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	26. 1677 Accesses	Meeting report Genomic triumph meets clinical reality Qasim Ayub, Yali Xue, Chris Tyler-Smith Genome Biology 2013, 14:307 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Genomic Disorders 2013 - from 60 years of DNA to human genomes in the clinic' meeting, held at Homerton College, Hills Road, Cambridge, UK, April 10-12, 2013.
	27. 1628 Accesses	Research CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes Quan Zhang, Mina Rho, Haixu Tang, Thomas G Doak, Yuzhen Ye Genome Biology 2013, 14:R40 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements
	28. 1576 Accesses	Research highlight Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine Sean M Cullen, Margaret A Goodell Genome Biology 2013, 14:116 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions
	29. 1493 Accesses	Research highlight Plastic, fantastic! Phenotypic variance in the transcriptional landscape of the grape berry Alisdair R Fernie, Takayuki Tohge Genome Biology 2013, 14:119 (7 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight covering Mario Pezzotti's research article analyzing the plasticity of grape berrys in response to environmental changes
	30. 1472 Accesses	Method A scaling normalization method for differential expression analysis of RNA-seq data Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel and empirical method for normalization of RNA-seq data is presented
	31. 1424 Accesses	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.
	32. 1402 Accesses	Research Inactive or moderately active human promoters are enriched for inter-individual epialleles Carolina Gemma, Sreeram V Ramagopalan, Thomas A Down, Huriya Beyan, Mohammed I Hawa, Michelle L Holland, Paul J Hurd, Gavin Giovannoni, R David Leslie, George C Ebers, Vardhman K Rakyan Genome Biology 2013, 14:R43 (25 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions
	33. 1386 Accesses	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 \| 1 comment \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
	34. 1298 Accesses	Method Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke Genome Biology 2011, 12:R18 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The optimization of PCR amplification steps in Illumina libraries significantly reduces sequencing bias
	35. 1265 Accesses	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.
	36. 1244 Accesses	Method Improving RNA-Seq expression estimates by correcting for fragment bias Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extension to Cufflinks corrects bias in RNA-seq datasets
	37. 1239 Accesses	Method Model-based Analysis of ChIP-Seq (MACS) Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu Genome Biology 2008, 9:R137 (17 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MACS performs model-based analysis of ChIP-Seq data generated by short read sequencers.
	38. 1190 Accesses	Research Comprehensive genotyping of the USA national maize inbred seed bank Maria C Romay, Mark J Millard, Jeffrey C Glaubitz, Jason A Peiffer, Kelly L Swarts, Terry M Casstevens, Robert J Elshire, Charlotte B Acharya, Sharon E Mitchell, Sherry A Flint-Garcia, Michael D McMullen, James B Holland, Edward S Buckler, Candice A Gardner Genome Biology 2013, 14:R55 (11 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time
	39. 1183 Accesses	Software The Transcription Factor Encyclopedia Dimas Yusuf, Stefanie L Butland, Magdalena I Swanson, Eugene Bolotin, Amy Ticoll, Warren A Cheung, Xiao Cindy Zhang, Christopher TD Dickman, Debra L Fulton, Jonathan S Lim, Jake M Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N de Leeuw, Elizabeth M Simpson, Gerhart U Ryffel, Eric W-F Lam, Ralf Kist, Miranda SC Wilson, Raquel Marco-Ferreres, Jan J Brosens, Leonardo L Beccari, Paola Bovolenta, Bérénice A Benayoun, Lara J Monteiro, Helma DC Schwenen, Lars Grontved, Elizabeth Wederell, Susanne Mandrup, Reiner A Veitia et al. Genome Biology 2012, 13:R24 (29 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system
	40. 1165 Accesses	Editorial Raymond Gosling: the man who crystallized genes Naomi Attar Genome Biology 2013, 14:402 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary "The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
	41. 1155 Accesses	Method Bioconductor: open software development for computational biology and bioinformatics Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang Genome Biology 2004, 5:R80 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.
	42. 1116 Accesses	Opinion Sixty years of genome biology W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
	43. 1123 Accesses	Research A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Hoeffner, Marcus Krueger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
	44. 1118 Accesses	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
	45. 1101 Accesses	Research Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper, Athos Bousvaros, Joshua Korzenik, Bruce E Sands, Ramnik J Xavier, Curtis Huttenhower Genome Biology 2012, 13:R79 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the microbes and microbial metabolism present in intestinal biopsies and stool samples from 231 IBD and healthy subjects
	46. 1105 Accesses	Research Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome María Muñoz-Amatriaín, Steven R Eichten, Thomas Wicker, Todd A Richmond, Martin Mascher, Burkhard Steuernagel, Uwe Scholz, Ruvini Ariyadasa, Manuel Spannagl, Thomas Nussbaumer, Klaus FX Mayer, Stefan Taudien, Matthias Platzer, Jeffrey A Jeddeloh, Nathan M Springer, Gary J Muehlbauer, Nils Stein Genome Biology 2013, 14:R58 (12 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations
	47. 1100 Accesses	Research Functional analysis of transcription factor binding sites in human promoters Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Aldred, Nathan D Trinklein, Richard M Myers, Zhiping Weng Genome Biology 2012, 13:R50 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary TFBSs are predicted from ENCODE data, and experiments in four cell lines find 70% to be functional
	48. 1089 Accesses	Research Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang, Xing Wang Deng Genome Biology 2013, 14:R57 (12 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids
	49. 1064 Accesses	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 \| Cited on BioMed Central \| Editor’s summary Error rates are compared in data from Illumina's HiSeq and GAIIx systems
	50. 1055 Accesses	Research Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis Srikanth Nagalla, Jeff W Chou, Mark C Willingham, Jimmy Ruiz, James P Vaughn, Purnima Dubey, Timothy L Lash, Stephen J Hamilton-Dutoit, Jonas Bergh, Christos Sotiriou, Michael A Black, Lance D Miller Genome Biology 2013, 14:R34 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes