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		Research Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level Olivier Harismendy, Vikas Bansal, Gaurav Bhatia, Masakazu Nakano, Michael Scott, Xiaoyun Wang, Colette Dib, Edouard Turlotte, Jack C Sipe, Sarah S Murray, Jean Deleuze, Vineet Bafna, Eric J Topol, Kelly A Frazer Genome Biology 2010, 11:R118 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Re-sequencing of human endocannabinoid metabolic genes from a large population reveals rare variants associated with extreme obesity.
		Research Comparative genomics reveals birth and death of fragile regions in mammalian evolution Max A Alekseyev, Pavel A Pevzner Genome Biology 2010, 11:R117 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new model explains the frequencies of breakpoints at genomic rearrangement hotspots by demonstrating that fragile sites undergo birth and death.
		Research highlight Metastasis suppression: a role of the Dice(r) Scott Valastyan, Robert A Weinberg Genome Biology 2010, 11:141 (30 November 2010) Abstract \| Full text \| PDF \| PubMed
		Comment Every dog has his day in court Gregory A Petsko Genome Biology 2010, 11:139 (30 November 2010) Full text \| PDF \| PubMed \| Editor’s summary The dog days of stem cell funding.
		Software Quake: quality-aware detection and correction of sequencing errors David R Kelley, Michael C Schatz, Steven L Salzberg Genome Biology 2010, 11:R116 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quake employs a sophisticated approach to error identification and correction in next generation sequencing data.
		Software Constructing a fish metabolic network model Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide fish metabolic model, MetaFishNet, is presented.
		Research Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew JG Simpson, Robert L Strausberg Genome Biology 2010, 11:R114 (25 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of the exome and transcriptome of a breast cancer cell line allows discovery of potentially tumorigenic loss of heterozygosity events.
		Research Genetic diversity in India and the inference of Eurasian population expansion Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, Fuli Yu Genome Biology 2010, 11:R113 (24 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SNP study demonstrates a high degree of Indian genetic diversity and suggests a significant isolation period between Out-of-Africa and Eurasian expansion.
		Method Patient-oriented gene set analysis for cancer mutation data Simina M Boca, Kenneth W Kinzler, Victor E Velculescu, Bert Vogelstein, Giovanni Parmigiani Genome Biology 2010, 11:R112 (23 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel patient-orientated gene set analysis method is presented and applied to a glioblastoma multiforme dataset
		Research Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise Nadia C Whitelaw, Suyinn Chong, Daniel K Morgan, Colm Nestor, Timothy J Bruxner, Alyson Ashe, Eleanore Lambley, Richard Meehan, Emma Whitelaw Genome Biology 2010, 11:R111 (19 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mutants for two epigenetic modifiers are found to be associated with increased intangible variation in phenotypes and in gene expression levels.
		Research Immunostaining of modified histones defines high-level features of the human metaphase epigenome Edith Terrenoire, Fiona McRonald, John A Halsall, Paula Page, Robert S Illingworth, A Malcolm R Taylor, Val Davison, Laura P O'Neill, Bryan M Turner Genome Biology 2010, 11:R110 (15 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Immunofluorescent mapping of histone modifications in single cells at metaphase demonstrates both stable and altered patterns through mitosis
		Research A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Simon R Ellwood, Zhaohui Liu, Rob A Syme, Zhibing Lai, James K Hane, Felicity Keiper, Caroline S Moffat, Richard P Oliver, Timothy L Friesen Genome Biology 2010, 11:R109 (10 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Characterization of barley filamentous fungal pathogen genome by paired-end Solexa sequencing, genome assembly and karyotyping, with insights into pathogenicity.
		Comment A Faustian bargain Gregory A Petsko Genome Biology 2010, 11:138 (31 October 2010) Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary An open letter to George M Philip, President of the State University of New York At Albany.
		Method Rapid haplotype inference for nuclear families Amy L Williams, David E Housman, Martin C Rinard, David K Gifford Genome Biology 2010, 11:R108 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hapi infers the haplotype of an individual based on sequence information from them and their parents.
		Research Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie C Dunning Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Morgens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2010, 11:R107 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Streptococcus pneumoniae genome analysis reveals that the presence of pathogenicity genes is not sufficient to determine virulence
		Meeting report Out of the sequencer and into the wiki as we face new challenges in genome informatics Zemin Ning, Stephen B Montgomery Genome Biology 2010, 11:308 (28 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint Cold Spring Harbor Laboratory/Wellcome Trust Conference 'Genome Informatics' meeting, 15-19 September 2010, Hinxton, Cambridge, UK.
		Method Differential expression analysis for sequence count data Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
		Research highlight Bet hedging in the underworld Xue-Xian Zhang, Paul B Rainey Genome Biology 2010, 11:137 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A soil bacterium hedges its bets on how long it will take to find a new plant host by producing two kinds of daughter cells.
