Genome Biology | Volume 9 Issue 1

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	Volume 9 Issue 1
	Comment
	Comment The story they missed Gregory A Petsko Genome Biology 2008, 9:101 (31 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The closer we get to post-educational employment, the smaller the percentage of women at every stage. Where do all the talented and accomplished women go?
	Review
	Review Anchoring the genome Diego Ottaviani, Elliott Lever, Petros Takousis, Denise Sheer Genome Biology 2008, 9:201 (22 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Specific attachment of chromosomal sites to the nuclear matrix is crucial to the control of transcription and DNA replication.
	Protein family review The Groucho/TLE/Grg family of transcriptional co-repressors Barbara H Jennings, David Ish-Horowicz Genome Biology 2008, 9:205 (31 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Groucho family of co-repressor proteins are essential for development and may also have a role in some human cancers.
	Minireview Deciphering histone 2A deubiquitination Michael J Clague, Judy M Coulson, Sylvie Urbé Genome Biology 2008, 9:202 (23 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The discovery of three different enzymes that deubiquitinate histone 2A.
	Minireview Yeast Polo-like kinase substrates are nailed with the right tools Vincent Archambault, David M Glover Genome Biology 2008, 9:203 (30 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new approach to identifying kinase substrates reveals a novel role for yeast Polo-like kinase in mitosis
	Minireview MicroRNA, sex determination and floral meristem determinacy in maize Jo Banks Genome Biology 2008, 9:204 (30 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sex determination in maize inflorescences is determined by microRNA action.
	Report
	Meeting report Toward more effective gene delivery Hannah H Chen, Ryan Cawood, Leonard W Seymour Genome Biology 2008, 9:301 (18 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the symposium 'In vivo barriers to gene delivery', Cold Spring Harbor, USA, 26-29 November 2007.
	Research
	Research Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome Jia Wu, Jiang Du, Joel Rozowsky, Zhengdong Zhang, Alexander E Urban, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder Genome Biology 2008, 9:R3 (3 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RACE sequencing of ENCODE regions shows that much of the human genome is represented in poly(A)+ RNA.
	Research Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli Morgan N Price, Paramvir S Dehal, Adam P Arkin Genome Biology 2008, 9:R4 (7 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most Escherichia coli transcription factors have paralogs, but these usually arose by horizontal gene transfer rather than by duplication within the E. coli lineage, as previously believed.
	Research Picoeukaryotic sequences in the Sargasso Sea metagenome Gwenael Piganeau, Yves Desdevises, Evelyne Derelle, Herve Moreau Genome Biology 2008, 9:R5 (7 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many sequences from picoeukaryotes were found in DNA sequence data assembled from Sargasso seawater.
	Research Genomic chart guiding embryonic stem cell cardiopoiesis Randolph S Faustino, Atta Behfar, Carmen Perez-Terzic, Andre Terzic Genome Biology 2008, 9:R6 (9 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene expression analysis of embryonic stem cells undergoing guided cardiogenic differentiation reveals the molecular fingerprint for committing to cardiac cell fate.
	Research Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium Yoshinori Tomoyasu, Sherry C Miller, Shuichiro Tomita, Michael Schoppmeier, Daniela Grossmann, Gregor Bucher Genome Biology 2008, 9:R10 (17 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tribolium resembles C. elegans in showing a robust systemic RNAi response, but does not have C. elegans-type RNAi mechanisms; insect systemic RNAi probably uses a different mechanism.
	Research Gene expression variation in African and European populations of Drosophila melanogaster Stephan Hutter, Sarah S Saminadin-Peter, Wolfgang Stephan, John Parsch Genome Biology 2008, 9:R12 (21 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of gene expression variation in 16 Drosophila melanogaster strains from two natural populations reveals traits that were important for local adaptation to the European and African environments.
	Research Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity Corneliu Henegar, Joan Tordjman, Vincent Achard, Danièle Lacasa, Isabelle Cremer, Michèle Guerre-Millo, Christine Poitou, Arnaud Basdevant, Vladimir Stich, Nathalie Viguerie, Dominique Langin, Pierre Bedossa, Jean-Daniel Zucker, Karine Clement Genome Biology 2008, 9:R14 (21 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the transcriptomic signature of white adipose tissue in obese human subjects revealed increased interstitial fibrosis and an infiltration of inflammatory cells into the tissue.
	Research Towards defining the nuclear proteome J Lynn Fink, Seetha Karunaratne, Amit Mittal, Donald M Gardiner, Nicholas Hamilton, Donna Mahony, Chikatoshi Kai, Harukazu Suzuki, Yosihide Hayashizaki, Rohan D Teasdale Genome Biology 2008, 9:R15 (23 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Direct evidence is reported for 2,568 mammalian proteins within the nuclear proteome, consisting of at least 14% of the entire proteome.
	Research Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus Christoph Welsch, Francisco S Domingues, Simone Susser, Iris Antes, Christoph Hartmann, Gabriele Mayr, Andreas Schlicker, Christoph Sarrazin, Mario Albrecht, Stefan Zeuzem, Thomas Lengauer Genome Biology 2008, 9:R16 (23 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Structural analysis of the inhibitor Telaprevir (VX-950) of the hepatitis C virus (HCV) protease NS3-4A shows that mutations at V36 and/or T54 result in impaired interaction with VX-950, explaining the development of viral breakthrough variants.
