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		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.
		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.
		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.
		Open letter Sequencing the genome of the Atlantic salmon (Salmo salar) William S Davidson, Ben F Koop, Steven JM Jones, Patricia Iturra, Rodrigo Vidal, Alejandro Maass, Inge Jonassen, Sigbjorn Lien, Stig W Omholt Genome Biology 2010, 11:403 (30 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids.
		Research The rate of the molecular clock and the cost of gratuitous protein synthesis Germán Plata, Max E Gottesman, Dennis Vitkup Genome Biology 2010, 11:R98 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The effect and cost of protein misfolding on protein evolution rate in E. coli is shown to be small compared with effects of protein synthesis.
		Research Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation Magali Naville, Daniel Gautheret Genome Biology 2010, 11:R97 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The large-scale detection of bacterial attenuators of transcription reveals a far more varied picture of transcriptional regulation than previously anticipated.
		Method Multi-species integrative biclustering Peter Waltman, Thadeous Kacmarczyk, Ashley R Bate, Daniel B Kearns, David J Reiss, Patrick Eichenberger, Richard Bonneau Genome Biology 2010, 11:R96 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary cMonkey allows biclustering of data from multiple species in order to identify gene groups with conserved regulatory modules
		Research Novel venom gene discovery in the platypus Camilla M Whittington, Anthony T Papenfuss, Devin P Locke, Elaine R Mardis, Richard K Wilson, Sahar Abubucker, Makedonka Mitreva, Emily SW Wong, Arthur L Hsu, Philip W Kuchel, Katherine Belov, Wesley C Warren Genome Biology 2010, 11:R95 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptome of the platypus venom gland reveals novel venom genes and sheds light on the evolution of mammalian venom.
		Review Rat traps: filling the toolbox for manipulating the rat genome Ruben van Boxtel, Edwin Cuppen Genome Biology 2010, 11:217 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Efficient gene targeting and mutant generation in the rat are increasing its usefulness as a model animal.
		Research highlight Host transcription in active and latent tuberculosis Sarah M Fortune, Eric J Rubin Genome Biology 2010, 11:135 (28 September 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study has identified a transcriptional signature for active tuberculosis, suggesting that the distinction between active and latent forms may not be absolute.
		Research Sequence and structure of Brassica rapa chromosome A3 Jeong-Hwan Mun, Soo-Jin Kwon, Young-Joo Seol, Jin A Kim, Mina Jin, Jung Sun Kim, Myung-Ho Lim, Soo-In Lee, Joon Ki Hong, Tae-Ho Park, Sang-Choon Lee, Beom-Jin Kim, Mi-Suk Seo, Seunghoon Baek, Min-Jee Lee, Ja Young Shin, Jang-Ho Hahn, Yoon-Jung Hwang, Ki-Byung Lim, Jee Young Park, Jonghoon Lee, Tae-Jin Yang, Hee-Ju Yu, Ik-Young Choi, Beom-Soon Choi, Su Ryun Choi, Nirala Ramchiary, Yong Pyo Lim, Fiona Fraser, Nizar Drou, Eleni Soumpourou, Martin Trick, Ian Bancroft, Andrew G Sharpe, Isobel AP Parkin, Jacqueline Batley, Dave Edwards, Beom-Seok Park et al. Genome Biology 2010, 11:R94 (27 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Brassica rapa A3 chromosome sequence and a comparative synteny analysis with Arabidopsis thaliana provides a model of plant genome evolution.
		Research highlight Unmasking a role for sex chromosomes in gene silencing Danielle M Maatouk, Blanche Capel Genome Biology 2010, 11:134 (27 September 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New research suggests that sex chromosome dimorphism helps to regulate gene silencing.
		Comment Shadows on the wall Gregory A Petsko Genome Biology 2010, 11:136 (23 September 2010) Full text \| PDF \| PubMed \| Editor’s summary Skepticism is healthy and the toppling of scientific paradigms shouldn’t be feared.
