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		Opinion The real cost of sequencing: higher than you think! Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein Genome Biology 2011, 12:125 (25 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
		Meeting report Computational biology: plus c'est la même chose, plus ça change Curtis Huttenhower Genome Biology 2011, 12:307 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint 19th Annual ISMB/10th Annual ECCB and the 7th ISCB Student Council Symposium, Vienna, Austria, 15-19 July 2011
		Research highlight Repeated phenotypic changes highlight molecular targets of convergent evolution Maggie R Wagner, Thomas Mitchell-Olds Genome Biology 2011, 12:124 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Maggie Wagner and Thomas Mitchell-Olds discuss how selection might preferentially target certain genes that have a strong phenotypic effect
		Software Cistrome: an integrative platform for transcriptional regulation studies Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu Genome Biology 2011, 12:R83 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Galaxy-based web application for integrative analysis of ChIP data
		Research Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast Brian T Wilhelm, Samuel Marguerat, Sofia Aligianni, Sandra Codlin, Stephen Watt, Jürg Bähler Genome Biology 2011, 12:R82 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of marks associated with introns in S. pombe finds distinct patterns of histones, open chromatin and PolII enrichment
		Research Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
		Method Single-cell copy number variation detection Jiqiu Cheng, Evelyne Vanneste, Peter Konings, Thierry Voet, Joris R Vermeesch, Yves Moreau Genome Biology 2011, 12:R80 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method is presented for detecting copy number variations from array CGH data specifically optimized for use with single cells
		Research highlight Sequencing skippy: the genome sequence of an Australian kangaroo, Macropus eugenii Elizabeth P Murchison, David J Adams Genome Biology 2011, 12:123 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sanger Institute's David Adams finds our kangaroo genome sequence article to be a fascinating window on mammalian evolution
		Method PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data David L Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L Skalsky, Jack D Keene, Uwe Ohler Genome Biology 2011, 12:R79 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data
		Research A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1 Melanie Blasius, Josep V Forment, Neha Thakkar, Sebastian A Wagner, Chunaram Choudhary, Stephen P Jackson Genome Biology 2011, 12:R78 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phospho-proteomics screen identifies many novel Chk1 substrates and a target site consensus motif
		Research Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage Min Zhu, Ming Yi, Chang Hee Kim, Chuxia Deng, Yi Li, Daniel Medina, Robert M Stephens, Jeffrey E Green Genome Biology 2011, 12:R77 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression profiling in mouse models of mammary tumors identifies miRNA signatures particular to lineages or driver oncogenes
		Research The head-regeneration transcriptome of the planarian Schmidtea mediterranea Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer Genome Biology 2011, 12:R76 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea
		Research Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford progeria syndrome cells Ishita S Mehta, Christopher H Eskiw, Halime D Arican, Ian R Kill, Joanna M Bridger Genome Biology 2011, 12:R74 (12 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Treating cultured cells from Hutchinson-Gilford progeria patients with farnesyltransferase inhibitors restores wildtype chromosome dynamics
		Research The contrasting roles of PPARδ and PPARγ in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue Lee D Roberts, Andrew J Murray, David Menassa, Tom Ashmore, Andrew W Nicholls, Julian L Griffin Genome Biology 2011, 12:R75 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A specific agonist demonstrates the contrast between PPAR-delta and PPAR-gamma function in lipid metabolism
		Method Hybrid selection for sequencing pathogen genomes from clinical samples Alexandre Melnikov, Kevin Galinsky, Peter Rogov, Timothy Fennell, Daria Van Tyne, Carsten Russ, Rachel Daniels, Kayla G Barnes, James Bochicchio, Daouda Ndiaye, Papa D Sene, Dyann F Wirth, Chad Nusbaum, Sarah K Volkman, Bruce W Birren, Andreas Gnirke, Daniel E Neafsey Genome Biology 2011, 12:R73 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Baits generated from Plasmodium DNA are used in solution hybridization to enrich parasite DNA from clinical samples to facilitate sequencing
		Method TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Daehwan Kim, Steven L Salzberg Genome Biology 2011, 12:R72 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm
		Method Single cell transcriptomics of neighboring hyphae of Aspergillus niger Charissa de Bekker, Oskar Bruning, Martijs J Jonker, Timo M Breit, Han AB Wösten Genome Biology 2011, 12:R71 (4 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for single cell transcriptomics is developed and is demonstrated on single hyphae of Aspergillus niger
