Genome Biology | Volume 8 Issue 6

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	Volume 8 Issue 6
	Comment
	Comment An idea whose time has gone Gregory A Petsko Genome Biology 2007, 8:107 (2 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The $60 million a year in public money that is being spent on the Protein Structure Initiative is enough to fund approximately 100-200 individual investigator-initiated research grants.
	Review
	Protein family review The calpains: modular designs and functional diversity Dorothy E Croall, Klaus Ersfeld Genome Biology 2007, 8:218 (2 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The eukaryotic calpains are a family of calcium-dependent papain-like proteases and their non-enzymatic relatives whose varied physiological functions are beginning to be fully explored.
	Minireview Topological variation in single-gene phylogenetic trees Jose Castresana Genome Biology 2007, 8:216 (13 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale phylogenetic study of the human lineage dramatically points up the problems of using single genes to build phylogenetic trees.
	Minireview Pyrosequencing positions nucleosomes precisely Tom Owen-Hughes, Maik Engeholm Genome Biology 2007, 8:217 (27 June 2007) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Massively parallel pyrosequencing used to map nucleosome positions genome-wide.
	Report
	Meeting report An epigenetic role for noncoding RNAs and intragenic DNA methylation James M Flanagan, Laurence Wild Genome Biology 2007, 8:307 (27 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Keystone Symposium 'Epigenetics: Regulation of Chromatin Structure in Development and Disease', Breckenridge, USA, 11-16 April 2007.
	Research
	Research Cloning and characterization of microRNAs from wheat (Triticum aestivum L.) Yingyin Yao, Ganggang Guo, Zhongfu Ni, Ramanjulu Sunkar, Jinkun Du, Jian-Kang Zhu, Qixin Sun Genome Biology 2007, 8:R96 (1 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A small RNA library was used to identify 58 miRNAs from 43 miRNA families from wheat (Triticum aestivum L.), and 46 potential targets were predicted.
	Research Computational and transcriptional evidence for microRNAs in the honey bee genome Daniel B Weaver, Juan M Anzola, Jay D Evans, Jeffrey G Reid, Justin T Reese, Kevin L Childs, Evgeny M Zdobnov, Manoj P Samanta, Jonathan Miller, Christine G Elsik Genome Biology 2007, 8:R97 (1 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A total of 68 non-redundant candidate honey bee miRNAs were identified computationally; several of them appear to have previously unrecognized orthologs in the Drosophila genome. Several miRNAs showed caste- or age-related differences in transcript abundance and are likely to be involved in regulating honey bee development.
	Research Mixture modeling of transcript abundance classes in natural populations Wen-Ping Hsieh, Gisele Passador-Gurgel, Eric A Stone, Greg Gibson Genome Biology 2007, 8:R98 (4 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression profiling of Drosophila melanogaster adult female heads for 108 nearly isogenic lines from two different populations, and of CEPH lymphoblastoid lines, shows that differential expression of transcripts among individuals is due to a complex interplay of cis- and trans-acting factors.
	Research Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Jinling Huang, Johann Gogarten Genome Biology 2007, 8:R99 (4 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary Phylogenomic analyses of the red alga Cyanidioschyzon merolae shows that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, suggesting an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote.
	Research Genetic flux over time in the Salmonella lineage Georgios S Vernikos, Nicholas R Thomson, Julian Parkhill Genome Biology 2007, 8:R100 (4 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary From a whole-genome comparative analysis of Salmonella, Escherichia coli and Shigella strains, the relative time of insertion of putative horizontally acquired genes in three Salmonella strains were inferred, highlighting the major impact of horizontal transfer in the evolution of the salmonellae.
	Research Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon Genome Biology 2007, 8:R101 (5 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Analysis of 280 experimentally-verified cis-regulatory modules from Drosophila reveal features both common to all and unique to distinct subclasses of modules.
	Research Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains Laurence Rohmer, Christine Fong, Simone Abmayr, Michael Wasnick, Theodore Larson Freeman, Matthew Radey, Tina Guina, Kerstin Svensson, Hillary S Hayden, Michael Jacobs, Larry A Gallagher, Colin Manoil, Robert K Ernst, Becky Drees, Danielle Buckley, Eric Haugen, Donald Bovee, Yang Zhou, Jean Chang, Ruth Levy, Regina Lim, Will Gillett, Don Guenthener, Allison Kang, Scott A Shaffer, Greg Taylor, Jinzhi Chen, Byron Gallis, David A D'Argenio, Mats Forsman, Maynard V Olson, David R Goodlett, Rajinder Kaul, Samuel I Miller, Mitchell J Brittnacher et al. Genome Biology 2007, 8:R102 (5 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary .Sequencing of the non-pathogenic Francisella tularensis sub-species novicida U112, and comparison with two pathogenic sub-species, provides insights into the evolution of pathogenicity in these species.