	Research Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling Scott H Robbins, Thierry Walzer, Doulaye Dembélé, Christelle Thibault, Axel Defays, Gilles Bessou, Huichun Xu, Eric Vivier, MacLean Sellars, Philippe Pierre, Franck R Sharp, Susan Chan, Philippe Kastner, Marc Dalod Genome Biology 2008, 9:R17 (24 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide expression profiling of mouse and human leukocytes reveal conserved transcriptional programs of plasmacytoid or conventional dendritic cell subsets.
	Research Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi Nora Khaldi, Jérôme Collemare, Marc-Henri Lebrun, Kenneth H Wolfe Genome Biology 2008, 9:R18 (24 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic and comparative genomic analysis of orthologs of the Magnaporthe grisea ACE1 cluster reveals evidence for horizontal transfer of part of this cluster from an M. grisea-like ancestor into an ancestor of Aspergillus clavatus.
	Research Translational control plays a prominent role in the hepatocytic differentiation of HepaRG liver progenitor cells Romain Parent, Laura Beretta Genome Biology 2008, 9:R19 (25 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript profiling of HepaRG cells shows that translational regulation is the main genomic event associated with hepatocytic differentiation.
	Research The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization Juliana Kagan, Itai Sharon, Oded Beja, Jonathan C Kuhn Genome Biology 2008, 9:R20 (27 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of the seven genes of the tryptophan pathway in the Sargasso Sea metagenome shows that the majority of contigs and scaffolds contain whole or split operons that are similar to previously analyzed trp gene organizations.
	Research A BAC-based integrated linkage map of the silkworm Bombyx mori Kimiko Yamamoto, Junko Nohata, Keiko Kadono-Okuda, Junko Narukawa, Motoe Sasanuma, Shun-ichi Sasanuma, Hiroshi Minami, Michihiko Shimomura, Yoshitaka Suetsugu, Yutaka Banno, Kazutoyo Osoegawa, Pieter J de Jong, Marian R Goldsmith, Kazuei Mita Genome Biology 2008, 9:R21 (28 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An integrated map of the Bombyx mori genome has been constructed using 361.1 Mb of BAC contigs and singletons together with a genetic map containing 1689 independent genes and synteny among Apis, Tribolium, and Bombyx was examined.
	Research Mechanisms of intron gain and loss in Cryptococcus Thomas J Sharpton, Daniel E Neafsey, James E Galagan, John W Taylor Genome Biology 2008, 9:R24 (30 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of five relatively closely related yeast Cryptococcus genomes suggests that recombination causes internal intron loss and that DNA repeat expansion can create new introns in a population.
	Method High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae Hun-Goo Lee, Hyo-Soo Lee, Sang-Hoon Jeon, Tae-Hoon Chung, Young-Sung Lim, Won-Ki Huh Genome Biology 2008, 9:R2 (3 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel approach for identifying condition-specific regulatory modules in yeast reveals functionally distinct coregulated submodules.
	Method Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman Genome Biology 2008, 9:R7 (11 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes.
	Method The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation Shirley Wu, Mike P Liang, Russ B Altman Genome Biology 2008, 9:R8 (16 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SeqFEATURE, a tool for protein function annotation, models protein functions described by sequence motifs using a structural representation. The tool shows significantly improved performance over other methods when sequence and structural similarity are low.
	Method Protein interactions in human genetic diseases Benjamin Schuster-Böckler, Alex Bateman Genome Biology 2008, 9:R9 (16 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented to identify residues that form part of an interaction interface, leading to the prediction that 1,428 OMIM mutations are related to an interaction defect.
	Method CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships Wei-Cheng Lo, Ping-Chiang Lyu Genome Biology 2008, 9:R11 (18 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CPSARST (Circular Permutation Search Aided by Ramachandran Sequential Transformation) is an efficient database search tool that provides a new way for rapidly detecting novel relationships among proteins.
	Method An improved method for detecting and delineating genomic regions with altered gene expression in cancer Björn Nilsson, Mikael Johansson, Anders Heyden, Sven Nelander, Thoas Fioretos Genome Biology 2008, 9:R13 (21 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented for identifying genomic regions with altered gene expression in gene expression maps.
	Method Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs Andra Ivan, Marc S Halfon, Saurabh Sinha Genome Biology 2008, 9:R22 (28 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Prediction of cis-regulatory modules ab initio, without any input of relevant motifs, is achieved with two novel methods.
	Method Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data Chang-Kyu Lee, Susan M Sunkin, Chihchau Kuan, Carol L Thompson, Sayan Pathak, Lydia Ng, Chris Lau, Shanna Fischer, Marty Mortrud, Cliff Slaughterbeck, Allan Jones, Ed Lein, Michael Hawrylycz Genome Biology 2008, 9:R23 (30 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This study introduces a novel method for standardized relative quantification of colorimetric in situ hybridization signal that enables a large-scale cross-platform expression level comparison of in situ hybridization with two publicly available microarray brain data sources.
	Software MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data Igor Ulitsky, Irit Gat-Viks, Ron Shamir Genome Biology 2008, 9:R1 (2 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new computational tool is presented that allows the integration of high-throughput experimental results with the probabilistic modeling of previously obtained information about cellular systems. The tool (MetaReg) is demonstrated on the leucine biosynthesis system in S.cerevisiae.
	Correspondence
	Correspondence Uncovering trends in gene naming Michael R Seringhaus, Philip D Cayting, Mark B Gerstein Genome Biology 2008, 9:401 (31 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of unusual gene names reveals trends underlying their choice.

