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		Method ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb Genome Biology 2011, 12:R67 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq
		Research The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology Gerard Manning, David S Reiner, Tineke Lauwaet, Michael Dacre, Alias Smith, Yufeng Zhai, Staffan Svard, Frances D Gillin Genome Biology 2011, 12:R66 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of sequenced genomes of Giardia lamblia reveals that it has the fewest number of kinases of any known eukaryote
		Research Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins Johan Nilsson, Mats Grahn, Anthony PH Wright Genome Biology 2011, 12:R65 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Enhanced positive codon selection in the intrinsically disordered regions of yeast proteins
		Research Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis Laure-Emmanuelle Zaragosi, Brigitte Wdziekonski, Kevin Brigand, Phi Villageois, Bernard Mari, Rainer Waldmann, Christian Dani, Pascal Barbry Genome Biology 2011, 12:R64 (18 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The miR-30 family of miRNAs is found to regulate adipogenesis by targeting RUNX2 mRNA
		Research Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque Xiaodong Fang, Yanfeng Zhang, Rui Zhang, Lixin Yang, Ming Li, Kaixiong Ye, Xiaosen Guo, Jun Wang, Bing Su Genome Biology 2011, 12:R63 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome of a Chinese rhesus macaque includes millions of SNPs relative to the (Indian) reference genome
		Research A comparative analysis of DNA methylation across human embryonic stem cell lines Pao-Yang Chen, Suhua Feng, Jong Joo, Steve E Jacobsen, Matteo Pellegrini Genome Biology 2011, 12:R62 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of DNA methylation in three human embryonic stem cell lines
		Correction Correction: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Jordana T Bell, Athma A Pai, Joseph K Pickrell, Daniel J Gaffney, Roger Pique-Regi, Jacob F Degner, Yoav Gilad, Jonathan K Pritchard Genome Biology 2011, 12:405 (3 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Profiling lymphoblastoid cell lines from HapMap individuals reveals a significant genetic component for inter-individual DNA methylation and gene expression
		Comment Risky business Gregory A Petsko Genome Biology 2011, 12:119 (30 June 2011) Full text \| PDF \| PubMed \| Editor’s summary Greater risk in funding scientific research could lead to better results
		Research Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy Michal Ozery-Flato, Chaim Linhart, Luba Trakhtenbrot, Shai Izraeli, Ron Shamir Genome Biology 2011, 12:R61 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A statistical analysis of the Mitelman database reveals an unexpected co-occurrence of chromosome gains and, similarly, of chromosome losses
		Protein family review The tubby family proteins Saikat Mukhopadhyay, Peter K Jackson Genome Biology 2011, 12:225 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tubby family proteins act as cellular bridges between phosphoinositides to other cellular structures and have roles in obesity and retinal disease
		Research highlight The jigsaw puzzle of our African ancestry: unsolved, or unsolvable? Chiara Batini, Mark A Jobling Genome Biology 2011, 12:118 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mark Jobling highlights a new Y chromosome phylogeny and discusses how it further fragments the puzzle of our African ancestry
		Research highlight Genomes of uncultured eukaryotes: sorting FACS from fiction Alexandra Z Worden, Christopher Dupont, Andrew E Allen Genome Biology 2011, 12:117 (27 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Direct genome sequencing of biliphytes, uncultured marine eukaryotes, from the environment shows the difficulties in separating out the signals from different genomes with this technique
		Method Metagenomic biomarker discovery and explanation Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower Genome Biology 2011, 12:R60 (24 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for distinguishing microbial populations from metagenomic data is presented
		Review The mouse genetics toolkit: revealing function and mechanism Louise van der Weyden, Jacqueline K White, David J Adams, Darren W Logan Genome Biology 2011, 12:224 (24 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many tools and technologies are now available for discovering disease genes, manipulating their function and understanding genetic variation in mice
		Research Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study Hiroki Goto, Benjamin Dickins, Enis Afgan, Ian M Paul, James Taylor, Kateryna D Makova, Anton Nekrutenko Genome Biology 2011, 12:R59 (23 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of 3 families with a Galaxy-based method for heteroplasmy identification suggests that within-individual mtDNA variation is infrequent
		Research Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content Carina F Mugal, Hans Ellegren Genome Biology 2011, 12:R58 (22 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CpG mutation rate variation in the human germline correlates with DNA methylation, GC content and the mutation rate of other nucleotides