	Research Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains Justin S Hogg, Fen Z Hu, Benjamin Janto, Robert Boissy, Jay Hayes, Randy Keefe, J Christopher Post, Garth D Ehrlich Genome Biology 2007, 8:R103 (5 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary The genomes of 9 non-typeable H. influenzae clinical isolates were sequenced and compared with a reference strain, allowing the characterisation and modelling of the core-and supra genomes of this organism.
	Research A functional map of NFκB signaling identifies novel modulators and multiple system controls Thomas A Halsey, Longlong Yang, John R Walker, John B Hogenesch, Russell S Thomas Genome Biology 2007, 8:R104 (6 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using cell-based genomic screens and functional assays, positive and negative modulators of NFκB signaling were identified and mapped onto the known NFκB signaling cascade.
	Research Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction Yavor Hadzhiev, Michael Lang, Raymond Ertzer, Axel Meyer, Uwe Strähle, Ferenc Müller Genome Biology 2007, 8:R106 (8 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Investigation of the ar-C midline enhancer of sonic hedgehog orthologs and paralogs from distantly related vertebrate lineages identified lineage-specific motif changes; exchanging motifs between paralog enhancers resulted in the reversal of enhancer specificity.
	Research Large-scale identification of human genes implicated in epidermal barrier function Eve Toulza, Nicolas R Mattiuzzo, Marie-Florence Galliano, Nathalie Jonca, Carole Dossat, Daniel Jacob, Antoine de Daruvar, Patrick Wincker, Guy Serre, Marina Guerrin Genome Biology 2007, 8:R107 (11 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Identification of genes expressed in epidermal granular keratinocytes by ORESTES, including a number that are highly specific for these cells.
	Research Functional coordination of alternative splicing in the mammalian central nervous system Matthew Fagnani, Yoseph Barash, Joanna Y Ip, Christine Misquitta, Qun Pan, Arneet L Saltzman, Ofer Shai, Leo Lee, Aviad Rozenhek, Naveed Mohammad, Sandrine Willaime-Morawek, Tomas Babak, Wen Zhang, Timothy R Hughes, Derek van der Kooy, Brendan J Frey, Benjamin J Blencowe Genome Biology 2007, 8:R108 (12 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microarray analysis provides new evidence suggesting that specific cellular processes in the mammalian CNS are coordinated at the level of alternative splicing, and that a complex splicing code underlies CNS-specific alternative splicing regulation.
	Research The human phylome Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón Genome Biology 2007, 8:R109 (13 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed.
	Research A semi-quantitative GeLC-MS analysis of temporal proteome expression in the emerging nosocomial pathogen Ochrobactrum anthropi Robert Graham, Mohit K Sharma, Nigel G Ternan, D Brent Weatherly, Rick L Tarleton, Geoff McMullan Genome Biology 2007, 8:R110 (13 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A semi-quantitative gel-based analysis identifies distinct proteomic profiles associated with specific growth points for the nosocomial pathogen Ochrobactrum anthropi.
	Research Detailed analysis of 15q11-q14 sequence corrects errors and gaps in the public access sequence to fully reveal large segmental duplications at breakpoints for Prader-Willi, Angelman, and inv dup(15) syndromes Andrew J Makoff, Rachel H Flomen Genome Biology 2007, 8:R114 (15 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed segmental map of the 15q11-q14 region of the human genome reveals two pairs of large direct repeats in regions associated with Prader-Willi and Angelman syndromes and other repeats that may increase susceptibility to other disorders.
	Research LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs Zhonglin Tang, Yong Li, Ping Wan, Xiaoping Li, Shuhong Zhao, Bang Liu, Bin Fan, Mengjin Zhu, Mei Yu, Kui Li Genome Biology 2007, 8:R115 (16 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of Tongcheng and Landrace pigs using long serial analysis of gene expression provides insight into the molecular mechanism underlying differences in muscle growth.
