Genome Biology | Volume 8 Issue 7

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	Volume 8 Issue 7
	Comment
	Comment A truly titanic figure in science Gregory A Petsko Genome Biology 2007, 8:108 (31 July 2007) Abstract \| Full text \| PDF \| Editor’s summary Very few people have had a younger heart or a more open mind than Dan Koshland. All he had to do to make a field more interesting was to enter it.
	Review
	Minireview My 2,000 best films: parallel phenotyping of Dictyostelium development Gareth Bloomfield, Robert R Kay Genome Biology 2007, 8:220 (23 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Developmental phenotyping of 2,000 Dictyostelium mutants using parallel time-lapse filming.
	Minireview Identification of structural aberrations in cancer by SNP array analysis Stefan Heinrichs, A Thomas Look Genome Biology 2007, 8:219 (31 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SNP microarrays are a powerful way of uncovering mutations relevant to cancer.
	Minireview A small RNA makes a Bic difference Howell F Moffett, Carl D Novina Genome Biology 2007, 8:221 (31 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Highly specific gene knockouts in mice for the microRNA miR155 show multiple defects in adaptive immunity.
	Report
	Meeting report The future for plants and plants for the future Yves Van de Peer Genome Biology 2007, 8:308 (11 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 2007 EMBO Conference Series on Plant Molecular Biology 'From basic genomics to systems biology', Ghent, Belgium, 2-4 May 2007.
	Meeting report Drosophila by the dozen Susan E Celniker, Roger A Hoskins Genome Biology 2007, 8:309 (13 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 48th Annual Drosophila Research Conference, Philadelphia, USA, 7-11 March 2007.
	Meeting report Cell signaling and cancer Eleni Bazigou, Charalampos Rallis Genome Biology 2007, 8:310 (23 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cancer Research UK London Research Institute Special Conference 'Signal Transduction', London, UK, 14-16 May 2007.
	Meeting report On the origin of neurons Jeremy N Pulvers, Judith Schenk, Yoko Arai, Ji-Feng Fei, Kanako Saito, Wieland B Huttner Genome Biology 2007, 8:311 (31 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the conference 'Neurogenesis 2007', Tokyo, Japan, 15-16 May 2007.
	Research
	Research A proteome-wide protein interaction map for Campylobacter jejuni Jodi R Parrish, Jingkai Yu, Guozhen Liu, Julie A Hines, Jason E Chan, Bernie A Mangiola, Huamei Zhang, Svetlana Pacifico, Farshad Fotouhi, Victor J DiRita, Trey Ideker, Phillip Andrews, Russell L Finley Genome Biology 2007, 8:R130 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 'Systematic identification of protein interactions for the bacterium Campylobacter jejuni using high-throughput yeast two-hybrid screens detected interactions for 80% of the organism's proteins.
	Research Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer Sergio Kaiser, Young-Kyu Park, Jeffrey L Franklin, Richard B Halberg, Ming Yu, Walter J Jessen, Johannes Freudenberg, Xiaodi Chen, Kevin Haigis, Anil G Jegga, Sue Kong, Bhuvaneswari Sakthivel, Huan Xu, Timothy Reichling, Mohammad Azhar, Gregory P Boivin, Reade B Roberts, Anika C Bissahoyo, Fausto Gonzales, Greg C Bloom, Steven Eschrich, Scott L Carter, Jeremy E Aronow, John Kleimeyer, Michael Kleimeyer, Vivek Ramaswamy, Stephen H Settle, Braden Boone, Shawn Levy, Jonathan M Graff et al. Genome Biology 2007, 8:R131 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Colon tumors from four independent mouse models and 100 human colorectal cancers all exhibited striking recapitulation of embryonic colon gene expression from embryonic days 13.5-18.5.
