Genome Biology | Volume 13 Issue 6

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	Volume 13 Issue 6
	Comment
	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.
	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 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
	Review
	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
	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
	Report
	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
	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 \| Cited on BioMed Central \| Editor’s summary Whole genome sequencing of 8 laboratory populations of E. coli casts light on the mechanisms by which populations evolve
	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 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 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
	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 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 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
	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
	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
	Software Toward almost closed genomes with GapFiller Marten Boetzer, Walter Pirovano Genome Biology 2012, 13:R56 (25 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GapFiller is a method for automatically filling gaps in short read genome assemblies using the existing sequencing data

	Volume 13 Issue 6
	Comment
	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.
	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 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
	Review
	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
	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
	Report
	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
	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 \| Cited on BioMed Central \| Editor’s summary Whole genome sequencing of 8 laboratory populations of E. coli casts light on the mechanisms by which populations evolve
	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 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 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
	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 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 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
	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
	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
	Software Toward almost closed genomes with GapFiller Marten Boetzer, Walter Pirovano Genome Biology 2012, 13:R56 (25 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GapFiller is a method for automatically filling gaps in short read genome assemblies using the existing sequencing data

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Volume 13 Issue 6

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