Genome Biology | Volume 8 Issue 5

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 8 Issue 5
	Comment
	Comment Inconvenient truths Gregory A Petsko Genome Biology 2007, 8:106 (31 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Science is not immune to meaningless locutions and genomics is rapidly acquiring its own set. They are used as a way of camouflaging the truth.
	Review
	Protein family review The integrins Yoshikazu Takada, Xiaojing Ye, Scott Simon Genome Biology 2007, 8:215 (1 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An overview of a family of cell-surface adhesion and signaling receptors that mediate cell-cell adhesion and cell-extracellular matrix adhesion.
	Minireview Mouse maps of gene expression in the brain Susan E Koester, Thomas R Insel Genome Biology 2007, 8:212 (18 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comprehensive atlases of gene expression in the mouse brain will provide a great resource for neurobiology.
	Minireview Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia Timothy Hughes, Diana Ekman, Himanshu Ardawatia, Arne Elofsson, David A Liberles Genome Biology 2007, 8:213 (22 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Can dosage compensation completely explain gene retention after whole-genome duplication?
	Minireview A rational route to probing membrane proteins Amy E Keating Genome Biology 2007, 8:214 (31 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Computationally designed peptides against transmembrane helices point to new approaches to studying membrane protein function.
	Report
	Meeting report The fungal frontier Jill R Blankenship, Aaron P Mitchell Genome Biology 2007, 8:305 (22 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 24th Fungal Genetics Conference, Asilomar, USA, 20-25 March 2007.
	Meeting report Chickens get their place in the sun Charalampos Rallis Genome Biology 2007, 8:306 (25 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the International Chick Meeting 'The Chick as a Model Organism: Genes, Development and Function', Barcelona, Spain, 11-14 April 2007.
	Research
	Research Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans Joel N Meyer, Windy A Boyd, Gregory A Azzam, Astrid C Haugen, Jonathan H Freedman, Bennett Van Houten Genome Biology 2007, 8:R70 (1 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Repair of UVC-induced DNA damage in Caenorhabditis elegans is similar kinetically and genetically to repair in humans, and it slows significantly in aging C. elegans.
	Research Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition Tristan Lefébure, Michael J Stanhope Genome Biology 2007, 8:R71 (2 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative evolutionary analyses of 26 Streptococcus genomes show that recombination and positive selection have both had important roles in the adaptation of different species to different hosts.
	Research Gene expression analysis of nuclear factor I-A deficient mice indicates delayed brain maturation Yong Wong, Christian Schulze, Thomas Streichert, Richard M Gronostajski, Melitta Schachner, Thomas Tilling Genome Biology 2007, 8:R72 (2 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Gene expression analysis of brains from mice deficient in nuclear factor I-A (Nfia^-/-mice) and from Nfia^+/+mice suggests that Nfia^-/-mice are delayed in early postnatal development, especially oligodendrocyte maturation.
	Research Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study Gabriella Rustici, Harm van Bakel, Daniel H Lackner, Frank C Holstege, Cisca Wijmenga, Jürg Bähler, Alvis Brazma Genome Biology 2007, 8:R73 (3 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of genome-wide responses to changing copper and iron levels in budding and fission yeast reveals conservation of only a small core set of genes and remarkable differences in the responses of the two yeasts to excess copper.
	Research Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors Jason I Herschkowitz, Karl Simin, Victor J Weigman, Igor Mikaelian, Jerry Usary, Zhiyuan Hu, Karen E Rasmussen, Laundette P Jones, Shahin Assefnia, Subhashini Chandrasekharan, Michael G Backlund, Yuzhi Yin, Andrey I Khramtsov, Roy Bastein, John Quackenbush, Robert I Glazer, Powel H Brown, Jeffrey E Green, Levy Kopelovich, Priscilla A Furth, Juan P Palazzo, Olufunmilayo I Olopade, Philip S Bernard, Gary A Churchill, Terry Van Dyke, Charles M Perou Genome Biology 2007, 8:R76 (10 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of mammary tumor gene-expression profiles from thirteen murine models using microarrays and with that of human breast tumors showed that many of the defining characteristics of human subtypes were conserved among mouse models.
