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		Research Epigenetic interplay between mouse endogenous retroviruses and host genes Rita Rebollo, Katharine Miceli-Royer, Ying Zhang, Sharareh Farivar, Liane Gagnier, Dixie L Mager Genome Biology 2012, 13:R89 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes proximal to mouse endogenous retroviral elements defend against the invasion of silencing methylation using both buffer regions and euchromatin propagation
		Research Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity Alok K Tewari, Galip Yardimci, Yoichiro Shibata, Nathan C Sheffield, Lingyun Song, Barry S Taylor, Stoyan G Georgiev, Gerhard A Coetzee, Uwe Ohler, Terrence S Furey, Gregory E Crawford, Phillip G Febbo Genome Biology 2012, 13:R88 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Androgen receptor binding to the genome occurs by multiple mechanisms and is associated with an increase in chromatin accessibility
		Software methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason Genome Biology 2012, 13:R87 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An R package (incorporating multiple analysis tools) automates and simplifies the characterization of methylation datasets
		Method Enhanced top-down characterization of histone post-translational modifications Zhixin Tian, Nikola Tolić, Rui Zhao, Ronald J Moore, Shawna M Hengel, Errol W Robinson, David L Stenoien, Si Wu, Richard D Smith, Ljiljana Paša-Tolić Genome Biology 2012, 13:R86 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An extremely sensitive, high-throughput mass spectrometry platform for the unambiguous identification of histone post-translational modifications
		Research H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions Manching Ku, Jacob D Jaffe, Richard P Koche, Esther Rheinbay, Mitsuhiro Endoh, Haruhiko Koseki, Steven A Carr, Bradley E Bernstein Genome Biology 2012, 13:R85 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The landscape of H2A.Z, including a novel post-transcriptionally modified variant, in ES and neural progenitor cells
		Research Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns Duncan Sproul, Robert R Kitchen, Colm E Nestor, J Michael Dixon, Andrew H Sims, David J Harrison, Bernard H Ramsahoye, Richard R Meehan Genome Biology 2012, 13:R84 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Aberrant promoter hypermethylation in cancer does not promote tumorigenesis, but instead reinforces repression inherited from pre-cancerous tissue
		Method BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry Genome Biology 2012, 13:R83 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An alignment, quality control and analysis pipeline for bisulfite sequencing data
		Method BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation Jing-Quan Lim, Chandana Tennakoon, Guoliang Li, Eleanor Wong, Yijun Ruan, Chia-Lin Wei, Wing-Kin Sung Genome Biology 2012, 13:R82 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BatMeth is a fast, accurate tool for mapping Illumina or SOLiD bisulfite sequencing reads
		Research Correlation of proteome-wide changes with social immunity behaviors provides insight into resistance to the parasitic mite, Varroa destructor, in the honey bee (Apis mellifera) Robert Parker, M Marta Guarna, Andony P Melathopoulos, Kyung-Mee Moon, Rick White, Elizabeth Huxter, Stephen F Pernal, Leonard J Foster Genome Biology 2012, 13:R81 (28 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of honeybees identifies proteins associated with the hygienic response to infestation with Varroa destructor mite
		Review Human pigmentation genes under environmental selection Richard A Sturm, David L Duffy Genome Biology 2012, 13:248 (27 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Review on what GWAS and comparative genomics have taught us about environmental selection on human pigmentation genes
		Research highlight Evolutionary insights into genome-wide nucleosome positioning Vijender Singh, Tom Owen-Hughes Genome Biology 2012, 13:170 (27 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A discussion of a recent article in Molecular Cell that uses different yeast species to determine the factors influencing nucleosome positioning
		Research Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH_cin Saccharomyces cerevisiae Rick Orij, Malene L Urbanus, Franco J Vizeacoumar, Guri Giaever, Charles Boone, Corey Nislow, Stanley Brul, Gertien J Smits Genome Biology 2012, 13:R80 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study in yeast finds that intracellular pH actively controls growth rate, potentially via signaling through inositol polyphosphates
		Research Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper, Athos Bousvaros, Joshua Korzenik, Bruce E Sands, Ramnik J Xavier, Curtis Huttenhower Genome Biology 2012, 13:R79 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of the microbes and microbial metabolism present in intestinal biopsies and stool samples from 231 IBD and healthy subjects
		Method RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations Joonhoon Kim, Jennifer L Reed Genome Biology 2012, 13:R78 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RELATCH is a method for predicting metabolic responses to genetic and environmental perturbations, based on the principle of relative optimality
