Genome Biology | All articles

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

Supplements

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	All
		Review Translational disease interpretation with molecular networks Anaïs Baudot, Gonzalo Gómez-López, Alfonso Valencia Genome Biology 2009, 10:221 (29 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The integration of medical information into gene and protein networks could lead to a better understanding of complex diseases.
		Comment What my genome told me - and what it didn't Gregory A Petsko Genome Biology 2009, 10:108 (29 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Lessons in personal genome analysis, social networking or health information?
		Research Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea Yvan Zivanovic, Jean Armengaud, Arnaud Lagorce, Christophe Leplat, Philippe Guérin, Murielle Dutertre, Véronique Anthouard, Patrick Forterre, Patrick Wincker, Fabrice Confalonieri Genome Biology 2009, 10:R70 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Thermococcus gammatolerans, a radioresistant archaeon, is described; a proteomic analysis reveals that radioresistance may be due to unknown DNA repair enzymes.
		Meeting report Interfacing systems biology and synthetic biology Allyson Lister, Varodom Charoensawan, Subhajyoti De, Katherine James, Sarath Chandra Janga, Julian Huppert Genome Biology 2009, 10:309 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of BioSysBio 2009, the IET conference on Synthetic Biology, Systems Biology and Bioinformatics, Cambridge, UK, 23-25 March 2009.
		Research iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens Genome Biology 2009, 10:R69 (25 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new and validated genome-scale metabolic model of Bacillus subtilis 168, iBsu1103, is presented that has significantly improved completeness and accuracy.
		Research Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses Xiyin Wang, Udo Gowik, Haibao Tang, John E Bowers, Peter Westhoff, Andrew H Paterson Genome Biology 2009, 10:R68 (23 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the sorghum, maize and rice genomes shows that gene duplication and functional innovation is common to evolution of most but not all genes in the C4 photosynthetic pathway
		Research Insights into female sperm storage from the spermathecal fluid proteome of the honeybee Apis mellifera Boris Baer, Holger Eubel, Nicolas L Taylor, Nicholas O'Toole, A Harvey Millar Genome Biology 2009, 10:R67 (18 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic and metabolic network analysis of honeybee queen spermathecal fluid provides insights into female long-term sperm storage mechanisms.
		Research Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress Simon M Dittami, Delphine Scornet, Jean-Louis Petit, Béatrice Ségurens, Corinne Da Silva, Erwan Corre, Michael Dondrup, Karl-Heinz Glatting, Rainer König, Lieven Sterck, Pierre Rouzé, Yves Van de Peer, J Mark Cock, Catherine Boyen, Thierry Tonon Genome Biology 2009, 10:R66 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The brown alga Ectocarpus siliculosus, unlike terrestrial plants, undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress.
		Research A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes Diego Cortez, Patrick Forterre, Simonetta Gribaldo Genome Biology 2009, 10:R65 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale survey of potential recently acquired integrative elements in 119 archaeal and bacterial genomes reveals that many recently acquired genes have originated from integrative elements
		Method A novel and universal method for microRNA RT-qPCR data normalization Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele Genome Biology 2009, 10:R64 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The mean expression value: a new method for accurate and reliable normalization of microRNA expression data from RT-qPCR experiments.
		Protein family review The WASP and WAVE family proteins Shusaku Kurisu, Tadaomi Takenawa Genome Biology 2009, 10:226 (15 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the cytoskeleton-organizing WASP and WAVE family proteins.
		Minireview Transposons that clean up after themselves Douglas L Chalker Genome Biology 2009, 10:224 (15 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transposon in the germline genome of the ciliate Oxytricha removes itself from the differentiating somatic genome during development.
		Research The conservation and evolutionary modularity of metabolism José M Peregrín-Alvarez, Chris Sanford, John Parkinson Genome Biology 2009, 10:R63 (12 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel evolutionary analysis of metabolic networks across 26 taxa reveals a highly-conserved but flexible core of metabolic enzymes.
		Research Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana Xiaoyu Zhang, Yana V Bernatavichute, Shawn Cokus, Matteo Pellegrini, Steven E Jacobsen Genome Biology 2009, 10:R62 (9 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the genome-wide distribution patterns of histone H3 lysine4 methylation in Arabidopsis thaliana seedlings shows that it has widespread roles in regulating gene expression.
