Genome Biology | Volume 8 Issue 10

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	Volume 8 Issue 10
	Comment
	Comment They fought the law and the law won Gregory A Petsko Genome Biology 2007, 8:111 (2 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The new science geo-engineering doesn't try to alter a few corn plants; it aims to tinker with the entire planet, based on the notion that ultimately we can actively manipulate the planet to have any climate pattern we want. But there is no way we can ever assess all of the likely consequences.
	Report
	Meeting report Shaping the future of interactome networks Patrick Aloy Genome Biology 2007, 8:316 (1 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report of the third Interactome Networks Conference, Hinxton, UK, 29 August-1 September 2007.
	Meeting report A cornucopia of delights for the mouse fancier Dominic P Norris, Sonja Nowotschin, Anna-Katerina Hadjantonakis Genome Biology 2007, 8:318 (1 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Mouse Molecular Genetics meeting, Hinxton, UK, 5-9 September 2007.
	Meeting report Tipping the balance in autoimmune disease Mary Collins Genome Biology 2007, 8:317 (2 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB Summer Research Conference on Autoimmunity, Saxtons River, USA, 14-29 July 2007.
	Research
	Research Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte Amal J Johnston, Patrick Meier, Jacqueline Gheyselinck, Samuel EJ Wuest, Michael Federer, Edith Schlagenhauf, Jörg D Becker, Ueli Grossniklaus Genome Biology 2007, 8:R204 (3 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic subtraction and expression profiling of wild-type Arabidopsis and a sporophytic mutant lacking an embryo sac identified 1,260 genes expressed in the embryo sac; a total of 527 genes were identified for their expression in ovules of mutants lacking an embryo sac.
	Research A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans Ana C Gomes, Isabel Miranda, Raquel M Silva, Gabriela R Moura, Benjamin Thomas, Alexandre Akoulitchev, Manuel AS Santos Genome Biology 2007, 8:R206 (4 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An unusual decoding of leucine CUG codons as serine in Candida albicans revealed unanticipated codon ambiguity, which expands the proteome of this human pathogen exponentially.
	Research All duplicates are not equal: the difference between small-scale and genome duplication Luke Hakes, John W Pinney, Simon C Lovell, Stephen G Oliver, David L Robertson Genome Biology 2007, 8:R209 (4 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The comparison of pairs of gene duplications generated by small-scale duplications with those created by large-scale duplications shows that they differ in quantifiable ways. It is suggested that this is directly due to biases on the paths to gene retention rather than association with different functional categories.
	Research Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia Jennifer Cohen, Linda J Van Marter, Yao Sun, Elizabeth Allred, Alan Leviton, Isaac S Kohane Genome Biology 2007, 8:R210 (4 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The expression profiles of umbilical cords from premature newborns reveal distinct patterns, including changes in the expression of chromatin remodeling factors, associated with the development of bronchopulmonary dysplasia.
	Research Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines Axel A Elling, Makedonka Mitreva, Justin Recknor, Xiaowu Gai, John Martin, Thomas R Maier, Jeffrey P McDermott, Tarek Hewezi, David McK Bird, Eric L Davis, Richard S Hussey, Dan Nettleton, James P McCarter, Thomas J Baum Genome Biology 2007, 8:R211 (5 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The generation and analysis of over 20,000 ESTs allowed the identification and expression profiling of 6,860 predicted genes in the nematode Heterodera glycines. This revealed that gene expression patterns in the dauer stage of Caenorhabditis elegans are not conserved in H. glycines.
	Research Host origin of plastid solute transporters in the first photosynthetic eukaryotes Heather M Tyra, Marc Linka, Andreas PM Weber, Debashish Bhattacharya Genome Biology 2007, 8:R212 (5 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of plastid transporter proteins in Arabidopsis suggests a host origin and provides new insights into plastid evolution.
	Research High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer Suet F Chin, Andrew E Teschendorff, John C Marioni, Yanzhong Wang, Nuno L Barbosa-Morais, Natalie P Thorne, Jose L Costa, Sarah E Pinder, Mark A van de Wiel, Andrew R Green, Ian O Ellis, Peggy L Porter, Simon Tavaré, James D Brenton, Bauke Ylstra, Carlos Caldas Genome Biology 2007, 8:R215 (7 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer, and provides a genome-wide list of common copy number alterations associated with aberrant expression and poor prognosis.