		Comment Why science and synchronized swimming should not be Olympic sports Neil Hall Genome Biology 2012, 13:171 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By Neil Hall
		Research highlight Functional predictions from inference and observation in sequence-based inflammatory bowel disease research Folker Meyer, William L Trimble, Eugene B Chang, Kim M Handley Genome Biology 2012, 13:169 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research Highlight: important advances in understanding the gut microbiome composition and microbial metabolism in patients with IBD
		Meeting report The yeast factory Daniela Delneri Genome Biology 2012, 13:320 (25 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 13th International Congress on Yeasts (ICY), held at Madison, Wisconsin, USA, 26-30 August 2012
		Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
		Research Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 Seth Frietze, Rui Wang, Lijing Yao, Yu Tak, Zhenqing Ye, Malaina Gaddis, Heather Witt, Peggy J Farnham, Victor X Jin Genome Biology 2012, 13:R52 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcription factor TCF7L2 can be tethered to the genome by GATA3, and therefore can target sites lacking its own motif
		Research The GENCODE pseudogene resource Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng Mu, Rachel Harte, Suganthi Balasubramanian, Andrea Tanzer, Mark Diekhans, Alexandre Reymond, Tim J Hubbard, Jennifer Harrow, Mark B Gerstein Genome Biology 2012, 13:R51 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The GENCODE pseudogene resource includes evidence for dead genes undergoing resurrection
		Research Functional analysis of transcription factor binding sites in human promoters Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Aldred, Nathan D Trinklein, Richard M Myers, Zhiping Weng Genome Biology 2012, 13:R50 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary TFBSs are predicted from ENCODE data, and experiments in four cell lines find 70% to be functional
		Research Analysis of variation at transcription factor binding sites in Drosophila and humans Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, Ewan Birney Genome Biology 2012, 13:R49 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription factor binding site variability in fly and human provides evidence for a buffering phenomenon
		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
		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

	All
		Research Epigenetic interplay between mouse endogenous retroviruses and host genes Rita Rebollo, Katharine Miceli-Royer, Ying Zhang, Sharareh Farivar, Liane Gagnier, Dixie L Mager Genome Biology 2012, 13:R89 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes proximal to mouse endogenous retroviral elements defend against the invasion of silencing methylation using both buffer regions and euchromatin propagation
		Research Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity Alok K Tewari, Galip Yardimci, Yoichiro Shibata, Nathan C Sheffield, Lingyun Song, Barry S Taylor, Stoyan G Georgiev, Gerhard A Coetzee, Uwe Ohler, Terrence S Furey, Gregory E Crawford, Phillip G Febbo Genome Biology 2012, 13:R88 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Androgen receptor binding to the genome occurs by multiple mechanisms and is associated with an increase in chromatin accessibility
		Software methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason Genome Biology 2012, 13:R87 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An R package (incorporating multiple analysis tools) automates and simplifies the characterization of methylation datasets
		Method Enhanced top-down characterization of histone post-translational modifications Zhixin Tian, Nikola Tolić, Rui Zhao, Ronald J Moore, Shawna M Hengel, Errol W Robinson, David L Stenoien, Si Wu, Richard D Smith, Ljiljana Paša-Tolić Genome Biology 2012, 13:R86 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An extremely sensitive, high-throughput mass spectrometry platform for the unambiguous identification of histone post-translational modifications
		Research H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions Manching Ku, Jacob D Jaffe, Richard P Koche, Esther Rheinbay, Mitsuhiro Endoh, Haruhiko Koseki, Steven A Carr, Bradley E Bernstein Genome Biology 2012, 13:R85 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The landscape of H2A.Z, including a novel post-transcriptionally modified variant, in ES and neural progenitor cells
		Research Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns Duncan Sproul, Robert R Kitchen, Colm E Nestor, J Michael Dixon, Andrew H Sims, David J Harrison, Bernard H Ramsahoye, Richard R Meehan Genome Biology 2012, 13:R84 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Aberrant promoter hypermethylation in cancer does not promote tumorigenesis, but instead reinforces repression inherited from pre-cancerous tissue
