar P Kuipers Genome Biology 2005, 6:P4 (3 March 2005) Abstract \| Full text \| PDF \| Editor’s summary In order to provide a quick and robust method for assessing data quality and sources of errors in DNA-microarray experiments a novel and cost-effective validation scheme was devised, implemented, and employed. The method was validated using Lactococcus lactis IL1403 amplicon-based DNA-microarray experiments. It was shown that the validation scheme allows determining conditions that could be improved to yield even higher DNA-microarray data quality.
	Deposited research article A non-parametric approach for identifying differentially expressed genes in factorial microarray experiments Qihua Tan, Jesper Dahlgaard, Werner Vach, Basem M Abdallah, Moustapha Kassem, Torben A Kruse Genome Biology 2005, 6:P5 (10 March 2005) Abstract \| Full text \| PDF \| Editor’s summary A non-parametric approach is prsented that uses bootstrap-assisted correspondence analysis to identify and validate genes that are differentially expressed in factorial microarray experiments which are characterized by simultaneous measurement of the effects of multiple experiment factors.
	Deposited research article Sequence complementarity of U2 snRNA and U2A' intron predicts intron function Maria Lundin Genome Biology 2005, 6:P6 (29 March 2005) Abstract \| Full text \| PDF \| Editor’s summary This paper exemplifies a putative function of an intron RNA (i5e6i6) of the U2 small nuclear ribonucleoprotein particle (U2 snRNP) A' specific protein (U2A') pre mRNA. A possible RNA-RNA structure formed by complementary sequences in U2A'i5e6i6 and U2 snRNA is conserved in vertebrates, suggesting a role of U2A'i5e6i6 in the 3'end processing of U2 snRNA primary transcript.
	Research news Zinc finger nucleases correct genes Graciela Flores Genome Biology 2005, 6:spotlight-20050404-01 (4 April 2005) Abstract \| Full text \| Editor’s summary Technique used successfully for IL2R-gamma receptor, mutated in X-linked SCID
	Research news Improving adenovirus vaccines Don Monroe Genome Biology 2005, 6:spotlight-20050405-01 (5 April 2005) Abstract \| Full text \| Editor’s summary Including the target in the viral capsid allows immune boost against Pseudomonas
	Research news Mouse, fly wound repair linked Charles Q Choi Genome Biology 2005, 6:spotlight-20050415-01 (15 April 2005) Abstract \| Full text \| Editor’s summary Reports suggest common control factors for the healing of mammal skin and insect cuticle
	Research news New model of leukocyte arrest Graciela Flores Genome Biology 2005, 6:spotlight-20050418-01 (18 April 2005) Abstract \| Full text \| Editor’s summary Paper suggests chemokines stop lymphocytes in a fraction of a second, faster than previously thought
	Research news Human RNA silences viral DNA Charles Q Choi Genome Biology 2005, 6:spotlight-20050422-01 (22 April 2005) Abstract \| Full text \| Editor’s summary MicroRNA plays an unexpected role in the process, researchers report in Science
	Research news Same-sex fungi can mate Charles Q Choi Genome Biology 2005, 6:spotlight-20050426-01 (26 April 2005) Abstract \| Full text \| Editor’s summary C. neoformans' sexual cycle could shed light on the evolution from asexuality to sex
	Research news A primitive energy pathway in fungus Charles Q Choi Genome Biology 2005, 6:spotlight-20050429-02 (29 April 2005) Abstract \| Full text \| Editor’s summary Energy-generating proton pump previously seen only in prokaryotes is identified in L. maculans
	Research news Gene may regulate need for sleep Harvey Black Genome Biology 2005, 6:spotlight-20050429-01 (29 April 2005) Abstract \| Full text \| Editor’s summary In Drosophila, a point mutation in Shaker results in flies that snooze much less than wildtype
	Research
	Research Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana Xiu-Jie Wang, Terry Gaasterland, Nam-Hai Chua Genome Biology 2005, 6:R30 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A new computational method for predicting cis-encoded natural antisense transcripts (NATs) in Arabidopsis identified 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed, and analysis of MPSS data suggested that for most pairs one of the two transcripts is predominantly expressed in a tissue-specific manner.