	Research Evolutionary conservation of regulated longevity assurance mechanisms Joshua J McElwee, Eugene Schuster, Eric Blanc, Matthew D Piper, James H Thomas, Dhaval S Patel, Colin Selman, Dominic J Withers, Janet M Thornton, Linda Partridge, David Gems Genome Biology 2007, 8:R132 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Short abstract: A multi-level cross-species comparative analysis of gene-expression changes accompanying increased longevity in mutant nematodes, fruit flies and mice with reduced insulin/IGF-1 signaling revealed candidate conserved mechanisms.
	Research Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system Stephen E Von Stetina, Joseph D Watson, Rebecca M Fox, Kellen L Olszewski, W Clay Spencer, Peter J Roy, David M Miller Genome Biology 2007, 8:R135 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel strategy for profiling Caenorhabditis elegans cells identifies transcripts highly enriched in either the embryonic or larval C. elegans nervous system, including 19 conserved transcripts of unknown function that are also expressed in the mammalian brain.
	Research Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes Gino JE Baart, Bert Zomer, Alex de Haan, Leo A van der Pol, E Coen Beuvery, Johannes Tramper, Dirk E Martens Genome Biology 2007, 8:R136 (6 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-scale flux model for primary metabolism of Neisseria meningitidis was constructed; a minimal medium for growth of N. meningitidis was designed using the model and tested successfully in batch and chemostat cultures.
	Research Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain Ivan Conte, Paola Bovolenta Genome Biology 2007, 8:R137 (6 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A cluster of highly conserved non-coding sequences surrounding the Six3 gene were identified in fish genomes, and transgenesis in medaka fish demonstrates that these sequences have enhancer, silencer and silencer blocker activities that are differentially combined to control the distribution of Six3.
	Research Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes Yoshitoshi Ogura, Tadasuke Ooka, Asadulghani, Jun Terajima, Jean-Philippe Nougayrède, Ken Kurokawa, Kousuke Tashiro, Toru Tobe, Keisuke Nakayama, Satoru Kuhara, Eric Oswald, Haruo Watanabe, Tetsuya Hayashi Genome Biology 2007, 8:R138 (10 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparing the genomes of O157 and non-O157 enterohemorrhagic Escherichia coli (EHEC) strains reveals the selective conservation of a large number of virulence determinants.
	Research A high utility integrated map of the pig genome Sean J Humphray, Carol E Scott, Richard Clark, Brandy Marron, Clare Bender, Nick Camm, Jayne Davis, Andrew Jenks, Angela Noon, Manish Patel, Harminder Sehra, Fengtang Yang, Margarita B Rogatcheva, Denis Milan, Patrick Chardon, Gary Rohrer, Dan Nonneman, Pieter de Jong, Stacey N Meyers, Alan Archibald, Jonathan E Beever, Lawrence B Schook, Jane Rogers Genome Biology 2007, 8:R139 (11 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly.
	Research Housekeeping genes tend to show reduced upstream sequence conservation Domènec Farré, Nicolás Bellora, Loris Mularoni, Xavier Messeguer, M Mar Albà Genome Biology 2007, 8:R140 (13 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mammalian housekeeping genes show significantly lower promoter sequence conservation, especially upstream of position -500 with respect to the transcription start site, than genes expressed in a subset of tissues.
	Research Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution Matthew W Hahn Genome Biology 2007, 8:R141 (16 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent bias in tree reconciliation methods is described that occurs when the inferred gene tree is not correct, casting doubt on previous conclusions about ancient duplications and losses in vertebrate genome history.
	Research siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P₃-mTOR signaling pathway as a primary regulator of transferrin uptake Thierry Galvez, Mary N Teruel, Won Heo, Joshua T Jones, Man Kim, Jen Liou, Jason W Myers, Tobias Meyer Genome Biology 2007, 8:R142 (19 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A survey of 1,804 human dicer-generated signaling siRNAs using automated quantitative imaging identified the phosphatidylinositol-3,4,5-trisphosphate-mTOR signaling pathway as a primary regulator of iron-transferrin uptake.
