Genome Biology | Volume 11 Issue 5

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	Volume 11 Issue 5
	Comment
	Editorial A decade and genome of change Clare Garvey Genome Biology 2010, 11:120 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Innovations in genomic technologies have generated huge advances in biomedical research over the last decade.
	Comment And they said it wouldn't last... Gregory A Petsko Genome Biology 2010, 11:121 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the 10 years that Genome Biology has been published the scientific changes have been amazing, as have the changes in the culture of science.
	Research highlight Interesting things come in small packages Edward F DeLong Genome Biology 2010, 11:118 (14 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An unusual uncultivated nitrogen-fixing cyanobacterium lacks many of the signature features of typical cyanobacteria.
	Research highlight Membrane traffic in the post-genomic era Peter Hein, Mark von Zastrow Genome Biology 2010, 11:119 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A multi-parametric genetic screening approach sheds light on integrated control of the endocytic pathway in mammalian cells.
	Review
	Review Between a chicken and a grape: estimating the number of human genes Mihaela Pertea, Steven L Salzberg Genome Biology 2010, 11:206 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The number of genes in the human genome is still an estimate.
	Review The case for cloud computing in genome informatics Lincoln D Stein Genome Biology 2010, 11:207 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 3 comments \| Editor’s summary With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics.
	Review The next frontier of systems biology: higher-order and interspecies interactions Michael A Fischbach, Nevan J Krogan Genome Biology 2010, 11:208 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systems biology is set to go beyond single species to the study of interspecies interactions.
	Review The origin and early evolution of eukaryotes in the light of phylogenomics Eugene V Koonin Genome Biology 2010, 11:209 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and new phylogenies of eukaryote groups suggest a scenario in which the mitochondrial endosymbiosis triggered the origin of eukaryotes.
	Review Direct sequencing of the human microbiome readily reveals community differences Justin Kuczynski, Elizabeth K Costello, Diana R Nemergut, Jesse Zaneveld, Christian L Lauber, Dan Knights, Omry Koren, Noah Fierer, Scott T Kelley, Ruth E Ley, Jeffrey I Gordon, Rob Knight Genome Biology 2010, 11:210 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Future sequencing of the human microbiota will require greater breadth rather than depth.
	Review Cancer genomics identifies determinants of tumor biology Elaine R Mardis Genome Biology 2010, 11:211 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Whole-genome analysis of human tumors has identified some unsuspected tumor-associated genes
	Review GWASs and the age of human as the model organism for autoimmune genetic research Robert Plenge Genome Biology 2010, 11:212 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Humans should perhaps be the model organism for autoimmune disease studies, considering the success of GWAS studies uncovering risk alleles.
	Report
	Meeting report Microbial signaling and systems biology Alistair JP Brown Genome Biology 2010, 11:302 (17 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the symposium on Signaling and Systems Biology held during the Society for General Microbiology Spring Meeting, 29-30 March 2010, Edinburgh, UK
	Meeting report Sequences to systems Manolis Kellis, John L Rinn Genome Biology 2010, 11:303 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the seventh annual meeting on Systems Biology: Global Regulation of Gene Expression, 23-27 March 2010, Cold Spring Harbor, USA.
	Meeting report mRNA: a complex(ed) life Michaela Müller, Karla M Neugebauer, Christian Eckmann Genome Biology 2010, 11:304 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the EMBL conference 'The Complex Life of mRNA: From Synthesis to Decay', Heidelberg, Germany, 18-21 March 2010.
	Research
	Research The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum Marcin Piechota, Michal Korostynski, Wojciech Solecki, Agnieszka Gieryk, Michal Slezak, Wiktor Bilecki, Barbara Ziolkowska, Elzbieta Kostrzewa, Iwona Cymerman, Lukasz Swiech, Jacek Jaworski, Ryszard Przewlocki Genome Biology 2010, 11:R48 (4 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcriptional response to six commonly-abused drugs was assessed in the mouse brain revealing common modules of drug-induced genes.
	Research Widespread remodeling of mid-coding sequence nucleosomes by Isw1 Itay Tirosh, Nadejda Sigal, Naama Barkai Genome Biology 2010, 11:R49 (10 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In yeast, the chromatin remodeler Isw1 shifts nucleosomes from mid-coding, to more 5’ regions of genes and may regulate transcriptional elongation.
	Research Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes Charles Hebert, Hugues Roest Crollius Genome Biology 2010, 11:R51 (12 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Human genes contain a 10 bp repeat of RR dinucleotides focused around the first nucleosome position suggesting a role in transcriptional control.
	Research Towards a comprehensive structural variation map of an individual human genome Andy W Pang, Jeffrey R MacDonald, Dalila Pinto, John Wei, Muhammad A Rafiq, Donald F Conrad, Hansoo Park, Matthew E Hurles, Charles Lee, J Craig Venter, Ewen F Kirkness, Samuel Levy, Lars Feuk, Stephen W Scherer Genome Biology 2010, 11:R52 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive map of structural variation in the human genome provides a reference dataset for analyses of future personal genomes.
	Research A human functional protein interaction network and its application to cancer data analysis Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.
	Research Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus Claudia Steglich, Debbie Lindell, Matthias Futschik, Trent Rector, Robert Steen, Sallie W Chisholm Genome Biology 2010, 11:R54 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA half lives in the slow growing cyanobacteria Prochlorococcus are surprisingly short and may enable rapid responses to environmental change.
	Research Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult Rachel A Heimeier, Biswajit Das, Daniel R Buchholz, Maria Fiorentino, Yun-Bo Shi Genome Biology 2010, 11:R55 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The developmental transcriptome of the Xenopus laevis intestine, from embryo to adult, reveals insights into the regulation of gut development in all vertebrates.
	Research Evidence for natural antisense transcript-mediated inhibition of microRNA function Mohammad Ali Faghihi, Ming Zhang, Jia Huang, Farzaneh Modarresi, Marcel P Van der Brug, Michael A Nalls, Mark R Cookson, Georges St-Laurent, Claes Wahlestedt Genome Biology 2010, 11:R56 (27 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The BACE1-antisense transcript and miR-485-5p have antagonistic regulatory effects on BACE1 transcript expression and are dysregulated in Alzheimer’s disease patients.
	Research Screening the human exome: a comparison of whole genome and whole transcriptome sequencing Elizabeth T Cirulli, Abanish Singh, Kevin V Shianna, Dongliang Ge, Jason P Smith, Jessica M Maia, Erin L Heinzen, James J Goedert, David B Goldstein, the Center for HIV/AIDS Vaccine Immunology (CHAVI) Genome Biology 2010, 11:R57 (28 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq is an efficient and cheaper alternative, compared with whole genome sequencing, for identifying coding variants in humans.
	Method Computational challenges in the analysis of ancient DNA Kay Prüfer, Udo Stenzel, Michael Hofreiter, Svante Pääbo, Janet Kelso, Richard E Green Genome Biology 2010, 11:R47 (6 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method of next-generation sequencing analysis is presented which takes into account the biases characteristic of ancient, including Neandertal, DNA samples.
	Method Modeling non-uniformity in short-read rates in RNA-Seq data Jun Li, Hui Jiang, Wing Wong Genome Biology 2010, 11:R50 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Methods for modeling read counts from short read RNA-seq data.

