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		Research Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder, Mark Gerstein Genome Biology 2012, 13:R48 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions
		Software ggbio: an R package for extending the grammar of graphics for genomic data Tengfei Yin, Dianne Cook, Michael Lawrence Genome Biology 2012, 13:R77 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent, robust and versatile software tool for visualizing genomic data
		Method A computational framework for boosting confidence in high-throughput protein-protein interaction datasets Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, Bonnie Berger Genome Biology 2012, 13:R76 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Coev2Net is a method for assigning confidence to high-throughput protein-protein interaction predictions
		Meeting report The rise of translational bioinformatics Yves A Lussier, Haiquan Li Genome Biology 2012, 13:319 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 20th International Conference On Intelligent Systems For Molecular Biology (ISMB), held at Long Beach, California, USA, July 15-17, 2012.
		Comment A modest proposal for an outreach section in scientific publications Chris Gunter, Anne Osterrieder Genome Biology 2012, 13:168 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By Chris Gunter and Anne Osterrieder
		Meeting report Turning pipe dreams into reality Peter Li, Jeremy Goecks, Tin-Lap Lee Genome Biology 2012, 13:318 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The 2012 Galaxy meeting shows how the bioinformatic tools within Galaxy are developing and automating data analysis in the life sciences
		Opinion The tomato genome: implications for plant breeding, genomics and evolution Aashish Ranjan, Yasunori Ichihashi, Neelima R Sinha Genome Biology 2012, 13:167 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The importance of the tomato genome for plant breeding and the future of crop research
		Research Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers Alayne L Brunner, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West Genome Biology 2012, 13:R75 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs
		Research Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage Hervé Moreau, Bram Verhelst, Arnaud Couloux, Evelyne Derelle, Stephane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F Hohmann-Marriott, Gwenael Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele Genome Biology 2012, 13:R74 (24 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome sequence of the marine green alga Bathycoccus prasinos, and a phylogenomic comparison with other Mammiellales species
		Research Novel origins of copy number variation in the dog genome Jonas Berglund, Elisa M Nevalainen, Anna-Maja Molin, Michele Perloski, The LUPA Consortium, Catherine André, Michael C Zody, Ted Sharpe, Christophe Hitte, Kerstin Lindblad-Toh, Hannes Lohi, Matthew T Webster Genome Biology 2012, 13:R73 (23 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary CNVs were analyzed in dogs from 17 breeds, and were found to be associated with different features compared to other mammals
		Research Sequencing and characterization of the FVB/NJ mouse genome Kim Wong, Suzannah Bumpstead, Louise Van Der Weyden, Laura G Reinholdt, Laurens G Wilming, David J Adams, Thomas M Keane Genome Biology 2012, 13:R72 (23 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the FVB/NJ mouse is sequenced, revealing variants specific to this strain
		Research A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers Nathan P Palmer, Patrick R Schmid, Bonnie Berger, Isaac S Kohane Genome Biology 2012, 13:R71 (21 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues
		Research The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite Andrea H Horakova, J Mauro Calabrese, Christine R McLaughlin, Deanna C Tremblay, Terry Magnuson, Brian P Chadwick Genome Biology 2012, 13:R70 (20 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A characterization of the X-linked homogenous tandem repeat DXZ4 in mouse, and a subsequent analysis of conservation across mammals
		Research Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian Genome Biology 2012, 13:R69 (17 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-wide mapping of 5-formylcytosine in ES cells reveals an enrichment in promoter and exon CpG islands, and an association with transcription
		Research Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins Gary LeRoy, Iouri Chepelev, Peter A DiMaggio, Mario A Blanco, Barry M Zee, Keji Zhao, Benjamin A Garcia Genome Biology 2012, 13:R68 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A novel proteogenomic strategy links the histone reader proteins Brd3 and Brd4 to HOX gene regulation
		Research highlight Genomes of extremophile crucifers: new platforms for comparative genomics and beyond Simon M Dittami, Thierry Tonon Genome Biology 2012, 13:166 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research Highlight: the genome sequences of extremophile crucifers provide valuable insights into the underlying mechanisms of stress tolerance in plants
		Open letter An encyclopedia of mouse DNA elements (Mouse ENCODE) Mouse ENCODE Consortium, John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al. Genome Biology 2012, 13:418 (13 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome
		Method Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule Genome Biology 2012, 13:R67 (3 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The CLIP and iCLIP methods are compared for their utility in determining RNA binding protein binding sites
		Review Autism genetics: searching for specificity and convergence Jamee M Berg, Daniel H Geschwind Genome Biology 2012, 13:247 (31 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Daniel Geschwind and Jamee Berg review the genes associated with autism spectrum disorders: how might their functions relate to one another?