	Research Accuracy and quality of massively parallel DNA pyrosequencing Susan M Huse, Julie A Huber, Hilary G Morrison, Mitchell L Sogin, David Welch Genome Biology 2007, 8:R143 (20 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Error rates were estimated for the Roche GS20 massively parallel pyrosequencing system, and several factors were identified that can be used to remove low-quality reads, improving the accuracy to 99.75% or better.
	Research Global analysis of patterns of gene expression during Drosophila embryogenesis Pavel Tomancak, Benjamin P Berman, Amy Beaton, Richard Weiszmann, Elaine Kwan, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2007, 8:R145 (23 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome were documented, of which 40% show tissue-restricted expression.
	Research Combined analysis reveals a core set of cycling genes Yong Lu, Shaun Mahony, Panayiotis V Benos, Roni Rosenfeld, Itamar Simon, Linda L Breeden, Ziv Bar-Joseph Genome Biology 2007, 8:R146 (24 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary The simultaneous analysis of expression data from multiple species reveals a core set of conserved cycling genes that is much larger than previously thought.
	Research Meta-analysis of primary target genes of peroxisome proliferator-activated receptors Merja Heinäniemi, J Oskari Uski, Tatjana Degenhardt, Carsten Carlberg Genome Biology 2007, 8:R147 (25 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combined experimental and in silico approach identifies Peroxisome Proliferator Activated Receptor (PPAR) binding sites and six novel target genes in the human genome.
	Research Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres Alicia Alonso, Björn Fritz, Dan Hasson, György Abrusan, Fanny Cheung, Kinya Yoda, Bernhard Radlwimmer, Andreas G Ladurner, Peter E Warburton Genome Biology 2007, 8:R148 (25 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The distribution of centromeric chromatin-associated proteins across human neocentromeric DNA shows that this chromatin consists of several CENP-A-containing sub-domains.
	Research Air-pollutant chemicals and oxidized lipids exhibit genome-wide synergistic effects on endothelial cells Ke Gong, Wei Zhao, Ning Li, Berenice Barajas, Michael Kleinman, Constantinos Sioutas, Steve Horvath, Aldons J Lusis, Andre Nel, Jesus A Araujo Genome Biology 2007, 8:R149 (26 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression analysis of human microvascular endothelial cells exposed to diesel exhaust particles and oxidized phospholipids revealed several upregulated gene modules, including genes involved in vascular inflammatory processes such as atherosclerosis.
	Research Human subtelomeric duplicon structure and organization Anthony Ambrosini, Sheila Paul, Sufen Hu, Harold Riethman Genome Biology 2007, 8:R151 (30 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sequence divergence within subtelomeric duplicon families varies considerably, as does the organization of duplicon blocks at subtelomere alleles; a class of duplicon blocks was identified that are subtelomere-specific.
	Research Using comparative genomics to reorder the human genome sequence into a virtual sheep genome Brian P Dalrymple, Ewen F Kirkness, Mikhail Nefedov, Sean McWilliam, Abhirami Ratnakumar, Wes Barris, Shaying Zhao, Jyoti Shetty, Jillian F Maddox, Margaret O'Grady, Frank Nicholas, Allan M Crawford, Tim Smith, Pieter J de Jong, John McEwan, V Hutton Oddy, Noelle E Cockett, the International Sheep Genomics Consortium Genome Biology 2007, 8:R152 (30 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using BAC-end sequences, a sparse marker map and the sequences of the human, dog and cow genomes, an accurate and detailed sub-gene level map of the sheep genome has been constructed.
	Research Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle Jennifer L Shock, Kael F Fischer, Joseph L DeRisi Genome Biology 2007, 8:R134 (7 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent bias in tree reconciliation methods is described that occurs when the inferred gene tree is not correct, casting doubt on previous conclusions about ancient duplications and losses in vertebrate genome history.
