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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
		Review High-throughput sequencing to decipher the genetic heterogeneity of deafness Zippora Brownstein, Yoni Bhonker, Karen B Avraham Genome Biology 2012, 13:245 (29 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary High-throughput sequencing approaches have accelerated the discovery of genes related to hearing loss, and may reshape clinical diagnosis of deafness
		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.
		Method A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level Stephan Binder, Georg Schendzielorz, Norma Stäbler, Karin Krumbach, Kristina Hoffmann, Michael Bott, Lothar Eggeling Genome Biology 2012, 13:R40 (28 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel high-throughput method that uses in vivo metabolite sensors to identify bacterial metabolite producers
		Research The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Thomas Pröschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Alexandre Lomsadze, Mark Borodovsky, Jean-Michel Claverie, Igor V Grigoriev, James L Van Etten Genome Biology 2012, 13:R39 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome of a polar eukaryotic microorganism, an alga called Coccomyxa subellipsoidea C-169, reveals universal strategies for cold adaptation
		Research Genomic diversity of the human intestinal parasite Entamoeba histolytica Gareth D Weedall, C Graham Clark, Pia Koldkjaer, Suzanne Kay, Iris Bruchhaus, Egbert Tannich, Steve Paterson, Neil Hall Genome Biology 2012, 13:R38 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Ten strains of Entamoeba histolytica are sequenced. Low levels of genetic diversity are found, and evidence for sexual reproduction is uncovered
		Research Comparative multi-omics systems analysis of Escherichia coli strains B and K-12 Sung Yoon, Mee-Jung Han, Haeyoung Jeong, Choong Lee, Xiao-Xia Xia, Dae-Hee Lee, Ji Shim, Sang Lee, Tae Oh, Jihyun F Kim Genome Biology 2012, 13:R37 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of multi-omics data and the generation of a genome-scale metabolic network to determine the phenotypic characteristics of E. coli
		Meeting report A Keystone for ncRNA Ezgi Hacisuleyman, Moran N Cabili, John L Rinn Genome Biology 2012, 13:315 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Rinn and colleagues give a report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012.
		Research A systematic screen reveals new elements acting at the G2/M cell cycle control Francisco J Navarro, Paul Nurse Genome Biology 2012, 13:R36 (24 May 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A screen for regulators of the G2/M transition in fission yeast reveals novel regulators of cell cycle control
		Research Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns Joachim Weischenfeldt, Johannes Waage, Geng Tian, Jing Zhao, Inge Damgaard, Janus Jakobsen, Karsten Kristiansen, Anders Krogh, Jun Wang, Bo T Porse Genome Biology 2012, 13:R35 (24 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An extensive in vivo analysis of how nonsense mediated mRNA decay regulates alternative splicing in two mouse tissues
		Method A new approach for detecting low-level mutations in next-generation sequence data Mingkun Li, Mark Stoneking Genome Biology 2012, 13:R34 (23 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method is presented for differentiating mutations present at low level in a sample from sequencing errors
		Research highlight Enhancer dysfunction: how the main regulators of gene expression contribute to cancer Siavash K Kurdistani Genome Biology 2012, 13:156 (23 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight on the role of variant epigenetics in establishing an enhancer element-mediated oncogenic transcriptional program
		Research highlight Layer cake: the first bite at gene expression diversity in the human brain Philipp Khaitovich Genome Biology 2012, 13:157 (22 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Philipp Khaitovich highlights research by Allan Jones and colleagues that assesses regional gene expression in the human brain neocortex
		Comment Goodbye, Columbus Gregory A Petsko Genome Biology 2012, 13:155 (18 May 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Guaranteeing experimental outcomes and findings: funding then and now
		Correction A quantitative literature-curated gold standard for kinase-substrate pairs Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Youn, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews Genome Biology 2012, 13:417 (10 May 2012) Abstract \| Full text \| PDF \| PubMed
		Research A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response Scott Schwartz, Iddo Friedberg, Ivan V Ivanov, Laurie A Davidson, Jennifer S Goldsby, David B Dahl, Damir Herman, Mei Wang, Sharon M Donovan, Robert S Chapkin Genome Biology 2012, 13:r32 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota
		Review Genetic architecture of body size in mammals Kathryn E Kemper, Peter M Visscher, Michael E Goddard Genome Biology 2012, 13:244 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Peter Visscher and colleagues survey the current known mutations affecting body size in humans, mice, dogs and livestock species
		Comment Economies of scale Gregory A Petsko Genome Biology 2012, 13:154 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The current glut of postdoctoral and graduate scientists can be addressed by applying economic principles.
