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		Correction Correction: Closing gaps in the human genome using sequencing by synthesis Manuel Garber, Michael C Zody, Harindra C Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2011, 12:403 (19 April 2011) Abstract \| Full text \| PDF \| PubMed
		Research Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma Christian P Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth, Diego A Martinez, Irina S Druzhinina, Michael Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A Horwitz, Prasun K Mukherjee, Mala Mukherjee, László Kredics, Luis D Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte G Cervantes-Badillo, Jean Challacombe, Olga Chertkov, Kevin McCluskey, Fanny Coulpier, Nandan Deshpande, Hans von Döhren, Daniel J Ebbole, Edgardo U Esquivel-Naranjo, Erzsébet Fekete, Michel Flipphi, Fabian Glaser, Elida Y Gómez-Rodríguez, Sabine Gruber et al. Genome Biology 2011, 12:R40 (18 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of two novel genomes from the biocontrol agent genus Trichoderma
		Software A quantitative literature-curated gold standard for kinase-substrate pairs Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Young, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews Genome Biology 2011, 12:R39 (14 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A yeast kinase interaction database is presented, for kinase-gene and kinase-protein interactions
		Research Discovery of permuted and recently split transfer RNAs in Archaea Patricia P Chan, Aaron E Cozen, Todd M Lowe Genome Biology 2011, 12:R38 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Discovery of novel split and permuted archaeal tRNAs argues against a single, early origin in Archaea
		Research Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome Christine R McLaughlin, Brian P Chadwick Genome Biology 2011, 12:R37 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potential roles of the human DXZ4 macrosatellite in CTCF binding and X inactivation are revealed through functional conservation in primates.
		Research highlight An enigmatic satellite William Amos Genome Biology 2011, 12:110 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A conserved, transcribed X-linked satellite DNA that defies X-inactivation.
		Research Genome-wide survey of post-meiotic segregation during yeast recombination Eugenio Mancera, Richard Bourgon, Wolfgang Huber, Lars M Steinmetz Genome Biology 2011, 12:R36 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide study of post-meiotic segregation, in which mismatches in heteroduplex DNA are left unrepaired, performed in yeast
		Opinion What does biologically meaningful mean? A perspective on gene regulatory network validation Albertha JM Walhout Genome Biology 2011, 12:109 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Deciding whether gene regulatory interactions are biologically meaningful is not as simple as it might seem.
		Method An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations John C Tan, Becky A Miller, Asako Tan, Jigar J Patel, Ian H Cheeseman, Tim JC Anderson, Magnus Manske, Gareth Maslen, Dominic P Kwiatkowski, Michael T Ferdig Genome Biology 2011, 12:R35 (8 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Plasmodium falciparum genotyping array for determining variation in field samples with human DNA contamination.
		Research The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin Genome Biology 2011, 12:R34 (7 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromatin accessibility influences the binding of Drosophila transcription factors.
		Research High recombination rates and hotspots in a Plasmodium falciparum genetic cross Hongying Jiang, Na Li, Vivek Gopalan, Martine M Zilversmit, Sudhir Varma, Vijayaraj Nagarajan, Jian Li, Jianbing Mu, Karen Hayton, Bruce Henschen, Ming Yi, Robert Stephens, Gilean McVean, Philip Awadalla, Thomas E Wellems, Xin-zhuan Su Genome Biology 2011, 12:R33 (4 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification of Plasmodium falciparum recombination rates, hotspots and a potential PRDM9 candidate.
		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
		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
		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 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
		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.
		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.
		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 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 \| Editor’s summary Re-sequencing of the Ws-2 Arabidopsis accession and a comparison with the reference accession reveals a novel circadian clock mutation.
		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 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
		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
		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 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 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.

	All
		Correction Correction: Closing gaps in the human genome using sequencing by synthesis Manuel Garber, Michael C Zody, Harindra C Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2011, 12:403 (19 April 2011) Abstract \| Full text \| PDF \| PubMed
		Research Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma Christian P Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth, Diego A Martinez, Irina S Druzhinina, Michael Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A Horwitz, Prasun K Mukherjee, Mala Mukherjee, László Kredics, Luis D Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte G Cervantes-Badillo, Jean Challacombe, Olga Chertkov, Kevin McCluskey, Fanny Coulpier, Nandan Deshpande, Hans von Döhren, Daniel J Ebbole, Edgardo U Esquivel-Naranjo, Erzsébet Fekete, Michel Flipphi, Fabian Glaser, Elida Y Gómez-Rodríguez, Sabine Gruber et al. Genome Biology 2011, 12:R40 (18 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of two novel genomes from the biocontrol agent genus Trichoderma
		Software A quantitative literature-curated gold standard for kinase-substrate pairs Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Young, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews Genome Biology 2011, 12:R39 (14 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A yeast kinase interaction database is presented, for kinase-gene and kinase-protein interactions
		Research Discovery of permuted and recently split transfer RNAs in Archaea Patricia P Chan, Aaron E Cozen, Todd M Lowe Genome Biology 2011, 12:R38 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Discovery of novel split and permuted archaeal tRNAs argues against a single, early origin in Archaea
		Research Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome Christine R McLaughlin, Brian P Chadwick Genome Biology 2011, 12:R37 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potential roles of the human DXZ4 macrosatellite in CTCF binding and X inactivation are revealed through functional conservation in primates.
		Research highlight An enigmatic satellite William Amos Genome Biology 2011, 12:110 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A conserved, transcribed X-linked satellite DNA that defies X-inactivation.
		Research Genome-wide survey of post-meiotic segregation during yeast recombination Eugenio Mancera, Richard Bourgon, Wolfgang Huber, Lars M Steinmetz Genome Biology 2011, 12:R36 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide study of post-meiotic segregation, in which mismatches in heteroduplex DNA are left unrepaired, performed in yeast
		Opinion What does biologically meaningful mean? A perspective on gene regulatory network validation Albertha JM Walhout Genome Biology 2011, 12:109 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Deciding whether gene regulatory interactions are biologically meaningful is not as simple as it might seem.
		Method An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations John C Tan, Becky A Miller, Asako Tan, Jigar J Patel, Ian H Cheeseman, Tim JC Anderson, Magnus Manske, Gareth Maslen, Dominic P Kwiatkowski, Michael T Ferdig Genome Biology 2011, 12:R35 (8 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Plasmodium falciparum genotyping array for determining variation in field samples with human DNA contamination.
		Research The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin Genome Biology 2011, 12:R34 (7 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromatin accessibility influences the binding of Drosophila transcription factors.
		Research High recombination rates and hotspots in a Plasmodium falciparum genetic cross Hongying Jiang, Na Li, Vivek Gopalan, Martine M Zilversmit, Sudhir Varma, Vijayaraj Nagarajan, Jian Li, Jianbing Mu, Karen Hayton, Bruce Henschen, Ming Yi, Robert Stephens, Gilean McVean, Philip Awadalla, Thomas E Wellems, Xin-zhuan Su Genome Biology 2011, 12:R33 (4 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification of Plasmodium falciparum recombination rates, hotspots and a potential PRDM9 candidate.
		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
		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
		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 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
		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.
		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.
		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 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 \| Editor’s summary Re-sequencing of the Ws-2 Arabidopsis accession and a comparison with the reference accession reveals a novel circadian clock mutation.
		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 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
		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
		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 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 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.