	Volume 9 Issue 1
	Comment
	Comment The story they missed Gregory A Petsko Genome Biology 2008, 9:101 (31 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The closer we get to post-educational employment, the smaller the percentage of women at every stage. Where do all the talented and accomplished women go?
	Review
	Review Anchoring the genome Diego Ottaviani, Elliott Lever, Petros Takousis, Denise Sheer Genome Biology 2008, 9:201 (22 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Specific attachment of chromosomal sites to the nuclear matrix is crucial to the control of transcription and DNA replication.
	Protein family review The Groucho/TLE/Grg family of transcriptional co-repressors Barbara H Jennings, David Ish-Horowicz Genome Biology 2008, 9:205 (31 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Groucho family of co-repressor proteins are essential for development and may also have a role in some human cancers.
	Minireview Deciphering histone 2A deubiquitination Michael J Clague, Judy M Coulson, Sylvie Urbé Genome Biology 2008, 9:202 (23 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The discovery of three different enzymes that deubiquitinate histone 2A.
	Minireview Yeast Polo-like kinase substrates are nailed with the right tools Vincent Archambault, David M Glover Genome Biology 2008, 9:203 (30 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new approach to identifying kinase substrates reveals a novel role for yeast Polo-like kinase in mitosis
	Minireview MicroRNA, sex determination and floral meristem determinacy in maize Jo Banks Genome Biology 2008, 9:204 (30 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sex determination in maize inflorescences is determined by microRNA action.
	Report
	Meeting report Toward more effective gene delivery Hannah H Chen, Ryan Cawood, Leonard W Seymour Genome Biology 2008, 9:301 (18 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the symposium 'In vivo barriers to gene delivery', Cold Spring Harbor, USA, 26-29 November 2007.
	Research
	Research Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome Jia Wu, Jiang Du, Joel Rozowsky, Zhengdong Zhang, Alexander E Urban, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder Genome Biology 2008, 9:R3 (3 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RACE sequencing of ENCODE regions shows that much of the human genome is represented in poly(A)+ RNA.
	Research Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli Morgan N Price, Paramvir S Dehal, Adam P Arkin Genome Biology 2008, 9:R4 (7 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most Escherichia coli transcription factors have paralogs, but these usually arose by horizontal gene transfer rather than by duplication within the E. coli lineage, as previously believed.
	Research Picoeukaryotic sequences in the Sargasso Sea metagenome Gwenael Piganeau, Yves Desdevises, Evelyne Derelle, Herve Moreau Genome Biology 2008, 9:R5 (7 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many sequences from picoeukaryotes were found in DNA sequence data assembled from Sargasso seawater.
	Research Genomic chart guiding embryonic stem cell cardiopoiesis Randolph S Faustino, Atta Behfar, Carmen Perez-Terzic, Andre Terzic Genome Biology 2008, 9:R6 (9 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene expression analysis of embryonic stem cells undergoing guided cardiogenic differentiation reveals the molecular fingerprint for committing to cardiac cell fate.
	Research Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium Yoshinori Tomoyasu, Sherry C Miller, Shuichiro Tomita, Michael Schoppmeier, Daniela Grossmann, Gregor Bucher Genome Biology 2008, 9:R10 (17 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tribolium resembles C. elegans in showing a robust systemic RNAi response, but does not have C. elegans-type RNAi mechanisms; insect systemic RNAi probably uses a different mechanism.
	Research Gene expression variation in African and European populations of Drosophila melanogaster Stephan Hutter, Sarah S Saminadin-Peter, Wolfgang Stephan, John Parsch Genome Biology 2008, 9:R12 (21 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of gene expression variation in 16 Drosophila melanogaster strains from two natural populations reveals traits that were important for local adaptation to the European and African environments.
