Genome Biology | Volume 9 Issue 6

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 9 Issue 6
	Comment
	Comment It is alive Gregory A Petsko Genome Biology 2008, 9:106 (23 June 2008) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary We need to familiarize ourselves with the facts of evolution, so that we can mount a spirited defense against creationism and the forces of ignorance.
	Review
	Review What makes pathogens pathogenic Garth D Ehrlich, N Luisa Hiller, Fen Hu Genome Biology 2008, 9:225 (24 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A review of the evolution of microbial pathogenicity in the context of the 'symbiome' of microbes and their multicellular hosts.
	Protein family review The AID/APOBEC family of nucleic acid mutators Silvestro G Conticello Genome Biology 2008, 9:229 (17 June 2008) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary An overview of the AID/APOBEC family of cytidine deaminases, enzymes that can mutate RNA and DNA.
	Minireview Wormnet: a crystal ball for Caenorhabditis elegans Stephen E Von Stetina, Susan E Mango Genome Biology 2008, 9:226 (2 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrated gene network for Caenorhabditis elegans encompasses most protein-coding genes.
	Minireview A fruitful outcome to the papaya genome project Fusheng Wei, Rod A Wing Genome Biology 2008, 9:227 (6 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Papaya provides the first draft genome sequence of a transgenic fruit.
	Minireview Does a new polyomavirus contribute to Merkel cell carcinoma? Kelly M Garneski, James A DeCaprio, Paul Nghiem Genome Biology 2008, 9:228 (17 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new polyomavirus has been discovered in Merkel cell carcinomas, but does it contribute to carcinogenesis?
	Report
	Meeting report Elucidating developmental gene networks Anja Hanisch, Annalisa Vezzaro, Charalampos Rallis Genome Biology 2008, 9:310 (2 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Joint Meeting of the British Societies for Cell and Developmental Biology, Warwick, UK, 31 March-3 April, 2008.
	Meeting report Complex responses to a diverse environment Mary Collins, David G Winkler, Lih-Ling Lin Genome Biology 2008, 9:311 (3 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Keystone Symposium 'Innate Immunity: Signaling Mechanisms', Keystone, USA, 24-29 February, 2008.
	Meeting report Caenorhabditis elegans comes of age Julian Ceron, Peter Swoboda Genome Biology 2008, 9:312 (16 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the European C. elegans 2008 meeting, Seville, Spain, 29 March-2 April 2008.
	Meeting report Sequencing the regulatory genome Stein Aerts, Stefanie Butland Genome Biology 2008, 9:313 (19 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Systems Biology: Global Regulation of Gene Expression', Cold Spring Harbor, USA, 27-30 March 2008.
	Research
	Research Inhibition of casein kinase 1-epsilon induces cancer-cell-selective, PERIOD2-dependent growth arrest Wan Seok Yang, Brent R Stockwell Genome Biology 2008, 9:R92 (2 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Casein kinase 1 epsilon is identified as a potential target for developing selective anticancer reagents.
	Research Chætognath transcriptome reveals ancestral and unique features among bilaterians Ferdinand Marlétaz, André Gilles, Xavier Caubit, Yvan Perez, Carole Dossat, Sylvie Samain, Gabor Gyapay, Patrick Wincker, Yannick Le Parco Genome Biology 2008, 9:R94 (4 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The chætognath transcriptome reveals unusual genomic features in the evolution of this protostome and suggests that it could be used as a model organism for bilaterians.
	Research The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution Georgina Hernández-Montes, J Javier Díaz-Mejía, Ernesto Pérez-Rueda, Lorenzo Segovia Genome Biology 2008, 9:R95 (9 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids is predicted using comparative genomics.
	Research Identification of motifs that function in the splicing of non-canonical introns Jill I Murray, Rodger B Voelker, Kristy L Henscheid, M Bryan Warf, J Andrew Berglund Genome Biology 2008, 9:R97 (12 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The enrichment of specific intronic splicing enhancers upstream of weak PY tracts suggests a novel mechanism for intron recognition that compensates for a weakened canonical pre-mRNA splicing motif.