	Method High-throughput analysis of spatio-temporal dynamics in Dictyostelium Satoshi Sawai, Xiao-Juan Guan, Adam Kuspa, Edward C Cox Genome Biology 2007, 8:R144 (21 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A time-lapse based approach is presented that allows a rapid examination of the spatio-temporal dynamics of Dictyostelium cell populations, enabling users to search and retrieve movies on a gene-by-gene and phenotype-by-phenotype basis.
	Method Novel metrics for evaluating the functional coherence of protein groups via protein semantic network Bin Zheng, Xinghua Lu Genome Biology 2007, 8:R153 (31 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Metrics are presented for assessing overall functional coherence of a group of proteins based on the associated biomedical literature.
	Software FlyMine: an integrated database for Drosophila and Anopheles genomics Rachel Lyne, Richard Smith, Kim Rutherford, Matthew Wakeling, Andrew Varley, Francois Guillier, Hilde Janssens, Wenyan Ji, Peter Mclaren, Philip North, Debashis Rana, Tom Riley, Julie Sullivan, Xavier Watkins, Mark Woodbridge, Kathryn Lilley, Steve Russell, Michael Ashburner, Kenji Mizuguchi, Gos Micklem Genome Biology 2007, 8:R129 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This novel web-based database provides unique accessibility and querying of integrated genomic and proteomic data for Drosophila and Anopheles.
	Software Strategy for encoding and comparison of gene expression signatures Yajun Yi, Chun Li, Clay Miller, Alfred L George Genome Biology 2007, 8:R133 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EXALT (EXpression signature AnaLysis Tool) enables comparisons of microarray data across experimental platforms and different laboratories.
	Software PHIDIAS: a pathogen-host interaction data integration and analysis system Zuoshuang Xiang, Yuying Tian, Yongqun He Genome Biology 2007, 8:R150 (30 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary PHIDIAS is a web-based database system serving as a centralized source to search, compare and analyse integrated genome sequences, conserved domains and transcriptional data related to pathogen-host interactions.

	Volume 8 Issue 7
	Comment
	Comment A truly titanic figure in science Gregory A Petsko Genome Biology 2007, 8:108 (31 July 2007) Abstract \| Full text \| PDF \| Editor’s summary Very few people have had a younger heart or a more open mind than Dan Koshland. All he had to do to make a field more interesting was to enter it.
	Review
	Minireview My 2,000 best films: parallel phenotyping of Dictyostelium development Gareth Bloomfield, Robert R Kay Genome Biology 2007, 8:220 (23 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Developmental phenotyping of 2,000 Dictyostelium mutants using parallel time-lapse filming.
	Minireview Identification of structural aberrations in cancer by SNP array analysis Stefan Heinrichs, A Thomas Look Genome Biology 2007, 8:219 (31 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SNP microarrays are a powerful way of uncovering mutations relevant to cancer.
	Minireview A small RNA makes a Bic difference Howell F Moffett, Carl D Novina Genome Biology 2007, 8:221 (31 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Highly specific gene knockouts in mice for the microRNA miR155 show multiple defects in adaptive immunity.
	Report
	Meeting report The future for plants and plants for the future Yves Van de Peer Genome Biology 2007, 8:308 (11 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 2007 EMBO Conference Series on Plant Molecular Biology 'From basic genomics to systems biology', Ghent, Belgium, 2-4 May 2007.
	Meeting report Drosophila by the dozen Susan E Celniker, Roger A Hoskins Genome Biology 2007, 8:309 (13 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 48th Annual Drosophila Research Conference, Philadelphia, USA, 7-11 March 2007.
	Meeting report Cell signaling and cancer Eleni Bazigou, Charalampos Rallis Genome Biology 2007, 8:310 (23 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cancer Research UK London Research Institute Special Conference 'Signal Transduction', London, UK, 14-16 May 2007.
