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	Volume 8 Issue 9
	Comment
	Comment Strange days Gregory A Petsko Genome Biology 2007, 8:110 (1 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary It's too bad that Al Gore who might be one of the few Democrats to be a good friend to science, who believes that reason, not faith or ideology, should decide issues, and who actually knows something about the world outside his own country, isn’t going to run for US president.
	Review
	Protein family review The protamine family of sperm nuclear proteins Rod Balhorn Genome Biology 2007, 8:227 (26 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An overview of the vertebrate members of a diverse family of basic DNA-binding proteins that are synthesized in the late-stage spermatids of many animals and plants and condense the spermatid genome into a genetically inactive state.
	Minireview Hidden weapons of microbial destruction in plant genomes John M Manners Genome Biology 2007, 8:225 (26 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent bioinformatic analyses of sequenced plant genomes reveal a previously unrecognized abundance of genes encoding antimicrobial cysteine-rich peptides, representing a formidable and dynamic defense arsenal against plant pests and pathogens.
	Minireview The monkey's perspective Todd R Disotell, Anthony J Tosi Genome Biology 2007, 8:226 (26 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sequencing of the genome of a female rhesus macaque (Macaca mulatta) of Indian origin will provide us with biomedical and evolutionary insights into both humans and Old World monkeys.
	Report
	Meeting report Global 'worming' Sreekanth H Chalasani, Evan H Feinberg, Massimo A Hilliard Genome Biology 2007, 8:314 (13 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 16th International Caenorhabditis elegans Meeting, Los Angeles, USA, 27 June-1 July 2007.
	Meeting report Complexity and integration in the control of inner-ear development Donald L Swiderski, Tzy-Wen Gong, Mirna Mustapha Genome Biology 2007, 8:315 (1 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Sixth Molecular Biology of Hearing and Deafness Conference, Hinxton, UK, 11-14 July 2007.
	Research
	Research Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere Miguel A Matilla, Manuel Espinosa-Urgel, José J Rodríguez-Herva, Juan L Ramos, María Ramos-González Genome Biology 2007, 8:R179 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A global analysis of Pseudomonas putida gene expression performed during the interaction with maize roots revealed how a bacterial population adjusts its genetic program to the specific conditions of this lifestyle.
	Research Functional constraint and small insertions and deletions in the ENCODE regions of the human genome Taane G Clark, Toby Andrew, Gregory M Cooper, Elliott H Margulies, James C Mullikin, David J Balding Genome Biology 2007, 8:R180 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Indel rates were observed to be reduced approximately twenty-fold in exonic ENCODE regions, five-fold in sequence that exhibits high evolutionary constraint in mammals and up to two-fold in some classes of regulatory elements.
	Research Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation Feng He, Jan Buer, An-Ping Zeng, Rudi Balling Genome Biology 2007, 8:R181 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By combining information on the yeast transcription network and high-resolution time-series data with a series of factors, support is provided for the concept that dynamic cumulative regulation is a major principle of quantitative transcriptional control.
	Research Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics Jibin Sun, Xin Lu, Ursula Rinas, An Zeng Genome Biology 2007, 8:R182 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genome-scale metabolic network and an in-depth genomic comparison of Aspergillus niger with seven other fungi is presented, revealing more than 1,100 enzyme-coding genes that are unique to A. niger.
	Research Transcriptomic and phenotypic analysis of murine embryonic stem cell derived BMP2⁺lineage cells: an insight into mesodermal patterning Michael Doss, Shuhua Chen, Johannes Winkler, Rita Hippler-Altenburg, Margareta Odenthal, Claudia Wickenhauser, Sridevi Balaraman, Herbert Schulz, Oliver Hummel, Norbert Hübner, Nandini Ghosh-Choudhury, Isaia Sotiriadou, Jürgen Hescheler, Agapios Sachinidis Genome Biology 2007, 8:R184 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptome analysis of BMP2⁺cells in comparison to the undifferentiated BMP2 ES cells and the control population from 7-day old embryoid bodies led to the identification of 479 specifically upregulated and 193 downregulated transcripts.