	Research GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p Job Dekker Genome Biology 2007, 8:R116 (18 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary GC-rich and AT-rich chromatin domains display distinct chromatin conformations and are marked by distinct patterns of histone modifications, and the histone deacetylase Rpd3p is an attenuator of these differences.
	Research Genetic background influences murine prostate gene expression: implications for cancer phenotypes Daniella Bianchi-Frias, Colin Pritchard, Brigham H Mecham, Ilsa M Coleman, Peter S Nelson Genome Biology 2007, 8:R117 (18 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Microarray analyses to quantitate transcript levels in the prostates of five inbred mouse strains identified differences in gene expression in benign epithelium that correlated with the differentiation state of adjacent tumors.
	Research Fast-evolving noncoding sequences in the human genome Christine P Bird, Barbara E Stranger, Maureen Liu, Daryl J Thomas, Catherine E Ingle, Claude Beazley, Webb Miller, Matthew E Hurles, Emmanouil T Dermitzakis Genome Biology 2007, 8:R118 (19 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Over 1,300 conserved non-coding sequences were identified that appear to have undergone dramatic human-specific changes in selective pressures; these are enriched in recent segmental duplications, suggesting a recent change in selective constraint following duplication.
	Research The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes Lorena E Rosaleny, Ana B Ruiz-García, José García-Martínez, José E Pérez-Ortín, Vicente Tordera Genome Biology 2007, 8:R119 (20 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A macroarray platform was used to identify binding sites of yeast histone acetyltransferase catalytic subunits and to correlate their positions with acetylation of lysine 14 of histone H3, revealing that Sas3p and Gcn5p are recruited to similar sets of intensely transcribed genes.
	Research Genome position and gene amplification Pavla Gajduskova, Antoine M Snijders, Serena Kwek, Ritu Roydasgupta, Jane Fridlyand, Taku Tokuyasu, Daniel Pinkel, Donna G Albertson Genome Biology 2007, 8:R120 (21 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells.
	Research Evolutionary history and functional implications of protein domains and their combinations in eukaryotes Masumi Itoh, Jose C Nacher, Kei-ichi Kuma, Susumu Goto, Minoru Kanehisa Genome Biology 2007, 8:R121 (25 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no similar trends were observed in other clades of eukaryotes.
	Research Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity Yuxia Cui, Sandra J McBride, Windy A Boyd, Scott Alper, Jonathan H Freedman Genome Biology 2007, 8:R122 (25 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Global analysis of the transcriptional response to cadmium exposure in Caenorhabditis elegans reveals roles for genes involved in cellular trafficking, metabolic processes and proteolysis, and for the signaling protein KEL-8.
	Research Observing metabolic functions at the genome scale Jean-Marc Schwartz, Claire Gaugain, Jose C Nacher, Antoine de Daruvar, Minoru Kanehisa Genome Biology 2007, 8:R123 (26 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A modular approach is presented that allows the observation of the transcriptional activity of metabolic functions at the genome scale.
	Research Estimation and correction of non-specific binding in a large-scale spike-in experiment Eugene F Schuster, Eric Blanc, Linda Partridge, Janet M Thornton Genome Biology 2007, 8:R126 (26 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combined statistical analysis using the MAS5 PM-MM, GC-NSB and PDNN methods to generate probeset values from microarray data results in an improved ability to detect differential expression and estimates of false discovery rates compared with the individual methods.
	Research Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome Noa Sela, Britta Mersch, Nurit Gal-Mark, Galit Lev-Maor, Agnes Hotz-Wagenblatt, Gil Ast Genome Biology 2007, 8:R127 (27 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of transposed elements in the human and mouse genomes reveals many effects on the transcriptomes, including a higher level of exonization of Alu elements than other elements.
	Research Morphine effects on striatal transcriptome in mice Michal Korostynski, Marcin Piechota, Dorota Kaminska, Wojciech Solecki, Ryszard Przewlocki Genome Biology 2007, 8:R128 (28 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Global transcriptional analysis of mouse striata following acute and chronic exposure to morphine reveals multiple physiological factors which may affect opioid-related phenotypes and implicates a number of gene networks, including glucocorticoid receptor regulated genes, in the response to this opioid.
	Method RAD marker microarrays enable rapid mapping of zebrafish mutations Michael R Miller, Tressa S Atwood, B Frank Eames, Johann K Eberhart, Yi-Lin Yan, John H Postlethwait, Eric A Johnson Genome Biology 2007, 8:R105 (6 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A RAD marker microarray was constructed to facilitate rapid genetic mapping of zebrafish mutations and used to localize previously unmapped mutations to genomic regions just a few centiMorgans in length.