		Research Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes Daniel F Simola, Chantal Francis, Paul D Sniegowski, Junhyong Kim Genome Biology 2010, 11:R105 (22 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Expression timing changes during the cell cycle in woodland and lab S. cerevisiae strains reveal modular timing changes in evolution.
		Method FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z Chen, Joel S Rozowsky, Ashutosh K Tewari, Naoki Kitabayashi, Benjamin J Moss, Mark S Chee, Francesca Demichelis, Mark A Rubin, Mark B Gerstein Genome Biology 2010, 11:R104 (21 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary FusionSeq is a method for identifying fusion transcripts from RNA-seq data. Novel fusions are identified in prostate cancer datasets.
		Research Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero, Teresa M Przytycka Genome Biology 2010, 11:R103 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An algorithm called LDsplit was developed to identify polymorphisms associated with meiotic recombination hotspots.
		Research An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation Gregory P Harhay, Timothy PL Smith, Leeson J Alexander, Christian D Haudenschild, John W Keele, Lakshmi K Matukumalli, Steven G Schroeder, Curtis P Van Tassell, Cathy R Gresham, Susan M Bridges, Shane C Burgess, Tad S Sonstegard Genome Biology 2010, 11:R102 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Digital gene expression has been used to analyse transcription in 92 bovine tissues.
		Research Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies Laura M Zahn, Xuan Ma, Naomi S Altman, Qing Zhang, P Kerr Wall, Donglan Tian, Cynthia J Gibas, Raad Gharaibeh, James H Leebens-Mack, Claude W dePamphilis, Hong Ma Genome Biology 2010, 11:R101 (15 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The California poppy’s transcriptome and its comparison with those of basal angiosperms reveals the poppy’s unique evolutionary position.
		Research Somatic structural rearrangements in genetically engineered mouse mammary tumors Ignacio Varela, Christiaan Klijn, Phillip J Stephens, Laura J Mudie, Lucy Stebbings, Danushka Galappaththige, Hanneke van der Gulden, Eva Schut, Sjoerd Klarenbeek, Peter J Campbell, Lodewyk FA Wessels, Michael R Stratton, Jos Jonkers, P Andrew Futreal, David J Adams Genome Biology 2010, 11:R100 (13 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Paired-end sequencing of mouse models of mammary tumors reveals the landscape of genome rearrangements and gene fusions.
		Review Capturing the dynamic epigenome Roger B Deal, Steven Henikoff Genome Biology 2010, 11:218 (8 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Direct measurements of chromatin dynamics are providing deeper insights into processes such as transcription, DNA replication and epigenetic inheritance.

	All
		Research Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level Olivier Harismendy, Vikas Bansal, Gaurav Bhatia, Masakazu Nakano, Michael Scott, Xiaoyun Wang, Colette Dib, Edouard Turlotte, Jack C Sipe, Sarah S Murray, Jean Deleuze, Vineet Bafna, Eric J Topol, Kelly A Frazer Genome Biology 2010, 11:R118 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Re-sequencing of human endocannabinoid metabolic genes from a large population reveals rare variants associated with extreme obesity.
		Research Comparative genomics reveals birth and death of fragile regions in mammalian evolution Max A Alekseyev, Pavel A Pevzner Genome Biology 2010, 11:R117 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new model explains the frequencies of breakpoints at genomic rearrangement hotspots by demonstrating that fragile sites undergo birth and death.
		Research highlight Metastasis suppression: a role of the Dice(r) Scott Valastyan, Robert A Weinberg Genome Biology 2010, 11:141 (30 November 2010) Abstract \| Full text \| PDF \| PubMed
		Comment Every dog has his day in court Gregory A Petsko Genome Biology 2010, 11:139 (30 November 2010) Full text \| PDF \| PubMed \| Editor’s summary The dog days of stem cell funding.
		Software Quake: quality-aware detection and correction of sequencing errors David R Kelley, Michael C Schatz, Steven L Salzberg Genome Biology 2010, 11:R116 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quake employs a sophisticated approach to error identification and correction in next generation sequencing data.
		Software Constructing a fish metabolic network model Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide fish metabolic model, MetaFishNet, is presented.
		Research Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew JG Simpson, Robert L Strausberg Genome Biology 2010, 11:R114 (25 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of the exome and transcriptome of a breast cancer cell line allows discovery of potentially tumorigenic loss of heterozygosity events.
		Research Genetic diversity in India and the inference of Eurasian population expansion Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, Fuli Yu Genome Biology 2010, 11:R113 (24 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SNP study demonstrates a high degree of Indian genetic diversity and suggests a significant isolation period between Out-of-Africa and Eurasian expansion.
		Method Patient-oriented gene set analysis for cancer mutation data Simina M Boca, Kenneth W Kinzler, Victor E Velculescu, Bert Vogelstein, Giovanni Parmigiani Genome Biology 2010, 11:R112 (23 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel patient-orientated gene set analysis method is presented and applied to a glioblastoma multiforme dataset
		Research Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise Nadia C Whitelaw, Suyinn Chong, Daniel K Morgan, Colm Nestor, Timothy J Bruxner, Alyson Ashe, Eleanore Lambley, Richard Meehan, Emma Whitelaw Genome Biology 2010, 11:R111 (19 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mutants for two epigenetic modifiers are found to be associated with increased intangible variation in phenotypes and in gene expression levels.
		Research Immunostaining of modified histones defines high-level features of the human metaphase epigenome Edith Terrenoire, Fiona McRonald, John A Halsall, Paula Page, Robert S Illingworth, A Malcolm R Taylor, Val Davison, Laura P O'Neill, Bryan M Turner Genome Biology 2010, 11:R110 (15 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Immunofluorescent mapping of histone modifications in single cells at metaphase demonstrates both stable and altered patterns through mitosis
		Research A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Simon R Ellwood, Zhaohui Liu, Rob A Syme, Zhibing Lai, James K Hane, Felicity Keiper, Caroline S Moffat, Richard P Oliver, Timothy L Friesen Genome Biology 2010, 11:R109 (10 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Characterization of barley filamentous fungal pathogen genome by paired-end Solexa sequencing, genome assembly and karyotyping, with insights into pathogenicity.
		Comment A Faustian bargain Gregory A Petsko Genome Biology 2010, 11:138 (31 October 2010) Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary An open letter to George M Philip, President of the State University of New York At Albany.
		Method Rapid haplotype inference for nuclear families Amy L Williams, David E Housman, Martin C Rinard, David K Gifford Genome Biology 2010, 11:R108 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hapi infers the haplotype of an individual based on sequence information from them and their parents.
		Research Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie C Dunning Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Morgens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2010, 11:R107 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Streptococcus pneumoniae genome analysis reveals that the presence of pathogenicity genes is not sufficient to determine virulence
		Meeting report Out of the sequencer and into the wiki as we face new challenges in genome informatics Zemin Ning, Stephen B Montgomery Genome Biology 2010, 11:308 (28 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint Cold Spring Harbor Laboratory/Wellcome Trust Conference 'Genome Informatics' meeting, 15-19 September 2010, Hinxton, Cambridge, UK.
		Method Differential expression analysis for sequence count data Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
		Research highlight Bet hedging in the underworld Xue-Xian Zhang, Paul B Rainey Genome Biology 2010, 11:137 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A soil bacterium hedges its bets on how long it will take to find a new plant host by producing two kinds of daughter cells.
		Research Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes Daniel F Simola, Chantal Francis, Paul D Sniegowski, Junhyong Kim Genome Biology 2010, 11:R105 (22 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Expression timing changes during the cell cycle in woodland and lab S. cerevisiae strains reveal modular timing changes in evolution.
		Method FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z Chen, Joel S Rozowsky, Ashutosh K Tewari, Naoki Kitabayashi, Benjamin J Moss, Mark S Chee, Francesca Demichelis, Mark A Rubin, Mark B Gerstein Genome Biology 2010, 11:R104 (21 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary FusionSeq is a method for identifying fusion transcripts from RNA-seq data. Novel fusions are identified in prostate cancer datasets.
		Research Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero, Teresa M Przytycka Genome Biology 2010, 11:R103 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An algorithm called LDsplit was developed to identify polymorphisms associated with meiotic recombination hotspots.
		Research An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation Gregory P Harhay, Timothy PL Smith, Leeson J Alexander, Christian D Haudenschild, John W Keele, Lakshmi K Matukumalli, Steven G Schroeder, Curtis P Van Tassell, Cathy R Gresham, Susan M Bridges, Shane C Burgess, Tad S Sonstegard Genome Biology 2010, 11:R102 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Digital gene expression has been used to analyse transcription in 92 bovine tissues.
		Research Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies Laura M Zahn, Xuan Ma, Naomi S Altman, Qing Zhang, P Kerr Wall, Donglan Tian, Cynthia J Gibas, Raad Gharaibeh, James H Leebens-Mack, Claude W dePamphilis, Hong Ma Genome Biology 2010, 11:R101 (15 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The California poppy’s transcriptome and its comparison with those of basal angiosperms reveals the poppy’s unique evolutionary position.
		Research Somatic structural rearrangements in genetically engineered mouse mammary tumors Ignacio Varela, Christiaan Klijn, Phillip J Stephens, Laura J Mudie, Lucy Stebbings, Danushka Galappaththige, Hanneke van der Gulden, Eva Schut, Sjoerd Klarenbeek, Peter J Campbell, Lodewyk FA Wessels, Michael R Stratton, Jos Jonkers, P Andrew Futreal, David J Adams Genome Biology 2010, 11:R100 (13 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Paired-end sequencing of mouse models of mammary tumors reveals the landscape of genome rearrangements and gene fusions.
		Review Capturing the dynamic epigenome Roger B Deal, Steven Henikoff Genome Biology 2010, 11:218 (8 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Direct measurements of chromatin dynamics are providing deeper insights into processes such as transcription, DNA replication and epigenetic inheritance.