Genome Biology | Volume 6 Issue 10

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	Volume 6 Issue 10
	Comment
	Comment Half right Gregory A Petsko Genome Biology 2005, 6:120 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Classifying research papers as true or false belittles and grossly oversimplifies the way most fields work.
	Review
	Review Global approaches to understanding ubiquitination Peter Kaiser, Lan Huang Genome Biology 2005, 6:233 (29 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The proteome-wide strategies that are being used to study aspects of ubiquitin biology are reviewed, including substrates, components of the proteasome and ubiquitin ligases, and deubiquitination.
	Minireview The ribosomal subunit assembly line Mensur Dlakić Genome Biology 2005, 6:234 (19 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent proteomic studies in in yeast and plants have identified nearly 200 yeast proteins that participate in the assembly of ribosomal subunits and their transport from the nucleus, and revealed considerable variability in the protein composition of individual plant ribosomes.
	Minireview Systems biology approaches in cell signaling research Raymond E Chen, Jeremy Thorner Genome Biology 2005, 6:235 (29 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies reveal important information about the rates of signal transmission and propagation and help establish some general regulatory characteristics of multi-tiered signaling cascades.
	Report
	Paper report Articles selected by Faculty of 1000: ectopic gene conversions; heterozygous insertions in C. elegans; plant RNA silencing suppression; phage insertion into the host genome; screening viral protein variants Genome Biology 2005, 6:352 (20 September 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering ectopic gene conversions; heterozygous insertions in C. elegans; plant RNA silencing suppression; phage insertion into the host genome; screening viral protein variants.
	Paper report Articles selected by Faculty of 1000: Wolbachia ankyrin domain-encoding genes; horizontal gene transfer rates; profiling mental retardation; murine exon evolution; rice and Arabidopsis transcriptomes Genome Biology 2005, 6:353 (3 October 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering Wolbachia ankyrin domain-encoding genes; horizontal gene transfer rates; profiling mental retardation; murine exon evolution; rice and Arabidopsis transcriptomes.
	Meeting report Microbial metagenomics Emmanuel F Mongodin, Joanne B Emerson, Karen E Nelson Genome Biology 2005, 6:347 (27 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 105th Annual Meeting of the American Society for Microbiology, Atlanta, USA, 5-9 June 2005.
	Meeting report Bioinformatics with a French accent Laurence D Hurst, Laurent Duret Genome Biology 2005, 6:349 (28 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the bioinformatics conference 'JOBIM: Journées ouvertes biologie informatiques mathématiques', Lyon, France, 6-8 July 2005.
	Meeting report A weed for all reasons Vivian F Irish, Christopher D Day Genome Biology 2005, 6:350 (28 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 16th International Arabidopsis Conference, Madison, USA, 15-19 June 2005.
	Meeting report Putting the 'bio' into bioinformatics Olga G Troyanskaya Genome Biology 2005, 6:351 (29 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 13th Annual Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, USA, 25-29 June 2005.
	Meeting report Digital drug discovery Michael A Goldman Genome Biology 2005, 6:348 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cambridge Healthtech Institute conference 'Beyond Genome', San Franciso, USA, 13-16 June 2005.
	Deposited research article A Protein Similarity Approach For Detecting Prophage Regions In Bacterial Genomes Geeta V Rao, Preeti Mehta, K V Srividhya, S Krishnaswamy Genome Biology 2005, 6:P11 (9 September 2005) Abstract \| Full text \| PDF \| Editor’s summary The e14 region from Escherichia coli is a decaying lambdoid prophage element. This study shows that a protein based comparative approach using BLAST can be used to identify similar lambdoid prophage elements in other bacterial genomes
	Research
	Research Sequence and structural analysis of BTB domain proteins Peter J Stogios, Gregory S Downs, Jimmy JS Jauhal, Sukhjeen K Nandra, Gilbert G Privé Genome Biology 2005, 6:R82 (15 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary An analysis of the protein architecture, genomic distribution and sequence conservation of BTB domain proteins in 17 fully sequenced eukaryotes reveals a high structural conservation and adaptation to different modes of self-association and interactions with non-BTB proteins.
	Research The dog and rat olfactory receptor repertoires Pascale Quignon, Mathieu Giraud, Maud Rimbault, Patricia Lavigne, Sandrine Tacher, Emmanuelle Morin, Elodie Retout, Anne-Sophie Valin, Kerstin Lindblad-Toh, Jacques Nicolas, Francis Galibert Genome Biology 2005, 6:R83 (28 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An almost complete list of odorant receptor genes in the dog (1,094 genes) and the rat (1,493 genes) is described. A comparison of odorant receptor repertoires in rat, dog, mouse and human is also included.
