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		Method Ray Meta: scalable de novo metagenome assembly and profiling Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
		Research A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts Eric J Suh, Matthew Y Remillard, Aster Legesse-Miller, Elizabeth L Johnson, Johanna MS Lemons, Talia R Chapman, Joshua J Forman, Mina Kojima, Eric S Silberman, Hilary A Coller Genome Biology 2012, 13:R121 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study identifying microRNAs both facilitating and delaying fibroblast cell cycle re-entry from quiescence
		Method cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data Evangelos Bellos, Michael R Johnson, Lachlan J M Coin Genome Biology 2012, 13:R120 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrative, probabilistic method for CNV discovery and genotyping
		Research Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing Margarida Cardoso-Moreira, J Arguello, Andrew G Clark Genome Biology 2012, 13:R119 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of breakpoints in Drosophila melanogaster genomes reveals similarities and differences with breakpoint formation in humans
		Research Microevolutionary analysis of Clostridium difficile genomes to investigate transmission Xavier Didelot, David W Eyre, Madeleine Cule, Camilla LC Ip, M Ansari, David Griffiths, Alison Vaughan, Lily O'Connor, Tanya Golubchik, Elizabeth M Batty, Paolo Piazza, Daniel J Wilson, Rory Bowden, Peter J Donnelly, Kate E Dingle, Mark Wilcox, A Walker, Derrick W Crook, Tim E A Peto, Rosalind M Harding Genome Biology 2012, 13:R118 (21 December 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Transmission events of Clostridium difficile are inferred from whole-genome sequencing of isolates and estimating divergence time of bacterial strains
		Research Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements Xue Dong, Julia Reimer, Ulrike Göbel, Julia Engelhorn, Fei He, Heiko Schoof, Franziska Turck Genome Biology 2012, 13:R117 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
		Meeting report Personal genomes and precision medicine Gareth Highnam, David Mittelman Genome Biology 2012, 13:324 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012
		Method FOCAL: an experimental design tool for systematizing metabolic discoveries and model development Christopher J Tervo, Jennifer L Reed Genome Biology 2012, 13:R116 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype
		Research Whole-genome reconstruction and mutational signatures in gastric cancer Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Zang, Fei Yao, Pierre-Étienne Jacques, Audrey SM Teo, Ioana Cutcutache, Zhenshui Zhang, Wah Lee, Yee Sia, Song Gao, Pramila N Ariyaratne, Andrea Ho, Xing Woo, Lavanya Veeravali, Choon Ong, Niantao Deng, Kartiki V Desai, Chiea Khor, Martin L Hibberd, Atif Shahab, Jaideepraj Rao, Mengchu Wu, Ming Teh, Feng Zhu, Sze Chin, Brendan Pang, Jimmy BY So, Guillaume Bourque et al. Genome Biology 2012, 13:R115 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer.
		Research Widespread promoter-mediated coordination of transcription and mRNA degradation Mally Dori-Bachash, Ophir Shalem, Yair S Manor, Yitzhak Pilpel, Itay Tirosh Genome Biology 2012, 13:R114 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription and degradation of mRNA in yeast is commonly coordinated through promoters
		Research Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data Matthew Parker, Xiang Chen, Armita Bahrami, James Dalton, Michael Rusch, Gang Wu, John Easton, Nai-Kong Cheung, Michael Dyer, Elaine R Mardis, Richard K Wilson, Charles Mullighan, Richard Gilbertson, Suzanne J Baker, Gerard Zambetti, David W Ellison, James R Downing, Jinghui Zhang, the Pediatric Cancer Genome Project Genome Biology 2012, 13:R113 (11 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of telomere length changes in a large collection of pediatric tumors
		Method A network module-based method for identifying cancer prognostic signatures Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis
		Method MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks Edward Vitkin, Tomer Shlomi Genome Biology 2012, 13:R111 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MIRAGE is a gap-filling method for metabolic networks based on functional genomics data which is demonstrated, then applied to cyanobacterial networks
		Research highlight Dicer partners expand the repertoire of miRNA targets Lukasz Jaskiewicz, Mihaela Zavolan Genome Biology 2012, 13:179 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Lukasz Jaskiewicz and Mihaela Zavolan discusses how cofactors modify Dicer processing and, consequently, transcriptional networks
		Comment Computational thinking in the era of big data biology Michael C Schatz Genome Biology 2012, 13:177 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary by Mike Schatz
		Research Human genes with CpG island promoters have a distinct transcription-associated chromatin organization Tanya Vavouri, Ben Lehner Genome Biology 2012, 13:R110 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
		Method Computational discovery of regulatory elements in a continuous expression space Mathieu Lajoie, Olivier Gascuel, Vincent Lefort, Laurent Bréhélin Genome Biology 2012, 13:R109 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method that identifies regulatory elements by estimating motif densities around each gene, using overlapping neighborhoods in expression space
		Research Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph, Till S Voss Genome Biology 2012, 13:R108 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins
		Research Transposable elements reveal a stem cell-specific class of long noncoding RNAs David Kelley, John Rinn Genome Biology 2012, 13:R107 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A characterization of the transposable element content of human lincRNAs to resolve the evolutionary origins of lincRNAs in the human genome
		Research highlight Why rodent pseudogenes refuse to retire Manyuan Long, Li Zhang Genome Biology 2012, 13:178 (20 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Functional entities or curmudgeonly junk? The ceRNA hypothesis may explain why many rodent pseudogenes resist evolutionary erosion
		Meeting report International plant molecular biology: a bright future for green science Sibum Sung, Enamul Huq, Z Jeffrey Chen Genome Biology 2012, 13:323 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th International Congress of Plant Molecular Biology, Jeju, South Korea, October 21-26, 2012.