	Research Transcriptional profiling of inductive mesenchyme to identify molecules involved in prostate development and disease Griet Vanpoucke, Brigid Orr, O Cathal Grace, Ray Chan, George R Ashley, Karin Williams, Omar E Franco, Simon W Hayward, Axel A Thomson Genome Biology 2007, 8:R213 (8 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of SAGE libraries for prostatic inductive mesenchyme and the complete prostatic rudiment revealed 219 transcripts that were enriched in, or specific to, inductive mesenchyme. Further analysis suggested that Scube1 is a novel stromal molecule involved in prostate development and tumorigenesis.
	Research MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype Cherie Blenkiron, Leonard D Goldstein, Natalie P Thorne, Inmaculada Spiteri, Suet-Feung Chin, Mark J Dunning, Nuno L Barbosa-Morais, Andrew E Teschendorff, Andrew R Green, Ian O Ellis, Simon Tavaré, Carlos Caldas, Eric A Miska Genome Biology 2007, 8:R214 (8 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Integrated analysis of miRNA expression and genomic changes in human breast tumors allows the classification of tumor subtypes.
	Research The ribosomal protein genes and Minute loci of Drosophila melanogaster Steven J Marygold, John Roote, Gunter Reuter, Andrew Lambertsson, Michael Ashburner, Gillian H Millburn, Paul M Harrison, Zhan Yu, Naoya Kenmochi, Thomas C Kaufman, Sally J Leevers, Kevin R Cook Genome Biology 2007, 8:R216 (10 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combined bioinformatic and genetic approach was used to conduct a systematic analysis of the relationship between ribosomal protein genes and Minute loci in Drosophila melanogaster, allowing the identification of 64 Minute loci corresponding to ribosomal genes.
	Research Transcriptional regulatory network for sexual differentiation in fission yeast Juan Mata, Anna Wilbrey, Jürg Bähler Genome Biology 2007, 8:R217 (10 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis of the transcriptome of fission yeast after genetic perturbation of 6 genes known to have a role in sexual differentiation reveals insights into the regulatory principles controlling the gene expression program driving this process.
	Research Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris Yong-Qiang He, Liang Zhang, Bo-Le Jiang, Zheng-Chun Zhang, Rong-Qi Xu, Dong-Jie Tang, Jing Qin, Wei Jiang, Xia Zhang, Jie Liao, Jin-Ru Cao, Sui-Sheng Zhang, Mei-Liang Wei, Xiao-Xia Liang, Guang-Tao Lu, Jia-Xun Feng, Baoshan Chen, Jing Cheng, Ji-Liang Tang Genome Biology 2007, 8:R218 (10 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Construction of a microarray based on the genome of Xanthomonas campestris pv.campestris (Xcc), and its use to analyse 18 other virulent Xcc strains, revealed insights into the genetic diversity and determinants of host specificity of Xcc strains.
	Research Responses of hyperthermophilic crenarchaea to UV irradiation Dorothee Götz, Sonia Paytubi, Stacey Munro, Magnus Lundgren, Rolf Bernander, Malcolm F White Genome Biology 2007, 8:R220 (11 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptional response to UV irradiation was analyzed in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius, showing a clear response to DNA damage but no increase in the expression of DNA repair genes.
	Research Gene expression profiling of Hfe^-/-liver and duodenum in mouse strains with differing susceptibilities to iron loading: identification of transcriptional regulatory targets of Hfe and potential hemochromatosis modifiers Hélène Coppin, Valérie Darnaud, Léon Kautz, Delphine Meynard, Marc Aubry, Jean Mosser, Maria Martinez, Marie-Paule Roth Genome Biology 2007, 8:R221 (18 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene expression profiling using microarrays of Hfe-/- liver and duodenum in mouse strains with differing susceptibilities to iron loading allowed the identification of transcriptional targets of the hemochromatosis-associated gene Hfe.
	Research Common gene expression strategies revealed by genome-wide analysis in yeast José García-Martínez, Fernando González-Candelas, José E Pérez-Ortín Genome Biology 2007, 8:R222 (19 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive analysis of six variables characterizing gene expression in yeast, including transcription and translation, mRNA and protein amounts, reveals a general tendency for levels of mRNA and protein to be harmonized, and for functionally related genes to have similar values for these variables.
	Research Comparative genomic analysis of fungal genomes reveals intron-rich ancestors Jason E Stajich, Fred S Dietrich, Scott W Roy Genome Biology 2007, 8:R223 (19 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of intron gain and loss in fungal genomes provides support for an intron-rich fungus-animal ancestor.
