Genome Biology | Volume 10 Issue 9

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	Volume 10 Issue 9
	Comment
	Comment An issue to remember Gregory A Petsko Genome Biology 2009, 10:111 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Thumbing through a recent copy of a journal reveals unexpected riches.
	Review
	Protein family review The netrin protein family Sathyanath Rajasekharan, Timothy E Kennedy Genome Biology 2009, 10:239 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The netrins are a family of extracellular proteins that direct cell and axon migration during embryogenesis.
	Minireview The promise and reality of personal genomics Bryndis Yngvadottir, Daniel G MacArthur, Hanjun Jin, Chris Tyler-Smith Genome Biology 2009, 10:237 (2 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The second personal genome sequence of a Korean tells something about genetic ancestry but still little of medical relevance.
	Minireview Predicting drug side-effects by chemical systems biology Nicholas P Tatonetti, Tianyun Liu, Russ B Altman Genome Biology 2009, 10:238 (2 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chemical systems biology approaches can explain unexpected observations of drug inefficacy or side-effects.
	Minireview Common variants in polygenic schizophrenia Joseph T Glessner, Hakon Hakonarson Genome Biology 2009, 10:236 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Schizophrenia is associated with both common single-nucleotide polymorphisms at the MHC locus and rare copy-number variants affecting many genes.
	Report
	Meeting report New tricks for an old-favorite model Charalampos Rallis Genome Biology 2009, 10:315 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 24th International Conference on Yeast Genetics and Molecular Biology, Manchester, UK, 19-24 July 2009.
	Research
	Research Nucleosome deposition and DNA methylation at coding region boundaries Jung Choi, Jae-Bum Bae, Jaemyun Lyu, Tae-Yoon Kim, Young-Joon Kim Genome Biology 2009, 10:R89 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nucleosomes and methylation have been observed to peak at both ends of protein coding units in a genome-wide survey.
	Research mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer Chao Cheng, Xuping Fu, Pedro Alves, Mark Gerstein Genome Biology 2009, 10:R90 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers
	Research A global survey identifies novel upstream components of the Ath5 neurogenic network Marcel Souren, Juan Martinez-Morales, Panagiota Makri, Beate Wittbrodt, Joachim Wittbrodt Genome Biology 2009, 10:R92 (7 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Regulators of vertebrate Ath5 expression were identified by high-throughput screening; extending the current gene regulatory model network controlling retinal neurogenesis.
	Research Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection Nicoletta Bivi, Milena Romanello, Richard Harrison, Ian Clarke, David C Hoyle, Luigi Moro, Fulvia Ortolani, Antonella Bonetti, Franco Quadrifoglio, Gianluca Tell, Daniela Delneri Genome Biology 2009, 10:R93 (10 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Growth competition assays using barcoded yeast deletion-mutants reveal the molecular targets of nitrogen containing bisphosphonates used for the treatment of bone cancers and osteoporosis.
	Research Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae Sandra Merz, Benedikt Westermann Genome Biology 2009, 10:R95 (14 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide deletion mutant analysis in budding yeast reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis.
	Research Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Santiago F Elena Genome Biology 2009, 10:R96 (15 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An Arabidopsis thaliana transcriptional network reveals regulatory mechanisms for the control of genes related to stress adaptation.
	Research Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.
	Research A cell surface interaction network of neural leucine-rich repeat receptors Christian Söllner, Gavin J Wright Genome Biology 2009, 10:R99 (18 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A network of Zebrafish extracellular neuroreceptor interactions are revealed using AVEXIS, a highly stringent interaction assay.
	Research Many LINE1 elements contribute to the transcriptome of human somatic cells Sanjida H Rangwala, Lili Zhang, Haig H Kazazian Genome Biology 2009, 10:R100 (22 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Over 600 LINE 1 elements are shown to be transcribed in humans; 400 of these are full-length elements in the reference genome.
	Research High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans Arun K Ramani, Andrew C Nelson, Philipp Kapranov, Ian Bell, Thomas R Gingeras, Andrew G Fraser Genome Biology 2009, 10:R101 (24 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high-resolution transcriptome of wild-type and nonsense-mediated decay (NMD) defective C. elegans during development reveals insights into the NMD pathway and it’s role in development.
	Research Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium Richard A Stabler, Miao He, Lisa Dawson, Melissa Martin, Esmeralda Valiente, Craig Corton, Trevor D Lawley, Mohammed Sebaihia, Michael A Quail, Graham Rose, Dale N Gerding, Maryse Gibert, Michel R Popoff, Julian Parkhill, Gordon Dougan, Brendan W Wren Genome Biology 2009, 10:R102 (25 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome comparison of non-epidemic and epidemic strains of Clostridium difficile reveals gene gains that could explain how a hypervirulent strain has emerged
	Method Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network Bolan Linghu, Evan S Snitkin, Zhenjun Hu, Yu Xia, Charles DeLisi Genome Biology 2009, 10:R91 (3 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes
	Method De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones Genome Biology 2009, 10:R94 (11 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for de novo assembly of a eukaryotic genome using Illumina, 454 and Sanger generated sequence data
	Software Simultaneous alignment of short reads against multiple genomes Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel Genome Biology 2009, 10:R98 (17 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New software for the alignment of short-read sequence data to multiple genomes allows identification of polymorphisms that cannot be identified by alignment to a single reference genome.
	Correspondence
	Correspondence Joining forces in the quest for orthologs Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis Genome Biology 2009, 10:403 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Building momentum to coordinate and leverage community orthology prediction resources.