	Research Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice Shixia Huang, Yi Li, Yidong Chen, Katrina Podsypanina, Mario Chamorro, Adam B Olshen, Kartiki V Desai, Anne Tann, David Petersen, Jeffrey E Green, Harold E Varmus Genome Biology 2005, 6:R84 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary cDNA microarray-derived expression profiles of MMTV-Wnt-1 and MMTV-Neu transgenic mice reveal several hundred genes to be differentially expressed at each stage of breast tumor development.
	Research The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure Eric Bapteste, Robert L Charlebois, Dave MacLeod, Céline Brochier Genome Biology 2005, 6:R85 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the taxonomic distribution, evolutionary rates and phylogenies of 65 proteins related to the nuclear pore complex shows high heterogeneity of evolutionary rates between these proteins.
	Research A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs Reut Shalgi, Michal Lapidot, Ron Shamir, Yitzhak Pilpel Genome Biology 2005, 6:R86 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By analyzing 3' UTR sequences and mRNA decay profiles in yeast, 53 sequence motifs have been identified that may be implicated in stabilization or destabilization of mRNA.
	Method Searching for differentially expressed gene combinations Marcel Dettling, Edward Gabrielson, Giovanni Parmigiani Genome Biology 2005, 6:R88 (19 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CorScor is a novel approach to identifying gene pairs with joint differential expression. It can be used to detect phenotype-related dependencies and interactions among genes.
	Method Inferring protein domain interactions from databases of interacting proteins Robert Riley, Christopher Lee, Chiara Sabatti, David Eisenberg Genome Biology 2005, 6:R89 (19 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary A new method for inferring domain interactions from databases of interacting proteins was used to deduce 3,005 high-confidence domain interactions from over 177,000 potential interactions.
	Method Explicit equilibrium modeling of transcription-factor binding and gene regulation Joshua A Granek, Neil D Clarke Genome Biology 2005, 6:R87 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational model, GOMER, is presented that predicts transcription-factor binding and incorporates effects of cooperativity and competition.

	Volume 6 Issue 10
	Comment
	Comment Half right Gregory A Petsko Genome Biology 2005, 6:120 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Classifying research papers as true or false belittles and grossly oversimplifies the way most fields work.
	Review
	Review Global approaches to understanding ubiquitination Peter Kaiser, Lan Huang Genome Biology 2005, 6:233 (29 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The proteome-wide strategies that are being used to study aspects of ubiquitin biology are reviewed, including substrates, components of the proteasome and ubiquitin ligases, and deubiquitination.
	Minireview The ribosomal subunit assembly line Mensur Dlakić Genome Biology 2005, 6:234 (19 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent proteomic studies in in yeast and plants have identified nearly 200 yeast proteins that participate in the assembly of ribosomal subunits and their transport from the nucleus, and revealed considerable variability in the protein composition of individual plant ribosomes.
	Minireview Systems biology approaches in cell signaling research Raymond E Chen, Jeremy Thorner Genome Biology 2005, 6:235 (29 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies reveal important information about the rates of signal transmission and propagation and help establish some general regulatory characteristics of multi-tiered signaling cascades.
	Report
	Paper report Articles selected by Faculty of 1000: ectopic gene conversions; heterozygous insertions in C. elegans; plant RNA silencing suppression; phage insertion into the host genome; screening viral protein variants Genome Biology 2005, 6:352 (20 September 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering ectopic gene conversions; heterozygous insertions in C. elegans; plant RNA silencing suppression; phage insertion into the host genome; screening viral protein variants.
	Paper report Articles selected by Faculty of 1000: Wolbachia ankyrin domain-encoding genes; horizontal gene transfer rates; profiling mental retardation; murine exon evolution; rice and Arabidopsis transcriptomes Genome Biology 2005, 6:353 (3 October 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering Wolbachia ankyrin domain-encoding genes; horizontal gene transfer rates; profiling mental retardation; murine exon evolution; rice and Arabidopsis transcriptomes.
	Meeting report Microbial metagenomics Emmanuel F Mongodin, Joanne B Emerson, Karen E Nelson Genome Biology 2005, 6:347 (27 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 105th Annual Meeting of the American Society for Microbiology, Atlanta, USA, 5-9 June 2005.