	Meeting report On the origin of neurons Jeremy N Pulvers, Judith Schenk, Yoko Arai, Ji-Feng Fei, Kanako Saito, Wieland B Huttner Genome Biology 2007, 8:311 (31 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the conference 'Neurogenesis 2007', Tokyo, Japan, 15-16 May 2007.
	Research
	Research A proteome-wide protein interaction map for Campylobacter jejuni Jodi R Parrish, Jingkai Yu, Guozhen Liu, Julie A Hines, Jason E Chan, Bernie A Mangiola, Huamei Zhang, Svetlana Pacifico, Farshad Fotouhi, Victor J DiRita, Trey Ideker, Phillip Andrews, Russell L Finley Genome Biology 2007, 8:R130 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 'Systematic identification of protein interactions for the bacterium Campylobacter jejuni using high-throughput yeast two-hybrid screens detected interactions for 80% of the organism's proteins.
	Research Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer Sergio Kaiser, Young-Kyu Park, Jeffrey L Franklin, Richard B Halberg, Ming Yu, Walter J Jessen, Johannes Freudenberg, Xiaodi Chen, Kevin Haigis, Anil G Jegga, Sue Kong, Bhuvaneswari Sakthivel, Huan Xu, Timothy Reichling, Mohammad Azhar, Gregory P Boivin, Reade B Roberts, Anika C Bissahoyo, Fausto Gonzales, Greg C Bloom, Steven Eschrich, Scott L Carter, Jeremy E Aronow, John Kleimeyer, Michael Kleimeyer, Vivek Ramaswamy, Stephen H Settle, Braden Boone, Shawn Levy, Jonathan M Graff et al. Genome Biology 2007, 8:R131 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Colon tumors from four independent mouse models and 100 human colorectal cancers all exhibited striking recapitulation of embryonic colon gene expression from embryonic days 13.5-18.5.
	Research Evolutionary conservation of regulated longevity assurance mechanisms Joshua J McElwee, Eugene Schuster, Eric Blanc, Matthew D Piper, James H Thomas, Dhaval S Patel, Colin Selman, Dominic J Withers, Janet M Thornton, Linda Partridge, David Gems Genome Biology 2007, 8:R132 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Short abstract: A multi-level cross-species comparative analysis of gene-expression changes accompanying increased longevity in mutant nematodes, fruit flies and mice with reduced insulin/IGF-1 signaling revealed candidate conserved mechanisms.
	Research Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system Stephen E Von Stetina, Joseph D Watson, Rebecca M Fox, Kellen L Olszewski, W Clay Spencer, Peter J Roy, David M Miller Genome Biology 2007, 8:R135 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel strategy for profiling Caenorhabditis elegans cells identifies transcripts highly enriched in either the embryonic or larval C. elegans nervous system, including 19 conserved transcripts of unknown function that are also expressed in the mammalian brain.
	Research Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes Gino JE Baart, Bert Zomer, Alex de Haan, Leo A van der Pol, E Coen Beuvery, Johannes Tramper, Dirk E Martens Genome Biology 2007, 8:R136 (6 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-scale flux model for primary metabolism of Neisseria meningitidis was constructed; a minimal medium for growth of N. meningitidis was designed using the model and tested successfully in batch and chemostat cultures.
	Research Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain Ivan Conte, Paola Bovolenta Genome Biology 2007, 8:R137 (6 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A cluster of highly conserved non-coding sequences surrounding the Six3 gene were identified in fish genomes, and transgenesis in medaka fish demonstrates that these sequences have enhancer, silencer and silencer blocker activities that are differentially combined to control the distribution of Six3.
	Research Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes Yoshitoshi Ogura, Tadasuke Ooka, Asadulghani, Jun Terajima, Jean-Philippe Nougayrède, Ken Kurokawa, Kousuke Tashiro, Toru Tobe, Keisuke Nakayama, Satoru Kuhara, Eric Oswald, Haruo Watanabe, Tetsuya Hayashi Genome Biology 2007, 8:R138 (10 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparing the genomes of O157 and non-O157 enterohemorrhagic Escherichia coli (EHEC) strains reveals the selective conservation of a large number of virulence determinants.