		Meeting report Strategies towards sequencing complex crop genomes James C Abbott, Sarah A Butcher Genome Biology 2012, 13:322 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Strategies for de novo assemblies of complex crop genomes workshop held at The Genome Analysis Centre, Norwich, UK, 8-10 October 2012.
		Research Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling Mariona Nadal-Ribelles, Núria Conde, Oscar Flores, Juan González-Vallinas, Eduardo Eyras, Modesto Orozco, Eulàlia de Nadal, Francesc Posas Genome Biology 2012, 13:R106 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hog1 bypasses gene expression regulation by targeting RNA polymerase II machinery and inducing chromatin remodeling at stress-responsive loci
		Method A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis Simon E Alfred, Anuradha Surendra, Chris Le, Ken Lin, Alexander Mok, Iain M Wallace, Michael Proctor, Malene L Urbanus, Guri Giaever, Corey Nislow Genome Biology 2012, 13:R105 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An automated small molecule screening method for Chlamydomonas reinhardtii, and its application to identify bioactive compounds for agriculture, biofuels and therapeutics
		Software InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor Alain Coletta, Colin Molter, Robin Duqué, David Steenhoff, Jonatan Taminau, Virginie de Schaetzen, Stijn Meganck, Cosmin Lazar, David Venet, Vincent Detours, Ann Nowé, Hugues Bersini, David Y Weiss Solís Genome Biology 2012, 13:R104 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A web-based data storage hub that connects genomics datasets to GUI and command line data analysis tools

	All
		Method Ray Meta: scalable de novo metagenome assembly and profiling Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
		Research A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts Eric J Suh, Matthew Y Remillard, Aster Legesse-Miller, Elizabeth L Johnson, Johanna MS Lemons, Talia R Chapman, Joshua J Forman, Mina Kojima, Eric S Silberman, Hilary A Coller Genome Biology 2012, 13:R121 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study identifying microRNAs both facilitating and delaying fibroblast cell cycle re-entry from quiescence
		Method cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data Evangelos Bellos, Michael R Johnson, Lachlan J M Coin Genome Biology 2012, 13:R120 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrative, probabilistic method for CNV discovery and genotyping
		Research Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing Margarida Cardoso-Moreira, J Arguello, Andrew G Clark Genome Biology 2012, 13:R119 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of breakpoints in Drosophila melanogaster genomes reveals similarities and differences with breakpoint formation in humans
		Research Microevolutionary analysis of Clostridium difficile genomes to investigate transmission Xavier Didelot, David W Eyre, Madeleine Cule, Camilla LC Ip, M Ansari, David Griffiths, Alison Vaughan, Lily O'Connor, Tanya Golubchik, Elizabeth M Batty, Paolo Piazza, Daniel J Wilson, Rory Bowden, Peter J Donnelly, Kate E Dingle, Mark Wilcox, A Walker, Derrick W Crook, Tim E A Peto, Rosalind M Harding Genome Biology 2012, 13:R118 (21 December 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Transmission events of Clostridium difficile are inferred from whole-genome sequencing of isolates and estimating divergence time of bacterial strains
		Research Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements Xue Dong, Julia Reimer, Ulrike Göbel, Julia Engelhorn, Fei He, Heiko Schoof, Franziska Turck Genome Biology 2012, 13:R117 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
		Meeting report Personal genomes and precision medicine Gareth Highnam, David Mittelman Genome Biology 2012, 13:324 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012
		Method FOCAL: an experimental design tool for systematizing metabolic discoveries and model development Christopher J Tervo, Jennifer L Reed Genome Biology 2012, 13:R116 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype
		Research Whole-genome reconstruction and mutational signatures in gastric cancer Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Zang, Fei Yao, Pierre-Étienne Jacques, Audrey SM Teo, Ioana Cutcutache, Zhenshui Zhang, Wah Lee, Yee Sia, Song Gao, Pramila N Ariyaratne, Andrea Ho, Xing Woo, Lavanya Veeravali, Choon Ong, Niantao Deng, Kartiki V Desai, Chiea Khor, Martin L Hibberd, Atif Shahab, Jaideepraj Rao, Mengchu Wu, Ming Teh, Feng Zhu, Sze Chin, Brendan Pang, Jimmy BY So, Guillaume Bourque et al. Genome Biology 2012, 13:R115 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer.