		Software BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation Anthony ML Liekens, Jeroen De Knijf, Walter Daelemans, Bart Goethals, Peter De Rijk, Jurgen Del-Favero Genome Biology 2011, 12:R57 (22 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Software for data integration and mining of biomedical data
		Research A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs Kate M Broadbent, Daniel Park, Ashley R Wolf, Daria Van Tyne, Jennifer S Sims, Ulf Ribacke, Sarah Volkman, Manoj Duraisingh, Dyann Wirth, Pardis C Sabeti, John L Rinn Genome Biology 2011, 12:R56 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional analysis of Plasmodium falciparum reveals developmentally regulated telomere-associated lncRNAs
		Method Sniper: improved SNP discovery by multiply mapping deep sequenced reads Daniel F Simola, Junhyong Kim Genome Biology 2011, 12:R55 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for improved SNP discovery in next-generation sequencing data
		Research 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells Hume Stroud, Suhua Feng, Shannon Morey Kinney, Sriharsa Pradhan, Steven E Jacobsen Genome Biology 2011, 12:R54 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide study in hESCs finds that the modified base 5-hydroxymethylcytosine is enriched in enhancer regions and gene bodies
		Research highlight Genome-wide mapping of the sixth base Dinh Diep, Kun Zhang Genome Biology 2011, 12:116 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mapping of 5-hydroxylmethylcytosine in mammalian genomes has unveiled its unique role in the epigenetic regulation of gene expression
		Meeting report Grand network convergence Joel S Bader Genome Biology 2011, 12:306 (17 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Systems Biology: Networks meeting, Cold Spring Harbor Laboratory, USA, 22-26 March, 2011
		Research Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa Li Wei, Long Yan, Tai Wang Genome Biology 2011, 12:R53 (16 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Deep sequencing reveals miRNAs expressed during rice pollen development
		Meeting report Bright days for yeast research Martin Převorovský, Charalampos Rallis Genome Biology 2011, 12:305 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the British Yeast Group Meeting, Brighton, UK, 23-25 March 2011
		Protein family review The lamin protein family Travis A Dittmer, Tom Misteli Genome Biology 2011, 12:222 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lamins are the major architectural proteins of animal nuclear membranes and are involved in a wide range of nuclear functions and human diseases.

	All
		Method ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb Genome Biology 2011, 12:R67 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq
		Research The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology Gerard Manning, David S Reiner, Tineke Lauwaet, Michael Dacre, Alias Smith, Yufeng Zhai, Staffan Svard, Frances D Gillin Genome Biology 2011, 12:R66 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of sequenced genomes of Giardia lamblia reveals that it has the fewest number of kinases of any known eukaryote
		Research Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins Johan Nilsson, Mats Grahn, Anthony PH Wright Genome Biology 2011, 12:R65 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Enhanced positive codon selection in the intrinsically disordered regions of yeast proteins
		Research Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis Laure-Emmanuelle Zaragosi, Brigitte Wdziekonski, Kevin Brigand, Phi Villageois, Bernard Mari, Rainer Waldmann, Christian Dani, Pascal Barbry Genome Biology 2011, 12:R64 (18 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The miR-30 family of miRNAs is found to regulate adipogenesis by targeting RUNX2 mRNA
		Research Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque Xiaodong Fang, Yanfeng Zhang, Rui Zhang, Lixin Yang, Ming Li, Kaixiong Ye, Xiaosen Guo, Jun Wang, Bing Su Genome Biology 2011, 12:R63 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome of a Chinese rhesus macaque includes millions of SNPs relative to the (Indian) reference genome
		Research A comparative analysis of DNA methylation across human embryonic stem cell lines Pao-Yang Chen, Suhua Feng, Jong Joo, Steve E Jacobsen, Matteo Pellegrini Genome Biology 2011, 12:R62 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of DNA methylation in three human embryonic stem cell lines
		Correction Correction: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Jordana T Bell, Athma A Pai, Joseph K Pickrell, Daniel J Gaffney, Roger Pique-Regi, Jacob F Degner, Yoav Gilad, Jonathan K Pritchard Genome Biology 2011, 12:405 (3 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Profiling lymphoblastoid cell lines from HapMap individuals reveals a significant genetic component for inter-individual DNA methylation and gene expression
		Comment Risky business Gregory A Petsko Genome Biology 2011, 12:119 (30 June 2011) Full text \| PDF \| PubMed \| Editor’s summary Greater risk in funding scientific research could lead to better results