	Research The embryonic muscle transcriptome of Caenorhabditis elegans Rebecca M Fox, Joseph D Watson, Stephen E Von Stetina, Joan McDermott, Thomas M Brodigan, Tetsunari Fukushige, Michael Krause, David M Miller Genome Biology 2007, 8:R188 (12 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fluorescence activated cell sorting and microarray profiling were used to identify 1,312 expressed genes that are enriched in myo-3::GFP-positive muscle cells of Caenorhabditis elegans.
	Research Social regulation of gene expression in human leukocytes Steve W Cole, Louise C Hawkley, Jesusa M Arevalo, Caroline Y Sung, Robert M Rose, John T Cacioppo Genome Biology 2007, 8:R189 (13 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of differentially expressed in circulating leukocytes from people who chronically experienced high versus low levels of subjective social isolation (loneliness) revealed over-expression of some anti-inflammatory genes and under-expression of some pro-inflammatory genes.
	Research Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer Martin Buess, Dimitry SA Nuyten, Trevor Hastie, Torsten Nielsen, Robert Pesich, Patrick O Brown Genome Biology 2007, 8:R191 (14 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an effort to deconvolute global gene-expression profiles, an interaction between some breast cancer cells and stromal fibroblasts was found to induce an interferon response, which may be associated with a greater propensity for tumor progression.
	Research Genome-wide investigation reveals pathogen-specific and shared signatures in the response of Caenorhabditis elegans to infection Daniel Wong, Daphne Bazopoulou, Nathalie Pujol, Nektarios Tavernarakis, Jonathan J Ewbank Genome Biology 2007, 8:R194 (17 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Microarray analysis of the transcriptional response of C. elegans to four bacterial pathogens revealed that different infections trigger responses, some of which are common to all four pathogens, such as necrotic cell death, which has been associated with infection in humans.
	Research Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species Anne Laurençon, Raphaëlle Dubruille, Evgeni Efimenko, Guillaume Grenier, Ryan Bissett, Elisabeth Cortier, Vivien Rolland, Peter Swoboda, Bénédicte Durand Genome Biology 2007, 8:R195 (17 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are involved in sensory ciliogenesis.
	Research Drawing the tree of eukaryotic life based on the analysis of 2,269 manually annotated myosins from 328 species Florian Odronitz, Martin Kollmar Genome Biology 2007, 8:R196 (18 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tree of eukaryotic life was reconstructed based on the analysis of 2,269 myosin motor domains from 328 organisms, confirming some accepted relationships of major taxa and resolving disputed and preliminary classifications.
	Research Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions Vera van Noort, Berend Snel, Martijn A Huynen Genome Biology 2007, 8:R197 (19 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By combining different types of large datasets that give evidence for protein-interactions, qualitative labels on the predicted protein interaction network of S. cerevisiae could be inferred, providing guidance towards direct experimental verification of the predicted interactions.
	Research Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life Alexey V Lobanov, Dmitri E Fomenko, Yan Zhang, Aniruddha Sengupta, Dolph L Hatfield, Vadim N Gladyshev Genome Biology 2007, 8:R198 (19 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In silico and metabolic labeling studies of the selenoproteomes of several eukaryotes revealed distinct selenoprotein patterns as well as an ancient origin of selenoproteins and massive, independent losses in land plants, fungi, nematodes, insects and some protists, suggesting that the environment plays an important role in selenoproteome evolution.
	Research Rooting the eutherian tree: the power and pitfalls of phylogenomics Hidenori Nishihara, Norihiro Okada, Masami Hasegawa Genome Biology 2007, 8:R199 (21 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an attempt to root the eutherian tree using genome-scale data with the maximum likelihood method, a concatenate analysis supports a putatively wrong tree, whereas separate analyses of different genes reduced the bias.