	Research Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools Weichun Huang, Joseph R Nevins, Uwe Ohler Genome Biology 2007, 8:R225 (24 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic simulation of promoter evolution were used to analyze functional site turnover in regulatory sequences.
	Research Surprising complexity of the ancestral apoptosis network Christian M Zmasek, Qing Zhang, Yuzhen Ye, Adam Godzik Genome Biology 2007, 8:R226 (24 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A comparative genomics approach revealed that the genes for several components of the apoptosis network with single copies in vertebrates have multiple paralogs in cnidarian-bilaterian ancestors, suggesting a complex evolutionary history for this network.
	Research Transcriptional profiling reveals barcode-like toxicogenomic responses in the zebrafish embryo Lixin Yang, Jules R Kemadjou, Christian Zinsmeister, Matthias Bauer, Jessica Legradi, Ferenc Müller, Michael Pankratz, Jens Jäkel, Uwe Strähle Genome Biology 2007, 8:R227 (25 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray profiling of zebrafish embryos exposed to a range of environmental toxicants revealed distinct expression profiles for each of the toxicants tested.
	Research Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization John C Marioni, Natalie P Thorne, Armand Valsesia, Tomas Fitzgerald, Richard Redon, Heike Fiegler, T Daniel Andrews, Barbara E Stranger, Andrew G Lynch, Emmanouil T Dermitzakis, Nigel P Carter, Simon Tavaré, Matthew E Hurles Genome Biology 2007, 8:R228 (25 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Datasets used for detecting copy number variation (CNV) are shown to be affected by a technical artifact. A novel CNV calling algorithm is presented which removes this artifact and identifies regions of CNV better than existing methods.
	Research On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees Tomàs Marques-Bonet, Jesús Sànchez-Ruiz, Lluís Armengol, Razi Khaja, Jaume Bertranpetit, Núria Lopez-Bigas, Mariano Rocchi, Elodie Gazave, Arcadi Navarro Genome Biology 2007, 8:R230 (30 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the genes located in rearranged human and chimpanzee chromosomes identified lower divergence than for those in colinear chromosomes.
	Research Phenotypic and transcriptional response to selection for alcohol sensitivity in Drosophila melanogaster Tatiana V Morozova, Robert RH Anholt, Trudy FC Mackay Genome Biology 2007, 8:R231 (31 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene-expression profiling combined with selection for genetically divergent Drosophila lines either highly sensitive or resistant to ethanol exposure has been used to identify candidate genes that affect alcohol sensitivity, including 23 novel genes that have human orthologs.
	Method Finding disease candidate genes by liquid association Ker-Chau Li, Aarno Palotie, Shinsheng Yuan, Denis Bronnikov, Daniel Chen, Xuelian Wei, Oi-Wa Choi, Janna Saarela, Leena Peltonen Genome Biology 2007, 8:R205 (4 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel approach to finding candidate genes by using gene-expression data has been developed and used to identify a multiple sclerosis susceptibility candidate genes.
	Method Harnessing naturally randomized transcription to infer regulatory relationships among genes Lin S Chen, Frank Emmert-Streib, John D Storey Genome Biology 2007, 8:R219 (11 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An approach is developed that utilizes randomized genotypes to rigorously infer causal regulatory relationships among genes at the transcriptional level. The approach is applied to an experiment in yeast, yielding new insights into the topology of the yeast transcriptional regulatory network.
	Method A BAC clone fingerprinting approach to the detection of human genome rearrangements Martin Krzywinski, Ian Bosdet, Carrie Mathewson, Natasja Wye, Jay Brebner, Readman Chiu, Richard Corbett, Matthew Field, Darlene Lee, Trevor Pugh, Stas Volik, Asim Siddiqui, Steven Jones, Jacquie Schein, Collin Collins, Marco Marra Genome Biology 2007, 8:R224 (22 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fingerprint Profiling (FPP) is a new method which uses restriction digest fingerprints of bacterial artificial chromosome (BAC) clones for detecting and classifying rearrangements in the human genome.
	Method Simplified ontologies allowing comparison of developmental mammalian gene expression Adele Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide Genome Biology 2007, 8:R229 (25 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Developmental eVOC ontologies presented are simplified orthogonal ontologies describing the temporal and spatial distribution of developmental human and mouse anatomy.
	Software PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation Elodie Portales-Casamar, Stefan Kirov, Jonathan Lim, Stuart Lithwick, Magdalena I Swanson, Amy Ticoll, Jay Snoddy, Wyeth W Wasserman Genome Biology 2007, 8:R207 (28 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction.