	Research Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-κB and other signal transcription factors in head and neck squamous cell carcinoma Bin Yan, Xinping Yang, Tin-Lap Lee, Jay Friedman, Jun Tang, Carter Van Waes, Zhong Chen Genome Biology 2007, 8:R78 (11 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray profiling of ten head and neck cancer lines revealed novel p53 and NF-κB transcriptional gene expression signatures which distinguished tumor cell subsets in association with their p53 status.
	Research Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house mouse subspecies François Bonhomme, Eric Rivals, Annie Orth, Gemma R Grant, Alec J Jeffreys, Philippe RJ Bois Genome Biology 2007, 8:R80 (14 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Global analysis of four minisatellite loci in House Mouse reveals unexpected long-range gene flow between populations and subspecies.
	Research Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome Shaun Mahony, David L Corcoran, Eleanor Feingold, Panayiotis V Benos Genome Biology 2007, 8:R84 (16 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of conservation of non-coding sequences, cis-regulatory elements and biological functions of regulated genes in opossum and other vertebrates enables better estimation of promoter conservation and transcription factor binding site turnover among mammals
	Research A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks Albert J Poustka, Alexander Kühn, Detlef Groth, Vesna Weise, Shunsuke Yaguchi, Robert D Burke, Ralf Herwig, Hans Lehrach, Georgia Panopoulou Genome Biology 2007, 8:R85 (16 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel territory-specific markers from the sea urchin Strongylocentrotus purpuratus have been identified using screens for genes that are differentially expressed in lithium-treated embryos, which form an excess of endomesoderm, and in zinc-treated embryos, in which endomesoderm specification is blocked.
	Research Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray Xiaohong Zhang, Omar De la Cruz, Jayant M Pinto, Dan Nicolae, Stuart Firestein, Yoav Gilad Genome Biology 2007, 8:R86 (17 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a microarray, expression of 76% of predicted human olfactory receptor genes was detected in olfactory epithelia, and many were expressed in non-olfactory tissues.
	Research Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly Neil F Lobo, Kathy S Campbell, Daniel Thaner, Becky deBruyn, Hean Koo, William M Gelbart, Brendan J Loftus, David W Severson, Frank H Collins Genome Biology 2007, 8:R88 (22 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In order to provide a set of manually curated and annotated sequences from the Aedes aegypti genome, mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using computational gene-finding, EST matches as well as comparative protein homology.
	Research GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism Dany JV Beste, Tracy Hooper, Graham Stewart, Bhushan Bonde, Claudio Avignone-Rossa, Michael E Bushell, Paul Wheeler, Steffen Klamt, Andrzej M Kierzek, Johnjoe McFadden Genome Biology 2007, 8:R89 (23 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GSMN-TB, a genome-scale metabolic model of M. tuberculosis, was constructed and validated using experimental data.
	Research Gene expression variation in Down's syndrome mice allows prioritization of candidate genes Marc Sultan, Ilaria Piccini, Daniela Balzereit, Ralf Herwig, Nidhi G Saran, Hans Lehrach, Roger H Reeves, Marie-Laure Yaspo Genome Biology 2007, 8:R91 (25 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA from eight Ts65Dn mice (a model of Down syndrome) and eight euploid mice were analysed by real-time PCR to examine inter-individual gene expression levels as a function of trisomy.
	Research Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages Antonio del Sol, Marcos J Araúzo-Bravo, Dolors Amoros, Ruth Nussinov Genome Biology 2007, 8:R92 (25 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method for studying signal transmission between functional sites by decomposing protein structures into modules demonstrates that protein domains consist of modules interconnected by residues that mediate signaling through the shortest pathways.
	Research Modular organization in the reductive evolution of protein-protein interaction networks Javier Tamames, Andrés Moya, Alfonso Valencia Genome Biology 2007, 8:R94 (28 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the reduction in genome size of Buchnera aphidicola from its common ancestor E. coli shows that the organization of networks into modules is the property that seems to be directly related with the evolutionary process of genome reduction.
	Research Unequal evolutionary conservation of human protein interactions in interologous networks Kevin R Brown, Igor Jurisica Genome Biology 2007, 8:R95 (29 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The conservation of protein-protein interaction networks can be examined by mapping human proteins to yeast and other model organisms, revealing that protein complexes are preferentially conserved, and that such conservation can yield biological insights.
	Method ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes Brian R King, Chittibabu Guda Genome Biology 2007, 8:R68 (1 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ngLOC is an n-gram-based Bayesian classification method that can predict the localization of a protein sequence over ten distinct subcellular organelles.