		Research Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits Daniel Wong, Ana Teixeira, Spyros Oikonomopoulos, Peter Humburg, Imtiaz Lone, David Saliba, Trevor Siggers, Martha Bulyk, Dimitar Angelov, Stefan Dimitrov, Irina A Udalova, Jiannis Ragoussis Genome Biology 2011, 12:R70 (29 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protein binding microarrays and Electrophoretic Mobility Shift Assay-Sequencing reveal non-canonical NFkappaB binding sites associated with polymorphisms
		Software ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data Brad A Friedman, Tom Maniatis Genome Biology 2011, 12:R69 (28 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A web-based RNA-seq and microarray analysis tool
		Open letter Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes Todd A Castoe, AP Jason de Koning, Kathryn T Hall, Ken D Yokoyama, Wanjun Gu, Eric N Smith, Cédric Feschotte, Peter Uetz, David A Ray, Jason Dobry, Robert Bogden, Stephen P Mackessy, Anne M Bronikowski, Wesley C Warren, Stephen M Secor, David D Pollock Genome Biology 2011, 12:406 (28 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the Burmese python is being sequenced, providing insights into the unique anatomy, physiology, and evolution of snakes
		Protein family review Atg8: an autophagy-related ubiquitin-like protein family Tomer Shpilka, Hilla Weidberg, Shmuel Pietrokovski, Zvulun Elazar Genome Biology 2011, 12:226 (27 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Atg8 family of autophagy-related ubiquitin-like proteins mediate remodeling of intracellular membranes and interact with many proteins to regulate trafficking and autophagy
		Research Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities Matthew N Bainbridge, Min Wang, Yuanqing Wu, Irene Newsham, Donna M Muzny, John L Jefferies, Thomas J Albert, Daniel L Burgess, Richard A Gibbs Genome Biology 2011, 12:R68 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Extension of exome capture beyond the commonly targeted regions reveals much higher variant densities in predicted exons
		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
		Comment Food of the dogs Gregory A Petsko Genome Biology 2011, 12:122 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Human evolution and the Paleofood movement
		Research highlight Sex lethal and upstream ORFs: a bait-and-trap system for ribosomes Peng Yao, Paul L Fox Genome Biology 2011, 12:121 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research highlight on a novel mechanism of eukaryotic gene regulation
		Research highlight An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data Weiqun Peng, Keji Zhao Genome Biology 2011, 12:120 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Keji Zhao discusses Genome Biology's method article on ZINBA, a novel peak-finding tool developed by Jason Lieb and colleagues
		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
		Opinion The real cost of sequencing: higher than you think! Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein Genome Biology 2011, 12:125 (25 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
		Meeting report Computational biology: plus c'est la même chose, plus ça change Curtis Huttenhower Genome Biology 2011, 12:307 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint 19th Annual ISMB/10th Annual ECCB and the 7th ISCB Student Council Symposium, Vienna, Austria, 15-19 July 2011
		Research highlight Repeated phenotypic changes highlight molecular targets of convergent evolution Maggie R Wagner, Thomas Mitchell-Olds Genome Biology 2011, 12:124 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Maggie Wagner and Thomas Mitchell-Olds discuss how selection might preferentially target certain genes that have a strong phenotypic effect
		Software Cistrome: an integrative platform for transcriptional regulation studies Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu Genome Biology 2011, 12:R83 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Galaxy-based web application for integrative analysis of ChIP data
		Research Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast Brian T Wilhelm, Samuel Marguerat, Sofia Aligianni, Sandra Codlin, Stephen Watt, Jürg Bähler Genome Biology 2011, 12:R82 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of marks associated with introns in S. pombe finds distinct patterns of histones, open chromatin and PolII enrichment
		Research Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
		Method Single-cell copy number variation detection Jiqiu Cheng, Evelyne Vanneste, Peter Konings, Thierry Voet, Joris R Vermeesch, Yves Moreau Genome Biology 2011, 12:R80 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method is presented for detecting copy number variations from array CGH data specifically optimized for use with single cells
		Research highlight Sequencing skippy: the genome sequence of an Australian kangaroo, Macropus eugenii Elizabeth P Murchison, David J Adams Genome Biology 2011, 12:123 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sanger Institute's David Adams finds our kangaroo genome sequence article to be a fascinating window on mammalian evolution
		Method PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data David L Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L Skalsky, Jack D Keene, Uwe Ohler Genome Biology 2011, 12:R79 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data
		Research A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1 Melanie Blasius, Josep V Forment, Neha Thakkar, Sebastian A Wagner, Chunaram Choudhary, Stephen P Jackson Genome Biology 2011, 12:R78 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phospho-proteomics screen identifies many novel Chk1 substrates and a target site consensus motif
