Genome Biology | Volume 6 Issue 12

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	Volume 6 Issue 12
	Comment
	Comment Who steals my identity steals trash Gregory A Petsko Genome Biology 2005, 6:122 (2 December 2005) Abstract \| Full text \| PDF \| Editor’s summary I've thought about this identity theft issue, and I've decided not to worry about it. My blasé feelings come from careful consideration of the consequences, not to me, but to the thief, of anyone who steals the identity of an academic scientist.
	Review
	Protein family review The expansin superfamily Javier Sampedro, Daniel J Cosgrove Genome Biology 2005, 6:242 (28 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expansins are plant proteins that loosen cell walls via a nonenzymatic mechanism; they are involved in cell expansion and other developmental events during which cell-wall modification occurs.
	Minireview Ancient genomes A Rus Hoelzel Genome Biology 2005, 6:239 (1 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In an application of modern genomic methods to material from the Pleistocene, a recent study has undertaken to clone and sequence a portion of the ancient genome of the cave bear.
	Minireview Splicing regulators: targets and drugs Gene Yeo Genome Biology 2005, 6:240 (1 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent work has revealed a complex network of distinct alternative splicing events in Drosophila as well as drugs that interfere specifically and directly with one class of splicing regulators in human cells.
	Minireview Predicting the sites of metastases Brian Z Ring, Douglas T Ross Genome Biology 2005, 6:241 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work has identified genes implicated in the tissue tropism of breast-cancer metastasis.
	Report
	Paper report Articles selected by Faculty of 1000 Biology: genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ε-Proteobacteria diversity. Genome Biology 2005, 6:362 (21 November 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 Biology covering genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ε-Proteobacteria diversity
	Paper report Articles selected by Faculty of 1000 Biology: yeast metabolite profiling; high-frequency homologous recombination; functional RNA motifs; phylogeny of Oryzeae; genomic variability within an organism. Genome Biology 2005, 6:363 (2 December 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 Biology covering yeast metabolite profiling; high-frequency homologous recombination; functional RNA motifs; phylogeny of Oryzeae; genomic variability within an organism
	Meeting report Understanding embryonic development: from screens to genes Lisa A Taneyhill Genome Biology 2005, 6:359 (24 November 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 64th Annual Meeting of the Society for Developmental Biology, San Francisco, USA, 27 July-1 August 2005.
	Meeting report Defining the proteome Jörg Bernhardt Genome Biology 2005, 6:360 (1 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Fourth Annual HUPO World Congress (HUPO2005) ‘From Defining the Proteome to Understanding Function’, Munich, Germany, 28 August-1 September 2005.
	Meeting report Transposon technology and vertebrate functional genomics Wenfeng An, Jef D Boeke Genome Biology 2005, 6:361 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Third Annual International Conference on Transposition and Animal Biotechnology, Minneapolis, USA, 23-24 June 2005, and the FASEB Summer Research Conference 'Mammalian Mobile Elements', Tuscon, USA, 4-9 June, 2005.
	Research
	Research Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3 Kengo Usui, Shintaro Katayama, Mutsumi Kanamori-Katayama, Chihiro Ogawa, Chikatoshi Kai, Makiko Okada, Jun Kawai, Takahiro Arakawa, Piero Carninci, Masayoshi Itoh, Koji Takio, Masashi Miyano, Satoru Kidoaki, Takehisa Matsuda, Yoshihide Hayashizaki, Harukazu Suzuki Genome Biology 2005, 6:R98 (18 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protein-protein interactions among 960 Pyrococcus soluble proteins have been analysed by mammalian two-hybrid analysis and thirteen interactions between annotated and unannotated proteins detected.
	Research The genomic response to 20-hydroxyecdysone at the onset of Drosophila metamorphosis Robert B Beckstead, Geanette Lam, Carl S Thummel Genome Biology 2005, 6:R99 (21 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome-wide transcriptional response to 20-hydroxyecdisone at the onset of Drosophila metamorphosis, as well as its dependency on one of the ecdysone receptors is described.
	Research Biased alternative polyadenylation in human tissues Haibo Zhang, Ju Lee, Bin Tian Genome Biology 2005, 6:R100 (28 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bioinformatic analyses of the occurrence and mechanism of alternative polyadenylation in different human tissues reveals systematic differences among tissues and suggests the involvement of both trans- and cis-regulatory elements.
