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	26. 1667 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
	27. 1661 Accesses	Research Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function Xiaoming Zhang, Jing Xia, Yifan E Lii, Blanca E Barrera-Figueroa, Xuefeng Zhou, Shang Gao, Lu Lu, Dongdong Niu, Zheng Chen, Christy Leung, Timothy Wong, Huiming Zhang, Jianhua Guo, Yi Li, Renyi Liu, Wanqi Liang, Jian-Kang Zhu, Weixiong Zhang, Hailing Jin Genome Biology 2012, 13:R20 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In Arabidopsis and rice, natural antisense transcripts are processed into siRNAs by DCL1 and DCL3
	28. 1580 Accesses	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
	29. 1576 Accesses	Research highlight The complex binding of PRDM9 Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
	30. 1484 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
	31. 1478 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. 1420 Accesses	Method Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson Genome Biology 2013, 14:R24 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples
	33. 1416 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
	34. 1392 Accesses	Meeting report The future of genomic medicine is here Konrad J Karczewski Genome Biology 2013, 14:304 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 6th annual Future of Genomic Medicine conference, held at the Scripps Seaside Forum, La Jolla, CA, USA, March 7-8, 2013
	35. 1342 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
	36. 1324 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.
	37. 1316 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
	38. 1283 Accesses	Research Contribution of transcriptional regulation to natural variations in Arabidopsis Wenqiong J Chen, Sherman H Chang, Matthew E Hudson, Wai-King Kwan, Jingqiu Li, Bram Estes, Daniel Knoll, Liang Shi, Tong Zhu Genome Biology 2005, 6:R32 (15 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Among five accessions 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis, identifying 60 genes that were differentially expressed in different accession backgrounds in an organ-dependent manner. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession.
	39. 1269 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.
	40. 1265 Accesses	Research Function-informed transcriptome analysis of Drosophila renal tubule Jing Wang, Laura Kean, Jingli Yang, Adrian K Allan, Shireen A Davies, Pawel Herzyk, Julian AT Dow Genome Biology 2004, 5:R69 (26 August 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Analysis of the transcriptome of the Drosophila melanogaster Malpighian (renal) tubule gives a radically new view of the function of the tubule, emphasising solute transport rather than fluid secretion.
	41. 1250 Accesses	Research The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude. Qingle Cai, Xiaoju Qian, Yongshan Lang, Yadan Luo, Shengkai Pan, Yuanyuan Hui, Caiyun Gou, Yue Cai, Meirong Hao, Jinyang Zhao, Songbo Wang, Zhaobao Wang, Xinming Zhang, Jinchao Liu, Longhai Luo, Yingrui Li, Jun Wang, Rongjun He, Fumin Lei, Jiaohui Xu Genome Biology 2013, 14:R29 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The ground tit genome, one of the highest quality avian genome assemblies to date, reveals potential mechanisms of high altitude adaptation
	42. 1244 Accesses	Research Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb-target genes James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendegast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells
	43. 1234 Accesses	Research Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data Jong Kim, John C Marioni Genome Biology 2013, 14:R7 (28 January 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new framework for modeling stochastic gene expression in single cells yields insights into the regulatory role of histone modifications
	44. 1212 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.
	45. 1137 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
	46. 1096 Accesses	Software MetAMOS: a modular and open source metagenomic assembly and analysis pipeline Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya, Brian Ondov, Aaron E Darling, Adam M Phillippy, Mihai Pop Genome Biology 2013, 14:R2 (15 January 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A modular, metagenomic analysis and assembly pipeline that inputs next-generation sequencing reads to generate genomic scaffolds and open reading frames
	47. 1091 Accesses	Research Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder, Mark Gerstein Genome Biology 2012, 13:R48 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions
	48. 1084 Accesses	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
	49. 1081 Accesses	Research Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes Pedro G Ferreira, Solenn Patalano, Ritika Chauhan, Richard Ffrench-Constant, Toni Gabaldon, Roderic Guigo, Seirian Sumner Genome Biology 2013, 14:R20 (26 February 2013) Abstract \| Provisional PDF \| PubMed \| 2 comments \| Editor’s summary An RNA-seq analysis of the genetic mechanisms controlling alternative phenotypes in the primitive eusocial wasp Polistes canadensis
	50. 1081 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 \| Editor’s summary An analysis of the microbes and microbial metabolism present in intestinal biopsies and stool samples from 231 IBD and healthy subjects