	Research Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis Robert Kleemann, Lars Verschuren, Marjan J van Erk, Yuri Nikolsky, Nicole HP Cnubben, Elwin R Verheij, Age K Smilde, Henk FJ Hendriks, Susanne Zadelaar, Graham J Smith, Valery Kaznacheev, Tatiana Nikolskaya, Anton Melnikov, Eva Hurt-Camejo, Jan van der Greef, Ben van Ommen, Teake Kooistra Genome Biology 2007, 8:R200 (24 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary With increasing dietary cholesterol intake the liver switches from a mainly resilient to a predominantly inflammatory state, which is associated with early lesion formation.
	Research Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression Jennifer Beane, Paola Sebastiani, Gang Liu, Jerome S Brody, Marc E Lenburg, Avrum Spira Genome Biology 2007, 8:R201 (25 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Oligonucleotide microarray analysis revealed 175 genes that are differentially expressed in large airway epithelial cells of people who currently smoke compared with those who never smoked, with 28 classified as irreversible, 6 as slowly reversible, and 139 as rapidly reversible.
	Research Regional differences in dosage compensation on the chicken Z chromosome Esther Melamed, Arthur P Arnold Genome Biology 2007, 8:R202 (27 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray data analysis revealed a cluster of well compensated genes in the MHM (male-hypermethylated) region on chicken chromosome Zp, whereas Zq is enriched in non-compensated genes. The non-coding MHM RNA may therefore play a role in dosage compensation in the female.
	Method Cross-species cluster co-conservation: a new method for generating protein interaction networks Anis Karimpour-Fard, Corrella S Detweiler, Kimberly D Erickson, Lawrence Hunter, Ryan T Gill Genome Biology 2007, 8:R185 (5 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cluster Co-Conservation (CCC) has been extended to a method for developing protein interaction networks based on co-conservation between protein pairs across multiple species, Cross-Species Cluster Co-Conservation (CS-CCC).
	Method Coverage and error models of protein-protein interaction data by directed graph analysis Tony Chiang, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, Wolfgang Huber Genome Biology 2007, 8:R186 (10 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Directed graph and multinomial error models were used to assess and characterize the error statistics in all published large-scale datasets for Saccharomyces cerevisiae
	Method The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data Gabriel S Eichler, Mark Reimers, David Kane, John N Weinstein Genome Biology 2007, 8:R187 (10 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The LeFE algorithm has been developed to address the complex, non-linear regulation of gene expression.
	Method InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale Haidong Wang, Eran Segal, Asa Ben-Hur, Qian-Ru Li, Marc Vidal, Daphne Koller Genome Biology 2007, 8:R192 (14 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary InSite is a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs.
	Method Identification of novel stem cell markers using gap analysis of gene expression data Paul M Krzyzanowski, Miguel A Andrade-Navarro Genome Biology 2007, 8:R193 (17 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for the detection of marker genes in large heterogeneous collections of gene expression data is described and applied to DNA microarray data generated from 83 mouse stem cell-related samples.
	Method A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila Ramanuj DasGupta, Kent Nybakken, Matthew Booker, Bernard Mathey-Prevot, Foster Gonsalves, Binita Changkakoty, Norbert Perrimon Genome Biology 2007, 8:R203 (28 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A second generation dsRNA library was used to re-assess factors that influence the outcome of transcriptional reporter-based whole-genome RNAi screens for the Wnt/Wingless (wg) and Hedgehog (hh)-signaling pathways.
	Software The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists Da Huang, Brad T Sherman, Qina Tan, Jack R Collins, W Gregory Alvord, Jean Roayaei, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki Genome Biology 2007, 8:R183 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The DAVID gene functional classification tool uses a novel fuzzy clustering algorithm to condense a list of genes or associated biological terms into organized classes of related genes or biology, called biological modules.
	Software DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data Michael Watson, Juliet Dukes, Abu-Bakr Abu-Median, Donald P King, Paul Britton Genome Biology 2007, 8:R190 (14 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DetectiV is a tool for analyzing pathogen-detection microarray datasets that allows simple visualisation, normalisation and significance testing.