	Method Celsius: a community resource for Affymetrix microarray data Allen Day, Marc RJ Carlson, Jun Dong, Brian D O'Connor, Stanley F Nelson Genome Biology 2007, 8:R112 (14 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Celsius is a new system that serves as a warehouse by aggregating Affymetrix files and associated metadata, and containing the largest publicly available source of Affymetrix microarray data.
	Method LongSAGE profiling of nine human embryonic stem cell lines Martin Hirst, Allen Delaney, Sean A Rogers, Angelique Schnerch, Deryck R Persaud, Michael D O'Connor, Thomas Zeng, Michelle Moksa, Keith Fichter, Diana Mah, Anne Go, Ryan D Morin, Agnes Baross, Yongjun Zhao, Jaswinder Khattra, Anna-Liisa Prabhu, Pawan Pandoh, Helen McDonald, Jennifer Asano, Noreen Dhalla, Kevin Ma, Stephanie Lee, Adrian Ally, Neil Chahal, Stephanie Menzies, Asim Siddiqui, Robert Holt, Steven Jones, Daniela S Gerhard, James A Thomson, Connie J Eaves, Marco A Marra et al. Genome Biology 2007, 8:R113 (14 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of a 2.6 million longSAGE sequence tag resource generated from nine human embryonic stem cell lines reveals an enrichment of RNA binding proteins and novel ES-specific transcripts.
	Method Measuring the accuracy of genome-size multiple alignments Amol Prakash, Martin Tompa Genome Biology 2007, 8:R124 (26 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel computational approach can assess the accuracy of genomic alignments, and reveals suspicious regions in the 17-vertebrate MULTIZ alignment available on the UCSC Genome Browser.
	Method Correcting for sequence biases in present/absent calls Eugene F Schuster, Eric Blanc, Linda Partridge, Janet M Thornton Genome Biology 2007, 8:R125 (26 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Correction of non-specific binding for both PM and MM probes using probe-sequence models can partially remove the probe-sequence bias in Affymetrix microarray experiments and result in better performance of the MAS 5.0 algorithm.

	Volume 8 Issue 6
	Comment
	Comment An idea whose time has gone Gregory A Petsko Genome Biology 2007, 8:107 (2 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The $60 million a year in public money that is being spent on the Protein Structure Initiative is enough to fund approximately 100-200 individual investigator-initiated research grants.
	Review
	Protein family review The calpains: modular designs and functional diversity Dorothy E Croall, Klaus Ersfeld Genome Biology 2007, 8:218 (2 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The eukaryotic calpains are a family of calcium-dependent papain-like proteases and their non-enzymatic relatives whose varied physiological functions are beginning to be fully explored.
	Minireview Topological variation in single-gene phylogenetic trees Jose Castresana Genome Biology 2007, 8:216 (13 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale phylogenetic study of the human lineage dramatically points up the problems of using single genes to build phylogenetic trees.
	Minireview Pyrosequencing positions nucleosomes precisely Tom Owen-Hughes, Maik Engeholm Genome Biology 2007, 8:217 (27 June 2007) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Massively parallel pyrosequencing used to map nucleosome positions genome-wide.
	Report
	Meeting report An epigenetic role for noncoding RNAs and intragenic DNA methylation James M Flanagan, Laurence Wild Genome Biology 2007, 8:307 (27 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Keystone Symposium 'Epigenetics: Regulation of Chromatin Structure in Development and Disease', Breckenridge, USA, 11-16 April 2007.
	Research
	Research Cloning and characterization of microRNAs from wheat (Triticum aestivum L.) Yingyin Yao, Ganggang Guo, Zhongfu Ni, Ramanjulu Sunkar, Jinkun Du, Jian-Kang Zhu, Qixin Sun Genome Biology 2007, 8:R96 (1 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A small RNA library was used to identify 58 miRNAs from 43 miRNA families from wheat (Triticum aestivum L.), and 46 potential targets were predicted.
	Research Computational and transcriptional evidence for microRNAs in the honey bee genome Daniel B Weaver, Juan M Anzola, Jay D Evans, Jeffrey G Reid, Justin T Reese, Kevin L Childs, Evgeny M Zdobnov, Manoj P Samanta, Jonathan Miller, Christine G Elsik Genome Biology 2007, 8:R97 (1 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A total of 68 non-redundant candidate honey bee miRNAs were identified computationally; several of them appear to have previously unrecognized orthologs in the Drosophila genome. Several miRNAs showed caste- or age-related differences in transcript abundance and are likely to be involved in regulating honey bee development.
