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		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
		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.