		Research highlight The aging epigenome: DNA methylation from the cradle to the grave Marc Winnefeld, Frank Lyko Genome Biology 2012, 13:165 (30 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Frank Lyko and Marc Winnefeld highlight a new survey of age-related epigenetic changes in newborn and centenarian methylomes
		Research Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation Markus Lommer, Michael Specht, Alexandra-Sophie Roy, Lars Kraemer, Reidar Andreson, Magdalena A Gutowska, Juliane Wolf, Sonja V Bergner, Markus B Schilhabel, Ulrich C Klostermeier, Robert G Beiko, Philip Rosenstiel, Michael Hippler, Julie LaRoche Genome Biology 2012, 13:R66 (26 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptomic and proteomic insights into the low-iron tolerance of Thalassoiosira oceanic, an oceanic diatom
		Research Developmental features of DNA methylation during activation of the embryonic zebrafish genome Ingrid S Andersen, Andrew H Reiner, Håvard Aanes, Peter Aleström, Philippe Collas Genome Biology 2012, 13:R65 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA methylation patterning at developmental genes is assayed before, during and after zygotic genome activation
		Research Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates Sean Conlan, Lilia A Mijares, NISC Comparative Sequencing Program, Jesse Becker, Robert W Blakesley, Gerard G Bouffard, Shelise Brooks, Holly Coleman, Jyoti Gupta, Natalie Gurson, Morgan Park, Brian Schmidt, Pamela J Thomas, Michael Otto, Heidi H Kong, Patrick R Murray, Julia A Segre Genome Biology 2012, 13:R64 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparative genomics of skin commensal and hospital infection-associated isolates uncovers a putative clinical biomarker
		Research highlight piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense Allison C Billi, Mallory A Freeberg, John K Kim Genome Biology 2012, 13:164 (20 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Kim and colleagues discuss transgenerational genome surveillance and the recognition of non-self by the worm piRNA system
		Research RNA processing in the minimal organism Nanoarchaeum equitans Lennart Randau Genome Biology 2012, 13:R63 (18 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq in the minimal archaeon Nanoarchaeum equitans reveals details of unusual RNA processing such as trans splicing of tRNA molecules
		Software CIDeR: multifactorial interaction networks in human diseases Martin Lechner, Veit Höhn, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Gabi Kastenmüller, Brigitte Waegele, Andreas Ruepp Genome Biology 2012, 13:R62 (18 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A database of interactions in neurological and metabolic disorders, with a wide range of search options and graphical outputs
		Meeting report Eastern genomics promises Scott C Edmunds Genome Biology 2012, 13:317 (17 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Bio-IT World Asia meeting, Marina Bay Sands, Singapore, 6-8 June 2012.
