Genome Biology | Volume 11 Issue 10

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	Volume 11 Issue 10
	Comment
	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.
	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.
	Review
	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.
	Report
	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.
	Research
	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.
	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 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 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 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.
	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
	Method Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA Nils Homer, Stanley F Nelson Genome Biology 2010, 11:R99 (8 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The novel short-read micro re-aligner SRMA improves variant discovery when aligning deep sequencing data to a reference genome.
	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.
	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
	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 \| Cited on BioMed Central \| Editor’s summary Hapi infers the haplotype of an individual based on sequence information from them and their parents.
	Correspondence
	Correspondence Do-it-yourself genetic testing Steven L Salzberg, Mihaela Pertea Genome Biology 2010, 11:404 (7 October 2010) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary How to test your BRCA status and why we need to prepare for the personal genomics age.

	Volume 11 Issue 10
	Comment
	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.
	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.
	Review
	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.
	Report
	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.
	Research
	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.
	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 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 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 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.
	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
	Method Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA Nils Homer, Stanley F Nelson Genome Biology 2010, 11:R99 (8 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The novel short-read micro re-aligner SRMA improves variant discovery when aligning deep sequencing data to a reference genome.
	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.
	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
	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 \| Cited on BioMed Central \| Editor’s summary Hapi infers the haplotype of an individual based on sequence information from them and their parents.
	Correspondence
	Correspondence Do-it-yourself genetic testing Steven L Salzberg, Mihaela Pertea Genome Biology 2010, 11:404 (7 October 2010) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary How to test your BRCA status and why we need to prepare for the personal genomics age.

Explore Genome Biology

Articles

Volume 11 Issue 10

Comment

Review

Report

Research

Correspondence