	Research Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes Qi Zhou, Jun Wang, Ling Huang, Wenhui Nie, Jinhuan Wang, Yan Liu, Xiangyi Zhao, Fengtang Yang, Wen Wang Genome Biology 2008, 9:R98 (14 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The nascent neo-sex chromosomes of black muntjacs show that regulatory mutations could accelerate the degeneration of the Y chromosome and contribute to the further evolution of dosage compensation.
	Research Identification of transcripts with enriched expression in the developing and adult pancreas Brad G Hoffman, Bogard Zavaglia, Joy Witzsche, Teresa Ruiz de Algara, Mike Beach, Pamela A Hoodless, Steven JM Jones, Marco A Marra, Cheryl D Helgason Genome Biology 2008, 9:R99 (14 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The expression profile of different developmental stages of the murine pancreas and predictions of transcription factor interactions, provides a framework for pancreas regulatory networks and development.
	Research Modified cell cycle status in a mouse model of altered neuronal vulnerability (slow Wallerian degeneration; Wld^s) Thomas M Wishart, Helen N Pemberton, Sally R James, Chris J McCabe, Thomas H Gillingwater Genome Biology 2008, 9:R101 (20 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Profiling of gene expression changes in mice harbouring the neurodegenerative Wlds mutation shows a strong correlation between changes in cell cycle pathways and altered vulnerability of terminally differentiated neurons.
	Research Genetic analysis of the human infective trypanosome Trypanosoma brucei gambiense: chromosomal segregation, crossing over, and the construction of a genetic map Anneli Cooper, Andy Tait, Lindsay Sweeney, Alison Tweedie, Liam Morrison, C Michael R Turner, Annette MacLeod Genome Biology 2008, 9:R103 (22 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-resolution genetic linkage map of the STIB 386 strain of Trypanosoma brucei gambiense is presented.
	Method A mouse plasma peptide atlas as a resource for disease proteomics Qing Zhang, Rajasree Menon, Eric W Deutsch, Sharon J Pitteri, Vitor M Faca, Hong Wang, Lisa F Newcomb, Ronald A DePinho, Nabeel Bardeesy, Daniela Dinulescu, Kenneth E Hung, Raju Kucherlapati, Tyler Jacks, Katerina Politi, Ruedi Aebersold, Gilbert S Omenn, David J States, Samir M Hanash Genome Biology 2008, 9:R93 (3 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A publicly available repository for high-quality peptide and protein data, identified by LC-MS/MS analysis.
	Method Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype Edward K Lobenhofer, J Todd Auman, Pamela E Blackshear, Gary A Boorman, Pierre R Bushel, Michael L Cunningham, Jennifer M Fostel, Kevin Gerrish, Alexandra N Heinloth, Richard D Irwin, David E Malarkey, B Alex Merrick, Stella O Sieber, Charles J Tucker, Sandra M Ward, Ralph E Wilson, Patrick Hurban, Raymond W Tennant, Richard S Paules Genome Biology 2008, 9:R100 (20 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Histopathology, clinical chemistry, hematology and gene expression data were collected from the rat liver and blood after treatment with eight known hepatotoxins.
	Method Assignment of isochores for all completely sequenced vertebrate genomes using a consensus Thorsten Schmidt, Dmitrij Frishman Genome Biology 2008, 9:R104 (30 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new consensus isochore assignment method and a database of isochore maps for all completely sequenced vertebrate genomes are presented.
	Software Anni 2.0: a multipurpose text-mining tool for the life sciences Rob Jelier, Martijn J Schuemie, Antoine Veldhoven, Lambert CJ Dorssers, Guido Jenster, Jan A Kors Genome Biology 2008, 9:R96 (12 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Anni 2.0 provides an ontology-based interface to MEDLINE.
	Software GMODWeb: a web framework for the generic model organism database Brian D O'Connor, Allen Day, Scott Cain, Olivier Arnaiz, Linda Sperling, Lincoln D Stein Genome Biology 2008, 9:R102 (20 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GMODWeb is a software framework designed to speed the development of websites for model organism databases.
	Correspondence
	Correspondence Circular reasoning rather than cyclic expression Lars Jensen, Ulrik de Lichtenberg, Thomas Jensen, Søren Brunak, Peer Bork Genome Biology 2008, 9:403 (23 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146.

