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		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 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.
		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.
		Method A standard variation file format for human genome sequences Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck Genome Biology 2010, 11:R88 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome variation format (GVF) and the 10Gen dataset provide a resource for the standardization of variant files and data analysis.
		Research Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species Moran Yassour, Jenna Pfiffner, Joshua Z Levin, Xian Adiconis, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, Aviv Regev Genome Biology 2010, 11:R87 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Strand-specific RNA sequencing in yeast species reveals antisense transcripts and their conserved expression across multiple species.
		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.
		Software Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team Genome Biology 2010, 11:R86 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy computing platform allows researchers to share data and data analysis workflows, facilitating easily reproducible analyses.
		Research Digital expression profiling of novel diatom transcripts provides insight into their biological functions Uma Maheswari, Kamel Jabbari, Jean-Louis Petit, Betina M Porcel, Andrew E Allen, Jean-Paul Cadoret, Alessandra De Martino, Marc Heijde, Raymond Kaas, Julie La Roche, Pascal J Lopez, Véronique Martin-Jézéquel, Agnès Meichenin, Thomas Mock, Micaela Schnitzler Parker, Assaf Vardi, E Virginia Armbrust, Jean Weissenbach, Michaël Katinka, Chris Bowler Genome Biology 2010, 11:R85 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Digital expression profiling of the diatom transcriptome under varying environmental conditions provides insights into the roles of novel diatom genes.
		Research highlight The missing graphical user interface for genomics Michael C Schatz Genome Biology 2010, 11:128 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy package for genomic analysis empowers regular users through a much-needed and user-friendly graphical web interface.
		Research Intronic motif pairs cooperate across exons to promote pre-mRNA splicing Shengdong Ke, Lawrence A Chasin Genome Biology 2010, 11:R84 (12 August 2010) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary New motifs are found to act synergistically across exons to define exon boundaries and promote pre-RNA splicing in the human genome.
		Software Cloud-scale RNA-sequencing differential expression analysis with Myrna Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
		Research Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Steven JM Jones, Janessa Laskin, Yvonne Y Li, Obi L Griffith, Jianghong An, Mikhail Bilenky, Yaron S Butterfield, Timothee Cezard, Eric Chuah, Richard Corbett, Anthony P Fejes, Malachi Griffith, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D Morin, Trevor J Pugh, Tesa Severson, Sohrab P Shah, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A Moore, David G Huntsman, Inanc Birol, Martin Hirst, Robert A Holt, Marco A Marra et al. Genome Biology 2010, 11:R82 (9 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genomes of a primary tumor and two metastases were sequenced, and the information used to guide treatment
		Research Multiple distinct small RNAs originate from the same microRNA precursors Weixiong Zhang, Shang Gao, Xuefeng Zhou, Jing Xia, Padmanabhan Chellappan, Xiang Zhou, Xiaoming Zhang, Hailing Jin Genome Biology 2010, 11:R81 (9 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Deep sequencing of Arabidopsis small RNAs reveals the existence of novel miRNA-like RNAs generated from miRNA precursor hairpins.
		Research Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development Nathalie Billon, Raivo Kolde, Jüri Reimand, Miguel C Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani Genome Biology 2010, 11:R80 (3 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A combined in silico and experimental analysis of mouse embryonic stem cell to adipocyte differentiation reveals new pathway dynamics and regulatory insights.
		Comment When the pie is too small Gregory A Petsko Genome Biology 2010, 11:127 (30 July 2010) Full text \| PDF \| PubMed \| Editor’s summary The NIH science funding pie has many mouths to feed; can a little go a long way?
		Review Nuclear transcription factors in mammalian mitochondria Sarah Leigh-Brown, José Enriquez, Duncan T Odom Genome Biology 2010, 11:215 (29 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Some nuclear-encoded transcription factors also act within mitochondria to regulate mitochondrial function.
		Research Paternally biased X inactivation in mouse neonatal brain Xu Wang, Paul D Soloway, Andrew G Clark Genome Biology 2010, 11:R79 (27 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pyrosequencing of X-linked genes in embryonic mouse brains reveals a small but statistically significant preference for inactivating the paternal X chromosome.
		Correspondence Genomic information infrastructure after the deluge Julian Parkhill, Ewan Birney, Paul Kersey Genome Biology 2010, 11:402 (26 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.
		Research Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing Anna Wetterbom, Adam Ameur, Lars Feuk, Ulf Gyllensten, Lucia Cavelier Genome Biology 2010, 11:R78 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of chimpanzee transcriptomes from different tissues and individuals using RNA-seq reveals novel transcribed regions.
		Research Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering Dwight Kuo, Kai Tan, Guy Zinman, Timothy Ravasi, Ziv Bar-Joseph, Trey Ideker Genome Biology 2010, 11:R77 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three yeast species respond to azole drugs in different ways and show different sensitivities to fluconazole
		Research highlight Annotating conserved and novel features of primate transcriptomes using sequencing Philipp Khaitovich Genome Biology 2010, 11:125 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of chimpanzee and human transcripts reveals transcripts lost in humans and highlights the incompleteness of non-human primate genome annotations.
		Method Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis Eric Letouzé, Yves Allory, Marc A Bollet, François Radvanyi, Frédéric Guyon Genome Biology 2010, 11:R76 (22 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TuMult is a method for reconstructing the history of cancer progression from copy number variations in several samples from a patient
		Research RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J Rando Genome Biology 2010, 11:R75 (16 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip for RNA PolII occupancy and transcription analysis reveals that mRNA levels in yeast do not correlate with PolII abundance on genes.
		Research Quantifying the mechanisms of domain gain in animal proteins Marija Buljan, Adam Frankish, Alex Bateman Genome Biology 2010, 11:R74 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The main mechanism of domain gain in metazoan proteins is shown to be the joining of exons from adjacent genes.
		Research highlight How do proteins gain new domains? Joseph A Marsh, Sarah A Teichmann Genome Biology 2010, 11:126 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.
		Research Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes Rebecca A Chodroff, Leo Goodstadt, Tamara M Sirey, Peter L Oliver, Kay E Davies, Eric D Green, Zoltán Molnár, Chris P Ponting Genome Biology 2010, 11:R72 (12 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Long non-coding RNAs are shown to have conserved sequence and expression in brain tissue across amniotes, suggesting a conserved functional role.

	All
		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 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.
		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.
		Method A standard variation file format for human genome sequences Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck Genome Biology 2010, 11:R88 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome variation format (GVF) and the 10Gen dataset provide a resource for the standardization of variant files and data analysis.
		Research Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species Moran Yassour, Jenna Pfiffner, Joshua Z Levin, Xian Adiconis, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, Aviv Regev Genome Biology 2010, 11:R87 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Strand-specific RNA sequencing in yeast species reveals antisense transcripts and their conserved expression across multiple species.
		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.
		Software Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team Genome Biology 2010, 11:R86 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy computing platform allows researchers to share data and data analysis workflows, facilitating easily reproducible analyses.
		Research Digital expression profiling of novel diatom transcripts provides insight into their biological functions Uma Maheswari, Kamel Jabbari, Jean-Louis Petit, Betina M Porcel, Andrew E Allen, Jean-Paul Cadoret, Alessandra De Martino, Marc Heijde, Raymond Kaas, Julie La Roche, Pascal J Lopez, Véronique Martin-Jézéquel, Agnès Meichenin, Thomas Mock, Micaela Schnitzler Parker, Assaf Vardi, E Virginia Armbrust, Jean Weissenbach, Michaël Katinka, Chris Bowler Genome Biology 2010, 11:R85 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Digital expression profiling of the diatom transcriptome under varying environmental conditions provides insights into the roles of novel diatom genes.
		Research highlight The missing graphical user interface for genomics Michael C Schatz Genome Biology 2010, 11:128 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy package for genomic analysis empowers regular users through a much-needed and user-friendly graphical web interface.
		Research Intronic motif pairs cooperate across exons to promote pre-mRNA splicing Shengdong Ke, Lawrence A Chasin Genome Biology 2010, 11:R84 (12 August 2010) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary New motifs are found to act synergistically across exons to define exon boundaries and promote pre-RNA splicing in the human genome.