		Research Widespread promoter-mediated coordination of transcription and mRNA degradation Mally Dori-Bachash, Ophir Shalem, Yair S Manor, Yitzhak Pilpel, Itay Tirosh Genome Biology 2012, 13:R114 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription and degradation of mRNA in yeast is commonly coordinated through promoters
		Research Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data Matthew Parker, Xiang Chen, Armita Bahrami, James Dalton, Michael Rusch, Gang Wu, John Easton, Nai-Kong Cheung, Michael Dyer, Elaine R Mardis, Richard K Wilson, Charles Mullighan, Richard Gilbertson, Suzanne J Baker, Gerard Zambetti, David W Ellison, James R Downing, Jinghui Zhang, the Pediatric Cancer Genome Project Genome Biology 2012, 13:R113 (11 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of telomere length changes in a large collection of pediatric tumors
		Method A network module-based method for identifying cancer prognostic signatures Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis
		Method MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks Edward Vitkin, Tomer Shlomi Genome Biology 2012, 13:R111 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MIRAGE is a gap-filling method for metabolic networks based on functional genomics data which is demonstrated, then applied to cyanobacterial networks
		Research highlight Dicer partners expand the repertoire of miRNA targets Lukasz Jaskiewicz, Mihaela Zavolan Genome Biology 2012, 13:179 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Lukasz Jaskiewicz and Mihaela Zavolan discusses how cofactors modify Dicer processing and, consequently, transcriptional networks
		Comment Computational thinking in the era of big data biology Michael C Schatz Genome Biology 2012, 13:177 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary by Mike Schatz
		Research Human genes with CpG island promoters have a distinct transcription-associated chromatin organization Tanya Vavouri, Ben Lehner Genome Biology 2012, 13:R110 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
		Method Computational discovery of regulatory elements in a continuous expression space Mathieu Lajoie, Olivier Gascuel, Vincent Lefort, Laurent Bréhélin Genome Biology 2012, 13:R109 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method that identifies regulatory elements by estimating motif densities around each gene, using overlapping neighborhoods in expression space
		Research Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph, Till S Voss Genome Biology 2012, 13:R108 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins
		Research Transposable elements reveal a stem cell-specific class of long noncoding RNAs David Kelley, John Rinn Genome Biology 2012, 13:R107 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A characterization of the transposable element content of human lincRNAs to resolve the evolutionary origins of lincRNAs in the human genome
		Research highlight Why rodent pseudogenes refuse to retire Manyuan Long, Li Zhang Genome Biology 2012, 13:178 (20 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Functional entities or curmudgeonly junk? The ceRNA hypothesis may explain why many rodent pseudogenes resist evolutionary erosion
		Meeting report International plant molecular biology: a bright future for green science Sibum Sung, Enamul Huq, Z Jeffrey Chen Genome Biology 2012, 13:323 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th International Congress of Plant Molecular Biology, Jeju, South Korea, October 21-26, 2012.
		Meeting report Strategies towards sequencing complex crop genomes James C Abbott, Sarah A Butcher Genome Biology 2012, 13:322 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Strategies for de novo assemblies of complex crop genomes workshop held at The Genome Analysis Centre, Norwich, UK, 8-10 October 2012.
		Research Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling Mariona Nadal-Ribelles, Núria Conde, Oscar Flores, Juan González-Vallinas, Eduardo Eyras, Modesto Orozco, Eulàlia de Nadal, Francesc Posas Genome Biology 2012, 13:R106 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hog1 bypasses gene expression regulation by targeting RNA polymerase II machinery and inducing chromatin remodeling at stress-responsive loci
		Method A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis Simon E Alfred, Anuradha Surendra, Chris Le, Ken Lin, Alexander Mok, Iain M Wallace, Michael Proctor, Malene L Urbanus, Guri Giaever, Corey Nislow Genome Biology 2012, 13:R105 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An automated small molecule screening method for Chlamydomonas reinhardtii, and its application to identify bioactive compounds for agriculture, biofuels and therapeutics
		Software InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor Alain Coletta, Colin Molter, Robin Duqué, David Steenhoff, Jonatan Taminau, Virginie de Schaetzen, Stijn Meganck, Cosmin Lazar, David Venet, Vincent Detours, Ann Nowé, Hugues Bersini, David Y Weiss Solís Genome Biology 2012, 13:R104 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A web-based data storage hub that connects genomics datasets to GUI and command line data analysis tools