	Method Towards the uniform distribution of null P values on Affymetrix microarrays Anthony A Fodor, Timothy L Tickle, Christine Richardson Genome Biology 2007, 8:R69 (1 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Estimating the P value from the overall distribution of scores on the microarray can produce P values that are much closer to a uniform distribution.
	Method Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies Björn Nilsson, Petra Håkansson, Mikael Johansson, Sven Nelander, Thoas Fioretos Genome Biology 2007, 8:R74 (8 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New ontological analysis methods are described for microarray data interpretation that, unlike existing approaches, are threshold-free and statistically powerful.
	Method cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers Thomas Brody, Wayne Rasband, Kevin Baler, Alexander Kuzin, Mukta Kundu, Ward F Odenwald Genome Biology 2007, 8:R75 (9 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary : The use of cis-Decoder, a new tool for discovery of conserved sequence elements that are shared between similarly regulating enhancers, suggests that enhancers use overlapping repertoires of highly conserved core elements.
	Method Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis Yingchun Liu, Markus Ringnér Genome Biology 2007, 8:R77 (11 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A strategy for identifying cell signaling pathways whose deregulation result in an observed expression signature is presented.
	Method Exon arrays provide accurate assessments of gene expression Karen Kapur, Yi Xing, Zhengqing Ouyang, Wing Wong Genome Biology 2007, 8:R82 (15 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A strategy for estimating gene expression on Affymetrix exon arrays suggests that these arrays may provide more accurate measurements of gene expression than traditional 3’ arrays.
	Method A distance difference matrix approach to identifying transcription factors that regulate differential gene expression Pieter De Bleser, Bart Hooghe, Dominique Vlieghe, Frans van Roy Genome Biology 2007, 8:R83 (16 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A distance difference matrix method is presented for identifying transcription factor binding sites of secondary factors responsible for the different responses of the target genes of one transcription factor.
	Method Monitoring of gene knockouts: genome-wide profiling of conditionally essential genes Lisa K Smith, Maria J Gomez, Konstantin Y Shatalin, Hyunwoo Lee, Alexander A Neyfakh Genome Biology 2007, 8:R87 (22 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Monitoring of gene knockouts is a new microarray-based genetic technique used for genome-wide identification of conditionally essential genes in bacteria
	Method Optimization and clinical validation of a pathogen detection microarray Christopher W Wong, Charlie Heng, Leong Wan Yee, Shirlena WL Soh, Cissy B Kartasasmita, Eric AF Simoes, Martin L Hibberd, Wing-Kin Sung, Lance D Miller Genome Biology 2007, 8:R93 (28 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New design and optimization of pathogen detection microarrays is shown to allow robust and accurate detection of a range of pathogens. The customized microarray platform includes a method for reducing PCR bias during DNA amplification.
	Software An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data Michał J Okoniewski, Tim Yates, Siân Dibben, Crispin J Miller Genome Biology 2007, 8:R79 (11 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An annotation database (X:MAP) and BioConductor/R package (exonmap) have been developed to support fine-grained analysis of exon array data.
	Software Tilescope: online analysis pipeline for high-density tiling microarray data Zhengdong D Zhang, Joel Rozowsky, Hugo YK Lam, Jiang Du, Michael Snyder, Mark Gerstein Genome Biology 2007, 8:R81 (14 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tilescope is a fully integrated and automated new data-processing pipeline for analyzing high-density tiling-array data.
	Software A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database José L Jiménez, Björn Hegemann, James RA Hutchins, Jan-Michael Peters, Richard Durbin Genome Biology 2007, 8:R90 (23 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary mtcPTM is a new database of phosphorylated protein sequences and atomic models. Analysis of the phosphosites in mtcPTM showed that phosphorylation sites are found in a highly heterogeneous range of structural and sequence contexts.
	Correspondence
	Correspondence Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns Rie Takahashi, Jeffrey H Miller Genome Biology 2007, 8:405 (3 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How to make music from the genome.
	Correspondence A recipe for high impact Murat Cokol, Raul Rodriguez-Esteban, Andrey Rzhetsky Genome Biology 2007, 8:406 (10 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary What makes an article high impact?