		Research highlight The greatest catch: big game fishing for mRNA-bound proteins Christopher R Sibley, Jan Attig, Jernej Ule Genome Biology 2012, 13:163 (17 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Jernej Ule and colleagues highlight two recent studies that have identified many novel RNA-binding proteins
		Method Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman Genome Biology 2012, 13:R61 (11 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A model-based SNP caller for bisulfite sequencing data improves methylation estimates and imprinting analysis
		Method A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples Serena Dollive, Gregory L Peterfreund, Scott Sherrill-Mix, Kyle Bittinger, Rohini Sinha, Christian Hoffmann, Christopher S Nabel, David A Hill, David Artis, Michael A Bachman, Rebecca Custers-Allen, Stephanie Grunberg, Gary D Wu, James D Lewis, Frederic D Bushman Genome Biology 2012, 13:R60 (3 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BROCC, a pipeline for the analysis of eukaryotes of microbiomes using conserved ribosomal rDNA sequences as markers
		Research E2F mediates enhanced alternative polyadenylation in proliferation Ran Elkon, Jarno Drost, Gijs van Haaften, Mathias Jenal, Mariette Schrier, Joachim AF Oude Vrielink, Reuven Agami Genome Biology 2012, 13:R59 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptome sequencing of two cell lines reveals shortened 3' UTRs and use of alternative polyadenylation sites associated with cell proliferation
		Research Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Tohru Masui, Yasuhiro Yasutomi, Naoki Osada Genome Biology 2012, 13:R58 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Malaysian cynomolgus macaque genome sheds light on structural variation between primate species
		Research Conserved rules govern genetic interaction degree across species Elizabeth N Koch, Michael Costanzo, Jeremy Bellay, Raamesh Deshpande, Kate Chatfield-Reed, Gordon Chua, Gennaro D'Urso, Brenda J Andrews, Charles Boone, Chad L Myers Genome Biology 2012, 13:R57 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic interaction degree is conserved between fission and budding yeast, but functional rewiring is also apparent
		Review The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities Jane WY Ng, Laura M Barrett, Andrew Wong, Diana Kuh, George Smith, Caroline L Relton Genome Biology 2012, 13:246 (29 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Longitudinal cohort studies provide an opportunity to study how changes in epigenetic patterns occur in response to diverse factors
		Comment Out of Africa Gregory A Petsko Genome Biology 2012, 13:162 (29 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko suggests five disreputable ways of making a fortune in science.
		Opinion Gene patents in the US - focusing on what really matters Allison W Dobson, James P Evans Genome Biology 2012, 13:161 (29 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary With new technologies, concerns about gene patent claims regarding isolated DNA are becoming less relevant
		Meeting report Dispatches from the functional phase of genome biology Luke Jostins Genome Biology 2012, 13:316 (27 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 25th annual meeting on The Biology of Genomes, Cold Spring Harbor, USA, 8-12 May 2012
		Research highlight Deciphering membrane protein structures from protein sequences Tilman Flock, AJ Venkatakrishnan, KR Vinothkumar, M Madan Babu Genome Biology 2012, 13:160 (27 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Madan Babu and colleagues discuss how co-evolving residue pairs can be exploited to predict membrane protein topology
		Software Toward almost closed genomes with GapFiller Marten Boetzer, Walter Pirovano Genome Biology 2012, 13:R56 (25 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary GapFiller is a method for automatically filling gaps in short read genome assemblies using the existing sequencing data
		Method m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence Jüri Reimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman, Nicholas M Luscombe Genome Biology 2012, 13:R55 (21 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A computational method that identifies process-specific regulators from high-throughput data. Its utility is shown in an analysis that identifies cell cycle regulators
		Research Regulation of alternative splicing by the circadian clock and food related cues Nicholas J McGlincy, Amandine Valomon, Johanna E Chesham, Elizabeth S Maywood, Michael H Hastings, Jernej Ule Genome Biology 2012, 13:R54 (21 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An extensive analysis of how the circadian clock and the physiological cue of feeding regulates alternative splicing in mice
		Research highlight Transposable elements: not as quiet as a mouse Rita Rebollo, Ying Zhang, Dixie L Mager Genome Biology 2012, 13:159 (20 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Identification of over 100,000 transposon element variants in 18 mouse genomes reveals the role of negative selection in their evolution
		Research Apple miRNAs and tasiRNAs with novel regulatory networks Rui Xia, Hong Zhu, Yong-qiang An, Eric P Beers, Zongrang Liu Genome Biology 2012, 13:R47 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive analysis of short regulatory RNAs including, miRNAs, siRNAs and tasiRNAs in the apple tree Malus domestica Golden Delicious
		Research Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms Fredrik Barrenäs, Sreenivas Chavali, Alexessander Alves, Lachlan Coin, Marjo-Riitta Jarvelin, Rebecka Jörnsten, Michael A Langston, Adaikalavan Ramasamy, Gary Rogers, Hui Wang, Mikael Benson Genome Biology 2012, 13:R46 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene network analysis can predict novel disease-associated genes and finds significant overlap between phenotypically disparate complex diseases