		Research Genome-wide analysis of mRNA decay patterns during early Drosophila development Stefan Thomsen, Simon Anders, Sarath Chandra Janga, Wolfgang Huber, Claudio R Alonso Genome Biology 2010, 11:R93 (21 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of mRNA decay in Drosophila embryos identifies maternally- and zygotically-encoded factors regulating mRNA degradation
		Method A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data Christopher Yau, Dmitri Mouradov, Robert N Jorissen, Stefano Colella, Ghazala Mirza, Graham Steers, Adrian Harris, Jiannis Ragoussis, Oliver Sieber, Christopher C Holmes Genome Biology 2010, 11:R92 (21 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary OncoSNP is a method for detecting CNVs in tumors from SNP array data that can account for contaminating healthy tissue.
		Research highlight Living the high life: high-altitude adaptation Laura B Scheinfeldt, Sarah A Tishkoff Genome Biology 2010, 11:133 (10 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide scans show that genetic variants associated with high-altitude adaptation in different geographic populations arose independently.
		Research Sequencing and analysis of an Irish human genome Pin Tong, James GD Prendergast, Amanda J Lohan, Susan M Farrington, Simon Cronin, Nial Friel, Dan G Bradley, Orla Hardiman, Alex Evans, James F Wilson, Brendan Loftus Genome Biology 2010, 11:R91 (7 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first Irish human genome was sequenced to 11-fold coverage. Over 3 million SNPs and nearly 200,000 indels are identified.
		Research highlight The first Irish genome and ways of improving sequence accuracy Young Seok Ju, Yun Joo Yoo, Jong-Il Kim, Jeong-Sun Seo Genome Biology 2010, 11:132 (7 September 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The whole-genome sequencing of an Irish person shows how imputation using previous known information improves the accuracy of low-read-depth sequencing.
		Method Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina Leslie Genome Biology 2010, 11:R90 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary mirSVR is a method for miRNA target prediction that, unusually, takes into account non-canonical binding sequences and non-conserved sites
		Research Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates Bernice Meng Qi Sim, Narisara Chantratita, Wen Fong Ooi, Tannistha Nandi, Ryan Tewhey, Vanaporn Wuthiekanun, Janjira Thaipadungpanit, Sarinna Tumapa, Pramila Ariyaratne, Wing-Kin Sung, Xiao Hui Sem, Hui Hoon Chua, Kalpana Ramnarayanan, Chi Ho Lin, Yichun Liu, Edward J Feil, Mindy B Glass, Gladys Tan, Sharon J Peacock, Patrick Tan Genome Biology 2010, 11:R89 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing and microarray analyses of non-pathogenic and pathogenic Burkholderia isolates reveals insight into the factors underlying the acquisition of pathogenesis.
		Comment The past is a foreign country Gregory A Petsko Genome Biology 2010, 11:131 (27 August 2010) Full text \| PDF \| Editor’s summary The scientific worldview of someone starting graduate school today is very different from that of previous generations.
		Research highlight Elucidating the molecular characteristics of organogenesis in human embryos Xin Geng, Guillermo Oliver Genome Biology 2010, 11:130 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptomic analysis of early human organogenesis reveals the molecular signature of these processes.
		Research highlight Transcription, one allele at a time Timothée Lionnet, Robert H Singer Genome Biology 2010, 11:129 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new technique for the imaging of transcription from a single gene in living cells highlights the dynamic nature of transcriptional regulation.
		Meeting report An illuminated view of molecular biology Yoseph Barash, Xinchen Wang Genome Biology 2010, 11:307 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 7th Special Interest Group meeting on Alternative Splicing, Boston, USA, 9-13 July 2010.
		Review Dosage compensation and the global re-balancing of aneuploid genomes Matthias Prestel, Christian Feller, Peter B Becker Genome Biology 2010, 11:216 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The dosage-compensation systems that equalize X-chromosome expression between sexes exemplify the intricacies of compensating for differences in gene copy number.