	Research Mixture modeling of transcript abundance classes in natural populations Wen-Ping Hsieh, Gisele Passador-Gurgel, Eric A Stone, Greg Gibson Genome Biology 2007, 8:R98 (4 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression profiling of Drosophila melanogaster adult female heads for 108 nearly isogenic lines from two different populations, and of CEPH lymphoblastoid lines, shows that differential expression of transcripts among individuals is due to a complex interplay of cis- and trans-acting factors.
	Research Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Jinling Huang, Johann Gogarten Genome Biology 2007, 8:R99 (4 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary Phylogenomic analyses of the red alga Cyanidioschyzon merolae shows that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, suggesting an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote.
	Research Genetic flux over time in the Salmonella lineage Georgios S Vernikos, Nicholas R Thomson, Julian Parkhill Genome Biology 2007, 8:R100 (4 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary From a whole-genome comparative analysis of Salmonella, Escherichia coli and Shigella strains, the relative time of insertion of putative horizontally acquired genes in three Salmonella strains were inferred, highlighting the major impact of horizontal transfer in the evolution of the salmonellae.
	Research Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon Genome Biology 2007, 8:R101 (5 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Analysis of 280 experimentally-verified cis-regulatory modules from Drosophila reveal features both common to all and unique to distinct subclasses of modules.
	Research Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains Laurence Rohmer, Christine Fong, Simone Abmayr, Michael Wasnick, Theodore Larson Freeman, Matthew Radey, Tina Guina, Kerstin Svensson, Hillary S Hayden, Michael Jacobs, Larry A Gallagher, Colin Manoil, Robert K Ernst, Becky Drees, Danielle Buckley, Eric Haugen, Donald Bovee, Yang Zhou, Jean Chang, Ruth Levy, Regina Lim, Will Gillett, Don Guenthener, Allison Kang, Scott A Shaffer, Greg Taylor, Jinzhi Chen, Byron Gallis, David A D'Argenio, Mats Forsman, Maynard V Olson, David R Goodlett, Rajinder Kaul, Samuel I Miller, Mitchell J Brittnacher et al. Genome Biology 2007, 8:R102 (5 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary .Sequencing of the non-pathogenic Francisella tularensis sub-species novicida U112, and comparison with two pathogenic sub-species, provides insights into the evolution of pathogenicity in these species.
	Research Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains Justin S Hogg, Fen Z Hu, Benjamin Janto, Robert Boissy, Jay Hayes, Randy Keefe, J Christopher Post, Garth D Ehrlich Genome Biology 2007, 8:R103 (5 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary The genomes of 9 non-typeable H. influenzae clinical isolates were sequenced and compared with a reference strain, allowing the characterisation and modelling of the core-and supra genomes of this organism.
	Research A functional map of NFκB signaling identifies novel modulators and multiple system controls Thomas A Halsey, Longlong Yang, John R Walker, John B Hogenesch, Russell S Thomas Genome Biology 2007, 8:R104 (6 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using cell-based genomic screens and functional assays, positive and negative modulators of NFκB signaling were identified and mapped onto the known NFκB signaling cascade.
	Research Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction Yavor Hadzhiev, Michael Lang, Raymond Ertzer, Axel Meyer, Uwe Strähle, Ferenc Müller Genome Biology 2007, 8:R106 (8 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Investigation of the ar-C midline enhancer of sonic hedgehog orthologs and paralogs from distantly related vertebrate lineages identified lineage-specific motif changes; exchanging motifs between paralog enhancers resulted in the reversal of enhancer specificity.
	Research Large-scale identification of human genes implicated in epidermal barrier function Eve Toulza, Nicolas R Mattiuzzo, Marie-Florence Galliano, Nathalie Jonca, Carole Dossat, Daniel Jacob, Antoine de Daruvar, Patrick Wincker, Guy Serre, Marina Guerrin Genome Biology 2007, 8:R107 (11 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Identification of genes expressed in epidermal granular keratinocytes by ORESTES, including a number that are highly specific for these cells.