	Volume 8 Issue 5
	Comment
	Comment Inconvenient truths Gregory A Petsko Genome Biology 2007, 8:106 (31 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Science is not immune to meaningless locutions and genomics is rapidly acquiring its own set. They are used as a way of camouflaging the truth.
	Review
	Protein family review The integrins Yoshikazu Takada, Xiaojing Ye, Scott Simon Genome Biology 2007, 8:215 (1 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An overview of a family of cell-surface adhesion and signaling receptors that mediate cell-cell adhesion and cell-extracellular matrix adhesion.
	Minireview Mouse maps of gene expression in the brain Susan E Koester, Thomas R Insel Genome Biology 2007, 8:212 (18 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comprehensive atlases of gene expression in the mouse brain will provide a great resource for neurobiology.
	Minireview Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia Timothy Hughes, Diana Ekman, Himanshu Ardawatia, Arne Elofsson, David A Liberles Genome Biology 2007, 8:213 (22 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Can dosage compensation completely explain gene retention after whole-genome duplication?
	Minireview A rational route to probing membrane proteins Amy E Keating Genome Biology 2007, 8:214 (31 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Computationally designed peptides against transmembrane helices point to new approaches to studying membrane protein function.
	Report
	Meeting report The fungal frontier Jill R Blankenship, Aaron P Mitchell Genome Biology 2007, 8:305 (22 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 24th Fungal Genetics Conference, Asilomar, USA, 20-25 March 2007.
	Meeting report Chickens get their place in the sun Charalampos Rallis Genome Biology 2007, 8:306 (25 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the International Chick Meeting 'The Chick as a Model Organism: Genes, Development and Function', Barcelona, Spain, 11-14 April 2007.
	Research
	Research Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans Joel N Meyer, Windy A Boyd, Gregory A Azzam, Astrid C Haugen, Jonathan H Freedman, Bennett Van Houten Genome Biology 2007, 8:R70 (1 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Repair of UVC-induced DNA damage in Caenorhabditis elegans is similar kinetically and genetically to repair in humans, and it slows significantly in aging C. elegans.
	Research Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition Tristan Lefébure, Michael J Stanhope Genome Biology 2007, 8:R71 (2 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative evolutionary analyses of 26 Streptococcus genomes show that recombination and positive selection have both had important roles in the adaptation of different species to different hosts.
	Research Gene expression analysis of nuclear factor I-A deficient mice indicates delayed brain maturation Yong Wong, Christian Schulze, Thomas Streichert, Richard M Gronostajski, Melitta Schachner, Thomas Tilling Genome Biology 2007, 8:R72 (2 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Gene expression analysis of brains from mice deficient in nuclear factor I-A (Nfia^-/-mice) and from Nfia^+/+mice suggests that Nfia^-/-mice are delayed in early postnatal development, especially oligodendrocyte maturation.
	Research Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study Gabriella Rustici, Harm van Bakel, Daniel H Lackner, Frank C Holstege, Cisca Wijmenga, Jürg Bähler, Alvis Brazma Genome Biology 2007, 8:R73 (3 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of genome-wide responses to changing copper and iron levels in budding and fission yeast reveals conservation of only a small core set of genes and remarkable differences in the responses of the two yeasts to excess copper.
	Research Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors Jason I Herschkowitz, Karl Simin, Victor J Weigman, Igor Mikaelian, Jerry Usary, Zhiyuan Hu, Karen E Rasmussen, Laundette P Jones, Shahin Assefnia, Subhashini Chandrasekharan, Michael G Backlund, Yuzhi Yin, Andrey I Khramtsov, Roy Bastein, John Quackenbush, Robert I Glazer, Powel H Brown, Jeffrey E Green, Levy Kopelovich, Priscilla A Furth, Juan P Palazzo, Olufunmilayo I Olopade, Philip S Bernard, Gary A Churchill, Terry Van Dyke, Charles M Perou Genome Biology 2007, 8:R76 (10 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of mammary tumor gene-expression profiles from thirteen murine models using microarrays and with that of human breast tumors showed that many of the defining characteristics of human subtypes were conserved among mouse models.
	Research Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-κB and other signal transcription factors in head and neck squamous cell carcinoma Bin Yan, Xinping Yang, Tin-Lap Lee, Jay Friedman, Jun Tang, Carter Van Waes, Zhong Chen Genome Biology 2007, 8:R78 (11 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray profiling of ten head and neck cancer lines revealed novel p53 and NF-κB transcriptional gene expression signatures which distinguished tumor cell subsets in association with their p53 status.