	Volume 10 Issue 9
	Comment
	Comment An issue to remember Gregory A Petsko Genome Biology 2009, 10:111 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Thumbing through a recent copy of a journal reveals unexpected riches.
	Review
	Protein family review The netrin protein family Sathyanath Rajasekharan, Timothy E Kennedy Genome Biology 2009, 10:239 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The netrins are a family of extracellular proteins that direct cell and axon migration during embryogenesis.
	Minireview The promise and reality of personal genomics Bryndis Yngvadottir, Daniel G MacArthur, Hanjun Jin, Chris Tyler-Smith Genome Biology 2009, 10:237 (2 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The second personal genome sequence of a Korean tells something about genetic ancestry but still little of medical relevance.
	Minireview Predicting drug side-effects by chemical systems biology Nicholas P Tatonetti, Tianyun Liu, Russ B Altman Genome Biology 2009, 10:238 (2 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chemical systems biology approaches can explain unexpected observations of drug inefficacy or side-effects.
	Minireview Common variants in polygenic schizophrenia Joseph T Glessner, Hakon Hakonarson Genome Biology 2009, 10:236 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Schizophrenia is associated with both common single-nucleotide polymorphisms at the MHC locus and rare copy-number variants affecting many genes.
	Report
	Meeting report New tricks for an old-favorite model Charalampos Rallis Genome Biology 2009, 10:315 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 24th International Conference on Yeast Genetics and Molecular Biology, Manchester, UK, 19-24 July 2009.
	Research
	Research Nucleosome deposition and DNA methylation at coding region boundaries Jung Choi, Jae-Bum Bae, Jaemyun Lyu, Tae-Yoon Kim, Young-Joon Kim Genome Biology 2009, 10:R89 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nucleosomes and methylation have been observed to peak at both ends of protein coding units in a genome-wide survey.
	Research mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer Chao Cheng, Xuping Fu, Pedro Alves, Mark Gerstein Genome Biology 2009, 10:R90 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers
	Research A global survey identifies novel upstream components of the Ath5 neurogenic network Marcel Souren, Juan Martinez-Morales, Panagiota Makri, Beate Wittbrodt, Joachim Wittbrodt Genome Biology 2009, 10:R92 (7 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Regulators of vertebrate Ath5 expression were identified by high-throughput screening; extending the current gene regulatory model network controlling retinal neurogenesis.
	Research Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection Nicoletta Bivi, Milena Romanello, Richard Harrison, Ian Clarke, David C Hoyle, Luigi Moro, Fulvia Ortolani, Antonella Bonetti, Franco Quadrifoglio, Gianluca Tell, Daniela Delneri Genome Biology 2009, 10:R93 (10 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Growth competition assays using barcoded yeast deletion-mutants reveal the molecular targets of nitrogen containing bisphosphonates used for the treatment of bone cancers and osteoporosis.
	Research Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae Sandra Merz, Benedikt Westermann Genome Biology 2009, 10:R95 (14 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide deletion mutant analysis in budding yeast reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis.
	Research Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Santiago F Elena Genome Biology 2009, 10:R96 (15 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An Arabidopsis thaliana transcriptional network reveals regulatory mechanisms for the control of genes related to stress adaptation.
	Research Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.
	Research A cell surface interaction network of neural leucine-rich repeat receptors Christian Söllner, Gavin J Wright Genome Biology 2009, 10:R99 (18 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A network of Zebrafish extracellular neuroreceptor interactions are revealed using AVEXIS, a highly stringent interaction assay.
	Research Many LINE1 elements contribute to the transcriptome of human somatic cells Sanjida H Rangwala, Lili Zhang, Haig H Kazazian Genome Biology 2009, 10:R100 (22 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Over 600 LINE 1 elements are shown to be transcribed in humans; 400 of these are full-length elements in the reference genome.
	Research High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans Arun K Ramani, Andrew C Nelson, Philipp Kapranov, Ian Bell, Thomas R Gingeras, Andrew G Fraser Genome Biology 2009, 10:R101 (24 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high-resolution transcriptome of wild-type and nonsense-mediated decay (NMD) defective C. elegans during development reveals insights into the NMD pathway and it’s role in development.
	Research Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium Richard A Stabler, Miao He, Lisa Dawson, Melissa Martin, Esmeralda Valiente, Craig Corton, Trevor D Lawley, Mohammed Sebaihia, Michael A Quail, Graham Rose, Dale N Gerding, Maryse Gibert, Michel R Popoff, Julian Parkhill, Gordon Dougan, Brendan W Wren Genome Biology 2009, 10:R102 (25 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome comparison of non-epidemic and epidemic strains of Clostridium difficile reveals gene gains that could explain how a hypervirulent strain has emerged
	Method Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network Bolan Linghu, Evan S Snitkin, Zhenjun Hu, Yu Xia, Charles DeLisi Genome Biology 2009, 10:R91 (3 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes
	Method De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones Genome Biology 2009, 10:R94 (11 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for de novo assembly of a eukaryotic genome using Illumina, 454 and Sanger generated sequence data
	Software Simultaneous alignment of short reads against multiple genomes Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel Genome Biology 2009, 10:R98 (17 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New software for the alignment of short-read sequence data to multiple genomes allows identification of polymorphisms that cannot be identified by alignment to a single reference genome.
	Correspondence
	Correspondence Joining forces in the quest for orthologs Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis Genome Biology 2009, 10:403 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Building momentum to coordinate and leverage community orthology prediction resources.

Explore Genome Biology

Articles

Volume 10 Issue 9

Comment

Review

Report

Research

Correspondence