	Research Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert Mikael Brosché, Basia Vinocur, Edward R Alatalo, Airi Lamminmäki, Thomas Teichmann, Eric A Ottow, Dimitar Djilianov, Dany Afif, Marie-Béatrice Bogeat-Triboulot, Arie Altman, Andrea Polle, Erwin Dreyer, Stephen Rudd, Lars Paulin, Petri Auvinen, Jaakko Kangasjärvi Genome Biology 2005, 6:R101 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Populus euphratica DNA microarray was constructed and used to analyze gene expression in trees growing in the desert. P. euphratica is shown to express a set of genes that is different from other Populus trees and these genes contribute to adaptation to saline growth conditions.
	Research Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm Aminata Touré, Emily J Clemente, Peter JI Ellis, Shantha K Mahadevaiah, Obah A Ojarikre, Penny AF Ball, Louise Reynard, Kate L Loveland, Paul S Burgoyne, Nabeel A Affara Genome Biology 2005, 6:R102 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis of the changes in the testis transcriptome resulting from deletions of the male-specific region on the mouse chromosome long arm (MSYq) identified novel Y chromosome-encoded transcripts.
	Research The design of transcription-factor binding sites is affected by combinatorial regulation Yonatan Bilu, Naama Barkai Genome Biology 2005, 6:R103 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Short abstract here
	Method The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates Laurence Ettwiller, Benedict Paten, Marcel Souren, Felix Loosli, Jochen Wittbrodt, Ewan Birney Genome Biology 2005, 6:R104 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several new methods and a specific alignment tool for investigating transcriptional motifs in vertebrates were used to identify all possible 12mers involved in transcription. Active instances of these motifs were identified using comparative analysis across vertebrates.
	Method A low-cost open-source SNP genotyping platform for association mapping applications Stuart J Macdonald, Tomi Pastinen, Anne Genissel, Theodore W Cornforth, Anthony D Long Genome Biology 2005, 6:R105 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An efficient, cost-effective and open-source approach is described for high-throughput genotyping of large fixed panels of diploid individuals.
	Software Ulysses - an application for the projection of molecular interactions across species Danielle Kemmer, Yong Huang, Sohrab P Shah, Jonathan Lim, Jochen Brumm, Macaire MS Yuen, John Ling, Tao Xu, Wyeth W Wasserman, BF Francis Ouellette Genome Biology 2005, 6:R106 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ulysses, a new software for the parallel analysis and display of protein interactions detected in various species, is described.

	Volume 6 Issue 12
	Comment
	Comment Who steals my identity steals trash Gregory A Petsko Genome Biology 2005, 6:122 (2 December 2005) Abstract \| Full text \| PDF \| Editor’s summary I've thought about this identity theft issue, and I've decided not to worry about it. My blasé feelings come from careful consideration of the consequences, not to me, but to the thief, of anyone who steals the identity of an academic scientist.
	Review
	Protein family review The expansin superfamily Javier Sampedro, Daniel J Cosgrove Genome Biology 2005, 6:242 (28 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expansins are plant proteins that loosen cell walls via a nonenzymatic mechanism; they are involved in cell expansion and other developmental events during which cell-wall modification occurs.
	Minireview Ancient genomes A Rus Hoelzel Genome Biology 2005, 6:239 (1 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In an application of modern genomic methods to material from the Pleistocene, a recent study has undertaken to clone and sequence a portion of the ancient genome of the cave bear.
	Minireview Splicing regulators: targets and drugs Gene Yeo Genome Biology 2005, 6:240 (1 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent work has revealed a complex network of distinct alternative splicing events in Drosophila as well as drugs that interfere specifically and directly with one class of splicing regulators in human cells.
	Minireview Predicting the sites of metastases Brian Z Ring, Douglas T Ross Genome Biology 2005, 6:241 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work has identified genes implicated in the tissue tropism of breast-cancer metastasis.
	Report
	Paper report Articles selected by Faculty of 1000 Biology: genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ε-Proteobacteria diversity. Genome Biology 2005, 6:362 (21 November 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 Biology covering genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ε-Proteobacteria diversity
	Paper report Articles selected by Faculty of 1000 Biology: yeast metabolite profiling; high-frequency homologous recombination; functional RNA motifs; phylogeny of Oryzeae; genomic variability within an organism. Genome Biology 2005, 6:363 (2 December 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 Biology covering yeast metabolite profiling; high-frequency homologous recombination; functional RNA motifs; phylogeny of Oryzeae; genomic variability within an organism
	Meeting report Understanding embryonic development: from screens to genes Lisa A Taneyhill Genome Biology 2005, 6:359 (24 November 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 64th Annual Meeting of the Society for Developmental Biology, San Francisco, USA, 27 July-1 August 2005.