	Research A high utility integrated map of the pig genome Sean J Humphray, Carol E Scott, Richard Clark, Brandy Marron, Clare Bender, Nick Camm, Jayne Davis, Andrew Jenks, Angela Noon, Manish Patel, Harminder Sehra, Fengtang Yang, Margarita B Rogatcheva, Denis Milan, Patrick Chardon, Gary Rohrer, Dan Nonneman, Pieter de Jong, Stacey N Meyers, Alan Archibald, Jonathan E Beever, Lawrence B Schook, Jane Rogers Genome Biology 2007, 8:R139 (11 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly.
	Research Housekeeping genes tend to show reduced upstream sequence conservation Domènec Farré, Nicolás Bellora, Loris Mularoni, Xavier Messeguer, M Mar Albà Genome Biology 2007, 8:R140 (13 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mammalian housekeeping genes show significantly lower promoter sequence conservation, especially upstream of position -500 with respect to the transcription start site, than genes expressed in a subset of tissues.
	Research Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution Matthew W Hahn Genome Biology 2007, 8:R141 (16 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent bias in tree reconciliation methods is described that occurs when the inferred gene tree is not correct, casting doubt on previous conclusions about ancient duplications and losses in vertebrate genome history.
	Research siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P₃-mTOR signaling pathway as a primary regulator of transferrin uptake Thierry Galvez, Mary N Teruel, Won Heo, Joshua T Jones, Man Kim, Jen Liou, Jason W Myers, Tobias Meyer Genome Biology 2007, 8:R142 (19 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A survey of 1,804 human dicer-generated signaling siRNAs using automated quantitative imaging identified the phosphatidylinositol-3,4,5-trisphosphate-mTOR signaling pathway as a primary regulator of iron-transferrin uptake.
	Research Accuracy and quality of massively parallel DNA pyrosequencing Susan M Huse, Julie A Huber, Hilary G Morrison, Mitchell L Sogin, David Welch Genome Biology 2007, 8:R143 (20 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Error rates were estimated for the Roche GS20 massively parallel pyrosequencing system, and several factors were identified that can be used to remove low-quality reads, improving the accuracy to 99.75% or better.
	Research Global analysis of patterns of gene expression during Drosophila embryogenesis Pavel Tomancak, Benjamin P Berman, Amy Beaton, Richard Weiszmann, Elaine Kwan, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2007, 8:R145 (23 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome were documented, of which 40% show tissue-restricted expression.
	Research Combined analysis reveals a core set of cycling genes Yong Lu, Shaun Mahony, Panayiotis V Benos, Roni Rosenfeld, Itamar Simon, Linda L Breeden, Ziv Bar-Joseph Genome Biology 2007, 8:R146 (24 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary The simultaneous analysis of expression data from multiple species reveals a core set of conserved cycling genes that is much larger than previously thought.
	Research Meta-analysis of primary target genes of peroxisome proliferator-activated receptors Merja Heinäniemi, J Oskari Uski, Tatjana Degenhardt, Carsten Carlberg Genome Biology 2007, 8:R147 (25 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combined experimental and in silico approach identifies Peroxisome Proliferator Activated Receptor (PPAR) binding sites and six novel target genes in the human genome.
	Research Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres Alicia Alonso, Björn Fritz, Dan Hasson, György Abrusan, Fanny Cheung, Kinya Yoda, Bernhard Radlwimmer, Andreas G Ladurner, Peter E Warburton Genome Biology 2007, 8:R148 (25 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The distribution of centromeric chromatin-associated proteins across human neocentromeric DNA shows that this chromatin consists of several CENP-A-containing sub-domains.