	Volume 8 Issue 9
	Comment
	Comment Strange days Gregory A Petsko Genome Biology 2007, 8:110 (1 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary It's too bad that Al Gore who might be one of the few Democrats to be a good friend to science, who believes that reason, not faith or ideology, should decide issues, and who actually knows something about the world outside his own country, isn’t going to run for US president.
	Review
	Protein family review The protamine family of sperm nuclear proteins Rod Balhorn Genome Biology 2007, 8:227 (26 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An overview of the vertebrate members of a diverse family of basic DNA-binding proteins that are synthesized in the late-stage spermatids of many animals and plants and condense the spermatid genome into a genetically inactive state.
	Minireview Hidden weapons of microbial destruction in plant genomes John M Manners Genome Biology 2007, 8:225 (26 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent bioinformatic analyses of sequenced plant genomes reveal a previously unrecognized abundance of genes encoding antimicrobial cysteine-rich peptides, representing a formidable and dynamic defense arsenal against plant pests and pathogens.
	Minireview The monkey's perspective Todd R Disotell, Anthony J Tosi Genome Biology 2007, 8:226 (26 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sequencing of the genome of a female rhesus macaque (Macaca mulatta) of Indian origin will provide us with biomedical and evolutionary insights into both humans and Old World monkeys.
	Report
	Meeting report Global 'worming' Sreekanth H Chalasani, Evan H Feinberg, Massimo A Hilliard Genome Biology 2007, 8:314 (13 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 16th International Caenorhabditis elegans Meeting, Los Angeles, USA, 27 June-1 July 2007.
	Meeting report Complexity and integration in the control of inner-ear development Donald L Swiderski, Tzy-Wen Gong, Mirna Mustapha Genome Biology 2007, 8:315 (1 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Sixth Molecular Biology of Hearing and Deafness Conference, Hinxton, UK, 11-14 July 2007.
	Research
	Research Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere Miguel A Matilla, Manuel Espinosa-Urgel, José J Rodríguez-Herva, Juan L Ramos, María Ramos-González Genome Biology 2007, 8:R179 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A global analysis of Pseudomonas putida gene expression performed during the interaction with maize roots revealed how a bacterial population adjusts its genetic program to the specific conditions of this lifestyle.
	Research Functional constraint and small insertions and deletions in the ENCODE regions of the human genome Taane G Clark, Toby Andrew, Gregory M Cooper, Elliott H Margulies, James C Mullikin, David J Balding Genome Biology 2007, 8:R180 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Indel rates were observed to be reduced approximately twenty-fold in exonic ENCODE regions, five-fold in sequence that exhibits high evolutionary constraint in mammals and up to two-fold in some classes of regulatory elements.
	Research Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation Feng He, Jan Buer, An-Ping Zeng, Rudi Balling Genome Biology 2007, 8:R181 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By combining information on the yeast transcription network and high-resolution time-series data with a series of factors, support is provided for the concept that dynamic cumulative regulation is a major principle of quantitative transcriptional control.
	Research Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics Jibin Sun, Xin Lu, Ursula Rinas, An Zeng Genome Biology 2007, 8:R182 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genome-scale metabolic network and an in-depth genomic comparison of Aspergillus niger with seven other fungi is presented, revealing more than 1,100 enzyme-coding genes that are unique to A. niger.
	Research Transcriptomic and phenotypic analysis of murine embryonic stem cell derived BMP2⁺lineage cells: an insight into mesodermal patterning Michael Doss, Shuhua Chen, Johannes Winkler, Rita Hippler-Altenburg, Margareta Odenthal, Claudia Wickenhauser, Sridevi Balaraman, Herbert Schulz, Oliver Hummel, Norbert Hübner, Nandini Ghosh-Choudhury, Isaia Sotiriadou, Jürgen Hescheler, Agapios Sachinidis Genome Biology 2007, 8:R184 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptome analysis of BMP2⁺cells in comparison to the undifferentiated BMP2 ES cells and the control population from 7-day old embryoid bodies led to the identification of 479 specifically upregulated and 193 downregulated transcripts.