	Volume 9 Issue 6
	Comment
	Comment It is alive Gregory A Petsko Genome Biology 2008, 9:106 (23 June 2008) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary We need to familiarize ourselves with the facts of evolution, so that we can mount a spirited defense against creationism and the forces of ignorance.
	Review
	Review What makes pathogens pathogenic Garth D Ehrlich, N Luisa Hiller, Fen Hu Genome Biology 2008, 9:225 (24 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A review of the evolution of microbial pathogenicity in the context of the 'symbiome' of microbes and their multicellular hosts.
	Protein family review The AID/APOBEC family of nucleic acid mutators Silvestro G Conticello Genome Biology 2008, 9:229 (17 June 2008) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary An overview of the AID/APOBEC family of cytidine deaminases, enzymes that can mutate RNA and DNA.
	Minireview Wormnet: a crystal ball for Caenorhabditis elegans Stephen E Von Stetina, Susan E Mango Genome Biology 2008, 9:226 (2 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrated gene network for Caenorhabditis elegans encompasses most protein-coding genes.
	Minireview A fruitful outcome to the papaya genome project Fusheng Wei, Rod A Wing Genome Biology 2008, 9:227 (6 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Papaya provides the first draft genome sequence of a transgenic fruit.
	Minireview Does a new polyomavirus contribute to Merkel cell carcinoma? Kelly M Garneski, James A DeCaprio, Paul Nghiem Genome Biology 2008, 9:228 (17 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new polyomavirus has been discovered in Merkel cell carcinomas, but does it contribute to carcinogenesis?
	Report
	Meeting report Elucidating developmental gene networks Anja Hanisch, Annalisa Vezzaro, Charalampos Rallis Genome Biology 2008, 9:310 (2 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Joint Meeting of the British Societies for Cell and Developmental Biology, Warwick, UK, 31 March-3 April, 2008.
	Meeting report Complex responses to a diverse environment Mary Collins, David G Winkler, Lih-Ling Lin Genome Biology 2008, 9:311 (3 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Keystone Symposium 'Innate Immunity: Signaling Mechanisms', Keystone, USA, 24-29 February, 2008.
	Meeting report Caenorhabditis elegans comes of age Julian Ceron, Peter Swoboda Genome Biology 2008, 9:312 (16 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the European C. elegans 2008 meeting, Seville, Spain, 29 March-2 April 2008.
	Meeting report Sequencing the regulatory genome Stein Aerts, Stefanie Butland Genome Biology 2008, 9:313 (19 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Systems Biology: Global Regulation of Gene Expression', Cold Spring Harbor, USA, 27-30 March 2008.
	Research
	Research Inhibition of casein kinase 1-epsilon induces cancer-cell-selective, PERIOD2-dependent growth arrest Wan Seok Yang, Brent R Stockwell Genome Biology 2008, 9:R92 (2 June 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Casein kinase 1 epsilon is identified as a potential target for developing selective anticancer reagents.
	Research Chætognath transcriptome reveals ancestral and unique features among bilaterians Ferdinand Marlétaz, André Gilles, Xavier Caubit, Yvan Perez, Carole Dossat, Sylvie Samain, Gabor Gyapay, Patrick Wincker, Yannick Le Parco Genome Biology 2008, 9:R94 (4 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The chætognath transcriptome reveals unusual genomic features in the evolution of this protostome and suggests that it could be used as a model organism for bilaterians.
	Research The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution Georgina Hernández-Montes, J Javier Díaz-Mejía, Ernesto Pérez-Rueda, Lorenzo Segovia Genome Biology 2008, 9:R95 (9 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids is predicted using comparative genomics.
	Research Identification of motifs that function in the splicing of non-canonical introns Jill I Murray, Rodger B Voelker, Kristy L Henscheid, M Bryan Warf, J Andrew Berglund Genome Biology 2008, 9:R97 (12 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The enrichment of specific intronic splicing enhancers upstream of weak PY tracts suggests a novel mechanism for intron recognition that compensates for a weakened canonical pre-mRNA splicing motif.