		Research highlight We are what we eat: how the diet of infants affects their gut microbiome Mihai Pop Genome Biology 2012, 13:152 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We are what we eat: Mihai Pop highlights our Research article investigating the impact of diet on an infant's gut
		Research Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel Marieke Simonis, Santosh S Atanur, Sam Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Game, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven JM Jones, Michal Pravenec, Tim J Aitman, Edwin Cuppen Genome Biology 2012, 13:r31 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome and transcriptome sequences of the founder strains of the HXB/BXH panel of recombinant inbred rat strains
		Review Current challenges in de novo plant genome sequencing and assembly Michael C Schatz, Jan Witkowski, W Richard McCombie Genome Biology 2012, 13:243 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
		Research highlight The Arabidopsis clock: time for an about-face? David E Somers Genome Biology 2012, 13:153 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Somers highlights three recent papers that arrive at a surprising conclusion about how TOC1 functions in the plant circadian clock
		Research Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium Simen M Kristoffersen, Chad Haase, M Ryan Weil, Karla D Passalacqua, Faheem Niazi, Stephen K Hutchison, Brian Desany, Anne-Brit Kolstø, Nicolas J Tourasse, Timothy D Read, Ole Økstad Genome Biology 2012, 13:R30 (26 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA-seq is used to determine mRNA decay rates to single nucleotide resolution in the Gram positive bacterium Bacillus cereus
		Software RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations Mauro AA Castro, Xin Wang, Michael NC Fletcher, Kerstin B Meyer, Florian Markowetz Genome Biology 2012, 13:R29 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for visualizing complex, large-scale networks that combines R/Bioconductor with Java, and allows the incorporation of plug-ins
		Research Mediation of Drosophila autosomal dosage effects and compensation by network interactions John H Malone, Dong-Yeon Cho, Nicolas R Mattiuzzo, Carlo G Artieri, Lichun Jiang, Ryan K Dale, Harold E Smith, Jennifer McDaniel, Sarah Munro, Marc Salit, Justen Andrews, Teresa M Przytycka, Brian Oliver Genome Biology 2012, 13:R28 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive RNA-seq analysis of autosomal dosage effects and compensation in 21 autosomal deficiency Drosophila lines
		Research Genome-wide identification and characterization of replication origins by deep sequencing Jia Xu, Yoshimi Yanagisawa, Alexander M Tsankov, Christopher Hart, Keita Aoki, Naveen Kommajosyula, Kathleen E Steinmann, James Bochicchio, Carsten Russ, Aviv Regev, Oliver J Rando, Chad Nusbaum, Hironori Niki, Patrice Milos, Zhiping Weng, Nicholas Rhind Genome Biology 2012, 13:R27 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Single-molecule deep sequencing and comparative genomics in three Schizosaccharomyces species sheds light on the nature of replication origins
		Research High levels of RNA-editing site conservation amongst 15 laboratory mouse strains Petr Danecek, Christoffer Nellåker, Rebecca E McIntyre, Jorge E Buendia-Buendia, Suzannah Bumpstead, Chris P Ponting, Jonathan Flint, Richard Durbin, Thomas M Keane, David J Adams Genome Biology 2012, 13:r26 (23 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extensive, genome-wide analysis of RNA editing in the brain transcriptomes of 15 mouse strains

	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
		Review High-throughput sequencing to decipher the genetic heterogeneity of deafness Zippora Brownstein, Yoni Bhonker, Karen B Avraham Genome Biology 2012, 13:245 (29 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary High-throughput sequencing approaches have accelerated the discovery of genes related to hearing loss, and may reshape clinical diagnosis of deafness
		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.