	Volume 11 Issue 5
	Comment
	Editorial A decade and genome of change Clare Garvey Genome Biology 2010, 11:120 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Innovations in genomic technologies have generated huge advances in biomedical research over the last decade.
	Comment And they said it wouldn't last... Gregory A Petsko Genome Biology 2010, 11:121 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the 10 years that Genome Biology has been published the scientific changes have been amazing, as have the changes in the culture of science.
	Research highlight Interesting things come in small packages Edward F DeLong Genome Biology 2010, 11:118 (14 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An unusual uncultivated nitrogen-fixing cyanobacterium lacks many of the signature features of typical cyanobacteria.
	Research highlight Membrane traffic in the post-genomic era Peter Hein, Mark von Zastrow Genome Biology 2010, 11:119 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A multi-parametric genetic screening approach sheds light on integrated control of the endocytic pathway in mammalian cells.
	Review
	Review Between a chicken and a grape: estimating the number of human genes Mihaela Pertea, Steven L Salzberg Genome Biology 2010, 11:206 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The number of genes in the human genome is still an estimate.
	Review The case for cloud computing in genome informatics Lincoln D Stein Genome Biology 2010, 11:207 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 3 comments \| Editor’s summary With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics.
	Review The next frontier of systems biology: higher-order and interspecies interactions Michael A Fischbach, Nevan J Krogan Genome Biology 2010, 11:208 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systems biology is set to go beyond single species to the study of interspecies interactions.
	Review The origin and early evolution of eukaryotes in the light of phylogenomics Eugene V Koonin Genome Biology 2010, 11:209 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and new phylogenies of eukaryote groups suggest a scenario in which the mitochondrial endosymbiosis triggered the origin of eukaryotes.
	Review Direct sequencing of the human microbiome readily reveals community differences Justin Kuczynski, Elizabeth K Costello, Diana R Nemergut, Jesse Zaneveld, Christian L Lauber, Dan Knights, Omry Koren, Noah Fierer, Scott T Kelley, Ruth E Ley, Jeffrey I Gordon, Rob Knight Genome Biology 2010, 11:210 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Future sequencing of the human microbiota will require greater breadth rather than depth.
	Review Cancer genomics identifies determinants of tumor biology Elaine R Mardis Genome Biology 2010, 11:211 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Whole-genome analysis of human tumors has identified some unsuspected tumor-associated genes
	Review GWASs and the age of human as the model organism for autoimmune genetic research Robert Plenge Genome Biology 2010, 11:212 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Humans should perhaps be the model organism for autoimmune disease studies, considering the success of GWAS studies uncovering risk alleles.
	Report
	Meeting report Microbial signaling and systems biology Alistair JP Brown Genome Biology 2010, 11:302 (17 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the symposium on Signaling and Systems Biology held during the Society for General Microbiology Spring Meeting, 29-30 March 2010, Edinburgh, UK
	Meeting report Sequences to systems Manolis Kellis, John L Rinn Genome Biology 2010, 11:303 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the seventh annual meeting on Systems Biology: Global Regulation of Gene Expression, 23-27 March 2010, Cold Spring Harbor, USA.
	Meeting report mRNA: a complex(ed) life Michaela Müller, Karla M Neugebauer, Christian Eckmann Genome Biology 2010, 11:304 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the EMBL conference 'The Complex Life of mRNA: From Synthesis to Decay', Heidelberg, Germany, 18-21 March 2010.
	Research