	All
		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.
		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.
		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.
		Open letter Sequencing the genome of the Atlantic salmon (Salmo salar) William S Davidson, Ben F Koop, Steven JM Jones, Patricia Iturra, Rodrigo Vidal, Alejandro Maass, Inge Jonassen, Sigbjorn Lien, Stig W Omholt Genome Biology 2010, 11:403 (30 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids.
		Research The rate of the molecular clock and the cost of gratuitous protein synthesis Germán Plata, Max E Gottesman, Dennis Vitkup Genome Biology 2010, 11:R98 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The effect and cost of protein misfolding on protein evolution rate in E. coli is shown to be small compared with effects of protein synthesis.
		Research Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation Magali Naville, Daniel Gautheret Genome Biology 2010, 11:R97 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The large-scale detection of bacterial attenuators of transcription reveals a far more varied picture of transcriptional regulation than previously anticipated.
		Method Multi-species integrative biclustering Peter Waltman, Thadeous Kacmarczyk, Ashley R Bate, Daniel B Kearns, David J Reiss, Patrick Eichenberger, Richard Bonneau Genome Biology 2010, 11:R96 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary cMonkey allows biclustering of data from multiple species in order to identify gene groups with conserved regulatory modules
		Research Novel venom gene discovery in the platypus Camilla M Whittington, Anthony T Papenfuss, Devin P Locke, Elaine R Mardis, Richard K Wilson, Sahar Abubucker, Makedonka Mitreva, Emily SW Wong, Arthur L Hsu, Philip W Kuchel, Katherine Belov, Wesley C Warren Genome Biology 2010, 11:R95 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptome of the platypus venom gland reveals novel venom genes and sheds light on the evolution of mammalian venom.
		Review Rat traps: filling the toolbox for manipulating the rat genome Ruben van Boxtel, Edwin Cuppen Genome Biology 2010, 11:217 (29 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Efficient gene targeting and mutant generation in the rat are increasing its usefulness as a model animal.
		Research highlight Host transcription in active and latent tuberculosis Sarah M Fortune, Eric J Rubin Genome Biology 2010, 11:135 (28 September 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study has identified a transcriptional signature for active tuberculosis, suggesting that the distinction between active and latent forms may not be absolute.
		Research Sequence and structure of Brassica rapa chromosome A3 Jeong-Hwan Mun, Soo-Jin Kwon, Young-Joo Seol, Jin A Kim, Mina Jin, Jung Sun Kim, Myung-Ho Lim, Soo-In Lee, Joon Ki Hong, Tae-Ho Park, Sang-Choon Lee, Beom-Jin Kim, Mi-Suk Seo, Seunghoon Baek, Min-Jee Lee, Ja Young Shin, Jang-Ho Hahn, Yoon-Jung Hwang, Ki-Byung Lim, Jee Young Park, Jonghoon Lee, Tae-Jin Yang, Hee-Ju Yu, Ik-Young Choi, Beom-Soon Choi, Su Ryun Choi, Nirala Ramchiary, Yong Pyo Lim, Fiona Fraser, Nizar Drou, Eleni Soumpourou, Martin Trick, Ian Bancroft, Andrew G Sharpe, Isobel AP Parkin, Jacqueline Batley, Dave Edwards, Beom-Seok Park et al. Genome Biology 2010, 11:R94 (27 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Brassica rapa A3 chromosome sequence and a comparative synteny analysis with Arabidopsis thaliana provides a model of plant genome evolution.
		Research highlight Unmasking a role for sex chromosomes in gene silencing Danielle M Maatouk, Blanche Capel Genome Biology 2010, 11:134 (27 September 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New research suggests that sex chromosome dimorphism helps to regulate gene silencing.
		Comment Shadows on the wall Gregory A Petsko Genome Biology 2010, 11:136 (23 September 2010) Full text \| PDF \| PubMed \| Editor’s summary Skepticism is healthy and the toppling of scientific paradigms shouldn’t be feared.