		Method A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level Stephan Binder, Georg Schendzielorz, Norma Stäbler, Karin Krumbach, Kristina Hoffmann, Michael Bott, Lothar Eggeling Genome Biology 2012, 13:R40 (28 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel high-throughput method that uses in vivo metabolite sensors to identify bacterial metabolite producers
		Research The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Thomas Pröschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Alexandre Lomsadze, Mark Borodovsky, Jean-Michel Claverie, Igor V Grigoriev, James L Van Etten Genome Biology 2012, 13:R39 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome of a polar eukaryotic microorganism, an alga called Coccomyxa subellipsoidea C-169, reveals universal strategies for cold adaptation
		Research Genomic diversity of the human intestinal parasite Entamoeba histolytica Gareth D Weedall, C Graham Clark, Pia Koldkjaer, Suzanne Kay, Iris Bruchhaus, Egbert Tannich, Steve Paterson, Neil Hall Genome Biology 2012, 13:R38 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Ten strains of Entamoeba histolytica are sequenced. Low levels of genetic diversity are found, and evidence for sexual reproduction is uncovered
		Research Comparative multi-omics systems analysis of Escherichia coli strains B and K-12 Sung Yoon, Mee-Jung Han, Haeyoung Jeong, Choong Lee, Xiao-Xia Xia, Dae-Hee Lee, Ji Shim, Sang Lee, Tae Oh, Jihyun F Kim Genome Biology 2012, 13:R37 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of multi-omics data and the generation of a genome-scale metabolic network to determine the phenotypic characteristics of E. coli
		Meeting report A Keystone for ncRNA Ezgi Hacisuleyman, Moran N Cabili, John L Rinn Genome Biology 2012, 13:315 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Rinn and colleagues give a report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012.
		Research A systematic screen reveals new elements acting at the G2/M cell cycle control Francisco J Navarro, Paul Nurse Genome Biology 2012, 13:R36 (24 May 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A screen for regulators of the G2/M transition in fission yeast reveals novel regulators of cell cycle control
		Research Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns Joachim Weischenfeldt, Johannes Waage, Geng Tian, Jing Zhao, Inge Damgaard, Janus Jakobsen, Karsten Kristiansen, Anders Krogh, Jun Wang, Bo T Porse Genome Biology 2012, 13:R35 (24 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An extensive in vivo analysis of how nonsense mediated mRNA decay regulates alternative splicing in two mouse tissues
		Method A new approach for detecting low-level mutations in next-generation sequence data Mingkun Li, Mark Stoneking Genome Biology 2012, 13:R34 (23 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method is presented for differentiating mutations present at low level in a sample from sequencing errors
		Research highlight Enhancer dysfunction: how the main regulators of gene expression contribute to cancer Siavash K Kurdistani Genome Biology 2012, 13:156 (23 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight on the role of variant epigenetics in establishing an enhancer element-mediated oncogenic transcriptional program
		Research highlight Layer cake: the first bite at gene expression diversity in the human brain Philipp Khaitovich Genome Biology 2012, 13:157 (22 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Philipp Khaitovich highlights research by Allan Jones and colleagues that assesses regional gene expression in the human brain neocortex
		Comment Goodbye, Columbus Gregory A Petsko Genome Biology 2012, 13:155 (18 May 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Guaranteeing experimental outcomes and findings: funding then and now
		Correction A quantitative literature-curated gold standard for kinase-substrate pairs Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Youn, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews Genome Biology 2012, 13:417 (10 May 2012) Abstract \| Full text \| PDF \| PubMed
		Research A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response Scott Schwartz, Iddo Friedberg, Ivan V Ivanov, Laurie A Davidson, Jennifer S Goldsby, David B Dahl, Damir Herman, Mei Wang, Sharon M Donovan, Robert S Chapkin Genome Biology 2012, 13:r32 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota
		Review Genetic architecture of body size in mammals Kathryn E Kemper, Peter M Visscher, Michael E Goddard Genome Biology 2012, 13:244 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Peter Visscher and colleagues survey the current known mutations affecting body size in humans, mice, dogs and livestock species
		Comment Economies of scale Gregory A Petsko Genome Biology 2012, 13:154 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The current glut of postdoctoral and graduate scientists can be addressed by applying economic principles.