	Research Air-pollutant chemicals and oxidized lipids exhibit genome-wide synergistic effects on endothelial cells Ke Gong, Wei Zhao, Ning Li, Berenice Barajas, Michael Kleinman, Constantinos Sioutas, Steve Horvath, Aldons J Lusis, Andre Nel, Jesus A Araujo Genome Biology 2007, 8:R149 (26 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression analysis of human microvascular endothelial cells exposed to diesel exhaust particles and oxidized phospholipids revealed several upregulated gene modules, including genes involved in vascular inflammatory processes such as atherosclerosis.
	Research Human subtelomeric duplicon structure and organization Anthony Ambrosini, Sheila Paul, Sufen Hu, Harold Riethman Genome Biology 2007, 8:R151 (30 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sequence divergence within subtelomeric duplicon families varies considerably, as does the organization of duplicon blocks at subtelomere alleles; a class of duplicon blocks was identified that are subtelomere-specific.
	Research Using comparative genomics to reorder the human genome sequence into a virtual sheep genome Brian P Dalrymple, Ewen F Kirkness, Mikhail Nefedov, Sean McWilliam, Abhirami Ratnakumar, Wes Barris, Shaying Zhao, Jyoti Shetty, Jillian F Maddox, Margaret O'Grady, Frank Nicholas, Allan M Crawford, Tim Smith, Pieter J de Jong, John McEwan, V Hutton Oddy, Noelle E Cockett, the International Sheep Genomics Consortium Genome Biology 2007, 8:R152 (30 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using BAC-end sequences, a sparse marker map and the sequences of the human, dog and cow genomes, an accurate and detailed sub-gene level map of the sheep genome has been constructed.
	Research Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle Jennifer L Shock, Kael F Fischer, Joseph L DeRisi Genome Biology 2007, 8:R134 (7 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent bias in tree reconciliation methods is described that occurs when the inferred gene tree is not correct, casting doubt on previous conclusions about ancient duplications and losses in vertebrate genome history.
	Method High-throughput analysis of spatio-temporal dynamics in Dictyostelium Satoshi Sawai, Xiao-Juan Guan, Adam Kuspa, Edward C Cox Genome Biology 2007, 8:R144 (21 July 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A time-lapse based approach is presented that allows a rapid examination of the spatio-temporal dynamics of Dictyostelium cell populations, enabling users to search and retrieve movies on a gene-by-gene and phenotype-by-phenotype basis.
	Method Novel metrics for evaluating the functional coherence of protein groups via protein semantic network Bin Zheng, Xinghua Lu Genome Biology 2007, 8:R153 (31 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Metrics are presented for assessing overall functional coherence of a group of proteins based on the associated biomedical literature.
	Software FlyMine: an integrated database for Drosophila and Anopheles genomics Rachel Lyne, Richard Smith, Kim Rutherford, Matthew Wakeling, Andrew Varley, Francois Guillier, Hilde Janssens, Wenyan Ji, Peter Mclaren, Philip North, Debashis Rana, Tom Riley, Julie Sullivan, Xavier Watkins, Mark Woodbridge, Kathryn Lilley, Steve Russell, Michael Ashburner, Kenji Mizuguchi, Gos Micklem Genome Biology 2007, 8:R129 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This novel web-based database provides unique accessibility and querying of integrated genomic and proteomic data for Drosophila and Anopheles.
	Software Strategy for encoding and comparison of gene expression signatures Yajun Yi, Chun Li, Clay Miller, Alfred L George Genome Biology 2007, 8:R133 (5 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EXALT (EXpression signature AnaLysis Tool) enables comparisons of microarray data across experimental platforms and different laboratories.
	Software PHIDIAS: a pathogen-host interaction data integration and analysis system Zuoshuang Xiang, Yuying Tian, Yongqun He Genome Biology 2007, 8:R150 (30 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary PHIDIAS is a web-based database system serving as a centralized source to search, compare and analyse integrated genome sequences, conserved domains and transcriptional data related to pathogen-host interactions.

Explore Genome Biology

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Volume 8 Issue 7

Comment

Review

Report

Research