		Minireview DNA breaks as triggers for antigenic variation in African trypanosomes Sam Alsford, David Horn, Lucy Glover Genome Biology 2009, 10:223 (8 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Double-strand breaks initiate coat protein switching in African trypanosomes.
		Research Metabolic-network-driven analysis of bacterial ecological strategies Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Nir Yosef, Roded Sharan, Uri Gophna, Eytan Ruppin Genome Biology 2009, 10:R61 (5 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bacterial ecological strategies revealed by metabolic network analysis show that ecological diversity correlates with metabolic flexibility, faster growth rate and intense co-habitation.
		Minireview Sequence patches on MAPK surfaces define protein-protein interactions Gary L Johnson, Shawn M Gomez Genome Biology 2009, 10:222 (5 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Redesigning ‘surface patches’ on a mitogen-activated protein kinase can change its interactions with other proteins.
		Method Closing gaps in the human genome using sequencing by synthesis Manuel Garber, Michael C Zody, Harindra M Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2009, 10:R60 (2 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for closing non-structural gaps in the human genome assembly using 454 sequencing is presented here.
		Research Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins Michelle Simon, John M Hancock Genome Biology 2009, 10:R59 (1 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of amino acid repeats in four mammalian and one bird genome shows that many are associated preferentially with intrinsically unstructured regions.
		Comment Render unto Darwin Gregory A Petsko Genome Biology 2009, 10:106 (1 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Science and religion; never the twain shall meet.
		Software The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process Erick Antezana, Mikel Egaña, Ward Blondé, Aitzol Illarramendi, Iñaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov, Martin Kuiper Genome Biology 2009, 10:R58 (29 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A software resource for the analysis of cell cycle related molecular networks.
		Meeting report Genome duality Silvia Kocanova, Kerstin Bystricky Genome Biology 2009, 10:308 (28 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on 'Higher Order Genome Architecture', the third meeting of the Marie Curie Conferences and Training Courses (MC-GARD), Edinburgh, UK, 1-5 April 2009.
		Opinion The 1001 Genomes Project for Arabidopsis thaliana Detlef Weigel, Richard Mott Genome Biology 2009, 10:107 (27 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 1001 Genomes project for Arabidopsis thaliana could provide an enormous boost for plant research for a modest financial investment.
		Research The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress Adriana L Alejandro-Osorio, Dana J Huebert, Dominic T Porcaro, Megan E Sonntag, Songdet Nillasithanukroh, Jessica L Will, Audrey P Gasch Genome Biology 2009, 10:R57 (26 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chromatin-immunoprecipitation and computational analysis implicate Rpd3p as an important co-factor in the network of genes regulating the yeast environmental stress response.
		Review Learning to get along despite struggling to get by Elizabeth A Ostrowski, Gad Shaulsky Genome Biology 2009, 10:218 (26 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A review of evolutionary theories for cooperation, with emphasis on the mechanisms that can favor cooperation and reduce conflict within multicellular organisms, enabling the transition from unicellular to multicellular life.
		Research Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms Michael L Clawson, James E Keen, Timothy PL Smith, Lisa M Durso, Tara G McDaneld, Robert E Mandrell, Margaret A Davis, James L Bono Genome Biology 2009, 10:R56 (22 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Novel SNPs from human and bovine O157:H7 E. coli isolates are mapped, revealing that the majority of human disease is caused by a bovine subset of this strain.
		Research Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease Radu Dobrin, Jun Zhu, Cliona Molony, Carmen Argman, Mark L Parrish, Sonia Carlson, Mark F Allan, Daniel Pomp, Eric E Schadt Genome Biology 2009, 10:R55 (22 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tissue-to-tissue coexpression networks between genes in hypothalamus, liver or adipose tissue enable identification of obesity-specific genes.
		Research Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development Masaomi Kato, Alexandre de Lencastre, Zachary Pincus, Frank J Slack Genome Biology 2009, 10:R54 (21 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A deep-sequencing approach to profiling gender-specific developmental regulation of small non-coding RNA expression in C. elegans reveals dynamic temporal expression and novel miRNAs and 21U RNAs.
		Research Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants Irene Bontell, Neil Hall, Kevin E Ashelford, JP Dubey, Jon P Boyle, Johan Lindh, Judith E Smith Genome Biology 2009, 10:R53 (20 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Extensive sequence analysis of eight Toxoplasma gondii isolates from Uganda has revealed chromosome sorting and local allelic variants.