	Research The embryonic muscle transcriptome of Caenorhabditis elegans Rebecca M Fox, Joseph D Watson, Stephen E Von Stetina, Joan McDermott, Thomas M Brodigan, Tetsunari Fukushige, Michael Krause, David M Miller Genome Biology 2007, 8:R188 (12 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fluorescence activated cell sorting and microarray profiling were used to identify 1,312 expressed genes that are enriched in myo-3::GFP-positive muscle cells of Caenorhabditis elegans.
	Research Social regulation of gene expression in human leukocytes Steve W Cole, Louise C Hawkley, Jesusa M Arevalo, Caroline Y Sung, Robert M Rose, John T Cacioppo Genome Biology 2007, 8:R189 (13 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of differentially expressed in circulating leukocytes from people who chronically experienced high versus low levels of subjective social isolation (loneliness) revealed over-expression of some anti-inflammatory genes and under-expression of some pro-inflammatory genes.
	Research Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer Martin Buess, Dimitry SA Nuyten, Trevor Hastie, Torsten Nielsen, Robert Pesich, Patrick O Brown Genome Biology 2007, 8:R191 (14 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an effort to deconvolute global gene-expression profiles, an interaction between some breast cancer cells and stromal fibroblasts was found to induce an interferon response, which may be associated with a greater propensity for tumor progression.
	Research Genome-wide investigation reveals pathogen-specific and shared signatures in the response of Caenorhabditis elegans to infection Daniel Wong, Daphne Bazopoulou, Nathalie Pujol, Nektarios Tavernarakis, Jonathan J Ewbank Genome Biology 2007, 8:R194 (17 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Microarray analysis of the transcriptional response of C. elegans to four bacterial pathogens revealed that different infections trigger responses, some of which are common to all four pathogens, such as necrotic cell death, which has been associated with infection in humans.
	Research Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species Anne Laurençon, Raphaëlle Dubruille, Evgeni Efimenko, Guillaume Grenier, Ryan Bissett, Elisabeth Cortier, Vivien Rolland, Peter Swoboda, Bénédicte Durand Genome Biology 2007, 8:R195 (17 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are involved in sensory ciliogenesis.
	Research Drawing the tree of eukaryotic life based on the analysis of 2,269 manually annotated myosins from 328 species Florian Odronitz, Martin Kollmar Genome Biology 2007, 8:R196 (18 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tree of eukaryotic life was reconstructed based on the analysis of 2,269 myosin motor domains from 328 organisms, confirming some accepted relationships of major taxa and resolving disputed and preliminary classifications.
	Research Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions Vera van Noort, Berend Snel, Martijn A Huynen Genome Biology 2007, 8:R197 (19 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By combining different types of large datasets that give evidence for protein-interactions, qualitative labels on the predicted protein interaction network of S. cerevisiae could be inferred, providing guidance towards direct experimental verification of the predicted interactions.
	Research Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life Alexey V Lobanov, Dmitri E Fomenko, Yan Zhang, Aniruddha Sengupta, Dolph L Hatfield, Vadim N Gladyshev Genome Biology 2007, 8:R198 (19 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In silico and metabolic labeling studies of the selenoproteomes of several eukaryotes revealed distinct selenoprotein patterns as well as an ancient origin of selenoproteins and massive, independent losses in land plants, fungi, nematodes, insects and some protists, suggesting that the environment plays an important role in selenoproteome evolution.
	Research Rooting the eutherian tree: the power and pitfalls of phylogenomics Hidenori Nishihara, Norihiro Okada, Masami Hasegawa Genome Biology 2007, 8:R199 (21 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an attempt to root the eutherian tree using genome-scale data with the maximum likelihood method, a concatenate analysis supports a putatively wrong tree, whereas separate analyses of different genes reduced the bias.