	Research Contribution of transcriptional regulation to natural variations in Arabidopsis Wenqiong J Chen, Sherman H Chang, Matthew E Hudson, Wai-King Kwan, Jingqiu Li, Bram Estes, Daniel Knoll, Liang Shi, Tong Zhu Genome Biology 2005, 6:R32 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Among five accessions 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis, identifying 60 genes that were differentially expressed in different accession backgrounds in an organ-dependent manner. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession.
	Research Conservation of tandem stop codons in yeasts Han Liang, Andre RO Cavalcanti, Laura F Landweber Genome Biology 2005, 6:R31 (16 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This study shows that a statistical excess of stop codons has evolved at the third codon downstream of the real stop codon UAA in yeasts. Comparative analysis indicates that stop codons at this location are considerably more conserved than sense codons, suggesting that these tandem stop codons are maintained by selection.
	Research A genomic approach to investigate developmental cell death in woody tissues of Populus trees Charleen Moreau, Nikolay Aksenov, Maribel Lorenzo, Bo Segerman, Christiane Funk, Peter Nilsson, Stefan Jansson, Hannele Tuominen Genome Biology 2005, 6:R34 (22 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Populus EST dataset was used for in silico transcript profiling of the programmed death of the xylem fibres in woody tissues of Populus stem. The analysis suggests the involvement of two novel extracellular serine proteases, nodulin-like proteins and an AtOST1 (Arabidopsis thaliana OPEN STOMATA 1) homolog in signaling fiber-cell death.
	Research An evolutionary and functional assessment of regulatory network motifs Aurélien Mazurie, Samuel Bottani, Massimo Vergassola Genome Biology 2005, 6:R35 (24 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Cross-species comparison and functional analysis of over-abundant motifs in an integrated network of yeast transcriptional and protein-protein interaction data showed that the over-abundance of the network motifs does not have any immediate functional or evolutive counterpart.
	Research Quantitative genomics of starvation stress resistance in Drosophila Susan T Harbison, Sherman Chang, Kim P Kamdar, Trudy FC Mackay Genome Biology 2005, 6:R36 (24 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The efficacy of transcriptional profiling for identifying networks of pleiotropic genes regulating complex traits was assessed. The transcriptional response to starvation stress in males and females of the Oregon-R and 2b Drosophila strains, as well as four recombinant inbred lines derived from them, was shown to be different between the sexes and to involve approximately 25% of the genome.
	Research Promoter features related to tissue specificity as measured by Shannon entropy Jonathan Schug, Winfried-Paul Schuller, Claudia Kappen, J Michael Salbaum, Maja Bucan, Christian J Stoeckert Genome Biology 2005, 6:R33 (29 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide analysis of promoters was carried out in the context of gene expression patterns in tissue surveys using human microarray and EST-based expression data. The study revealed that most genes show statistically significant tissue-dependent variations of expression level and identified components of promoters that distinguish tissue-specific from ubiquitous genes.
	Research The microbial selenoproteome of the Sargasso Sea Yan Zhang, Dmitri E Fomenko, Vadim N Gladyshev Genome Biology 2005, 6:R37 (29 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the selenoproteome of the largest microbial sequence dataset, the Sargasso Sea environmental genome sequences, identified 310 selenoprotein genes that clustered into 25 families. This included 101 new selenoprotein genes that belonged to 15 families, doubling the number of prokaryotic selenoprotein families.
	Method Pilot Anopheles gambiae full-length cDNA study: sequencing and initial characterization of 35,575 clones Shawn M Gomez, Karin Eiglmeier, Beatrice Segurens, Pierre Dehoux, Arnaud Couloux, Claude Scarpelli, Patrick Wincker, Jean Weissenbach, Paul T Brey, Charles W Roth Genome Biology 2005, 6:R39 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A preliminary analysis of over 35,000 clones from a full-length enriched cDNA library from the malaria mosquito vector Anopheles gambiae identifies nearly 3,700 genes, including a large number of genes that had not been annotated previously.
	Method Derivation of genetic interaction networks from quantitative phenotype data Becky L Drees, Vesteinn Thorsson, Gregory W Carter, Alexander W Rives, Marisa Z Raymond, Iliana Avila-Campillo, Paul Shannon, Timothy Galitski Genome Biology 2005, 6:R38 (31 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic interaction networks were derived from quantitative phenotype data by analyzing agar-invasion phenotypes of mutant yeast strains, which showed specific modes of genetic interaction with specific biological processes.

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Volume 6 Issue 4

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