	Research Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity Corneliu Henegar, Joan Tordjman, Vincent Achard, Danièle Lacasa, Isabelle Cremer, Michèle Guerre-Millo, Christine Poitou, Arnaud Basdevant, Vladimir Stich, Nathalie Viguerie, Dominique Langin, Pierre Bedossa, Jean-Daniel Zucker, Karine Clement Genome Biology 2008, 9:R14 (21 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the transcriptomic signature of white adipose tissue in obese human subjects revealed increased interstitial fibrosis and an infiltration of inflammatory cells into the tissue.
	Research Towards defining the nuclear proteome J Lynn Fink, Seetha Karunaratne, Amit Mittal, Donald M Gardiner, Nicholas Hamilton, Donna Mahony, Chikatoshi Kai, Harukazu Suzuki, Yosihide Hayashizaki, Rohan D Teasdale Genome Biology 2008, 9:R15 (23 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Direct evidence is reported for 2,568 mammalian proteins within the nuclear proteome, consisting of at least 14% of the entire proteome.
	Research Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus Christoph Welsch, Francisco S Domingues, Simone Susser, Iris Antes, Christoph Hartmann, Gabriele Mayr, Andreas Schlicker, Christoph Sarrazin, Mario Albrecht, Stefan Zeuzem, Thomas Lengauer Genome Biology 2008, 9:R16 (23 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Structural analysis of the inhibitor Telaprevir (VX-950) of the hepatitis C virus (HCV) protease NS3-4A shows that mutations at V36 and/or T54 result in impaired interaction with VX-950, explaining the development of viral breakthrough variants.
	Research Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling Scott H Robbins, Thierry Walzer, Doulaye Dembélé, Christelle Thibault, Axel Defays, Gilles Bessou, Huichun Xu, Eric Vivier, MacLean Sellars, Philippe Pierre, Franck R Sharp, Susan Chan, Philippe Kastner, Marc Dalod Genome Biology 2008, 9:R17 (24 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide expression profiling of mouse and human leukocytes reveal conserved transcriptional programs of plasmacytoid or conventional dendritic cell subsets.
	Research Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi Nora Khaldi, Jérôme Collemare, Marc-Henri Lebrun, Kenneth H Wolfe Genome Biology 2008, 9:R18 (24 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic and comparative genomic analysis of orthologs of the Magnaporthe grisea ACE1 cluster reveals evidence for horizontal transfer of part of this cluster from an M. grisea-like ancestor into an ancestor of Aspergillus clavatus.
	Research Translational control plays a prominent role in the hepatocytic differentiation of HepaRG liver progenitor cells Romain Parent, Laura Beretta Genome Biology 2008, 9:R19 (25 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript profiling of HepaRG cells shows that translational regulation is the main genomic event associated with hepatocytic differentiation.
	Research The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization Juliana Kagan, Itai Sharon, Oded Beja, Jonathan C Kuhn Genome Biology 2008, 9:R20 (27 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of the seven genes of the tryptophan pathway in the Sargasso Sea metagenome shows that the majority of contigs and scaffolds contain whole or split operons that are similar to previously analyzed trp gene organizations.
	Research A BAC-based integrated linkage map of the silkworm Bombyx mori Kimiko Yamamoto, Junko Nohata, Keiko Kadono-Okuda, Junko Narukawa, Motoe Sasanuma, Shun-ichi Sasanuma, Hiroshi Minami, Michihiko Shimomura, Yoshitaka Suetsugu, Yutaka Banno, Kazutoyo Osoegawa, Pieter J de Jong, Marian R Goldsmith, Kazuei Mita Genome Biology 2008, 9:R21 (28 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An integrated map of the Bombyx mori genome has been constructed using 361.1 Mb of BAC contigs and singletons together with a genetic map containing 1689 independent genes and synteny among Apis, Tribolium, and Bombyx was examined.