	Volume 8 Issue 10
	Comment
	Comment They fought the law and the law won Gregory A Petsko Genome Biology 2007, 8:111 (2 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The new science geo-engineering doesn't try to alter a few corn plants; it aims to tinker with the entire planet, based on the notion that ultimately we can actively manipulate the planet to have any climate pattern we want. But there is no way we can ever assess all of the likely consequences.
	Report
	Meeting report Shaping the future of interactome networks Patrick Aloy Genome Biology 2007, 8:316 (1 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report of the third Interactome Networks Conference, Hinxton, UK, 29 August-1 September 2007.
	Meeting report A cornucopia of delights for the mouse fancier Dominic P Norris, Sonja Nowotschin, Anna-Katerina Hadjantonakis Genome Biology 2007, 8:318 (1 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Mouse Molecular Genetics meeting, Hinxton, UK, 5-9 September 2007.
	Meeting report Tipping the balance in autoimmune disease Mary Collins Genome Biology 2007, 8:317 (2 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB Summer Research Conference on Autoimmunity, Saxtons River, USA, 14-29 July 2007.
	Research
	Research Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte Amal J Johnston, Patrick Meier, Jacqueline Gheyselinck, Samuel EJ Wuest, Michael Federer, Edith Schlagenhauf, Jörg D Becker, Ueli Grossniklaus Genome Biology 2007, 8:R204 (3 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic subtraction and expression profiling of wild-type Arabidopsis and a sporophytic mutant lacking an embryo sac identified 1,260 genes expressed in the embryo sac; a total of 527 genes were identified for their expression in ovules of mutants lacking an embryo sac.
	Research A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans Ana C Gomes, Isabel Miranda, Raquel M Silva, Gabriela R Moura, Benjamin Thomas, Alexandre Akoulitchev, Manuel AS Santos Genome Biology 2007, 8:R206 (4 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An unusual decoding of leucine CUG codons as serine in Candida albicans revealed unanticipated codon ambiguity, which expands the proteome of this human pathogen exponentially.
	Research All duplicates are not equal: the difference between small-scale and genome duplication Luke Hakes, John W Pinney, Simon C Lovell, Stephen G Oliver, David L Robertson Genome Biology 2007, 8:R209 (4 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The comparison of pairs of gene duplications generated by small-scale duplications with those created by large-scale duplications shows that they differ in quantifiable ways. It is suggested that this is directly due to biases on the paths to gene retention rather than association with different functional categories.
	Research Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia Jennifer Cohen, Linda J Van Marter, Yao Sun, Elizabeth Allred, Alan Leviton, Isaac S Kohane Genome Biology 2007, 8:R210 (4 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The expression profiles of umbilical cords from premature newborns reveal distinct patterns, including changes in the expression of chromatin remodeling factors, associated with the development of bronchopulmonary dysplasia.
	Research Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines Axel A Elling, Makedonka Mitreva, Justin Recknor, Xiaowu Gai, John Martin, Thomas R Maier, Jeffrey P McDermott, Tarek Hewezi, David McK Bird, Eric L Davis, Richard S Hussey, Dan Nettleton, James P McCarter, Thomas J Baum Genome Biology 2007, 8:R211 (5 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The generation and analysis of over 20,000 ESTs allowed the identification and expression profiling of 6,860 predicted genes in the nematode Heterodera glycines. This revealed that gene expression patterns in the dauer stage of Caenorhabditis elegans are not conserved in H. glycines.
	Research Host origin of plastid solute transporters in the first photosynthetic eukaryotes Heather M Tyra, Marc Linka, Andreas PM Weber, Debashish Bhattacharya Genome Biology 2007, 8:R212 (5 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of plastid transporter proteins in Arabidopsis suggests a host origin and provides new insights into plastid evolution.
	Research High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer Suet F Chin, Andrew E Teschendorff, John C Marioni, Yanzhong Wang, Nuno L Barbosa-Morais, Natalie P Thorne, Jose L Costa, Sarah E Pinder, Mark A van de Wiel, Andrew R Green, Ian O Ellis, Peggy L Porter, Simon Tavaré, James D Brenton, Bauke Ylstra, Carlos Caldas Genome Biology 2007, 8:R215 (7 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer, and provides a genome-wide list of common copy number alterations associated with aberrant expression and poor prognosis.