	Research Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house mouse subspecies François Bonhomme, Eric Rivals, Annie Orth, Gemma R Grant, Alec J Jeffreys, Philippe RJ Bois Genome Biology 2007, 8:R80 (14 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Global analysis of four minisatellite loci in House Mouse reveals unexpected long-range gene flow between populations and subspecies.
	Research Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome Shaun Mahony, David L Corcoran, Eleanor Feingold, Panayiotis V Benos Genome Biology 2007, 8:R84 (16 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of conservation of non-coding sequences, cis-regulatory elements and biological functions of regulated genes in opossum and other vertebrates enables better estimation of promoter conservation and transcription factor binding site turnover among mammals
	Research A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks Albert J Poustka, Alexander Kühn, Detlef Groth, Vesna Weise, Shunsuke Yaguchi, Robert D Burke, Ralf Herwig, Hans Lehrach, Georgia Panopoulou Genome Biology 2007, 8:R85 (16 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel territory-specific markers from the sea urchin Strongylocentrotus purpuratus have been identified using screens for genes that are differentially expressed in lithium-treated embryos, which form an excess of endomesoderm, and in zinc-treated embryos, in which endomesoderm specification is blocked.
	Research Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray Xiaohong Zhang, Omar De la Cruz, Jayant M Pinto, Dan Nicolae, Stuart Firestein, Yoav Gilad Genome Biology 2007, 8:R86 (17 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a microarray, expression of 76% of predicted human olfactory receptor genes was detected in olfactory epithelia, and many were expressed in non-olfactory tissues.
	Research Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly Neil F Lobo, Kathy S Campbell, Daniel Thaner, Becky deBruyn, Hean Koo, William M Gelbart, Brendan J Loftus, David W Severson, Frank H Collins Genome Biology 2007, 8:R88 (22 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In order to provide a set of manually curated and annotated sequences from the Aedes aegypti genome, mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using computational gene-finding, EST matches as well as comparative protein homology.
	Research GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism Dany JV Beste, Tracy Hooper, Graham Stewart, Bhushan Bonde, Claudio Avignone-Rossa, Michael E Bushell, Paul Wheeler, Steffen Klamt, Andrzej M Kierzek, Johnjoe McFadden Genome Biology 2007, 8:R89 (23 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GSMN-TB, a genome-scale metabolic model of M. tuberculosis, was constructed and validated using experimental data.
	Research Gene expression variation in Down's syndrome mice allows prioritization of candidate genes Marc Sultan, Ilaria Piccini, Daniela Balzereit, Ralf Herwig, Nidhi G Saran, Hans Lehrach, Roger H Reeves, Marie-Laure Yaspo Genome Biology 2007, 8:R91 (25 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA from eight Ts65Dn mice (a model of Down syndrome) and eight euploid mice were analysed by real-time PCR to examine inter-individual gene expression levels as a function of trisomy.
	Research Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages Antonio del Sol, Marcos J Araúzo-Bravo, Dolors Amoros, Ruth Nussinov Genome Biology 2007, 8:R92 (25 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method for studying signal transmission between functional sites by decomposing protein structures into modules demonstrates that protein domains consist of modules interconnected by residues that mediate signaling through the shortest pathways.
	Research Modular organization in the reductive evolution of protein-protein interaction networks Javier Tamames, Andrés Moya, Alfonso Valencia Genome Biology 2007, 8:R94 (28 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the reduction in genome size of Buchnera aphidicola from its common ancestor E. coli shows that the organization of networks into modules is the property that seems to be directly related with the evolutionary process of genome reduction.
	Research Unequal evolutionary conservation of human protein interactions in interologous networks Kevin R Brown, Igor Jurisica Genome Biology 2007, 8:R95 (29 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The conservation of protein-protein interaction networks can be examined by mapping human proteins to yeast and other model organisms, revealing that protein complexes are preferentially conserved, and that such conservation can yield biological insights.
	Method ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes Brian R King, Chittibabu Guda Genome Biology 2007, 8:R68 (1 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ngLOC is an n-gram-based Bayesian classification method that can predict the localization of a protein sequence over ten distinct subcellular organelles.
