Genome Biology | Volume 12 Issue 2

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	Volume 12 Issue 2
	Comment
	Comment There is a sanity clause Gregory A Petsko Genome Biology 2011, 12:105 (25 February 2011) Full text \| PDF \| PubMed \| Editor’s summary Supply versus demand part II: will funding basic research lead to medical advances?
	Research highlight A Drosophila model for the role of epigenetics in brain function and development Roman M Stilling, André Fischer Genome Biology 2011, 12:103 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genetic studies in Drosophila give insights into the possible role of epigenetic regulation of gene expression in a human mental retardation syndrome.
	Research highlight Piecing together the FTO jigsaw Timothy M Frayling, Ken Ong Genome Biology 2011, 12:104 (24 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two recent studies of the FTO gene provide more information on how it affects body mass index
	Review
	Review The domestic dog: man's best friend in the genomic era Adam R Boyko Genome Biology 2011, 12:216 (22 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The tremendous phenotypic diversity of domestic dog breeds, coupled with the availability of dog genome sequences, point to the dog as as an important model organism for complex-trait analysis
	Review The properties and applications of single-molecule DNA sequencing John F Thompson, Patrice M Milos Genome Biology 2011, 12:217 (24 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Single-molecule sequencing works directly from biological samples and generates very long reads, making it well suited for diagnostic and clinical applications.
	Research
	Research The role of codon selection in regulation of translation efficiency deduced from synthetic libraries Sivan Navon, Yitzhak Pilpel Genome Biology 2011, 12:R12 (1 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 5’ proximal translation bottlenecks are correlated with high expression levels in an E. coli synthetic gene library
	Research Bringing order to protein disorder through comparative genomics and genetic interactions Jeremy Bellay, Sangjo Han, Magali Michaut, TaeHyung Kim, Michael Costanzo, Brenda J Andrews, Charles Boone, Gary D Bader, Chad L Myers, Philip M Kim Genome Biology 2011, 12:R14 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics combined with genetic interaction analyses reveals three distinct functional classes of protein disorder
	Research Genomewide characterization of non-polyadenylated RNAs Li Yang, Michael O Duff, Brenton R Graveley, Gordon G Carmichael, Ling-Ling Chen Genome Biology 2011, 12:R16 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An RNA-seq study of two cell types finds that a significant proportion of mRNAs are not polyadenylated.
	Research Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli Maarten Vercruysse, Maarten Fauvart, Ann Jans, Serge Beullens, Kristien Braeken, Lore Cloots, Kristof Engelen, Kathleen Marchal, Jan Michiels Genome Biology 2011, 12:R17 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The stress response of Rhizobium etli is dissected through transcriptomics of a mutant that does not synthesize the alarmone molecule ppGpp
	Research Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Richard Sucgang, Alan Kuo, Xiangjun Tian, William Salerno, Anup Parikh, Christa L Feasley, Eileen Dalin, Hank Tu, Eryong Huang, Kerrie Barry, Erika Lindquist, Harris Shapiro, David Bruce, Jeremy Schmutz, Asaf Salamov, Petra Fey, Pascale Gaudet, Christophe Anjard, M Madan Babu, Siddhartha Basu, Yulia Bushmanova, Hanke van der Wel, Mariko Katoh-Kurasawa, Christopher Dinh, Pedro M Coutinho, Tamao Saito, Marek Elias, Pauline Schaap, Robert R Kay, Bernard Henrissat, Ludwig Eichinger, Francisco Rivero, Nicholas H Putnam, Christopher M West, William F Loomis, Rex L Chisholm, Gad Shaulsky, Joan E Strassmann, David C Queller, Adam Kuspa, Igor V Grigoriev et al. Genome Biology 2011, 12:R20 (28 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Dictyostelium purpureum is reported and compared with that of D. discoideum
	Method MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data Yiwen Chen, Clifford A Meyer, Tao Liu, Wei Li, Jun S Liu, Xiaole Shirley Liu Genome Biology 2011, 12:R11 (1 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MM-ChIP is a method for integrating cross-platform and between laboratory ChIP-seq or ChIP-chip datasets.
	Method Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads Ernest Turro, Shu-Yi Su, Ângela Gonçalves, Lachlan JM Coin, Sylvia Richardson, Alex Lewin Genome Biology 2011, 12:R13 (10 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for estimating isoform-specific expression and allelic imbalance in diploid organisms from RNA-seq data
	Method A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets Chao Cheng, Koon-Kiu Yan, Kevin Y Yip, Joel Rozowsky, Roger Alexander, Chong Shou, Mark Gerstein Genome Biology 2011, 12:R15 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for analyzing matched RNA-seq and ChIP datasets reveals that expression correlates to histone modifications but not a histone code
	Method Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke Genome Biology 2011, 12:R18 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The optimization of PCR amplification steps in Illumina libraries significantly reduces sequencing bias
	Method Dating the age of admixture via wavelet transform analysis of genome-wide data Irina Pugach, Rostislav Matveyev, Andreas Wollstein, Manfred Kayser, Mark Stoneking Genome Biology 2011, 12:R19 (25 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A combination of PCA and wavelet transform analysis defines admixture structure and dates its history
	Correspondence
	Correspondence Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses Albert J Vilella, Ewan Birney, Paul Flicek, Javier Herrero Genome Biology 2011, 12:401 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol 2010, 11:R16.