	Meeting report Defining the proteome Jörg Bernhardt Genome Biology 2005, 6:360 (1 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Fourth Annual HUPO World Congress (HUPO2005) ‘From Defining the Proteome to Understanding Function’, Munich, Germany, 28 August-1 September 2005.
	Meeting report Transposon technology and vertebrate functional genomics Wenfeng An, Jef D Boeke Genome Biology 2005, 6:361 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Third Annual International Conference on Transposition and Animal Biotechnology, Minneapolis, USA, 23-24 June 2005, and the FASEB Summer Research Conference 'Mammalian Mobile Elements', Tuscon, USA, 4-9 June, 2005.
	Research
	Research Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3 Kengo Usui, Shintaro Katayama, Mutsumi Kanamori-Katayama, Chihiro Ogawa, Chikatoshi Kai, Makiko Okada, Jun Kawai, Takahiro Arakawa, Piero Carninci, Masayoshi Itoh, Koji Takio, Masashi Miyano, Satoru Kidoaki, Takehisa Matsuda, Yoshihide Hayashizaki, Harukazu Suzuki Genome Biology 2005, 6:R98 (18 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protein-protein interactions among 960 Pyrococcus soluble proteins have been analysed by mammalian two-hybrid analysis and thirteen interactions between annotated and unannotated proteins detected.
	Research The genomic response to 20-hydroxyecdysone at the onset of Drosophila metamorphosis Robert B Beckstead, Geanette Lam, Carl S Thummel Genome Biology 2005, 6:R99 (21 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome-wide transcriptional response to 20-hydroxyecdisone at the onset of Drosophila metamorphosis, as well as its dependency on one of the ecdysone receptors is described.
	Research Biased alternative polyadenylation in human tissues Haibo Zhang, Ju Lee, Bin Tian Genome Biology 2005, 6:R100 (28 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bioinformatic analyses of the occurrence and mechanism of alternative polyadenylation in different human tissues reveals systematic differences among tissues and suggests the involvement of both trans- and cis-regulatory elements.
	Research Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert Mikael Brosché, Basia Vinocur, Edward R Alatalo, Airi Lamminmäki, Thomas Teichmann, Eric A Ottow, Dimitar Djilianov, Dany Afif, Marie-Béatrice Bogeat-Triboulot, Arie Altman, Andrea Polle, Erwin Dreyer, Stephen Rudd, Lars Paulin, Petri Auvinen, Jaakko Kangasjärvi Genome Biology 2005, 6:R101 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Populus euphratica DNA microarray was constructed and used to analyze gene expression in trees growing in the desert. P. euphratica is shown to express a set of genes that is different from other Populus trees and these genes contribute to adaptation to saline growth conditions.
	Research Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm Aminata Touré, Emily J Clemente, Peter JI Ellis, Shantha K Mahadevaiah, Obah A Ojarikre, Penny AF Ball, Louise Reynard, Kate L Loveland, Paul S Burgoyne, Nabeel A Affara Genome Biology 2005, 6:R102 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis of the changes in the testis transcriptome resulting from deletions of the male-specific region on the mouse chromosome long arm (MSYq) identified novel Y chromosome-encoded transcripts.
	Research The design of transcription-factor binding sites is affected by combinatorial regulation Yonatan Bilu, Naama Barkai Genome Biology 2005, 6:R103 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Short abstract here
	Method The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates Laurence Ettwiller, Benedict Paten, Marcel Souren, Felix Loosli, Jochen Wittbrodt, Ewan Birney Genome Biology 2005, 6:R104 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several new methods and a specific alignment tool for investigating transcriptional motifs in vertebrates were used to identify all possible 12mers involved in transcription. Active instances of these motifs were identified using comparative analysis across vertebrates.
	Method A low-cost open-source SNP genotyping platform for association mapping applications Stuart J Macdonald, Tomi Pastinen, Anne Genissel, Theodore W Cornforth, Anthony D Long Genome Biology 2005, 6:R105 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An efficient, cost-effective and open-source approach is described for high-throughput genotyping of large fixed panels of diploid individuals.
	Software Ulysses - an application for the projection of molecular interactions across species Danielle Kemmer, Yong Huang, Sohrab P Shah, Jonathan Lim, Jochen Brumm, Macaire MS Yuen, John Ling, Tao Xu, Wyeth W Wasserman, BF Francis Ouellette Genome Biology 2005, 6:R106 (2 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ulysses, a new software for the parallel analysis and display of protein interactions detected in various species, is described.

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Volume 6 Issue 12

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