		Research Conserved features of cohesin binding along fission yeast chromosomes Christine K Schmidt, Neil Brookes, Frank Uhlmann Genome Biology 2009, 10:R52 (19 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-resolution analysis of cohesin localization on fission yeast chromosomes reveals that several determinants, previously thought to be organism-specific, come together to shape overall distribution.
		Minireview Rare protection against type 1 diabetes Robert M Plenge Genome Biology 2009, 10:219 (15 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Next-generation DNA sequencing reveals rare alleles protective from type 1 diabetes.
		Research Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens Mark W Silby, Ana M Cerdeño-Tárraga, Georgios S Vernikos, Stephen R Giddens, Robert W Jackson, Gail M Preston, Xue-Xian Zhang, Christina D Moon, Stefanie M Gehrig, Scott AC Godfrey, Christopher G Knight, Jacob G Malone, Zena Robinson, Andrew J Spiers, Simon Harris, Gregory L Challis, Alice M Yaxley, David Harris, Kathy Seeger, Lee Murphy, Simon Rutter, Rob Squares, Michael A Quail, Elizabeth Saunders, Konstantinos Mavromatis, Thomas S Brettin, Stephen D Bentley, Joanne Hothersall, Elton Stephens, Christopher M Thomas, Julian Parkhill, Stuart B Levy, Paul B Rainey, Nicholas R Thomson et al. Genome Biology 2009, 10:R51 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the genome sequences of three Pseudomonas fluorescens strains reveals a heterogeneity reminiscent of a species complex rather than a single species
		Research Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data Yvonne JK Edwards, Anna E Lobley, Melissa M Pentony, David T Jones Genome Biology 2009, 10:R50 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Signals for microRNA targeting and ubiquitination are enriched in intrinsically disordered proteins, but some highly disordered proteins can escape rapid degradation.
		Minireview Induced pluripotent stem cells free of exogenous reprogramming factors Ramzey Abujarour, Sheng Ding Genome Biology 2009, 10:220 (6 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The search continues to find ways of efficiently generating induced pluripotent stem cells free of vectors and transgenes.
		Research Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila Deborah E Stage, Thomas H Eickbush Genome Biology 2009, 10:R49 (5 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative analysis of 12 Drosophila genomes reveals insights into the evolution and mechanism of integration of R1 and R2 retrotransposons.
		Research Co-evolutionary networks of genes and cellular processes across fungal species Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2009, 10:R48 (5 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two new measures of evolution are used to study co-evolutionary networks of fungal genes and cellular processes; links between co-evolution and co-functionality are revealed.
		Research Systemic analysis of the response of Aspergillus niger to ambient pH Mikael R Andersen, Linda Lehmann, Jens Nielsen Genome Biology 2009, 10:R47 (1 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systems modeling of Aspergillus niger under different pH conditions reveals novel pH-regulated metabolic genes and signaling genes in the pal/pacC pathway.
		Software MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations Jens Keilwagen, Jan Baumbach, Thomas A Kohl, Ivo Grosse Genome Biology 2009, 10:R46 (1 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MotifAdjuster helps to detect errors in binding site annotations.
		Comment Guilt by association Gregory A Petsko Genome Biology 2009, 10:104 (29 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Given that the effectiveness of genome-wide association studies for finding disease genes is being debated, an alternative would be to look for diseases linked to inherited metabolic disorders.
		Minireview Ribosomal footprints on a transcriptome landscape David R Morris Genome Biology 2009, 10:215 (28 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next-generation sequencing technology can be used to assess rates and regulation of translation across the entire yeast transcriptome.
		Research Microbial co-habitation and lateral gene transfer: what transposases can tell us Sean D Hooper, Konstantinos Mavromatis, Nikos C Kyrpides Genome Biology 2009, 10:R45 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Interactions between microbial communities are revealed using a network of lateral gene transfer events.
		Method Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure Reuben Thomas, Julia M Gohlke, Geffrey F Stopper, Frederick M Parham, Christopher J Portier Genome Biology 2009, 10:R44 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is proposed that finds enriched pathways relevant to a studied condition, using molecular and network data.