		Method BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry Genome Biology 2012, 13:R83 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An alignment, quality control and analysis pipeline for bisulfite sequencing data
		Method BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation Jing-Quan Lim, Chandana Tennakoon, Guoliang Li, Eleanor Wong, Yijun Ruan, Chia-Lin Wei, Wing-Kin Sung Genome Biology 2012, 13:R82 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BatMeth is a fast, accurate tool for mapping Illumina or SOLiD bisulfite sequencing reads
		Research Correlation of proteome-wide changes with social immunity behaviors provides insight into resistance to the parasitic mite, Varroa destructor, in the honey bee (Apis mellifera) Robert Parker, M Marta Guarna, Andony P Melathopoulos, Kyung-Mee Moon, Rick White, Elizabeth Huxter, Stephen F Pernal, Leonard J Foster Genome Biology 2012, 13:R81 (28 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of honeybees identifies proteins associated with the hygienic response to infestation with Varroa destructor mite
		Review Human pigmentation genes under environmental selection Richard A Sturm, David L Duffy Genome Biology 2012, 13:248 (27 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Review on what GWAS and comparative genomics have taught us about environmental selection on human pigmentation genes
		Research highlight Evolutionary insights into genome-wide nucleosome positioning Vijender Singh, Tom Owen-Hughes Genome Biology 2012, 13:170 (27 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A discussion of a recent article in Molecular Cell that uses different yeast species to determine the factors influencing nucleosome positioning
		Research Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH_cin Saccharomyces cerevisiae Rick Orij, Malene L Urbanus, Franco J Vizeacoumar, Guri Giaever, Charles Boone, Corey Nislow, Stanley Brul, Gertien J Smits Genome Biology 2012, 13:R80 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study in yeast finds that intracellular pH actively controls growth rate, potentially via signaling through inositol polyphosphates
		Research Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper, Athos Bousvaros, Joshua Korzenik, Bruce E Sands, Ramnik J Xavier, Curtis Huttenhower Genome Biology 2012, 13:R79 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of the microbes and microbial metabolism present in intestinal biopsies and stool samples from 231 IBD and healthy subjects
		Method RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations Joonhoon Kim, Jennifer L Reed Genome Biology 2012, 13:R78 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RELATCH is a method for predicting metabolic responses to genetic and environmental perturbations, based on the principle of relative optimality
		Comment Why science and synchronized swimming should not be Olympic sports Neil Hall Genome Biology 2012, 13:171 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By Neil Hall
		Research highlight Functional predictions from inference and observation in sequence-based inflammatory bowel disease research Folker Meyer, William L Trimble, Eugene B Chang, Kim M Handley Genome Biology 2012, 13:169 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research Highlight: important advances in understanding the gut microbiome composition and microbial metabolism in patients with IBD
		Meeting report The yeast factory Daniela Delneri Genome Biology 2012, 13:320 (25 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 13th International Congress on Yeasts (ICY), held at Madison, Wisconsin, USA, 26-30 August 2012
		Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
		Research Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 Seth Frietze, Rui Wang, Lijing Yao, Yu Tak, Zhenqing Ye, Malaina Gaddis, Heather Witt, Peggy J Farnham, Victor X Jin Genome Biology 2012, 13:R52 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcription factor TCF7L2 can be tethered to the genome by GATA3, and therefore can target sites lacking its own motif
		Research The GENCODE pseudogene resource Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng Mu, Rachel Harte, Suganthi Balasubramanian, Andrea Tanzer, Mark Diekhans, Alexandre Reymond, Tim J Hubbard, Jennifer Harrow, Mark B Gerstein Genome Biology 2012, 13:R51 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The GENCODE pseudogene resource includes evidence for dead genes undergoing resurrection
		Research Functional analysis of transcription factor binding sites in human promoters Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Aldred, Nathan D Trinklein, Richard M Myers, Zhiping Weng Genome Biology 2012, 13:R50 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary TFBSs are predicted from ENCODE data, and experiments in four cell lines find 70% to be functional
		Research Analysis of variation at transcription factor binding sites in Drosophila and humans Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, Ewan Birney Genome Biology 2012, 13:R49 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription factor binding site variability in fly and human provides evidence for a buffering phenomenon
		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
		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