	Research Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes Qi Zhou, Jun Wang, Ling Huang, Wenhui Nie, Jinhuan Wang, Yan Liu, Xiangyi Zhao, Fengtang Yang, Wen Wang Genome Biology 2008, 9:R98 (14 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The nascent neo-sex chromosomes of black muntjacs show that regulatory mutations could accelerate the degeneration of the Y chromosome and contribute to the further evolution of dosage compensation.
	Research Identification of transcripts with enriched expression in the developing and adult pancreas Brad G Hoffman, Bogard Zavaglia, Joy Witzsche, Teresa Ruiz de Algara, Mike Beach, Pamela A Hoodless, Steven JM Jones, Marco A Marra, Cheryl D Helgason Genome Biology 2008, 9:R99 (14 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The expression profile of different developmental stages of the murine pancreas and predictions of transcription factor interactions, provides a framework for pancreas regulatory networks and development.
	Research Modified cell cycle status in a mouse model of altered neuronal vulnerability (slow Wallerian degeneration; Wld^s) Thomas M Wishart, Helen N Pemberton, Sally R James, Chris J McCabe, Thomas H Gillingwater Genome Biology 2008, 9:R101 (20 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Profiling of gene expression changes in mice harbouring the neurodegenerative Wlds mutation shows a strong correlation between changes in cell cycle pathways and altered vulnerability of terminally differentiated neurons.
	Research Genetic analysis of the human infective trypanosome Trypanosoma brucei gambiense: chromosomal segregation, crossing over, and the construction of a genetic map Anneli Cooper, Andy Tait, Lindsay Sweeney, Alison Tweedie, Liam Morrison, C Michael R Turner, Annette MacLeod Genome Biology 2008, 9:R103 (22 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-resolution genetic linkage map of the STIB 386 strain of Trypanosoma brucei gambiense is presented.
	Method A mouse plasma peptide atlas as a resource for disease proteomics Qing Zhang, Rajasree Menon, Eric W Deutsch, Sharon J Pitteri, Vitor M Faca, Hong Wang, Lisa F Newcomb, Ronald A DePinho, Nabeel Bardeesy, Daniela Dinulescu, Kenneth E Hung, Raju Kucherlapati, Tyler Jacks, Katerina Politi, Ruedi Aebersold, Gilbert S Omenn, David J States, Samir M Hanash Genome Biology 2008, 9:R93 (3 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A publicly available repository for high-quality peptide and protein data, identified by LC-MS/MS analysis.
	Method Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype Edward K Lobenhofer, J Todd Auman, Pamela E Blackshear, Gary A Boorman, Pierre R Bushel, Michael L Cunningham, Jennifer M Fostel, Kevin Gerrish, Alexandra N Heinloth, Richard D Irwin, David E Malarkey, B Alex Merrick, Stella O Sieber, Charles J Tucker, Sandra M Ward, Ralph E Wilson, Patrick Hurban, Raymond W Tennant, Richard S Paules Genome Biology 2008, 9:R100 (20 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Histopathology, clinical chemistry, hematology and gene expression data were collected from the rat liver and blood after treatment with eight known hepatotoxins.
	Method Assignment of isochores for all completely sequenced vertebrate genomes using a consensus Thorsten Schmidt, Dmitrij Frishman Genome Biology 2008, 9:R104 (30 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new consensus isochore assignment method and a database of isochore maps for all completely sequenced vertebrate genomes are presented.
	Software Anni 2.0: a multipurpose text-mining tool for the life sciences Rob Jelier, Martijn J Schuemie, Antoine Veldhoven, Lambert CJ Dorssers, Guido Jenster, Jan A Kors Genome Biology 2008, 9:R96 (12 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Anni 2.0 provides an ontology-based interface to MEDLINE.
	Software GMODWeb: a web framework for the generic model organism database Brian D O'Connor, Allen Day, Scott Cain, Olivier Arnaiz, Linda Sperling, Lincoln D Stein Genome Biology 2008, 9:R102 (20 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GMODWeb is a software framework designed to speed the development of websites for model organism databases.
	Correspondence
	Correspondence Circular reasoning rather than cyclic expression Lars Jensen, Ulrik de Lichtenberg, Thomas Jensen, Søren Brunak, Peer Bork Genome Biology 2008, 9:403 (23 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146.

Explore Genome Biology

Articles

Volume 9 Issue 6

Comment

Review

Report

Research

Correspondence