		Research The bovine lactation genome: insights into the evolution of mammalian milk Danielle G Lemay, David J Lynn, William F Martin, Margaret C Neville, Theresa M Casey, Gonzalo Rincon, Evgenia V Kriventseva, Wesley C Barris, Angie S Hinrichs, Adrian J Molenaar, Katherine S Pollard, Nauman J Maqbool, Kuljeet Singh, Regan Murney, Evgeny M Zdobnov, Ross L Tellam, Juan F Medrano, J Bruce German, Monique Rijnkels Genome Biology 2009, 10:R43 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of milk protein and mammary genes in the bovine genome with those from other mammals gives insights into the evolution of lactation.
		Research A whole-genome assembly of the domestic cow, Bos taurus Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke, Steven L Salzberg Genome Biology 2009, 10:R42 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A cow whole-genome assembly of 2.86 billion base pairs that closes gaps and corrects previously-described inversions and deletions as well as describing a portion of the Y chromosome.
		Opinion Back to Bermuda: how is science best served? Deanna M Church, LaDeana W Hillier Genome Biology 2009, 10:105 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements.
		Minireview Malaria sporozoite proteome leaves a trail Marissa Vignali, Cate Speake, Patrick E Duffy Genome Biology 2009, 10:216 (21 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the proteomes of malaria sporozoites at different stages and mutation of selected genes reveals proteins necessary for infection of the vertebrate host.
		Minireview From transcription start site to cell biology Philipp Kapranov Genome Biology 2009, 10:217 (20 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNAs transcribed from previously unsuspected start sites add yet greater complexity to the mammalian transcriptome.
		Research Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation Atsutaka Kubosaki, Yasuhiro Tomaru, Michihira Tagami, Erik Arner, Hisashi Miura, Takahiro Suzuki, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki Genome Biology 2009, 10:R41 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Genome-wide analysis of EGR-1 binding sites reveals co-localization with CpG islands and histone H3 lysine 9 binding. SP-1 binding occupancies near EGR-1 binding sites are dramatically altered.
		Method The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair RR Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub Genome Biology 2009, 10:R40 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome-scale data collected by the FANTOM4 collaborative research project are presented as an integrated web resource.
		Software FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions Jessica Severin, Andrew M Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J Balwierz, Michiel JL de Hoon, David A Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O Daub, Alistair RR Forrest Genome Biology 2009, 10:R39 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets.

	All
		Review Translational disease interpretation with molecular networks Anaïs Baudot, Gonzalo Gómez-López, Alfonso Valencia Genome Biology 2009, 10:221 (29 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The integration of medical information into gene and protein networks could lead to a better understanding of complex diseases.
		Comment What my genome told me - and what it didn't Gregory A Petsko Genome Biology 2009, 10:108 (29 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Lessons in personal genome analysis, social networking or health information?
		Research Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea Yvan Zivanovic, Jean Armengaud, Arnaud Lagorce, Christophe Leplat, Philippe Guérin, Murielle Dutertre, Véronique Anthouard, Patrick Forterre, Patrick Wincker, Fabrice Confalonieri Genome Biology 2009, 10:R70 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Thermococcus gammatolerans, a radioresistant archaeon, is described; a proteomic analysis reveals that radioresistance may be due to unknown DNA repair enzymes.
		Meeting report Interfacing systems biology and synthetic biology Allyson Lister, Varodom Charoensawan, Subhajyoti De, Katherine James, Sarath Chandra Janga, Julian Huppert Genome Biology 2009, 10:309 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of BioSysBio 2009, the IET conference on Synthetic Biology, Systems Biology and Bioinformatics, Cambridge, UK, 23-25 March 2009.
		Research iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens Genome Biology 2009, 10:R69 (25 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new and validated genome-scale metabolic model of Bacillus subtilis 168, iBsu1103, is presented that has significantly improved completeness and accuracy.
		Research Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses Xiyin Wang, Udo Gowik, Haibao Tang, John E Bowers, Peter Westhoff, Andrew H Paterson Genome Biology 2009, 10:R68 (23 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the sorghum, maize and rice genomes shows that gene duplication and functional innovation is common to evolution of most but not all genes in the C4 photosynthetic pathway
		Research Insights into female sperm storage from the spermathecal fluid proteome of the honeybee Apis mellifera Boris Baer, Holger Eubel, Nicolas L Taylor, Nicholas O'Toole, A Harvey Millar Genome Biology 2009, 10:R67 (18 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic and metabolic network analysis of honeybee queen spermathecal fluid provides insights into female long-term sperm storage mechanisms.