		Research Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage Min Zhu, Ming Yi, Chang Hee Kim, Chuxia Deng, Yi Li, Daniel Medina, Robert M Stephens, Jeffrey E Green Genome Biology 2011, 12:R77 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression profiling in mouse models of mammary tumors identifies miRNA signatures particular to lineages or driver oncogenes
		Research The head-regeneration transcriptome of the planarian Schmidtea mediterranea Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer Genome Biology 2011, 12:R76 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea
		Research Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford progeria syndrome cells Ishita S Mehta, Christopher H Eskiw, Halime D Arican, Ian R Kill, Joanna M Bridger Genome Biology 2011, 12:R74 (12 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Treating cultured cells from Hutchinson-Gilford progeria patients with farnesyltransferase inhibitors restores wildtype chromosome dynamics
		Research The contrasting roles of PPARδ and PPARγ in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue Lee D Roberts, Andrew J Murray, David Menassa, Tom Ashmore, Andrew W Nicholls, Julian L Griffin Genome Biology 2011, 12:R75 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A specific agonist demonstrates the contrast between PPAR-delta and PPAR-gamma function in lipid metabolism
		Method Hybrid selection for sequencing pathogen genomes from clinical samples Alexandre Melnikov, Kevin Galinsky, Peter Rogov, Timothy Fennell, Daria Van Tyne, Carsten Russ, Rachel Daniels, Kayla G Barnes, James Bochicchio, Daouda Ndiaye, Papa D Sene, Dyann F Wirth, Chad Nusbaum, Sarah K Volkman, Bruce W Birren, Andreas Gnirke, Daniel E Neafsey Genome Biology 2011, 12:R73 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Baits generated from Plasmodium DNA are used in solution hybridization to enrich parasite DNA from clinical samples to facilitate sequencing
		Method TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Daehwan Kim, Steven L Salzberg Genome Biology 2011, 12:R72 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm
		Method Single cell transcriptomics of neighboring hyphae of Aspergillus niger Charissa de Bekker, Oskar Bruning, Martijs J Jonker, Timo M Breit, Han AB Wösten Genome Biology 2011, 12:R71 (4 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for single cell transcriptomics is developed and is demonstrated on single hyphae of Aspergillus niger
		Research Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits Daniel Wong, Ana Teixeira, Spyros Oikonomopoulos, Peter Humburg, Imtiaz Lone, David Saliba, Trevor Siggers, Martha Bulyk, Dimitar Angelov, Stefan Dimitrov, Irina A Udalova, Jiannis Ragoussis Genome Biology 2011, 12:R70 (29 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protein binding microarrays and Electrophoretic Mobility Shift Assay-Sequencing reveal non-canonical NFkappaB binding sites associated with polymorphisms
		Software ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data Brad A Friedman, Tom Maniatis Genome Biology 2011, 12:R69 (28 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A web-based RNA-seq and microarray analysis tool
		Open letter Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes Todd A Castoe, AP Jason de Koning, Kathryn T Hall, Ken D Yokoyama, Wanjun Gu, Eric N Smith, Cédric Feschotte, Peter Uetz, David A Ray, Jason Dobry, Robert Bogden, Stephen P Mackessy, Anne M Bronikowski, Wesley C Warren, Stephen M Secor, David D Pollock Genome Biology 2011, 12:406 (28 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the Burmese python is being sequenced, providing insights into the unique anatomy, physiology, and evolution of snakes
		Protein family review Atg8: an autophagy-related ubiquitin-like protein family Tomer Shpilka, Hilla Weidberg, Shmuel Pietrokovski, Zvulun Elazar Genome Biology 2011, 12:226 (27 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Atg8 family of autophagy-related ubiquitin-like proteins mediate remodeling of intracellular membranes and interact with many proteins to regulate trafficking and autophagy
		Research Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities Matthew N Bainbridge, Min Wang, Yuanqing Wu, Irene Newsham, Donna M Muzny, John L Jefferies, Thomas J Albert, Daniel L Burgess, Richard A Gibbs Genome Biology 2011, 12:R68 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Extension of exome capture beyond the commonly targeted regions reveals much higher variant densities in predicted exons
		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
		Comment Food of the dogs Gregory A Petsko Genome Biology 2011, 12:122 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Human evolution and the Paleofood movement
		Research highlight Sex lethal and upstream ORFs: a bait-and-trap system for ribosomes Peng Yao, Paul L Fox Genome Biology 2011, 12:121 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research highlight on a novel mechanism of eukaryotic gene regulation
		Research highlight An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data Weiqun Peng, Keji Zhao Genome Biology 2011, 12:120 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Keji Zhao discusses Genome Biology's method article on ZINBA, a novel peak-finding tool developed by Jason Lieb and colleagues
		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.