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	1.	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
	2.	Comment Sequestration: inadvertently killing biomedical research to score political points Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction
	3.	Research RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grützner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
	4.	Software ggbio: an R package for extending the grammar of graphics for genomic data Tengfei Yin, Dianne Cook, Michael Lawrence Genome Biology 2012, 13:R77 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent, robust and versatile software tool for visualizing genomic data
	5.	Research A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers Nathan P Palmer, Patrick R Schmid, Bonnie Berger, Isaac S Kohane Genome Biology 2012, 13:R71 (21 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues
	6.	Research Aging effects on DNA methylation modules in human brain and blood tissue Steve Horvath, Yafeng Zhang, Peter Langfelder, René S Kahn, Marco PM Boks, Kristel van Eijk, Leonard H van den Berg, Roel A Ophoff Genome Biology 2012, 13:R97 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An age-related co-methylation module in human brain and blood tissue includes genes associated with Alzheimer's disease
	7.	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
	8.	Editorial Raymond Gosling: the man who crystallized genes Naomi Attar Genome Biology 2013, 14:402 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary "The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
	9.	Method Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda Genome Biology 2013, 14:R31 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
	10.	Review From RNA-seq reads to differential expression results Alicia Oshlack, Mark D Robinson, Matthew D Young Genome Biology 2010, 11:220 (22 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
	11.	Research Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer Genome Biology 2013, 14:R14 (15 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
	12.	Correspondence The advantages of SMRT sequencing Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform
	13.	Software REAPR: a universal tool for genome assembly evaluation Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman, Thomas D Otto Genome Biology 2013, 14:R47 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new user-friendly software tool for genome assembly evaluation
	14.	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
	15.	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
	16.	Research A blood based 12-miRNA signature of Alzheimer disease patients Petra Leidinger, Christina Backes, Stephanie Deutscher, Katja Schmitt, Sabine C Muller, Karen Frese, Jan Haas, Klemens Ruprecht, Friedemann Paul, Cord Stahler, Christoph JG Lang, Benjamin Meder, Tamas Bartfai, Eckart Meese, Andreas Keller Genome Biology 2013, 14:R78 (29 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A 12-miRNA signature in blood samples can be used to detect Alzheimer’s disease and other neurological disorders
	17.	Research Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance David Martino, Yuk Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
	18.	Method Ray Meta: scalable de novo metagenome assembly and profiling Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
	19.	Method FOCAL: an experimental design tool for systematizing metabolic discoveries and model development Christopher J Tervo, Jennifer L Reed Genome Biology 2012, 13:R116 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype
	20.	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
	21.	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
	22.	Comment How to evaluate a graduate studentship, or choosing the right doctoral advisor Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Duncan Odom has some sage advice for those considering PhD options
	23.	Research A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans Anna C Need, Dalia Kasperavičiūtė, Elizabeth T Cirulli, David B Goldstein Genome Biology 2009, 10:R7 (22 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A principal components analysis of genomic information showed that individuals with full Jewish ancestry formed a clearly distinct cluster from those individuals with no Jewish ancestry.
	24.	Software EpiExplorer: live exploration and global analysis of large epigenomic datasets Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer, Christoph Bock Genome Biology 2012, 13:R96 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A text indexing algorithm enables extremely rapid, global analysis of large epigenomic datasets
	25.	Research Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph, Till S Voss Genome Biology 2012, 13:R108 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins