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		Research Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level Olivier Harismendy, Vikas Bansal, Gaurav Bhatia, Masakazu Nakano, Michael Scott, Xiaoyun Wang, Colette Dib, Edouard Turlotte, Jack C Sipe, Sarah S Murray, Jean Deleuze, Vineet Bafna, Eric J Topol, Kelly A Frazer Genome Biology 2010, 11:R118 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Re-sequencing of human endocannabinoid metabolic genes from a large population reveals rare variants associated with extreme obesity.
		Research Comparative genomics reveals birth and death of fragile regions in mammalian evolution Max A Alekseyev, Pavel A Pevzner Genome Biology 2010, 11:R117 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new model explains the frequencies of breakpoints at genomic rearrangement hotspots by demonstrating that fragile sites undergo birth and death.
		Research highlight Metastasis suppression: a role of the Dice(r) Scott Valastyan, Robert A Weinberg Genome Biology 2010, 11:141 (30 November 2010) Abstract \| Full text \| PDF \| PubMed
		Comment Every dog has his day in court Gregory A Petsko Genome Biology 2010, 11:139 (30 November 2010) Full text \| PDF \| PubMed \| Editor’s summary The dog days of stem cell funding.
		Software Quake: quality-aware detection and correction of sequencing errors David R Kelley, Michael C Schatz, Steven L Salzberg Genome Biology 2010, 11:R116 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quake employs a sophisticated approach to error identification and correction in next generation sequencing data.
		Software Constructing a fish metabolic network model Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide fish metabolic model, MetaFishNet, is presented.
		Research Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew JG Simpson, Robert L Strausberg Genome Biology 2010, 11:R114 (25 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of the exome and transcriptome of a breast cancer cell line allows discovery of potentially tumorigenic loss of heterozygosity events.
		Research Genetic diversity in India and the inference of Eurasian population expansion Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, Fuli Yu Genome Biology 2010, 11:R113 (24 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SNP study demonstrates a high degree of Indian genetic diversity and suggests a significant isolation period between Out-of-Africa and Eurasian expansion.
		Method Patient-oriented gene set analysis for cancer mutation data Simina M Boca, Kenneth W Kinzler, Victor E Velculescu, Bert Vogelstein, Giovanni Parmigiani Genome Biology 2010, 11:R112 (23 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel patient-orientated gene set analysis method is presented and applied to a glioblastoma multiforme dataset
		Research Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise Nadia C Whitelaw, Suyinn Chong, Daniel K Morgan, Colm Nestor, Timothy J Bruxner, Alyson Ashe, Eleanore Lambley, Richard Meehan, Emma Whitelaw Genome Biology 2010, 11:R111 (19 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mutants for two epigenetic modifiers are found to be associated with increased intangible variation in phenotypes and in gene expression levels.
		Research Immunostaining of modified histones defines high-level features of the human metaphase epigenome Edith Terrenoire, Fiona McRonald, John A Halsall, Paula Page, Robert S Illingworth, A Malcolm R Taylor, Val Davison, Laura P O'Neill, Bryan M Turner Genome Biology 2010, 11:R110 (15 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Immunofluorescent mapping of histone modifications in single cells at metaphase demonstrates both stable and altered patterns through mitosis
		Research A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Simon R Ellwood, Zhaohui Liu, Rob A Syme, Zhibing Lai, James K Hane, Felicity Keiper, Caroline S Moffat, Richard P Oliver, Timothy L Friesen Genome Biology 2010, 11:R109 (10 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Characterization of barley filamentous fungal pathogen genome by paired-end Solexa sequencing, genome assembly and karyotyping, with insights into pathogenicity.
		Comment A Faustian bargain Gregory A Petsko Genome Biology 2010, 11:138 (31 October 2010) Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary An open letter to George M Philip, President of the State University of New York At Albany.
		Method Rapid haplotype inference for nuclear families Amy L Williams, David E Housman, Martin C Rinard, David K Gifford Genome Biology 2010, 11:R108 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hapi infers the haplotype of an individual based on sequence information from them and their parents.
		Research Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie C Dunning Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Morgens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2010, 11:R107 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Streptococcus pneumoniae genome analysis reveals that the presence of pathogenicity genes is not sufficient to determine virulence
		Meeting report Out of the sequencer and into the wiki as we face new challenges in genome informatics Zemin Ning, Stephen B Montgomery Genome Biology 2010, 11:308 (28 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint Cold Spring Harbor Laboratory/Wellcome Trust Conference 'Genome Informatics' meeting, 15-19 September 2010, Hinxton, Cambridge, UK.
		Method Differential expression analysis for sequence count data Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
		Research highlight Bet hedging in the underworld Xue-Xian Zhang, Paul B Rainey Genome Biology 2010, 11:137 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A soil bacterium hedges its bets on how long it will take to find a new plant host by producing two kinds of daughter cells.
		Research Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes Daniel F Simola, Chantal Francis, Paul D Sniegowski, Junhyong Kim Genome Biology 2010, 11:R105 (22 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Expression timing changes during the cell cycle in woodland and lab S. cerevisiae strains reveal modular timing changes in evolution.
		Method FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z Chen, Joel S Rozowsky, Ashutosh K Tewari, Naoki Kitabayashi, Benjamin J Moss, Mark S Chee, Francesca Demichelis, Mark A Rubin, Mark B Gerstein Genome Biology 2010, 11:R104 (21 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary FusionSeq is a method for identifying fusion transcripts from RNA-seq data. Novel fusions are identified in prostate cancer datasets.
		Research Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero, Teresa M Przytycka Genome Biology 2010, 11:R103 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An algorithm called LDsplit was developed to identify polymorphisms associated with meiotic recombination hotspots.
		Research An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation Gregory P Harhay, Timothy PL Smith, Leeson J Alexander, Christian D Haudenschild, John W Keele, Lakshmi K Matukumalli, Steven G Schroeder, Curtis P Van Tassell, Cathy R Gresham, Susan M Bridges, Shane C Burgess, Tad S Sonstegard Genome Biology 2010, 11:R102 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Digital gene expression has been used to analyse transcription in 92 bovine tissues.
		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.
		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
		Research Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level Olivier Harismendy, Vikas Bansal, Gaurav Bhatia, Masakazu Nakano, Michael Scott, Xiaoyun Wang, Colette Dib, Edouard Turlotte, Jack C Sipe, Sarah S Murray, Jean Deleuze, Vineet Bafna, Eric J Topol, Kelly A Frazer Genome Biology 2010, 11:R118 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Re-sequencing of human endocannabinoid metabolic genes from a large population reveals rare variants associated with extreme obesity.
		Research Comparative genomics reveals birth and death of fragile regions in mammalian evolution Max A Alekseyev, Pavel A Pevzner Genome Biology 2010, 11:R117 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new model explains the frequencies of breakpoints at genomic rearrangement hotspots by demonstrating that fragile sites undergo birth and death.
		Research highlight Metastasis suppression: a role of the Dice(r) Scott Valastyan, Robert A Weinberg Genome Biology 2010, 11:141 (30 November 2010) Abstract \| Full text \| PDF \| PubMed
		Comment Every dog has his day in court Gregory A Petsko Genome Biology 2010, 11:139 (30 November 2010) Full text \| PDF \| PubMed \| Editor’s summary The dog days of stem cell funding.
		Software Quake: quality-aware detection and correction of sequencing errors David R Kelley, Michael C Schatz, Steven L Salzberg Genome Biology 2010, 11:R116 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quake employs a sophisticated approach to error identification and correction in next generation sequencing data.
		Software Constructing a fish metabolic network model Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide fish metabolic model, MetaFishNet, is presented.
		Research Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew JG Simpson, Robert L Strausberg Genome Biology 2010, 11:R114 (25 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of the exome and transcriptome of a breast cancer cell line allows discovery of potentially tumorigenic loss of heterozygosity events.
		Research Genetic diversity in India and the inference of Eurasian population expansion Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, Fuli Yu Genome Biology 2010, 11:R113 (24 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SNP study demonstrates a high degree of Indian genetic diversity and suggests a significant isolation period between Out-of-Africa and Eurasian expansion.
		Method Patient-oriented gene set analysis for cancer mutation data Simina M Boca, Kenneth W Kinzler, Victor E Velculescu, Bert Vogelstein, Giovanni Parmigiani Genome Biology 2010, 11:R112 (23 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel patient-orientated gene set analysis method is presented and applied to a glioblastoma multiforme dataset
		Research Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise Nadia C Whitelaw, Suyinn Chong, Daniel K Morgan, Colm Nestor, Timothy J Bruxner, Alyson Ashe, Eleanore Lambley, Richard Meehan, Emma Whitelaw Genome Biology 2010, 11:R111 (19 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mutants for two epigenetic modifiers are found to be associated with increased intangible variation in phenotypes and in gene expression levels.
		Research Immunostaining of modified histones defines high-level features of the human metaphase epigenome Edith Terrenoire, Fiona McRonald, John A Halsall, Paula Page, Robert S Illingworth, A Malcolm R Taylor, Val Davison, Laura P O'Neill, Bryan M Turner Genome Biology 2010, 11:R110 (15 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Immunofluorescent mapping of histone modifications in single cells at metaphase demonstrates both stable and altered patterns through mitosis
		Research A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Simon R Ellwood, Zhaohui Liu, Rob A Syme, Zhibing Lai, James K Hane, Felicity Keiper, Caroline S Moffat, Richard P Oliver, Timothy L Friesen Genome Biology 2010, 11:R109 (10 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Characterization of barley filamentous fungal pathogen genome by paired-end Solexa sequencing, genome assembly and karyotyping, with insights into pathogenicity.
		Comment A Faustian bargain Gregory A Petsko Genome Biology 2010, 11:138 (31 October 2010) Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary An open letter to George M Philip, President of the State University of New York At Albany.
		Method Rapid haplotype inference for nuclear families Amy L Williams, David E Housman, Martin C Rinard, David K Gifford Genome Biology 2010, 11:R108 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hapi infers the haplotype of an individual based on sequence information from them and their parents.
		Research Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie C Dunning Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Morgens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2010, 11:R107 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Streptococcus pneumoniae genome analysis reveals that the presence of pathogenicity genes is not sufficient to determine virulence
		Meeting report Out of the sequencer and into the wiki as we face new challenges in genome informatics Zemin Ning, Stephen B Montgomery Genome Biology 2010, 11:308 (28 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint Cold Spring Harbor Laboratory/Wellcome Trust Conference 'Genome Informatics' meeting, 15-19 September 2010, Hinxton, Cambridge, UK.
		Method Differential expression analysis for sequence count data Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
		Research highlight Bet hedging in the underworld Xue-Xian Zhang, Paul B Rainey Genome Biology 2010, 11:137 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A soil bacterium hedges its bets on how long it will take to find a new plant host by producing two kinds of daughter cells.
		Research Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes Daniel F Simola, Chantal Francis, Paul D Sniegowski, Junhyong Kim Genome Biology 2010, 11:R105 (22 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Expression timing changes during the cell cycle in woodland and lab S. cerevisiae strains reveal modular timing changes in evolution.
		Method FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z Chen, Joel S Rozowsky, Ashutosh K Tewari, Naoki Kitabayashi, Benjamin J Moss, Mark S Chee, Francesca Demichelis, Mark A Rubin, Mark B Gerstein Genome Biology 2010, 11:R104 (21 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary FusionSeq is a method for identifying fusion transcripts from RNA-seq data. Novel fusions are identified in prostate cancer datasets.
		Research Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero, Teresa M Przytycka Genome Biology 2010, 11:R103 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An algorithm called LDsplit was developed to identify polymorphisms associated with meiotic recombination hotspots.
		Research An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation Gregory P Harhay, Timothy PL Smith, Leeson J Alexander, Christian D Haudenschild, John W Keele, Lakshmi K Matukumalli, Steven G Schroeder, Curtis P Van Tassell, Cathy R Gresham, Susan M Bridges, Shane C Burgess, Tad S Sonstegard Genome Biology 2010, 11:R102 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Digital gene expression has been used to analyse transcription in 92 bovine tissues.
		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.
		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.