		Research Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress Simon M Dittami, Delphine Scornet, Jean-Louis Petit, Béatrice Ségurens, Corinne Da Silva, Erwan Corre, Michael Dondrup, Karl-Heinz Glatting, Rainer König, Lieven Sterck, Pierre Rouzé, Yves Van de Peer, J Mark Cock, Catherine Boyen, Thierry Tonon Genome Biology 2009, 10:R66 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The brown alga Ectocarpus siliculosus, unlike terrestrial plants, undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress.
		Research A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes Diego Cortez, Patrick Forterre, Simonetta Gribaldo Genome Biology 2009, 10:R65 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale survey of potential recently acquired integrative elements in 119 archaeal and bacterial genomes reveals that many recently acquired genes have originated from integrative elements
		Method A novel and universal method for microRNA RT-qPCR data normalization Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele Genome Biology 2009, 10:R64 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The mean expression value: a new method for accurate and reliable normalization of microRNA expression data from RT-qPCR experiments.
		Protein family review The WASP and WAVE family proteins Shusaku Kurisu, Tadaomi Takenawa Genome Biology 2009, 10:226 (15 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the cytoskeleton-organizing WASP and WAVE family proteins.
		Minireview Transposons that clean up after themselves Douglas L Chalker Genome Biology 2009, 10:224 (15 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transposon in the germline genome of the ciliate Oxytricha removes itself from the differentiating somatic genome during development.
		Research The conservation and evolutionary modularity of metabolism José M Peregrín-Alvarez, Chris Sanford, John Parkinson Genome Biology 2009, 10:R63 (12 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel evolutionary analysis of metabolic networks across 26 taxa reveals a highly-conserved but flexible core of metabolic enzymes.
		Research Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana Xiaoyu Zhang, Yana V Bernatavichute, Shawn Cokus, Matteo Pellegrini, Steven E Jacobsen Genome Biology 2009, 10:R62 (9 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the genome-wide distribution patterns of histone H3 lysine4 methylation in Arabidopsis thaliana seedlings shows that it has widespread roles in regulating gene expression.
		Minireview DNA breaks as triggers for antigenic variation in African trypanosomes Sam Alsford, David Horn, Lucy Glover Genome Biology 2009, 10:223 (8 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Double-strand breaks initiate coat protein switching in African trypanosomes.
		Research Metabolic-network-driven analysis of bacterial ecological strategies Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Nir Yosef, Roded Sharan, Uri Gophna, Eytan Ruppin Genome Biology 2009, 10:R61 (5 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bacterial ecological strategies revealed by metabolic network analysis show that ecological diversity correlates with metabolic flexibility, faster growth rate and intense co-habitation.
		Minireview Sequence patches on MAPK surfaces define protein-protein interactions Gary L Johnson, Shawn M Gomez Genome Biology 2009, 10:222 (5 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Redesigning ‘surface patches’ on a mitogen-activated protein kinase can change its interactions with other proteins.
		Method Closing gaps in the human genome using sequencing by synthesis Manuel Garber, Michael C Zody, Harindra M Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2009, 10:R60 (2 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for closing non-structural gaps in the human genome assembly using 454 sequencing is presented here.
		Research Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins Michelle Simon, John M Hancock Genome Biology 2009, 10:R59 (1 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of amino acid repeats in four mammalian and one bird genome shows that many are associated preferentially with intrinsically unstructured regions.
		Comment Render unto Darwin Gregory A Petsko Genome Biology 2009, 10:106 (1 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Science and religion; never the twain shall meet.
		Software The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process Erick Antezana, Mikel Egaña, Ward Blondé, Aitzol Illarramendi, Iñaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov, Martin Kuiper Genome Biology 2009, 10:R58 (29 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A software resource for the analysis of cell cycle related molecular networks.
		Meeting report Genome duality Silvia Kocanova, Kerstin Bystricky Genome Biology 2009, 10:308 (28 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on 'Higher Order Genome Architecture', the third meeting of the Marie Curie Conferences and Training Courses (MC-GARD), Edinburgh, UK, 1-5 April 2009.
		Opinion The 1001 Genomes Project for Arabidopsis thaliana Detlef Weigel, Richard Mott Genome Biology 2009, 10:107 (27 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 1001 Genomes project for Arabidopsis thaliana could provide an enormous boost for plant research for a modest financial investment.