	Method Towards the uniform distribution of null P values on Affymetrix microarrays Anthony A Fodor, Timothy L Tickle, Christine Richardson Genome Biology 2007, 8:R69 (1 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Estimating the P value from the overall distribution of scores on the microarray can produce P values that are much closer to a uniform distribution.
	Method Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies Björn Nilsson, Petra Håkansson, Mikael Johansson, Sven Nelander, Thoas Fioretos Genome Biology 2007, 8:R74 (8 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New ontological analysis methods are described for microarray data interpretation that, unlike existing approaches, are threshold-free and statistically powerful.
	Method cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers Thomas Brody, Wayne Rasband, Kevin Baler, Alexander Kuzin, Mukta Kundu, Ward F Odenwald Genome Biology 2007, 8:R75 (9 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary : The use of cis-Decoder, a new tool for discovery of conserved sequence elements that are shared between similarly regulating enhancers, suggests that enhancers use overlapping repertoires of highly conserved core elements.
	Method Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis Yingchun Liu, Markus Ringnér Genome Biology 2007, 8:R77 (11 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A strategy for identifying cell signaling pathways whose deregulation result in an observed expression signature is presented.
	Method Exon arrays provide accurate assessments of gene expression Karen Kapur, Yi Xing, Zhengqing Ouyang, Wing Wong Genome Biology 2007, 8:R82 (15 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A strategy for estimating gene expression on Affymetrix exon arrays suggests that these arrays may provide more accurate measurements of gene expression than traditional 3’ arrays.
	Method A distance difference matrix approach to identifying transcription factors that regulate differential gene expression Pieter De Bleser, Bart Hooghe, Dominique Vlieghe, Frans van Roy Genome Biology 2007, 8:R83 (16 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A distance difference matrix method is presented for identifying transcription factor binding sites of secondary factors responsible for the different responses of the target genes of one transcription factor.
	Method Monitoring of gene knockouts: genome-wide profiling of conditionally essential genes Lisa K Smith, Maria J Gomez, Konstantin Y Shatalin, Hyunwoo Lee, Alexander A Neyfakh Genome Biology 2007, 8:R87 (22 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Monitoring of gene knockouts is a new microarray-based genetic technique used for genome-wide identification of conditionally essential genes in bacteria
	Method Optimization and clinical validation of a pathogen detection microarray Christopher W Wong, Charlie Heng, Leong Wan Yee, Shirlena WL Soh, Cissy B Kartasasmita, Eric AF Simoes, Martin L Hibberd, Wing-Kin Sung, Lance D Miller Genome Biology 2007, 8:R93 (28 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New design and optimization of pathogen detection microarrays is shown to allow robust and accurate detection of a range of pathogens. The customized microarray platform includes a method for reducing PCR bias during DNA amplification.
	Software An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data Michał J Okoniewski, Tim Yates, Siân Dibben, Crispin J Miller Genome Biology 2007, 8:R79 (11 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An annotation database (X:MAP) and BioConductor/R package (exonmap) have been developed to support fine-grained analysis of exon array data.
	Software Tilescope: online analysis pipeline for high-density tiling microarray data Zhengdong D Zhang, Joel Rozowsky, Hugo YK Lam, Jiang Du, Michael Snyder, Mark Gerstein Genome Biology 2007, 8:R81 (14 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tilescope is a fully integrated and automated new data-processing pipeline for analyzing high-density tiling-array data.
	Software A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database José L Jiménez, Björn Hegemann, James RA Hutchins, Jan-Michael Peters, Richard Durbin Genome Biology 2007, 8:R90 (23 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary mtcPTM is a new database of phosphorylated protein sequences and atomic models. Analysis of the phosphosites in mtcPTM showed that phosphorylation sites are found in a highly heterogeneous range of structural and sequence contexts.
	Correspondence
	Correspondence Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns Rie Takahashi, Jeffrey H Miller Genome Biology 2007, 8:405 (3 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How to make music from the genome.
	Correspondence A recipe for high impact Murat Cokol, Raul Rodriguez-Esteban, Andrey Rzhetsky Genome Biology 2007, 8:406 (10 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary What makes an article high impact?

Explore Genome Biology

Articles

Volume 8 Issue 5

Comment

Review

Report

Research

Correspondence