		Software Cloud-scale RNA-sequencing differential expression analysis with Myrna Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
		Research Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Steven JM Jones, Janessa Laskin, Yvonne Y Li, Obi L Griffith, Jianghong An, Mikhail Bilenky, Yaron S Butterfield, Timothee Cezard, Eric Chuah, Richard Corbett, Anthony P Fejes, Malachi Griffith, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D Morin, Trevor J Pugh, Tesa Severson, Sohrab P Shah, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A Moore, David G Huntsman, Inanc Birol, Martin Hirst, Robert A Holt, Marco A Marra et al. Genome Biology 2010, 11:R82 (9 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genomes of a primary tumor and two metastases were sequenced, and the information used to guide treatment
		Research Multiple distinct small RNAs originate from the same microRNA precursors Weixiong Zhang, Shang Gao, Xuefeng Zhou, Jing Xia, Padmanabhan Chellappan, Xiang Zhou, Xiaoming Zhang, Hailing Jin Genome Biology 2010, 11:R81 (9 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Deep sequencing of Arabidopsis small RNAs reveals the existence of novel miRNA-like RNAs generated from miRNA precursor hairpins.
		Research Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development Nathalie Billon, Raivo Kolde, Jüri Reimand, Miguel C Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani Genome Biology 2010, 11:R80 (3 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A combined in silico and experimental analysis of mouse embryonic stem cell to adipocyte differentiation reveals new pathway dynamics and regulatory insights.
		Comment When the pie is too small Gregory A Petsko Genome Biology 2010, 11:127 (30 July 2010) Full text \| PDF \| PubMed \| Editor’s summary The NIH science funding pie has many mouths to feed; can a little go a long way?
		Review Nuclear transcription factors in mammalian mitochondria Sarah Leigh-Brown, José Enriquez, Duncan T Odom Genome Biology 2010, 11:215 (29 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Some nuclear-encoded transcription factors also act within mitochondria to regulate mitochondrial function.
		Research Paternally biased X inactivation in mouse neonatal brain Xu Wang, Paul D Soloway, Andrew G Clark Genome Biology 2010, 11:R79 (27 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pyrosequencing of X-linked genes in embryonic mouse brains reveals a small but statistically significant preference for inactivating the paternal X chromosome.
		Correspondence Genomic information infrastructure after the deluge Julian Parkhill, Ewan Birney, Paul Kersey Genome Biology 2010, 11:402 (26 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.
		Research Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing Anna Wetterbom, Adam Ameur, Lars Feuk, Ulf Gyllensten, Lucia Cavelier Genome Biology 2010, 11:R78 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of chimpanzee transcriptomes from different tissues and individuals using RNA-seq reveals novel transcribed regions.
		Research Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering Dwight Kuo, Kai Tan, Guy Zinman, Timothy Ravasi, Ziv Bar-Joseph, Trey Ideker Genome Biology 2010, 11:R77 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three yeast species respond to azole drugs in different ways and show different sensitivities to fluconazole
		Research highlight Annotating conserved and novel features of primate transcriptomes using sequencing Philipp Khaitovich Genome Biology 2010, 11:125 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of chimpanzee and human transcripts reveals transcripts lost in humans and highlights the incompleteness of non-human primate genome annotations.
		Method Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis Eric Letouzé, Yves Allory, Marc A Bollet, François Radvanyi, Frédéric Guyon Genome Biology 2010, 11:R76 (22 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TuMult is a method for reconstructing the history of cancer progression from copy number variations in several samples from a patient
		Research RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J Rando Genome Biology 2010, 11:R75 (16 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip for RNA PolII occupancy and transcription analysis reveals that mRNA levels in yeast do not correlate with PolII abundance on genes.
		Research Quantifying the mechanisms of domain gain in animal proteins Marija Buljan, Adam Frankish, Alex Bateman Genome Biology 2010, 11:R74 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The main mechanism of domain gain in metazoan proteins is shown to be the joining of exons from adjacent genes.
		Research highlight How do proteins gain new domains? Joseph A Marsh, Sarah A Teichmann Genome Biology 2010, 11:126 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.
		Research Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes Rebecca A Chodroff, Leo Goodstadt, Tamara M Sirey, Peter L Oliver, Kay E Davies, Eric D Green, Zoltán Molnár, Chris P Ponting Genome Biology 2010, 11:R72 (12 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Long non-coding RNAs are shown to have conserved sequence and expression in brain tissue across amniotes, suggesting a conserved functional role.