		Research The genomic landscape shaped by selection on transposable elements across 18 mouse strains Christoffer Nellåker, Thomas M Keane, Binnaz Yalcin, Kim Wong, Avigail Agam, T Grant Belgard, Jonathan Flint, David J Adams, Wayne N Frankel, Chris P Ponting Genome Biology 2012, 13:R45 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive catalog of transposable elements across 18 mouse strains, and a subsequent analysis of selection acting on these transposable elements
		Method SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack Genome Biology 2012, 13:R44 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for normalizing the Illumina 450k methylation array data, allowing analysis of the genome-wide methylation status of the human genome
		Research Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood Matthew N Davies, Manuela Volta, Ruth Pidsley, Katie Lunnon, Abhishek Dixit, Simon Lovestone, Cristian Coarfa, R Alan Harris, Aleksandar Milosavljevic, Claire Troakes, Safa Al-Sarraj, Richard Dobson, Leonard C Schalkwyk, Jonathan Mill Genome Biology 2012, 13:R43 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differentially methylated regions are annotated using matched blood and brain samples from multiple individuals
		Research Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples Nicola Segata, Susan Haake, Peter Mannon, Katherine P Lemon, Levi Waldron, Dirk Gevers, Curtis Huttenhower, Jacques Izard Genome Biology 2012, 13:R42 (14 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Human Microbiome Project's analysis of ten sites in the digestive tract of healthy human adults
		Research The multiplicity of divergence mechanisms in a single evolving population Ram P Maharjan, Thomas Ferenci, Peter R Reeves, Yang Li, Bin Liu, Lei Wang Genome Biology 2012, 13:R41 (8 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Whole genome sequencing of 8 laboratory populations of E. coli casts light on the mechanisms by which populations evolve
		Opinion Power to the people: a wiki-governance model for biobanks Edward S Dove, Yann Joly, Bartha M Knoppers Genome Biology 2012, 13:158 (29 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Edward Dove and colleagues propose a wiki-governance model for biobanks that gives citizens the ability to collaborate in biobank governance and policymaking.

	All
		Research Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder, Mark Gerstein Genome Biology 2012, 13:R48 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions
		Software ggbio: an R package for extending the grammar of graphics for genomic data Tengfei Yin, Dianne Cook, Michael Lawrence Genome Biology 2012, 13:R77 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent, robust and versatile software tool for visualizing genomic data
		Method A computational framework for boosting confidence in high-throughput protein-protein interaction datasets Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, Bonnie Berger Genome Biology 2012, 13:R76 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Coev2Net is a method for assigning confidence to high-throughput protein-protein interaction predictions
		Meeting report The rise of translational bioinformatics Yves A Lussier, Haiquan Li Genome Biology 2012, 13:319 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 20th International Conference On Intelligent Systems For Molecular Biology (ISMB), held at Long Beach, California, USA, July 15-17, 2012.
		Comment A modest proposal for an outreach section in scientific publications Chris Gunter, Anne Osterrieder Genome Biology 2012, 13:168 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By Chris Gunter and Anne Osterrieder
		Meeting report Turning pipe dreams into reality Peter Li, Jeremy Goecks, Tin-Lap Lee Genome Biology 2012, 13:318 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The 2012 Galaxy meeting shows how the bioinformatic tools within Galaxy are developing and automating data analysis in the life sciences
		Opinion The tomato genome: implications for plant breeding, genomics and evolution Aashish Ranjan, Yasunori Ichihashi, Neelima R Sinha Genome Biology 2012, 13:167 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The importance of the tomato genome for plant breeding and the future of crop research
		Research Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers Alayne L Brunner, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West Genome Biology 2012, 13:R75 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs
		Research Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage Hervé Moreau, Bram Verhelst, Arnaud Couloux, Evelyne Derelle, Stephane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F Hohmann-Marriott, Gwenael Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele Genome Biology 2012, 13:R74 (24 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome sequence of the marine green alga Bathycoccus prasinos, and a phylogenomic comparison with other Mammiellales species
		Research Novel origins of copy number variation in the dog genome Jonas Berglund, Elisa M Nevalainen, Anna-Maja Molin, Michele Perloski, The LUPA Consortium, Catherine André, Michael C Zody, Ted Sharpe, Christophe Hitte, Kerstin Lindblad-Toh, Hannes Lohi, Matthew T Webster Genome Biology 2012, 13:R73 (23 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary CNVs were analyzed in dogs from 17 breeds, and were found to be associated with different features compared to other mammals