	Research Transcriptional profiling of inductive mesenchyme to identify molecules involved in prostate development and disease Griet Vanpoucke, Brigid Orr, O Cathal Grace, Ray Chan, George R Ashley, Karin Williams, Omar E Franco, Simon W Hayward, Axel A Thomson Genome Biology 2007, 8:R213 (8 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of SAGE libraries for prostatic inductive mesenchyme and the complete prostatic rudiment revealed 219 transcripts that were enriched in, or specific to, inductive mesenchyme. Further analysis suggested that Scube1 is a novel stromal molecule involved in prostate development and tumorigenesis.
	Research MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype Cherie Blenkiron, Leonard D Goldstein, Natalie P Thorne, Inmaculada Spiteri, Suet-Feung Chin, Mark J Dunning, Nuno L Barbosa-Morais, Andrew E Teschendorff, Andrew R Green, Ian O Ellis, Simon Tavaré, Carlos Caldas, Eric A Miska Genome Biology 2007, 8:R214 (8 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Integrated analysis of miRNA expression and genomic changes in human breast tumors allows the classification of tumor subtypes.
	Research The ribosomal protein genes and Minute loci of Drosophila melanogaster Steven J Marygold, John Roote, Gunter Reuter, Andrew Lambertsson, Michael Ashburner, Gillian H Millburn, Paul M Harrison, Zhan Yu, Naoya Kenmochi, Thomas C Kaufman, Sally J Leevers, Kevin R Cook Genome Biology 2007, 8:R216 (10 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combined bioinformatic and genetic approach was used to conduct a systematic analysis of the relationship between ribosomal protein genes and Minute loci in Drosophila melanogaster, allowing the identification of 64 Minute loci corresponding to ribosomal genes.
	Research Transcriptional regulatory network for sexual differentiation in fission yeast Juan Mata, Anna Wilbrey, Jürg Bähler Genome Biology 2007, 8:R217 (10 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis of the transcriptome of fission yeast after genetic perturbation of 6 genes known to have a role in sexual differentiation reveals insights into the regulatory principles controlling the gene expression program driving this process.
	Research Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris Yong-Qiang He, Liang Zhang, Bo-Le Jiang, Zheng-Chun Zhang, Rong-Qi Xu, Dong-Jie Tang, Jing Qin, Wei Jiang, Xia Zhang, Jie Liao, Jin-Ru Cao, Sui-Sheng Zhang, Mei-Liang Wei, Xiao-Xia Liang, Guang-Tao Lu, Jia-Xun Feng, Baoshan Chen, Jing Cheng, Ji-Liang Tang Genome Biology 2007, 8:R218 (10 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Construction of a microarray based on the genome of Xanthomonas campestris pv.campestris (Xcc), and its use to analyse 18 other virulent Xcc strains, revealed insights into the genetic diversity and determinants of host specificity of Xcc strains.
	Research Responses of hyperthermophilic crenarchaea to UV irradiation Dorothee Götz, Sonia Paytubi, Stacey Munro, Magnus Lundgren, Rolf Bernander, Malcolm F White Genome Biology 2007, 8:R220 (11 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptional response to UV irradiation was analyzed in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius, showing a clear response to DNA damage but no increase in the expression of DNA repair genes.
	Research Gene expression profiling of Hfe^-/-liver and duodenum in mouse strains with differing susceptibilities to iron loading: identification of transcriptional regulatory targets of Hfe and potential hemochromatosis modifiers Hélène Coppin, Valérie Darnaud, Léon Kautz, Delphine Meynard, Marc Aubry, Jean Mosser, Maria Martinez, Marie-Paule Roth Genome Biology 2007, 8:R221 (18 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene expression profiling using microarrays of Hfe-/- liver and duodenum in mouse strains with differing susceptibilities to iron loading allowed the identification of transcriptional targets of the hemochromatosis-associated gene Hfe.
	Research Common gene expression strategies revealed by genome-wide analysis in yeast José García-Martínez, Fernando González-Candelas, José E Pérez-Ortín Genome Biology 2007, 8:R222 (19 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive analysis of six variables characterizing gene expression in yeast, including transcription and translation, mRNA and protein amounts, reveals a general tendency for levels of mRNA and protein to be harmonized, and for functionally related genes to have similar values for these variables.
	Research Comparative genomic analysis of fungal genomes reveals intron-rich ancestors Jason E Stajich, Fred S Dietrich, Scott W Roy Genome Biology 2007, 8:R223 (19 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of intron gain and loss in fungal genomes provides support for an intron-rich fungus-animal ancestor.
	Research Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools Weichun Huang, Joseph R Nevins, Uwe Ohler Genome Biology 2007, 8:R225 (24 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic simulation of promoter evolution were used to analyze functional site turnover in regulatory sequences.