		Research The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress Adriana L Alejandro-Osorio, Dana J Huebert, Dominic T Porcaro, Megan E Sonntag, Songdet Nillasithanukroh, Jessica L Will, Audrey P Gasch Genome Biology 2009, 10:R57 (26 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chromatin-immunoprecipitation and computational analysis implicate Rpd3p as an important co-factor in the network of genes regulating the yeast environmental stress response.
		Review Learning to get along despite struggling to get by Elizabeth A Ostrowski, Gad Shaulsky Genome Biology 2009, 10:218 (26 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A review of evolutionary theories for cooperation, with emphasis on the mechanisms that can favor cooperation and reduce conflict within multicellular organisms, enabling the transition from unicellular to multicellular life.
		Research Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms Michael L Clawson, James E Keen, Timothy PL Smith, Lisa M Durso, Tara G McDaneld, Robert E Mandrell, Margaret A Davis, James L Bono Genome Biology 2009, 10:R56 (22 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Novel SNPs from human and bovine O157:H7 E. coli isolates are mapped, revealing that the majority of human disease is caused by a bovine subset of this strain.
		Research Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease Radu Dobrin, Jun Zhu, Cliona Molony, Carmen Argman, Mark L Parrish, Sonia Carlson, Mark F Allan, Daniel Pomp, Eric E Schadt Genome Biology 2009, 10:R55 (22 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tissue-to-tissue coexpression networks between genes in hypothalamus, liver or adipose tissue enable identification of obesity-specific genes.
		Research Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development Masaomi Kato, Alexandre de Lencastre, Zachary Pincus, Frank J Slack Genome Biology 2009, 10:R54 (21 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A deep-sequencing approach to profiling gender-specific developmental regulation of small non-coding RNA expression in C. elegans reveals dynamic temporal expression and novel miRNAs and 21U RNAs.
		Research Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants Irene Bontell, Neil Hall, Kevin E Ashelford, JP Dubey, Jon P Boyle, Johan Lindh, Judith E Smith Genome Biology 2009, 10:R53 (20 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Extensive sequence analysis of eight Toxoplasma gondii isolates from Uganda has revealed chromosome sorting and local allelic variants.
		Research Conserved features of cohesin binding along fission yeast chromosomes Christine K Schmidt, Neil Brookes, Frank Uhlmann Genome Biology 2009, 10:R52 (19 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-resolution analysis of cohesin localization on fission yeast chromosomes reveals that several determinants, previously thought to be organism-specific, come together to shape overall distribution.
		Minireview Rare protection against type 1 diabetes Robert M Plenge Genome Biology 2009, 10:219 (15 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Next-generation DNA sequencing reveals rare alleles protective from type 1 diabetes.
		Research Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens Mark W Silby, Ana M Cerdeño-Tárraga, Georgios S Vernikos, Stephen R Giddens, Robert W Jackson, Gail M Preston, Xue-Xian Zhang, Christina D Moon, Stefanie M Gehrig, Scott AC Godfrey, Christopher G Knight, Jacob G Malone, Zena Robinson, Andrew J Spiers, Simon Harris, Gregory L Challis, Alice M Yaxley, David Harris, Kathy Seeger, Lee Murphy, Simon Rutter, Rob Squares, Michael A Quail, Elizabeth Saunders, Konstantinos Mavromatis, Thomas S Brettin, Stephen D Bentley, Joanne Hothersall, Elton Stephens, Christopher M Thomas, Julian Parkhill, Stuart B Levy, Paul B Rainey, Nicholas R Thomson et al. Genome Biology 2009, 10:R51 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the genome sequences of three Pseudomonas fluorescens strains reveals a heterogeneity reminiscent of a species complex rather than a single species
		Research Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data Yvonne JK Edwards, Anna E Lobley, Melissa M Pentony, David T Jones Genome Biology 2009, 10:R50 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Signals for microRNA targeting and ubiquitination are enriched in intrinsically disordered proteins, but some highly disordered proteins can escape rapid degradation.
		Minireview Induced pluripotent stem cells free of exogenous reprogramming factors Ramzey Abujarour, Sheng Ding Genome Biology 2009, 10:220 (6 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The search continues to find ways of efficiently generating induced pluripotent stem cells free of vectors and transgenes.
