Genome Biology | Volume 12 Issue 3

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	Volume 12 Issue 3
	Comment
	Editorial Closure of the NCBI SRA and implications for the long-term future of genomics data storage GB Editorial Team Genome Biology 2011, 12:402 (22 March 2011) Full text \| PDF \| PubMed \| Editor’s summary Closure of the NCBI SRA and implications for the long-term future of genomics data storage
	Comment The walking dead Gregory A Petsko Genome Biology 2011, 12:108 (31 March 2011) Full text \| PDF \| PubMed \| Editor’s summary Creationism, academic freedom and funding: keeping the zombie out of science.
	Research highlight The role of imprinted genes in humans Gudrun E Moore, Rebecca Oakey Genome Biology 2011, 12:106 (21 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Imprinting in humans seems to be less prevalent than in mice.
	Research highlight Control of endogenous gene expression timing by introns Annelie Oswald, Andrew C Oates Genome Biology 2011, 12:107 (29 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of gene expression from transgenes and endogenous genes with or without introns reveals a time-regulating role of introns in natural biological systems
	Review
	Review High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype Rosangela Sozzani, Philip N Benfey Genome Biology 2011, 12:219 (28 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of new methods for high-throughput phenotyping of multicellular organisms.
	Protein family review The transient receptor potential family of ion channels Bernd Nilius, Grzegorz Owsianik Genome Biology 2011, 12:218 (17 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transient receptor potential (TRP) of ion channels activate voltage-dependent ion channels and are involved in physiological processes such as sensation of stimuli and ion homeostasis
	Report
	Meeting report 'Next-generation' sequencing becomes 'now-generation' Daniel E Neafsey, Brian J Haas Genome Biology 2011, 12:303 (18 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology & Technology conference, Marco Island, USA, 2-5 February 2011.
	Research
	Research Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation Claudia C Weber, Laurence D Hurst Genome Biology 2011, 12:R23 (17 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The conservation of syntenic gene order previously described in yeast is not apparent in D. melanogaster
	Research Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells Alexander Cecil, Carina Rikanović, Knut Ohlsen, Chunguang Liang, Jörg Bernhardt, Tobias A Oelschlaeger, Tanja Gulder, Gerhard Bringmann, Ulrike Holzgrabe, Matthias Unger, Thomas Dandekar Genome Biology 2011, 12:R24 (21 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression analysis and metabolic modeling offer insights into an antibiotic’s target
	Research Genome-wide assessment of imprinted expression in human cells Lisanne Morcos, Bing Ge, Vonda Koka, Kevin CL Lam, Dmitry K Pokholok, Kevin L Gunderson, Alexandre Montpetit, Dominique J Verlaan, Tomi Pastinen Genome Biology 2011, 12:R25 (21 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide survey of allelic expression bias in human cells suggests only a very small number of human genes are imprinted
	Research Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities Frank J Stewart, Adrian K Sharma, Jessica A Bryant, John M Eppley, Edward F DeLong Genome Biology 2011, 12:R26 (22 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of several metagenomic datasets reveals that highly expressed genes are more conserved than less highly expressed ones
	Research A genome-wide view of mutation rate co-variation using multivariate analyses Guruprasad Ananda, Francesca Chiaromonte, Kateryna D Makova Genome Biology 2011, 12:R27 (22 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Local genomic features influence the rate of different types of mutations in primate genomes
	Research Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite France Denoeud, Michaël Roussel, Benjamin Noel, Ivan Wawrzyniak, Corinne Da Silva, Marie Diogon, Eric Viscogliosi, Céline Brochier-Armanet, Arnaud Couloux, Julie Poulain, Béatrice Segurens, Véronique Anthouard, Catherine Texier, Nicolas Blot, Philippe Poirier, Geok Choo Ng, Kevin SW Tan, François Artiguenave, Olivier Jaillon, Jean-Marc Aury, Frédéric Delbac, Patrick Wincker, Christian P Vivarès, Hicham El Alaoui Genome Biology 2011, 12:R29 (25 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The genome sequence of the anaerobic stramenopile, Blastocystis, reveals the pathogenic potential of this important human parasite.
	Method hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets Todd A Johnson, Yoshihito Niimura, Hiroshi Tanaka, Yusuke Nakamura, Tatsuhiko Tsunoda Genome Biology 2011, 12:R21 (11 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Novel methods are presented for the detection and analysis of homozygous tracts from genotype data
	Method Improving RNA-Seq expression estimates by correcting for fragment bias Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extension to Cufflinks corrects bias in RNA-seq datasets
	Method Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis Kevin Ashelford, Maria E Eriksson, Christopher M Allen, Rosalinda D'Amore, Mikael Johansson, Peter Gould, Suzanne Kay, Andrew J Millar, Neil Hall, Anthony Hall Genome Biology 2011, 12:R28 (23 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Re-sequencing of the Ws-2 Arabidopsis accession and a comparison with the reference accession reveals a novel circadian clock mutation.
	Method ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes Alessandro M Varani, Patricia Siguier, Edith Gourbeyre, Vincent Charneau, Mick Chandler Genome Biology 2011, 12:R30 (28 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ISsaga is a tool for identifying and annotating insertion sequences in prokaryotic genomes.
	Method A vertebrate case study of the quality of assemblies derived from next-generation sequences Liang Ye, LaDeana W Hillier, Patrick Minx, Nay Thane, Devin P Locke, John C Martin, Lei Chen, Makedonka Mitreva, Jason R Miller, Kevin V Haub, David J Dooling, Elaine R Mardis, Richard K Wilson, George M Weinstock, Wesley C Warren Genome Biology 2011, 12:R31 (31 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In a comparative analysis, the chicken genome is assembled using Sanger, Illumina or 454 reads from the same biological sample
	Method The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics Tara A Gianoulis, Ashish Agarwal, Michael Snyder, Mark B Gerstein Genome Biology 2011, 12:R32 (31 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Making connections between unrelated tabulated genomics datasets

	Volume 12 Issue 3
	Comment
	Editorial Closure of the NCBI SRA and implications for the long-term future of genomics data storage GB Editorial Team Genome Biology 2011, 12:402 (22 March 2011) Full text \| PDF \| PubMed \| Editor’s summary Closure of the NCBI SRA and implications for the long-term future of genomics data storage
	Comment The walking dead Gregory A Petsko Genome Biology 2011, 12:108 (31 March 2011) Full text \| PDF \| PubMed \| Editor’s summary Creationism, academic freedom and funding: keeping the zombie out of science.
	Research highlight The role of imprinted genes in humans Gudrun E Moore, Rebecca Oakey Genome Biology 2011, 12:106 (21 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Imprinting in humans seems to be less prevalent than in mice.
	Research highlight Control of endogenous gene expression timing by introns Annelie Oswald, Andrew C Oates Genome Biology 2011, 12:107 (29 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of gene expression from transgenes and endogenous genes with or without introns reveals a time-regulating role of introns in natural biological systems
	Review
	Review High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype Rosangela Sozzani, Philip N Benfey Genome Biology 2011, 12:219 (28 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of new methods for high-throughput phenotyping of multicellular organisms.
	Protein family review The transient receptor potential family of ion channels Bernd Nilius, Grzegorz Owsianik Genome Biology 2011, 12:218 (17 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transient receptor potential (TRP) of ion channels activate voltage-dependent ion channels and are involved in physiological processes such as sensation of stimuli and ion homeostasis
	Report
	Meeting report 'Next-generation' sequencing becomes 'now-generation' Daniel E Neafsey, Brian J Haas Genome Biology 2011, 12:303 (18 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology & Technology conference, Marco Island, USA, 2-5 February 2011.