	Research Mechanisms of intron gain and loss in Cryptococcus Thomas J Sharpton, Daniel E Neafsey, James E Galagan, John W Taylor Genome Biology 2008, 9:R24 (30 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of five relatively closely related yeast Cryptococcus genomes suggests that recombination causes internal intron loss and that DNA repeat expansion can create new introns in a population.
	Method High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae Hun-Goo Lee, Hyo-Soo Lee, Sang-Hoon Jeon, Tae-Hoon Chung, Young-Sung Lim, Won-Ki Huh Genome Biology 2008, 9:R2 (3 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel approach for identifying condition-specific regulatory modules in yeast reveals functionally distinct coregulated submodules.
	Method Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman Genome Biology 2008, 9:R7 (11 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes.
	Method The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation Shirley Wu, Mike P Liang, Russ B Altman Genome Biology 2008, 9:R8 (16 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SeqFEATURE, a tool for protein function annotation, models protein functions described by sequence motifs using a structural representation. The tool shows significantly improved performance over other methods when sequence and structural similarity are low.
	Method Protein interactions in human genetic diseases Benjamin Schuster-Böckler, Alex Bateman Genome Biology 2008, 9:R9 (16 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented to identify residues that form part of an interaction interface, leading to the prediction that 1,428 OMIM mutations are related to an interaction defect.
	Method CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships Wei-Cheng Lo, Ping-Chiang Lyu Genome Biology 2008, 9:R11 (18 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CPSARST (Circular Permutation Search Aided by Ramachandran Sequential Transformation) is an efficient database search tool that provides a new way for rapidly detecting novel relationships among proteins.
	Method An improved method for detecting and delineating genomic regions with altered gene expression in cancer Björn Nilsson, Mikael Johansson, Anders Heyden, Sven Nelander, Thoas Fioretos Genome Biology 2008, 9:R13 (21 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented for identifying genomic regions with altered gene expression in gene expression maps.
	Method Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs Andra Ivan, Marc S Halfon, Saurabh Sinha Genome Biology 2008, 9:R22 (28 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Prediction of cis-regulatory modules ab initio, without any input of relevant motifs, is achieved with two novel methods.
	Method Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data Chang-Kyu Lee, Susan M Sunkin, Chihchau Kuan, Carol L Thompson, Sayan Pathak, Lydia Ng, Chris Lau, Shanna Fischer, Marty Mortrud, Cliff Slaughterbeck, Allan Jones, Ed Lein, Michael Hawrylycz Genome Biology 2008, 9:R23 (30 January 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This study introduces a novel method for standardized relative quantification of colorimetric in situ hybridization signal that enables a large-scale cross-platform expression level comparison of in situ hybridization with two publicly available microarray brain data sources.
	Software MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data Igor Ulitsky, Irit Gat-Viks, Ron Shamir Genome Biology 2008, 9:R1 (2 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new computational tool is presented that allows the integration of high-throughput experimental results with the probabilistic modeling of previously obtained information about cellular systems. The tool (MetaReg) is demonstrated on the leucine biosynthesis system in S.cerevisiae.
	Correspondence
	Correspondence Uncovering trends in gene naming Michael R Seringhaus, Philip D Cayting, Mark B Gerstein Genome Biology 2008, 9:401 (31 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of unusual gene names reveals trends underlying their choice.

Explore Genome Biology

Articles

Volume 9 Issue 1

Comment

Review

Report

Research

Correspondence