	Research Functional coordination of alternative splicing in the mammalian central nervous system Matthew Fagnani, Yoseph Barash, Joanna Y Ip, Christine Misquitta, Qun Pan, Arneet L Saltzman, Ofer Shai, Leo Lee, Aviad Rozenhek, Naveed Mohammad, Sandrine Willaime-Morawek, Tomas Babak, Wen Zhang, Timothy R Hughes, Derek van der Kooy, Brendan J Frey, Benjamin J Blencowe Genome Biology 2007, 8:R108 (12 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microarray analysis provides new evidence suggesting that specific cellular processes in the mammalian CNS are coordinated at the level of alternative splicing, and that a complex splicing code underlies CNS-specific alternative splicing regulation.
	Research The human phylome Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón Genome Biology 2007, 8:R109 (13 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed.
	Research A semi-quantitative GeLC-MS analysis of temporal proteome expression in the emerging nosocomial pathogen Ochrobactrum anthropi Robert Graham, Mohit K Sharma, Nigel G Ternan, D Brent Weatherly, Rick L Tarleton, Geoff McMullan Genome Biology 2007, 8:R110 (13 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A semi-quantitative gel-based analysis identifies distinct proteomic profiles associated with specific growth points for the nosocomial pathogen Ochrobactrum anthropi.
	Research Detailed analysis of 15q11-q14 sequence corrects errors and gaps in the public access sequence to fully reveal large segmental duplications at breakpoints for Prader-Willi, Angelman, and inv dup(15) syndromes Andrew J Makoff, Rachel H Flomen Genome Biology 2007, 8:R114 (15 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed segmental map of the 15q11-q14 region of the human genome reveals two pairs of large direct repeats in regions associated with Prader-Willi and Angelman syndromes and other repeats that may increase susceptibility to other disorders.
	Research LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs Zhonglin Tang, Yong Li, Ping Wan, Xiaoping Li, Shuhong Zhao, Bang Liu, Bin Fan, Mengjin Zhu, Mei Yu, Kui Li Genome Biology 2007, 8:R115 (16 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of Tongcheng and Landrace pigs using long serial analysis of gene expression provides insight into the molecular mechanism underlying differences in muscle growth.
	Research GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p Job Dekker Genome Biology 2007, 8:R116 (18 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary GC-rich and AT-rich chromatin domains display distinct chromatin conformations and are marked by distinct patterns of histone modifications, and the histone deacetylase Rpd3p is an attenuator of these differences.
	Research Genetic background influences murine prostate gene expression: implications for cancer phenotypes Daniella Bianchi-Frias, Colin Pritchard, Brigham H Mecham, Ilsa M Coleman, Peter S Nelson Genome Biology 2007, 8:R117 (18 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Microarray analyses to quantitate transcript levels in the prostates of five inbred mouse strains identified differences in gene expression in benign epithelium that correlated with the differentiation state of adjacent tumors.
	Research Fast-evolving noncoding sequences in the human genome Christine P Bird, Barbara E Stranger, Maureen Liu, Daryl J Thomas, Catherine E Ingle, Claude Beazley, Webb Miller, Matthew E Hurles, Emmanouil T Dermitzakis Genome Biology 2007, 8:R118 (19 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Over 1,300 conserved non-coding sequences were identified that appear to have undergone dramatic human-specific changes in selective pressures; these are enriched in recent segmental duplications, suggesting a recent change in selective constraint following duplication.
	Research The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes Lorena E Rosaleny, Ana B Ruiz-García, José García-Martínez, José E Pérez-Ortín, Vicente Tordera Genome Biology 2007, 8:R119 (20 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A macroarray platform was used to identify binding sites of yeast histone acetyltransferase catalytic subunits and to correlate their positions with acetylation of lysine 14 of histone H3, revealing that Sas3p and Gcn5p are recruited to similar sets of intensely transcribed genes.
	Research Genome position and gene amplification Pavla Gajduskova, Antoine M Snijders, Serena Kwek, Ritu Roydasgupta, Jane Fridlyand, Taku Tokuyasu, Daniel Pinkel, Donna G Albertson Genome Biology 2007, 8:R120 (21 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells.
	Research Evolutionary history and functional implications of protein domains and their combinations in eukaryotes Masumi Itoh, Jose C Nacher, Kei-ichi Kuma, Susumu Goto, Minoru Kanehisa Genome Biology 2007, 8:R121 (25 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no similar trends were observed in other clades of eukaryotes.
