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	1.	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
	2.	Comment Economies of scale Gregory A Petsko Genome Biology 2012, 13:154 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The current glut of postdoctoral and graduate scientists can be addressed by applying economic principles.
	3.	Review Current challenges in de novo plant genome sequencing and assembly Michael C Schatz, Jan Witkowski, W Richard McCombie Genome Biology 2012, 13:243 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
	4.	Review Genetic architecture of body size in mammals Kathryn E Kemper, Peter M Visscher, Michael E Goddard Genome Biology 2012, 13:244 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Peter Visscher and colleagues survey the current known mutations affecting body size in humans, mice, dogs and livestock species
	5.	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
	6.	Comment Goodbye, Columbus Gregory A Petsko Genome Biology 2012, 13:155 (18 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Guaranteeing experimental outcomes and findings: funding then and now
	7.	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.
	8.	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.
	9.	Research GeneChip analysis of human embryonic stem cell differentiation into hemangioblasts: an in silico dissection of mixed phenotypes Shi-Jiang Lu, Jennifer A Hipp, Qiang Feng, Jason D Hipp, Robert Lanza, Anthony Atala Genome Biology 2007, 8:R240 (13 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of human embryonic stem cells differentiating into blast cells reveals that erythroblasts are the predominant cell type in the blast cell population. In silico comparisons with publicly available data sets revealed the presence of endothelia, cardiomyocytes and hematopoietic lineages.
	10.	Research Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity Fernando Ulloa-Montoya, Benjamin L Kidder, Karen A Pauwelyn, Lucas G Chase, Aernout Luttun, Annelies Crabbe, Martine Geraerts, Alexei A Sharov, Yulan Piao, Minoru SH Ko, Wei-Shou Hu, Catherine M Verfaillie Genome Biology 2007, 8:R163 (6 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Comparison of the transcriptomes of pluripotent embryonic stem cells, multipotent adult progenitor cells and lineage restricted mesenchymal stem cells identified a unique gene expression profile of multipotent adult progenitor cells.
	11.	Research Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia Xiaobo Xia, Andrew L Kung Genome Biology 2009, 10:R113 (14 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip and microarray expression studies show that, in response to hypoxia, HIF-1 preferentially binds to and up-regulates already active genes.
	12.	Research Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens Mark W Silby, Ana M Cerdeño-Tárraga, Georgios S Vernikos, Stephen R Giddens, Robert W Jackson, Gail M Preston, Xue-Xian Zhang, Christina D Moon, Stefanie M Gehrig, Scott AC Godfrey, Christopher G Knight, Jacob G Malone, Zena Robinson, Andrew J Spiers, Simon Harris, Gregory L Challis, Alice M Yaxley, David Harris, Kathy Seeger, Lee Murphy, Simon Rutter, Rob Squares, Michael A Quail, Elizabeth Saunders, Konstantinos Mavromatis, Thomas S Brettin, Stephen D Bentley, Joanne Hothersall, Elton Stephens, Christopher M Thomas, Julian Parkhill, Stuart B Levy, Paul B Rainey, Nicholas R Thomson et al. Genome Biology 2009, 10:R51 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the genome sequences of three Pseudomonas fluorescens strains reveals a heterogeneity reminiscent of a species complex rather than a single species
	13.	Method Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen Genome Biology 2009, 10:R79 (22 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A set of methods is presented for normalization, quantification of noise and co-expression analysis for gene expression studies using deep sequencing.
	14.	Research Somatic structural rearrangements in genetically engineered mouse mammary tumors Ignacio Varela, Christiaan Klijn, Phillip J Stephens, Laura J Mudie, Lucy Stebbings, Danushka Galappaththige, Hanneke van der Gulden, Eva Schut, Sjoerd Klarenbeek, Peter J Campbell, Lodewyk FA Wessels, Michael R Stratton, Jos Jonkers, P Andrew Futreal, David J Adams Genome Biology 2010, 11:R100 (13 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Paired-end sequencing of mouse models of mammary tumors reveals the landscape of genome rearrangements and gene fusions.
	15.	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.
	16.	Research The developmental expression dynamics of Drosophila melanogaster transcription factors Boris Adryan, Sarah A Teichmann Genome Biology 2010, 11:R40 (12 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High levels of combinatorial complexity of transcription factors during embryogenesis in Drosophila melanogaster shed light on mechanisms of transcriptional control.
	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.	Research Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer Wigard P Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S Vermaat, Markus J van Roosmalen, Stef van Lieshout, Isaac J Nijman, Wijnand Roessingh, Ruben van 't Slot, José van de Belt, Victor Guryev, Marco Koudijs, Emile Voest, Edwin Cuppen Genome Biology 2011, 12:R103 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chromothripsis is found to be a common mechanism driving structural rearrangement in primary colorectal cancer and metastases
	19.	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
	20.	Research MicroRNAs and their isomiRs function cooperatively to target common biological pathways Nicole Cloonan, Shivangi Wani, Qinying Xu, Jian Gu, Kristi Lea, Sheila Heater, Catalin Barbacioru, Anita L Steptoe, Hilary C Martin, Ehsan Nourbakhsh, Keerthana Krishnan, Brooke Gardiner, Xiaohui Wang, Katia Nones, Jason A Steen, Nicholas A Matigian, David L Wood, Karin S Kassahn, Nic Waddell, Jill Shepherd, Clarence Lee, Jeff Ichikawa, Kevin McKernan, Kelli Bramlett, Scott Kuersten, Sean M Grimmond Genome Biology 2011, 12:R126 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary IsomiRs act cooperatively with canonical miRNAs to regulate gene expression
	21.	Method EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield Genome Biology 2011, 12:R44 (19 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Reconstructing full length rRNA sequences from short reads to estimate microbial community structure
	22.	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 \| Editor’s summary A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm
	23.	Comment Apocalypse now? Gregory A Petsko Genome Biology 2012, 13:151 (30 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko identifies some signs of the coming end of the world and, in that context, urges readers to pay close attention to the coming US presidential election
	24.	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
	25.	Research High levels of RNA-editing site conservation amongst 15 laboratory mouse strains Petr Danecek, Christoffer Nellåker, Rebecca E McIntyre, Jorge E Buendia-Buendia, Suzannah Bumpstead, Chris P Ponting, Jonathan Flint, Richard Durbin, Thomas M Keane, David J Adams Genome Biology 2012, 13:26 (23 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An extensive, genome-wide analysis of RNA editing in the brain transcriptomes of 15 mouse strains