		Research highlight We are what we eat: how the diet of infants affects their gut microbiome Mihai Pop Genome Biology 2012, 13:152 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We are what we eat: Mihai Pop highlights our Research article investigating the impact of diet on an infant's gut
		Research Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel Marieke Simonis, Santosh S Atanur, Sam Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Game, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven JM Jones, Michal Pravenec, Tim J Aitman, Edwin Cuppen Genome Biology 2012, 13:r31 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome and transcriptome sequences of the founder strains of the HXB/BXH panel of recombinant inbred rat strains
		Review Current challenges in de novo plant genome sequencing and assembly Michael C Schatz, Jan Witkowski, W Richard McCombie Genome Biology 2012, 13:243 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
		Research highlight The Arabidopsis clock: time for an about-face? David E Somers Genome Biology 2012, 13:153 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Somers highlights three recent papers that arrive at a surprising conclusion about how TOC1 functions in the plant circadian clock
		Research Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium Simen M Kristoffersen, Chad Haase, M Ryan Weil, Karla D Passalacqua, Faheem Niazi, Stephen K Hutchison, Brian Desany, Anne-Brit Kolstø, Nicolas J Tourasse, Timothy D Read, Ole Økstad Genome Biology 2012, 13:R30 (26 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA-seq is used to determine mRNA decay rates to single nucleotide resolution in the Gram positive bacterium Bacillus cereus
		Software RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations Mauro AA Castro, Xin Wang, Michael NC Fletcher, Kerstin B Meyer, Florian Markowetz Genome Biology 2012, 13:R29 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for visualizing complex, large-scale networks that combines R/Bioconductor with Java, and allows the incorporation of plug-ins
		Research Mediation of Drosophila autosomal dosage effects and compensation by network interactions John H Malone, Dong-Yeon Cho, Nicolas R Mattiuzzo, Carlo G Artieri, Lichun Jiang, Ryan K Dale, Harold E Smith, Jennifer McDaniel, Sarah Munro, Marc Salit, Justen Andrews, Teresa M Przytycka, Brian Oliver Genome Biology 2012, 13:R28 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive RNA-seq analysis of autosomal dosage effects and compensation in 21 autosomal deficiency Drosophila lines
		Research Genome-wide identification and characterization of replication origins by deep sequencing Jia Xu, Yoshimi Yanagisawa, Alexander M Tsankov, Christopher Hart, Keita Aoki, Naveen Kommajosyula, Kathleen E Steinmann, James Bochicchio, Carsten Russ, Aviv Regev, Oliver J Rando, Chad Nusbaum, Hironori Niki, Patrice Milos, Zhiping Weng, Nicholas Rhind Genome Biology 2012, 13:R27 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Single-molecule deep sequencing and comparative genomics in three Schizosaccharomyces species sheds light on the nature of replication origins
		Research High levels of RNA-editing site conservation amongst 15 laboratory mouse strains Petr Danecek, Christoffer Nellåker, Rebecca E McIntyre, Jorge E Buendia-Buendia, Suzannah Bumpstead, Chris P Ponting, Jonathan Flint, Richard Durbin, Thomas M Keane, David J Adams Genome Biology 2012, 13:r26 (23 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extensive, genome-wide analysis of RNA editing in the brain transcriptomes of 15 mouse strains