	Research
	Research Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation Claudia C Weber, Laurence D Hurst Genome Biology 2011, 12:R23 (17 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The conservation of syntenic gene order previously described in yeast is not apparent in D. melanogaster
	Research Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells Alexander Cecil, Carina Rikanović, Knut Ohlsen, Chunguang Liang, Jörg Bernhardt, Tobias A Oelschlaeger, Tanja Gulder, Gerhard Bringmann, Ulrike Holzgrabe, Matthias Unger, Thomas Dandekar Genome Biology 2011, 12:R24 (21 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression analysis and metabolic modeling offer insights into an antibiotic’s target
	Research Genome-wide assessment of imprinted expression in human cells Lisanne Morcos, Bing Ge, Vonda Koka, Kevin CL Lam, Dmitry K Pokholok, Kevin L Gunderson, Alexandre Montpetit, Dominique J Verlaan, Tomi Pastinen Genome Biology 2011, 12:R25 (21 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide survey of allelic expression bias in human cells suggests only a very small number of human genes are imprinted
	Research Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities Frank J Stewart, Adrian K Sharma, Jessica A Bryant, John M Eppley, Edward F DeLong Genome Biology 2011, 12:R26 (22 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of several metagenomic datasets reveals that highly expressed genes are more conserved than less highly expressed ones
	Research A genome-wide view of mutation rate co-variation using multivariate analyses Guruprasad Ananda, Francesca Chiaromonte, Kateryna D Makova Genome Biology 2011, 12:R27 (22 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Local genomic features influence the rate of different types of mutations in primate genomes
	Research Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite France Denoeud, Michaël Roussel, Benjamin Noel, Ivan Wawrzyniak, Corinne Da Silva, Marie Diogon, Eric Viscogliosi, Céline Brochier-Armanet, Arnaud Couloux, Julie Poulain, Béatrice Segurens, Véronique Anthouard, Catherine Texier, Nicolas Blot, Philippe Poirier, Geok Choo Ng, Kevin SW Tan, François Artiguenave, Olivier Jaillon, Jean-Marc Aury, Frédéric Delbac, Patrick Wincker, Christian P Vivarès, Hicham El Alaoui Genome Biology 2011, 12:R29 (25 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The genome sequence of the anaerobic stramenopile, Blastocystis, reveals the pathogenic potential of this important human parasite.
	Method hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets Todd A Johnson, Yoshihito Niimura, Hiroshi Tanaka, Yusuke Nakamura, Tatsuhiko Tsunoda Genome Biology 2011, 12:R21 (11 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Novel methods are presented for the detection and analysis of homozygous tracts from genotype data
	Method Improving RNA-Seq expression estimates by correcting for fragment bias Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extension to Cufflinks corrects bias in RNA-seq datasets
	Method Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis Kevin Ashelford, Maria E Eriksson, Christopher M Allen, Rosalinda D'Amore, Mikael Johansson, Peter Gould, Suzanne Kay, Andrew J Millar, Neil Hall, Anthony Hall Genome Biology 2011, 12:R28 (23 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Re-sequencing of the Ws-2 Arabidopsis accession and a comparison with the reference accession reveals a novel circadian clock mutation.
	Method ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes Alessandro M Varani, Patricia Siguier, Edith Gourbeyre, Vincent Charneau, Mick Chandler Genome Biology 2011, 12:R30 (28 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ISsaga is a tool for identifying and annotating insertion sequences in prokaryotic genomes.
	Method A vertebrate case study of the quality of assemblies derived from next-generation sequences Liang Ye, LaDeana W Hillier, Patrick Minx, Nay Thane, Devin P Locke, John C Martin, Lei Chen, Makedonka Mitreva, Jason R Miller, Kevin V Haub, David J Dooling, Elaine R Mardis, Richard K Wilson, George M Weinstock, Wesley C Warren Genome Biology 2011, 12:R31 (31 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In a comparative analysis, the chicken genome is assembled using Sanger, Illumina or 454 reads from the same biological sample
	Method The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics Tara A Gianoulis, Ashish Agarwal, Michael Snyder, Mark B Gerstein Genome Biology 2011, 12:R32 (31 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Making connections between unrelated tabulated genomics datasets

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Volume 12 Issue 3

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