		Research Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy Michal Ozery-Flato, Chaim Linhart, Luba Trakhtenbrot, Shai Izraeli, Ron Shamir Genome Biology 2011, 12:R61 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A statistical analysis of the Mitelman database reveals an unexpected co-occurrence of chromosome gains and, similarly, of chromosome losses
		Protein family review The tubby family proteins Saikat Mukhopadhyay, Peter K Jackson Genome Biology 2011, 12:225 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tubby family proteins act as cellular bridges between phosphoinositides to other cellular structures and have roles in obesity and retinal disease
		Research highlight The jigsaw puzzle of our African ancestry: unsolved, or unsolvable? Chiara Batini, Mark A Jobling Genome Biology 2011, 12:118 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mark Jobling highlights a new Y chromosome phylogeny and discusses how it further fragments the puzzle of our African ancestry
		Research highlight Genomes of uncultured eukaryotes: sorting FACS from fiction Alexandra Z Worden, Christopher Dupont, Andrew E Allen Genome Biology 2011, 12:117 (27 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Direct genome sequencing of biliphytes, uncultured marine eukaryotes, from the environment shows the difficulties in separating out the signals from different genomes with this technique
		Method Metagenomic biomarker discovery and explanation Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower Genome Biology 2011, 12:R60 (24 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for distinguishing microbial populations from metagenomic data is presented
		Review The mouse genetics toolkit: revealing function and mechanism Louise van der Weyden, Jacqueline K White, David J Adams, Darren W Logan Genome Biology 2011, 12:224 (24 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many tools and technologies are now available for discovering disease genes, manipulating their function and understanding genetic variation in mice
		Research Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study Hiroki Goto, Benjamin Dickins, Enis Afgan, Ian M Paul, James Taylor, Kateryna D Makova, Anton Nekrutenko Genome Biology 2011, 12:R59 (23 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of 3 families with a Galaxy-based method for heteroplasmy identification suggests that within-individual mtDNA variation is infrequent
		Research Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content Carina F Mugal, Hans Ellegren Genome Biology 2011, 12:R58 (22 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CpG mutation rate variation in the human germline correlates with DNA methylation, GC content and the mutation rate of other nucleotides
		Software BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation Anthony ML Liekens, Jeroen De Knijf, Walter Daelemans, Bart Goethals, Peter De Rijk, Jurgen Del-Favero Genome Biology 2011, 12:R57 (22 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Software for data integration and mining of biomedical data
		Research A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs Kate M Broadbent, Daniel Park, Ashley R Wolf, Daria Van Tyne, Jennifer S Sims, Ulf Ribacke, Sarah Volkman, Manoj Duraisingh, Dyann Wirth, Pardis C Sabeti, John L Rinn Genome Biology 2011, 12:R56 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional analysis of Plasmodium falciparum reveals developmentally regulated telomere-associated lncRNAs
		Method Sniper: improved SNP discovery by multiply mapping deep sequenced reads Daniel F Simola, Junhyong Kim Genome Biology 2011, 12:R55 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for improved SNP discovery in next-generation sequencing data
		Research 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells Hume Stroud, Suhua Feng, Shannon Morey Kinney, Sriharsa Pradhan, Steven E Jacobsen Genome Biology 2011, 12:R54 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide study in hESCs finds that the modified base 5-hydroxymethylcytosine is enriched in enhancer regions and gene bodies
		Research highlight Genome-wide mapping of the sixth base Dinh Diep, Kun Zhang Genome Biology 2011, 12:116 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mapping of 5-hydroxylmethylcytosine in mammalian genomes has unveiled its unique role in the epigenetic regulation of gene expression
		Meeting report Grand network convergence Joel S Bader Genome Biology 2011, 12:306 (17 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Systems Biology: Networks meeting, Cold Spring Harbor Laboratory, USA, 22-26 March, 2011
		Research Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa Li Wei, Long Yan, Tai Wang Genome Biology 2011, 12:R53 (16 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Deep sequencing reveals miRNAs expressed during rice pollen development
		Meeting report Bright days for yeast research Martin Převorovský, Charalampos Rallis Genome Biology 2011, 12:305 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the British Yeast Group Meeting, Brighton, UK, 23-25 March 2011
		Protein family review The lamin protein family Travis A Dittmer, Tom Misteli Genome Biology 2011, 12:222 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lamins are the major architectural proteins of animal nuclear membranes and are involved in a wide range of nuclear functions and human diseases.