		Research Genome-wide analysis of mRNA decay patterns during early Drosophila development Stefan Thomsen, Simon Anders, Sarath Chandra Janga, Wolfgang Huber, Claudio R Alonso Genome Biology 2010, 11:R93 (21 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of mRNA decay in Drosophila embryos identifies maternally- and zygotically-encoded factors regulating mRNA degradation
		Method A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data Christopher Yau, Dmitri Mouradov, Robert N Jorissen, Stefano Colella, Ghazala Mirza, Graham Steers, Adrian Harris, Jiannis Ragoussis, Oliver Sieber, Christopher C Holmes Genome Biology 2010, 11:R92 (21 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary OncoSNP is a method for detecting CNVs in tumors from SNP array data that can account for contaminating healthy tissue.
		Research highlight Living the high life: high-altitude adaptation Laura B Scheinfeldt, Sarah A Tishkoff Genome Biology 2010, 11:133 (10 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide scans show that genetic variants associated with high-altitude adaptation in different geographic populations arose independently.
		Research Sequencing and analysis of an Irish human genome Pin Tong, James GD Prendergast, Amanda J Lohan, Susan M Farrington, Simon Cronin, Nial Friel, Dan G Bradley, Orla Hardiman, Alex Evans, James F Wilson, Brendan Loftus Genome Biology 2010, 11:R91 (7 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first Irish human genome was sequenced to 11-fold coverage. Over 3 million SNPs and nearly 200,000 indels are identified.
		Research highlight The first Irish genome and ways of improving sequence accuracy Young Seok Ju, Yun Joo Yoo, Jong-Il Kim, Jeong-Sun Seo Genome Biology 2010, 11:132 (7 September 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The whole-genome sequencing of an Irish person shows how imputation using previous known information improves the accuracy of low-read-depth sequencing.
		Method Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina Leslie Genome Biology 2010, 11:R90 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary mirSVR is a method for miRNA target prediction that, unusually, takes into account non-canonical binding sequences and non-conserved sites
		Research Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates Bernice Meng Qi Sim, Narisara Chantratita, Wen Fong Ooi, Tannistha Nandi, Ryan Tewhey, Vanaporn Wuthiekanun, Janjira Thaipadungpanit, Sarinna Tumapa, Pramila Ariyaratne, Wing-Kin Sung, Xiao Hui Sem, Hui Hoon Chua, Kalpana Ramnarayanan, Chi Ho Lin, Yichun Liu, Edward J Feil, Mindy B Glass, Gladys Tan, Sharon J Peacock, Patrick Tan Genome Biology 2010, 11:R89 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing and microarray analyses of non-pathogenic and pathogenic Burkholderia isolates reveals insight into the factors underlying the acquisition of pathogenesis.
		Comment The past is a foreign country Gregory A Petsko Genome Biology 2010, 11:131 (27 August 2010) Full text \| PDF \| Editor’s summary The scientific worldview of someone starting graduate school today is very different from that of previous generations.
		Research highlight Elucidating the molecular characteristics of organogenesis in human embryos Xin Geng, Guillermo Oliver Genome Biology 2010, 11:130 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptomic analysis of early human organogenesis reveals the molecular signature of these processes.
		Research highlight Transcription, one allele at a time Timothée Lionnet, Robert H Singer Genome Biology 2010, 11:129 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new technique for the imaging of transcription from a single gene in living cells highlights the dynamic nature of transcriptional regulation.
		Meeting report An illuminated view of molecular biology Yoseph Barash, Xinchen Wang Genome Biology 2010, 11:307 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 7th Special Interest Group meeting on Alternative Splicing, Boston, USA, 9-13 July 2010.
		Review Dosage compensation and the global re-balancing of aneuploid genomes Matthias Prestel, Christian Feller, Peter B Becker Genome Biology 2010, 11:216 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The dosage-compensation systems that equalize X-chromosome expression between sexes exemplify the intricacies of compensating for differences in gene copy number.