	Research Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis Robert Kleemann, Lars Verschuren, Marjan J van Erk, Yuri Nikolsky, Nicole HP Cnubben, Elwin R Verheij, Age K Smilde, Henk FJ Hendriks, Susanne Zadelaar, Graham J Smith, Valery Kaznacheev, Tatiana Nikolskaya, Anton Melnikov, Eva Hurt-Camejo, Jan van der Greef, Ben van Ommen, Teake Kooistra Genome Biology 2007, 8:R200 (24 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary With increasing dietary cholesterol intake the liver switches from a mainly resilient to a predominantly inflammatory state, which is associated with early lesion formation.
	Research Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression Jennifer Beane, Paola Sebastiani, Gang Liu, Jerome S Brody, Marc E Lenburg, Avrum Spira Genome Biology 2007, 8:R201 (25 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Oligonucleotide microarray analysis revealed 175 genes that are differentially expressed in large airway epithelial cells of people who currently smoke compared with those who never smoked, with 28 classified as irreversible, 6 as slowly reversible, and 139 as rapidly reversible.
	Research Regional differences in dosage compensation on the chicken Z chromosome Esther Melamed, Arthur P Arnold Genome Biology 2007, 8:R202 (27 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray data analysis revealed a cluster of well compensated genes in the MHM (male-hypermethylated) region on chicken chromosome Zp, whereas Zq is enriched in non-compensated genes. The non-coding MHM RNA may therefore play a role in dosage compensation in the female.
	Method Cross-species cluster co-conservation: a new method for generating protein interaction networks Anis Karimpour-Fard, Corrella S Detweiler, Kimberly D Erickson, Lawrence Hunter, Ryan T Gill Genome Biology 2007, 8:R185 (5 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cluster Co-Conservation (CCC) has been extended to a method for developing protein interaction networks based on co-conservation between protein pairs across multiple species, Cross-Species Cluster Co-Conservation (CS-CCC).
	Method Coverage and error models of protein-protein interaction data by directed graph analysis Tony Chiang, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, Wolfgang Huber Genome Biology 2007, 8:R186 (10 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Directed graph and multinomial error models were used to assess and characterize the error statistics in all published large-scale datasets for Saccharomyces cerevisiae
	Method The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data Gabriel S Eichler, Mark Reimers, David Kane, John N Weinstein Genome Biology 2007, 8:R187 (10 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The LeFE algorithm has been developed to address the complex, non-linear regulation of gene expression.
	Method InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale Haidong Wang, Eran Segal, Asa Ben-Hur, Qian-Ru Li, Marc Vidal, Daphne Koller Genome Biology 2007, 8:R192 (14 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary InSite is a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs.
	Method Identification of novel stem cell markers using gap analysis of gene expression data Paul M Krzyzanowski, Miguel A Andrade-Navarro Genome Biology 2007, 8:R193 (17 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for the detection of marker genes in large heterogeneous collections of gene expression data is described and applied to DNA microarray data generated from 83 mouse stem cell-related samples.
	Method A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila Ramanuj DasGupta, Kent Nybakken, Matthew Booker, Bernard Mathey-Prevot, Foster Gonsalves, Binita Changkakoty, Norbert Perrimon Genome Biology 2007, 8:R203 (28 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A second generation dsRNA library was used to re-assess factors that influence the outcome of transcriptional reporter-based whole-genome RNAi screens for the Wnt/Wingless (wg) and Hedgehog (hh)-signaling pathways.
	Software The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists Da Huang, Brad T Sherman, Qina Tan, Jack R Collins, W Gregory Alvord, Jean Roayaei, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki Genome Biology 2007, 8:R183 (4 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The DAVID gene functional classification tool uses a novel fuzzy clustering algorithm to condense a list of genes or associated biological terms into organized classes of related genes or biology, called biological modules.
	Software DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data Michael Watson, Juliet Dukes, Abu-Bakr Abu-Median, Donald P King, Paul Britton Genome Biology 2007, 8:R190 (14 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DetectiV is a tool for analyzing pathogen-detection microarray datasets that allows simple visualisation, normalisation and significance testing.

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