	Research Surprising complexity of the ancestral apoptosis network Christian M Zmasek, Qing Zhang, Yuzhen Ye, Adam Godzik Genome Biology 2007, 8:R226 (24 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A comparative genomics approach revealed that the genes for several components of the apoptosis network with single copies in vertebrates have multiple paralogs in cnidarian-bilaterian ancestors, suggesting a complex evolutionary history for this network.
	Research Transcriptional profiling reveals barcode-like toxicogenomic responses in the zebrafish embryo Lixin Yang, Jules R Kemadjou, Christian Zinsmeister, Matthias Bauer, Jessica Legradi, Ferenc Müller, Michael Pankratz, Jens Jäkel, Uwe Strähle Genome Biology 2007, 8:R227 (25 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray profiling of zebrafish embryos exposed to a range of environmental toxicants revealed distinct expression profiles for each of the toxicants tested.
	Research Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization John C Marioni, Natalie P Thorne, Armand Valsesia, Tomas Fitzgerald, Richard Redon, Heike Fiegler, T Daniel Andrews, Barbara E Stranger, Andrew G Lynch, Emmanouil T Dermitzakis, Nigel P Carter, Simon Tavaré, Matthew E Hurles Genome Biology 2007, 8:R228 (25 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Datasets used for detecting copy number variation (CNV) are shown to be affected by a technical artifact. A novel CNV calling algorithm is presented which removes this artifact and identifies regions of CNV better than existing methods.
	Research On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees Tomàs Marques-Bonet, Jesús Sànchez-Ruiz, Lluís Armengol, Razi Khaja, Jaume Bertranpetit, Núria Lopez-Bigas, Mariano Rocchi, Elodie Gazave, Arcadi Navarro Genome Biology 2007, 8:R230 (30 October 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the genes located in rearranged human and chimpanzee chromosomes identified lower divergence than for those in colinear chromosomes.
	Research Phenotypic and transcriptional response to selection for alcohol sensitivity in Drosophila melanogaster Tatiana V Morozova, Robert RH Anholt, Trudy FC Mackay Genome Biology 2007, 8:R231 (31 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene-expression profiling combined with selection for genetically divergent Drosophila lines either highly sensitive or resistant to ethanol exposure has been used to identify candidate genes that affect alcohol sensitivity, including 23 novel genes that have human orthologs.
	Method Finding disease candidate genes by liquid association Ker-Chau Li, Aarno Palotie, Shinsheng Yuan, Denis Bronnikov, Daniel Chen, Xuelian Wei, Oi-Wa Choi, Janna Saarela, Leena Peltonen Genome Biology 2007, 8:R205 (4 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel approach to finding candidate genes by using gene-expression data has been developed and used to identify a multiple sclerosis susceptibility candidate genes.
	Method Harnessing naturally randomized transcription to infer regulatory relationships among genes Lin S Chen, Frank Emmert-Streib, John D Storey Genome Biology 2007, 8:R219 (11 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An approach is developed that utilizes randomized genotypes to rigorously infer causal regulatory relationships among genes at the transcriptional level. The approach is applied to an experiment in yeast, yielding new insights into the topology of the yeast transcriptional regulatory network.
	Method A BAC clone fingerprinting approach to the detection of human genome rearrangements Martin Krzywinski, Ian Bosdet, Carrie Mathewson, Natasja Wye, Jay Brebner, Readman Chiu, Richard Corbett, Matthew Field, Darlene Lee, Trevor Pugh, Stas Volik, Asim Siddiqui, Steven Jones, Jacquie Schein, Collin Collins, Marco Marra Genome Biology 2007, 8:R224 (22 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fingerprint Profiling (FPP) is a new method which uses restriction digest fingerprints of bacterial artificial chromosome (BAC) clones for detecting and classifying rearrangements in the human genome.
	Method Simplified ontologies allowing comparison of developmental mammalian gene expression Adele Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide Genome Biology 2007, 8:R229 (25 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Developmental eVOC ontologies presented are simplified orthogonal ontologies describing the temporal and spatial distribution of developmental human and mouse anatomy.
	Software PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation Elodie Portales-Casamar, Stefan Kirov, Jonathan Lim, Stuart Lithwick, Magdalena I Swanson, Amy Ticoll, Jay Snoddy, Wyeth W Wasserman Genome Biology 2007, 8:R207 (28 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction.

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Volume 8 Issue 10

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