	Meeting report Bioinformatics with a French accent Laurence D Hurst, Laurent Duret Genome Biology 2005, 6:349 (28 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the bioinformatics conference 'JOBIM: Journées ouvertes biologie informatiques mathématiques', Lyon, France, 6-8 July 2005.
	Meeting report A weed for all reasons Vivian F Irish, Christopher D Day Genome Biology 2005, 6:350 (28 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 16th International Arabidopsis Conference, Madison, USA, 15-19 June 2005.
	Meeting report Putting the 'bio' into bioinformatics Olga G Troyanskaya Genome Biology 2005, 6:351 (29 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 13th Annual Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, USA, 25-29 June 2005.
	Meeting report Digital drug discovery Michael A Goldman Genome Biology 2005, 6:348 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cambridge Healthtech Institute conference 'Beyond Genome', San Franciso, USA, 13-16 June 2005.
	Deposited research article A Protein Similarity Approach For Detecting Prophage Regions In Bacterial Genomes Geeta V Rao, Preeti Mehta, K V Srividhya, S Krishnaswamy Genome Biology 2005, 6:P11 (9 September 2005) Abstract \| Full text \| PDF \| Editor’s summary The e14 region from Escherichia coli is a decaying lambdoid prophage element. This study shows that a protein based comparative approach using BLAST can be used to identify similar lambdoid prophage elements in other bacterial genomes
	Research
	Research Sequence and structural analysis of BTB domain proteins Peter J Stogios, Gregory S Downs, Jimmy JS Jauhal, Sukhjeen K Nandra, Gilbert G Privé Genome Biology 2005, 6:R82 (15 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary An analysis of the protein architecture, genomic distribution and sequence conservation of BTB domain proteins in 17 fully sequenced eukaryotes reveals a high structural conservation and adaptation to different modes of self-association and interactions with non-BTB proteins.
	Research The dog and rat olfactory receptor repertoires Pascale Quignon, Mathieu Giraud, Maud Rimbault, Patricia Lavigne, Sandrine Tacher, Emmanuelle Morin, Elodie Retout, Anne-Sophie Valin, Kerstin Lindblad-Toh, Jacques Nicolas, Francis Galibert Genome Biology 2005, 6:R83 (28 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An almost complete list of odorant receptor genes in the dog (1,094 genes) and the rat (1,493 genes) is described. A comparison of odorant receptor repertoires in rat, dog, mouse and human is also included.
	Research Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice Shixia Huang, Yi Li, Yidong Chen, Katrina Podsypanina, Mario Chamorro, Adam B Olshen, Kartiki V Desai, Anne Tann, David Petersen, Jeffrey E Green, Harold E Varmus Genome Biology 2005, 6:R84 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary cDNA microarray-derived expression profiles of MMTV-Wnt-1 and MMTV-Neu transgenic mice reveal several hundred genes to be differentially expressed at each stage of breast tumor development.
	Research The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure Eric Bapteste, Robert L Charlebois, Dave MacLeod, Céline Brochier Genome Biology 2005, 6:R85 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the taxonomic distribution, evolutionary rates and phylogenies of 65 proteins related to the nuclear pore complex shows high heterogeneity of evolutionary rates between these proteins.
	Research A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs Reut Shalgi, Michal Lapidot, Ron Shamir, Yitzhak Pilpel Genome Biology 2005, 6:R86 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By analyzing 3' UTR sequences and mRNA decay profiles in yeast, 53 sequence motifs have been identified that may be implicated in stabilization or destabilization of mRNA.
	Method Searching for differentially expressed gene combinations Marcel Dettling, Edward Gabrielson, Giovanni Parmigiani Genome Biology 2005, 6:R88 (19 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CorScor is a novel approach to identifying gene pairs with joint differential expression. It can be used to detect phenotype-related dependencies and interactions among genes.
	Method Inferring protein domain interactions from databases of interacting proteins Robert Riley, Christopher Lee, Chiara Sabatti, David Eisenberg Genome Biology 2005, 6:R89 (19 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary A new method for inferring domain interactions from databases of interacting proteins was used to deduce 3,005 high-confidence domain interactions from over 177,000 potential interactions.
	Method Explicit equilibrium modeling of transcription-factor binding and gene regulation Joshua A Granek, Neil D Clarke Genome Biology 2005, 6:R87 (30 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational model, GOMER, is presented that predicts transcription-factor binding and incorporates effects of cooperativity and competition.

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Volume 6 Issue 10

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