	Volume 12 Issue 2
	Comment
	Comment There is a sanity clause Gregory A Petsko Genome Biology 2011, 12:105 (25 February 2011) Full text \| PDF \| PubMed \| Editor’s summary Supply versus demand part II: will funding basic research lead to medical advances?
	Research highlight A Drosophila model for the role of epigenetics in brain function and development Roman M Stilling, André Fischer Genome Biology 2011, 12:103 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genetic studies in Drosophila give insights into the possible role of epigenetic regulation of gene expression in a human mental retardation syndrome.
	Research highlight Piecing together the FTO jigsaw Timothy M Frayling, Ken Ong Genome Biology 2011, 12:104 (24 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two recent studies of the FTO gene provide more information on how it affects body mass index
	Review
	Review The domestic dog: man's best friend in the genomic era Adam R Boyko Genome Biology 2011, 12:216 (22 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The tremendous phenotypic diversity of domestic dog breeds, coupled with the availability of dog genome sequences, point to the dog as as an important model organism for complex-trait analysis
	Review The properties and applications of single-molecule DNA sequencing John F Thompson, Patrice M Milos Genome Biology 2011, 12:217 (24 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Single-molecule sequencing works directly from biological samples and generates very long reads, making it well suited for diagnostic and clinical applications.
	Research
	Research The role of codon selection in regulation of translation efficiency deduced from synthetic libraries Sivan Navon, Yitzhak Pilpel Genome Biology 2011, 12:R12 (1 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 5’ proximal translation bottlenecks are correlated with high expression levels in an E. coli synthetic gene library
	Research Bringing order to protein disorder through comparative genomics and genetic interactions Jeremy Bellay, Sangjo Han, Magali Michaut, TaeHyung Kim, Michael Costanzo, Brenda J Andrews, Charles Boone, Gary D Bader, Chad L Myers, Philip M Kim Genome Biology 2011, 12:R14 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics combined with genetic interaction analyses reveals three distinct functional classes of protein disorder
	Research Genomewide characterization of non-polyadenylated RNAs Li Yang, Michael O Duff, Brenton R Graveley, Gordon G Carmichael, Ling-Ling Chen Genome Biology 2011, 12:R16 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An RNA-seq study of two cell types finds that a significant proportion of mRNAs are not polyadenylated.
	Research Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli Maarten Vercruysse, Maarten Fauvart, Ann Jans, Serge Beullens, Kristien Braeken, Lore Cloots, Kristof Engelen, Kathleen Marchal, Jan Michiels Genome Biology 2011, 12:R17 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The stress response of Rhizobium etli is dissected through transcriptomics of a mutant that does not synthesize the alarmone molecule ppGpp
	Research Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Richard Sucgang, Alan Kuo, Xiangjun Tian, William Salerno, Anup Parikh, Christa L Feasley, Eileen Dalin, Hank Tu, Eryong Huang, Kerrie Barry, Erika Lindquist, Harris Shapiro, David Bruce, Jeremy Schmutz, Asaf Salamov, Petra Fey, Pascale Gaudet, Christophe Anjard, M Madan Babu, Siddhartha Basu, Yulia Bushmanova, Hanke van der Wel, Mariko Katoh-Kurasawa, Christopher Dinh, Pedro M Coutinho, Tamao Saito, Marek Elias, Pauline Schaap, Robert R Kay, Bernard Henrissat, Ludwig Eichinger, Francisco Rivero, Nicholas H Putnam, Christopher M West, William F Loomis, Rex L Chisholm, Gad Shaulsky, Joan E Strassmann, David C Queller, Adam Kuspa, Igor V Grigoriev et al. Genome Biology 2011, 12:R20 (28 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Dictyostelium purpureum is reported and compared with that of D. discoideum
	Method MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data Yiwen Chen, Clifford A Meyer, Tao Liu, Wei Li, Jun S Liu, Xiaole Shirley Liu Genome Biology 2011, 12:R11 (1 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MM-ChIP is a method for integrating cross-platform and between laboratory ChIP-seq or ChIP-chip datasets.
	Method Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads Ernest Turro, Shu-Yi Su, Ângela Gonçalves, Lachlan JM Coin, Sylvia Richardson, Alex Lewin Genome Biology 2011, 12:R13 (10 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for estimating isoform-specific expression and allelic imbalance in diploid organisms from RNA-seq data
	Method A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets Chao Cheng, Koon-Kiu Yan, Kevin Y Yip, Joel Rozowsky, Roger Alexander, Chong Shou, Mark Gerstein Genome Biology 2011, 12:R15 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for analyzing matched RNA-seq and ChIP datasets reveals that expression correlates to histone modifications but not a histone code
	Method Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke Genome Biology 2011, 12:R18 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The optimization of PCR amplification steps in Illumina libraries significantly reduces sequencing bias
	Method Dating the age of admixture via wavelet transform analysis of genome-wide data Irina Pugach, Rostislav Matveyev, Andreas Wollstein, Manfred Kayser, Mark Stoneking Genome Biology 2011, 12:R19 (25 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A combination of PCA and wavelet transform analysis defines admixture structure and dates its history
	Correspondence
	Correspondence Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses Albert J Vilella, Ewan Birney, Paul Flicek, Javier Herrero Genome Biology 2011, 12:401 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol 2010, 11:R16.

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Volume 12 Issue 2

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