	Research Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity Yuxia Cui, Sandra J McBride, Windy A Boyd, Scott Alper, Jonathan H Freedman Genome Biology 2007, 8:R122 (25 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Global analysis of the transcriptional response to cadmium exposure in Caenorhabditis elegans reveals roles for genes involved in cellular trafficking, metabolic processes and proteolysis, and for the signaling protein KEL-8.
	Research Observing metabolic functions at the genome scale Jean-Marc Schwartz, Claire Gaugain, Jose C Nacher, Antoine de Daruvar, Minoru Kanehisa Genome Biology 2007, 8:R123 (26 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A modular approach is presented that allows the observation of the transcriptional activity of metabolic functions at the genome scale.
	Research Estimation and correction of non-specific binding in a large-scale spike-in experiment Eugene F Schuster, Eric Blanc, Linda Partridge, Janet M Thornton Genome Biology 2007, 8:R126 (26 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combined statistical analysis using the MAS5 PM-MM, GC-NSB and PDNN methods to generate probeset values from microarray data results in an improved ability to detect differential expression and estimates of false discovery rates compared with the individual methods.
	Research Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome Noa Sela, Britta Mersch, Nurit Gal-Mark, Galit Lev-Maor, Agnes Hotz-Wagenblatt, Gil Ast Genome Biology 2007, 8:R127 (27 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of transposed elements in the human and mouse genomes reveals many effects on the transcriptomes, including a higher level of exonization of Alu elements than other elements.
	Research Morphine effects on striatal transcriptome in mice Michal Korostynski, Marcin Piechota, Dorota Kaminska, Wojciech Solecki, Ryszard Przewlocki Genome Biology 2007, 8:R128 (28 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Global transcriptional analysis of mouse striata following acute and chronic exposure to morphine reveals multiple physiological factors which may affect opioid-related phenotypes and implicates a number of gene networks, including glucocorticoid receptor regulated genes, in the response to this opioid.
	Method RAD marker microarrays enable rapid mapping of zebrafish mutations Michael R Miller, Tressa S Atwood, B Frank Eames, Johann K Eberhart, Yi-Lin Yan, John H Postlethwait, Eric A Johnson Genome Biology 2007, 8:R105 (6 June 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A RAD marker microarray was constructed to facilitate rapid genetic mapping of zebrafish mutations and used to localize previously unmapped mutations to genomic regions just a few centiMorgans in length.
	Method Celsius: a community resource for Affymetrix microarray data Allen Day, Marc RJ Carlson, Jun Dong, Brian D O'Connor, Stanley F Nelson Genome Biology 2007, 8:R112 (14 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Celsius is a new system that serves as a warehouse by aggregating Affymetrix files and associated metadata, and containing the largest publicly available source of Affymetrix microarray data.
	Method LongSAGE profiling of nine human embryonic stem cell lines Martin Hirst, Allen Delaney, Sean A Rogers, Angelique Schnerch, Deryck R Persaud, Michael D O'Connor, Thomas Zeng, Michelle Moksa, Keith Fichter, Diana Mah, Anne Go, Ryan D Morin, Agnes Baross, Yongjun Zhao, Jaswinder Khattra, Anna-Liisa Prabhu, Pawan Pandoh, Helen McDonald, Jennifer Asano, Noreen Dhalla, Kevin Ma, Stephanie Lee, Adrian Ally, Neil Chahal, Stephanie Menzies, Asim Siddiqui, Robert Holt, Steven Jones, Daniela S Gerhard, James A Thomson, Connie J Eaves, Marco A Marra et al. Genome Biology 2007, 8:R113 (14 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of a 2.6 million longSAGE sequence tag resource generated from nine human embryonic stem cell lines reveals an enrichment of RNA binding proteins and novel ES-specific transcripts.
	Method Measuring the accuracy of genome-size multiple alignments Amol Prakash, Martin Tompa Genome Biology 2007, 8:R124 (26 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel computational approach can assess the accuracy of genomic alignments, and reveals suspicious regions in the 17-vertebrate MULTIZ alignment available on the UCSC Genome Browser.
	Method Correcting for sequence biases in present/absent calls Eugene F Schuster, Eric Blanc, Linda Partridge, Janet M Thornton Genome Biology 2007, 8:R125 (26 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Correction of non-specific binding for both PM and MM probes using probe-sequence models can partially remove the probe-sequence bias in Affymetrix microarray experiments and result in better performance of the MAS 5.0 algorithm.

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