	Research The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum Marcin Piechota, Michal Korostynski, Wojciech Solecki, Agnieszka Gieryk, Michal Slezak, Wiktor Bilecki, Barbara Ziolkowska, Elzbieta Kostrzewa, Iwona Cymerman, Lukasz Swiech, Jacek Jaworski, Ryszard Przewlocki Genome Biology 2010, 11:R48 (4 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcriptional response to six commonly-abused drugs was assessed in the mouse brain revealing common modules of drug-induced genes.
	Research Widespread remodeling of mid-coding sequence nucleosomes by Isw1 Itay Tirosh, Nadejda Sigal, Naama Barkai Genome Biology 2010, 11:R49 (10 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In yeast, the chromatin remodeler Isw1 shifts nucleosomes from mid-coding, to more 5’ regions of genes and may regulate transcriptional elongation.
	Research Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes Charles Hebert, Hugues Roest Crollius Genome Biology 2010, 11:R51 (12 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Human genes contain a 10 bp repeat of RR dinucleotides focused around the first nucleosome position suggesting a role in transcriptional control.
	Research Towards a comprehensive structural variation map of an individual human genome Andy W Pang, Jeffrey R MacDonald, Dalila Pinto, John Wei, Muhammad A Rafiq, Donald F Conrad, Hansoo Park, Matthew E Hurles, Charles Lee, J Craig Venter, Ewen F Kirkness, Samuel Levy, Lars Feuk, Stephen W Scherer Genome Biology 2010, 11:R52 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive map of structural variation in the human genome provides a reference dataset for analyses of future personal genomes.
	Research A human functional protein interaction network and its application to cancer data analysis Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.
	Research Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus Claudia Steglich, Debbie Lindell, Matthias Futschik, Trent Rector, Robert Steen, Sallie W Chisholm Genome Biology 2010, 11:R54 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA half lives in the slow growing cyanobacteria Prochlorococcus are surprisingly short and may enable rapid responses to environmental change.
	Research Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult Rachel A Heimeier, Biswajit Das, Daniel R Buchholz, Maria Fiorentino, Yun-Bo Shi Genome Biology 2010, 11:R55 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The developmental transcriptome of the Xenopus laevis intestine, from embryo to adult, reveals insights into the regulation of gut development in all vertebrates.
	Research Evidence for natural antisense transcript-mediated inhibition of microRNA function Mohammad Ali Faghihi, Ming Zhang, Jia Huang, Farzaneh Modarresi, Marcel P Van der Brug, Michael A Nalls, Mark R Cookson, Georges St-Laurent, Claes Wahlestedt Genome Biology 2010, 11:R56 (27 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The BACE1-antisense transcript and miR-485-5p have antagonistic regulatory effects on BACE1 transcript expression and are dysregulated in Alzheimer’s disease patients.
	Research Screening the human exome: a comparison of whole genome and whole transcriptome sequencing Elizabeth T Cirulli, Abanish Singh, Kevin V Shianna, Dongliang Ge, Jason P Smith, Jessica M Maia, Erin L Heinzen, James J Goedert, David B Goldstein, the Center for HIV/AIDS Vaccine Immunology (CHAVI) Genome Biology 2010, 11:R57 (28 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq is an efficient and cheaper alternative, compared with whole genome sequencing, for identifying coding variants in humans.
	Method Computational challenges in the analysis of ancient DNA Kay Prüfer, Udo Stenzel, Michael Hofreiter, Svante Pääbo, Janet Kelso, Richard E Green Genome Biology 2010, 11:R47 (6 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method of next-generation sequencing analysis is presented which takes into account the biases characteristic of ancient, including Neandertal, DNA samples.
	Method Modeling non-uniformity in short-read rates in RNA-Seq data Jun Li, Hui Jiang, Wing Wong Genome Biology 2010, 11:R50 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Methods for modeling read counts from short read RNA-seq data.

Explore Genome Biology

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Volume 11 Issue 5

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Review

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