		Research Sequencing and characterization of the FVB/NJ mouse genome Kim Wong, Suzannah Bumpstead, Louise Van Der Weyden, Laura G Reinholdt, Laurens G Wilming, David J Adams, Thomas M Keane Genome Biology 2012, 13:R72 (23 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the FVB/NJ mouse is sequenced, revealing variants specific to this strain
		Research A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers Nathan P Palmer, Patrick R Schmid, Bonnie Berger, Isaac S Kohane Genome Biology 2012, 13:R71 (21 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues
		Research The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite Andrea H Horakova, J Mauro Calabrese, Christine R McLaughlin, Deanna C Tremblay, Terry Magnuson, Brian P Chadwick Genome Biology 2012, 13:R70 (20 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A characterization of the X-linked homogenous tandem repeat DXZ4 in mouse, and a subsequent analysis of conservation across mammals
		Research Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian Genome Biology 2012, 13:R69 (17 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-wide mapping of 5-formylcytosine in ES cells reveals an enrichment in promoter and exon CpG islands, and an association with transcription
		Research Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins Gary LeRoy, Iouri Chepelev, Peter A DiMaggio, Mario A Blanco, Barry M Zee, Keji Zhao, Benjamin A Garcia Genome Biology 2012, 13:R68 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A novel proteogenomic strategy links the histone reader proteins Brd3 and Brd4 to HOX gene regulation
		Research highlight Genomes of extremophile crucifers: new platforms for comparative genomics and beyond Simon M Dittami, Thierry Tonon Genome Biology 2012, 13:166 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research Highlight: the genome sequences of extremophile crucifers provide valuable insights into the underlying mechanisms of stress tolerance in plants
		Open letter An encyclopedia of mouse DNA elements (Mouse ENCODE) Mouse ENCODE Consortium, John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al. Genome Biology 2012, 13:418 (13 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome
		Method Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule Genome Biology 2012, 13:R67 (3 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The CLIP and iCLIP methods are compared for their utility in determining RNA binding protein binding sites
		Review Autism genetics: searching for specificity and convergence Jamee M Berg, Daniel H Geschwind Genome Biology 2012, 13:247 (31 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Daniel Geschwind and Jamee Berg review the genes associated with autism spectrum disorders: how might their functions relate to one another?
		Research highlight The aging epigenome: DNA methylation from the cradle to the grave Marc Winnefeld, Frank Lyko Genome Biology 2012, 13:165 (30 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Frank Lyko and Marc Winnefeld highlight a new survey of age-related epigenetic changes in newborn and centenarian methylomes
		Research Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation Markus Lommer, Michael Specht, Alexandra-Sophie Roy, Lars Kraemer, Reidar Andreson, Magdalena A Gutowska, Juliane Wolf, Sonja V Bergner, Markus B Schilhabel, Ulrich C Klostermeier, Robert G Beiko, Philip Rosenstiel, Michael Hippler, Julie LaRoche Genome Biology 2012, 13:R66 (26 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptomic and proteomic insights into the low-iron tolerance of Thalassoiosira oceanic, an oceanic diatom
		Research Developmental features of DNA methylation during activation of the embryonic zebrafish genome Ingrid S Andersen, Andrew H Reiner, Håvard Aanes, Peter Aleström, Philippe Collas Genome Biology 2012, 13:R65 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA methylation patterning at developmental genes is assayed before, during and after zygotic genome activation
		Research Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates Sean Conlan, Lilia A Mijares, NISC Comparative Sequencing Program, Jesse Becker, Robert W Blakesley, Gerard G Bouffard, Shelise Brooks, Holly Coleman, Jyoti Gupta, Natalie Gurson, Morgan Park, Brian Schmidt, Pamela J Thomas, Michael Otto, Heidi H Kong, Patrick R Murray, Julia A Segre Genome Biology 2012, 13:R64 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparative genomics of skin commensal and hospital infection-associated isolates uncovers a putative clinical biomarker
		Research highlight piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense Allison C Billi, Mallory A Freeberg, John K Kim Genome Biology 2012, 13:164 (20 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Kim and colleagues discuss transgenerational genome surveillance and the recognition of non-self by the worm piRNA system
		Research RNA processing in the minimal organism Nanoarchaeum equitans Lennart Randau Genome Biology 2012, 13:R63 (18 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq in the minimal archaeon Nanoarchaeum equitans reveals details of unusual RNA processing such as trans splicing of tRNA molecules
		Software CIDeR: multifactorial interaction networks in human diseases Martin Lechner, Veit Höhn, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Gabi Kastenmüller, Brigitte Waegele, Andreas Ruepp Genome Biology 2012, 13:R62 (18 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A database of interactions in neurological and metabolic disorders, with a wide range of search options and graphical outputs
		Meeting report Eastern genomics promises Scott C Edmunds Genome Biology 2012, 13:317 (17 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Bio-IT World Asia meeting, Marina Bay Sands, Singapore, 6-8 June 2012.