		Research Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila Deborah E Stage, Thomas H Eickbush Genome Biology 2009, 10:R49 (5 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative analysis of 12 Drosophila genomes reveals insights into the evolution and mechanism of integration of R1 and R2 retrotransposons.
		Research Co-evolutionary networks of genes and cellular processes across fungal species Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2009, 10:R48 (5 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two new measures of evolution are used to study co-evolutionary networks of fungal genes and cellular processes; links between co-evolution and co-functionality are revealed.
		Research Systemic analysis of the response of Aspergillus niger to ambient pH Mikael R Andersen, Linda Lehmann, Jens Nielsen Genome Biology 2009, 10:R47 (1 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systems modeling of Aspergillus niger under different pH conditions reveals novel pH-regulated metabolic genes and signaling genes in the pal/pacC pathway.
		Software MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations Jens Keilwagen, Jan Baumbach, Thomas A Kohl, Ivo Grosse Genome Biology 2009, 10:R46 (1 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MotifAdjuster helps to detect errors in binding site annotations.
		Comment Guilt by association Gregory A Petsko Genome Biology 2009, 10:104 (29 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Given that the effectiveness of genome-wide association studies for finding disease genes is being debated, an alternative would be to look for diseases linked to inherited metabolic disorders.
		Minireview Ribosomal footprints on a transcriptome landscape David R Morris Genome Biology 2009, 10:215 (28 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next-generation sequencing technology can be used to assess rates and regulation of translation across the entire yeast transcriptome.
		Research Microbial co-habitation and lateral gene transfer: what transposases can tell us Sean D Hooper, Konstantinos Mavromatis, Nikos C Kyrpides Genome Biology 2009, 10:R45 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Interactions between microbial communities are revealed using a network of lateral gene transfer events.
		Method Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure Reuben Thomas, Julia M Gohlke, Geffrey F Stopper, Frederick M Parham, Christopher J Portier Genome Biology 2009, 10:R44 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is proposed that finds enriched pathways relevant to a studied condition, using molecular and network data.
		Research The bovine lactation genome: insights into the evolution of mammalian milk Danielle G Lemay, David J Lynn, William F Martin, Margaret C Neville, Theresa M Casey, Gonzalo Rincon, Evgenia V Kriventseva, Wesley C Barris, Angie S Hinrichs, Adrian J Molenaar, Katherine S Pollard, Nauman J Maqbool, Kuljeet Singh, Regan Murney, Evgeny M Zdobnov, Ross L Tellam, Juan F Medrano, J Bruce German, Monique Rijnkels Genome Biology 2009, 10:R43 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of milk protein and mammary genes in the bovine genome with those from other mammals gives insights into the evolution of lactation.
		Research A whole-genome assembly of the domestic cow, Bos taurus Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke, Steven L Salzberg Genome Biology 2009, 10:R42 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A cow whole-genome assembly of 2.86 billion base pairs that closes gaps and corrects previously-described inversions and deletions as well as describing a portion of the Y chromosome.
		Opinion Back to Bermuda: how is science best served? Deanna M Church, LaDeana W Hillier Genome Biology 2009, 10:105 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements.
		Minireview Malaria sporozoite proteome leaves a trail Marissa Vignali, Cate Speake, Patrick E Duffy Genome Biology 2009, 10:216 (21 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the proteomes of malaria sporozoites at different stages and mutation of selected genes reveals proteins necessary for infection of the vertebrate host.
		Minireview From transcription start site to cell biology Philipp Kapranov Genome Biology 2009, 10:217 (20 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNAs transcribed from previously unsuspected start sites add yet greater complexity to the mammalian transcriptome.
		Research Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation Atsutaka Kubosaki, Yasuhiro Tomaru, Michihira Tagami, Erik Arner, Hisashi Miura, Takahiro Suzuki, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki Genome Biology 2009, 10:R41 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Genome-wide analysis of EGR-1 binding sites reveals co-localization with CpG islands and histone H3 lysine 9 binding. SP-1 binding occupancies near EGR-1 binding sites are dramatically altered.
		Method The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair RR Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub Genome Biology 2009, 10:R40 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome-scale data collected by the FANTOM4 collaborative research project are presented as an integrated web resource.
		Software FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions Jessica Severin, Andrew M Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J Balwierz, Michiel JL de Hoon, David A Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O Daub, Alistair RR Forrest Genome Biology 2009, 10:R39 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets.