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	1.	Comment A Faustian bargain Gregory A Petsko Genome Biology 2010, 11:138 (31 October 2010) Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary An open letter to George M Philip, President of the State University of New York At Albany.
	2.	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
	3.	Method Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes Georgia Giannoukos, Dawn M Ciulla, Katherine Huang, Brian J Haas, Jacques Izard, Joshua Z Levin, Jonathan Livny, Ashlee M Earl, Dirk Gevers, Doyle V Ward, Chad Nusbaum, Bruce W Birren, Andreas Gnirke Genome Biology 2012, 13:R23 (28 March 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A method is presented for transcriptome sequencing of complex bacterial mixtures or communities
	4.	Method Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer Genome Biology 2011, 12:R124 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples
	5.	Research Implications for health and disease in the genetic signature of the Ashkenazi Jewish population Saurav Guha, Jeffrey A Rosenfeld, Anil K Malhotra, Annette T Lee, Peter K Gregersen, John M Kane, Itsik Pe'er, Ariel Darvasi, Todd Lencz Genome Biology 2012, 13:R2 (25 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A population-specific genetic signature, derived from a large genotyping study, helps explain why some diseases are overrepresented in the Ashkenazi population
	6.	Research Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems André E Minoche, Juliane C Dohm, Heinz Himmelbauer Genome Biology 2011, 12:R112 (8 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Error rates are compared in data from Illumina's HiSeq and GAIIx systems
	7.	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.
	8.	Research Moving pictures of the human microbiome J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I Gordon, Rob Knight Genome Biology 2011, 12:R50 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The dynamism of microbiome populations is seen in daily samples from a landmark multi-body site, multi-individual study
	9.	Research Genetic adaptation to high altitude in the Ethiopian highlands Laura B Scheinfeldt, Sameer Soi, Simon Thompson, Alessia Ranciaro, Dawit Woldemeskel, William Beggs, Charla Lambert, Joseph P Jarvis, Dawit Abate, Gurja Belay, Sarah A Tishkoff Genome Biology 2012, 13:R1 (20 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genetics of hypoxia selection in an Ethiopian high-altitude population are distinct from Andean and Tibetan genotypes, suggestive of convergent evolution
	10.	Method A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data Desmond S Lun, Ashley Sherrid, Brian Weiner, David R Sherman, James E Galagan Genome Biology 2009, 10:R142 (22 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CSdeconv is a novel method for determining the location of transcription factor binding from ChIP-seq data that discriminates closely-spaced sites.
	11.	Research Comparison of solution-based exome capture methods for next generation sequencing Anna-Maija Sulonen, Pekka Ellonen, Henrikki Almusa, Maija Lepistö, Samuli Eldfors, Sari Hannula, Timo Miettinen, Henna Tyynismaa, Perttu Salo, Caroline Heckman, Heikki Joensuu, Taneli Raivio, Anu Suomalainen, Janna Saarela Genome Biology 2011, 12:R94 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Roche NimbleGen and Agilent solution-based exome capture kits are compared. NimbleGen kits give more accurate alignments to target regions
	12.	Research A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response Scott Schwartz, Iddo Friedberg, Ivan V Ivanov, Laurie A Davidson, Jennifer S Goldsby, David B Dahl, Damir Herman, Mei Wang, Sharon M Donovan, Robert Chapkin Genome Biology 2012, 13:R32 (30 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota
	13.	Review Computational and statistical approaches to analyzing variants identified by exome sequencing Nathan O Stitziel, Adam Kiezun, Shamil Sunyaev Genome Biology 2011, 12:227 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Many computational and statistical methods are now available to narrow down causal variants in exome sequencing data, for both Mendelian and complex diseases
	14.	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 \| Editor’s summary ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq
	15.	Opinion What does biologically meaningful mean? A perspective on gene regulatory network validation Albertha JM Walhout Genome Biology 2011, 12:109 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Deciding whether gene regulatory interactions are biologically meaningful is not as simple as it might seem.
	16.	Review Bacterial epidemiology and biology - lessons from genome sequencing Julian Parkhill, Brendan W Wren Genome Biology 2011, 12:230 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Brendan Wren and Julian Parkhill on how a new era in microbial genomics has solved ancient controversies and promises to revolutionize our understanding of bacterial pathogens
	17.	Research The draft genome and transcriptome of Cannabis sativa Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
	18.	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 \| Editor’s summary Software for data integration and mining of biomedical data
	19.	Software CellProfiler: image analysis software for identifying and quantifying cell phenotypes Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Kang, Ola Friman, David A Guertin, Joo Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini Genome Biology 2006, 7:R100 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CellProfiler, the first free, open-source system for flexible and high-throughput cell image analysis is described.
	20.	Method An integrative probabilistic model for identification of structural variation in sequencing data Suzanne S Sindi, Selim Onal, Luke Peng, Hsin-Ta Wu, Benjamin J Raphael Genome Biology 2012, 13:R22 (27 March 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary GASVpro is a method for structural variant detection that takes in to account both paired read and read depth signals
	21.	Opinion Comparing protein abundance and mRNA expression levels on a genomic scale Dov Greenbaum, Christopher Colangelo, Kenneth Williams, Mark Gerstein Genome Biology 2003, 4:117 (29 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We review the results of attempts to correlate protein abundance with mRNA expression levels, focusing on yeast.
	22.	Software RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations Mauro AA Castro, Xin Wang, Michael NC Fletcher, Kerstin B Meyer, Florian Markowetz Genome Biology 2012, 13:R29 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for visualizing complex, large-scale networks that combines R/Bioconductor with Java, and allows the incorporation of plug-ins
	23.	Method Path finding methods accounting for stoichiometry in metabolic networks Jon Pey, Joaquín Prada, John E Beasley, Francisco J Planes Genome Biology 2011, 12:R49 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The incorporation of stoichiometry into path finding improves metabolic network analysis
	24.	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 \| F1000 Biology \| Editor’s summary Deep sequencing reveals miRNAs expressed during rice pollen development
	25.	Research Benchmarking ortholog identification methods using functional genomics data Tim Hulsen, Martijn A Huynen, Jacob de Vlieg, Peter MA Groenen Genome Biology 2006, 7:R31 (13 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A benchmarking of the most popular orthologous identification methods using functional genomics data identifies the two best methods.