		Research highlight The greatest catch: big game fishing for mRNA-bound proteins Christopher R Sibley, Jan Attig, Jernej Ule Genome Biology 2012, 13:163 (17 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Jernej Ule and colleagues highlight two recent studies that have identified many novel RNA-binding proteins
		Method Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman Genome Biology 2012, 13:R61 (11 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A model-based SNP caller for bisulfite sequencing data improves methylation estimates and imprinting analysis
		Method A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples Serena Dollive, Gregory L Peterfreund, Scott Sherrill-Mix, Kyle Bittinger, Rohini Sinha, Christian Hoffmann, Christopher S Nabel, David A Hill, David Artis, Michael A Bachman, Rebecca Custers-Allen, Stephanie Grunberg, Gary D Wu, James D Lewis, Frederic D Bushman Genome Biology 2012, 13:R60 (3 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BROCC, a pipeline for the analysis of eukaryotes of microbiomes using conserved ribosomal rDNA sequences as markers
		Research E2F mediates enhanced alternative polyadenylation in proliferation Ran Elkon, Jarno Drost, Gijs van Haaften, Mathias Jenal, Mariette Schrier, Joachim AF Oude Vrielink, Reuven Agami Genome Biology 2012, 13:R59 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptome sequencing of two cell lines reveals shortened 3' UTRs and use of alternative polyadenylation sites associated with cell proliferation
		Research Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Tohru Masui, Yasuhiro Yasutomi, Naoki Osada Genome Biology 2012, 13:R58 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Malaysian cynomolgus macaque genome sheds light on structural variation between primate species
		Research Conserved rules govern genetic interaction degree across species Elizabeth N Koch, Michael Costanzo, Jeremy Bellay, Raamesh Deshpande, Kate Chatfield-Reed, Gordon Chua, Gennaro D'Urso, Brenda J Andrews, Charles Boone, Chad L Myers Genome Biology 2012, 13:R57 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic interaction degree is conserved between fission and budding yeast, but functional rewiring is also apparent
		Review The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities Jane WY Ng, Laura M Barrett, Andrew Wong, Diana Kuh, George Smith, Caroline L Relton Genome Biology 2012, 13:246 (29 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Longitudinal cohort studies provide an opportunity to study how changes in epigenetic patterns occur in response to diverse factors
		Comment Out of Africa Gregory A Petsko Genome Biology 2012, 13:162 (29 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko suggests five disreputable ways of making a fortune in science.
		Opinion Gene patents in the US - focusing on what really matters Allison W Dobson, James P Evans Genome Biology 2012, 13:161 (29 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary With new technologies, concerns about gene patent claims regarding isolated DNA are becoming less relevant
		Meeting report Dispatches from the functional phase of genome biology Luke Jostins Genome Biology 2012, 13:316 (27 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 25th annual meeting on The Biology of Genomes, Cold Spring Harbor, USA, 8-12 May 2012
		Research highlight Deciphering membrane protein structures from protein sequences Tilman Flock, AJ Venkatakrishnan, KR Vinothkumar, M Madan Babu Genome Biology 2012, 13:160 (27 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Madan Babu and colleagues discuss how co-evolving residue pairs can be exploited to predict membrane protein topology
		Software Toward almost closed genomes with GapFiller Marten Boetzer, Walter Pirovano Genome Biology 2012, 13:R56 (25 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary GapFiller is a method for automatically filling gaps in short read genome assemblies using the existing sequencing data
		Method m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence Jüri Reimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman, Nicholas M Luscombe Genome Biology 2012, 13:R55 (21 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A computational method that identifies process-specific regulators from high-throughput data. Its utility is shown in an analysis that identifies cell cycle regulators
		Research Regulation of alternative splicing by the circadian clock and food related cues Nicholas J McGlincy, Amandine Valomon, Johanna E Chesham, Elizabeth S Maywood, Michael H Hastings, Jernej Ule Genome Biology 2012, 13:R54 (21 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An extensive analysis of how the circadian clock and the physiological cue of feeding regulates alternative splicing in mice
		Research highlight Transposable elements: not as quiet as a mouse Rita Rebollo, Ying Zhang, Dixie L Mager Genome Biology 2012, 13:159 (20 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Identification of over 100,000 transposon element variants in 18 mouse genomes reveals the role of negative selection in their evolution
		Research Apple miRNAs and tasiRNAs with novel regulatory networks Rui Xia, Hong Zhu, Yong-qiang An, Eric P Beers, Zongrang Liu Genome Biology 2012, 13:R47 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive analysis of short regulatory RNAs including, miRNAs, siRNAs and tasiRNAs in the apple tree Malus domestica Golden Delicious
		Research Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms Fredrik Barrenäs, Sreenivas Chavali, Alexessander Alves, Lachlan Coin, Marjo-Riitta Jarvelin, Rebecka Jörnsten, Michael A Langston, Adaikalavan Ramasamy, Gary Rogers, Hui Wang, Mikael Benson Genome Biology 2012, 13:R46 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene network analysis can predict novel disease-associated genes and finds significant overlap between phenotypically disparate complex diseases
		Research The genomic landscape shaped by selection on transposable elements across 18 mouse strains Christoffer Nellåker, Thomas M Keane, Binnaz Yalcin, Kim Wong, Avigail Agam, T Grant Belgard, Jonathan Flint, David J Adams, Wayne N Frankel, Chris P Ponting Genome Biology 2012, 13:R45 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive catalog of transposable elements across 18 mouse strains, and a subsequent analysis of selection acting on these transposable elements
		Method SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack Genome Biology 2012, 13:R44 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for normalizing the Illumina 450k methylation array data, allowing analysis of the genome-wide methylation status of the human genome
		Research Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood Matthew N Davies, Manuela Volta, Ruth Pidsley, Katie Lunnon, Abhishek Dixit, Simon Lovestone, Cristian Coarfa, R Alan Harris, Aleksandar Milosavljevic, Claire Troakes, Safa Al-Sarraj, Richard Dobson, Leonard C Schalkwyk, Jonathan Mill Genome Biology 2012, 13:R43 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differentially methylated regions are annotated using matched blood and brain samples from multiple individuals
		Research Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples Nicola Segata, Susan Haake, Peter Mannon, Katherine P Lemon, Levi Waldron, Dirk Gevers, Curtis Huttenhower, Jacques Izard Genome Biology 2012, 13:R42 (14 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Human Microbiome Project's analysis of ten sites in the digestive tract of healthy human adults
		Research The multiplicity of divergence mechanisms in a single evolving population Ram P Maharjan, Thomas Ferenci, Peter R Reeves, Yang Li, Bin Liu, Lei Wang Genome Biology 2012, 13:R41 (8 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Whole genome sequencing of 8 laboratory populations of E. coli casts light on the mechanisms by which populations evolve
		Opinion Power to the people: a wiki-governance model for biobanks Edward S Dove, Yann Joly, Bartha M Knoppers Genome Biology 2012, 13:158 (29 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Edward Dove and colleagues propose a wiki-governance model for biobanks that gives citizens the ability to collaborate in biobank governance and policymaking.