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	51. 1001 Accesses	Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data
	52. 988 Accesses	Method User guide for mapping-by-sequencing in Arabidopsis Geo Velikkakam James, Vipul Patel, Karl JV Nordstrom, Jonas R Klasen, Patrice A Salome, Detlef Weigel, Korbinian Schneeberger Genome Biology 2013, 14:R61 (17 June 2013) Abstract \| Provisional PDF \| Editor’s summary Method for mapping-by-sequencing in Arabidopsis, using the Pop-seq software, and application to barley and rice as well
	53. 949 Accesses	Method jMOSAiCS: joint analysis of multiple ChIP-seq datasets Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sündüz Kele Genome Biology 2013, 14:R38 (29 April 2013) Abstract \| Provisional PDF \| Editor’s summary A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
	54. 922 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 Gabaldón, Roderic Guigó, Seirian Sumner Genome Biology 2013, 14:R20 (26 February 2013) Abstract \| Full text \| 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
	55. 923 Accesses	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 \| Cited on BioMed Central \| Editor’s summary Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
	56. 913 Accesses	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 \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented for transcriptome sequencing of complex bacterial mixtures or communities
	57. 913 Accesses	Research Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
	58. 892 Accesses	Research Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis Veronica Gregis, Fernando Andrés, Alice Sessa, Rosalinda F Guerra, Sara Simonini, Julieta L Mateos, Stefano Torti, Federico Zambelli, Gian Marco Prazzoli, Katrine N Bjerkan, Paul E Grini, Giulio Pavesi, Lucia Colombo, George Coupland, Martin M Kater Genome Biology 2013, 14:R56 (11 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of SVP-regulated pathways that control vegetative and floral meristem development
	59. 879 Accesses	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.
	60. 873 Accesses	Research Evaluation of next generation sequencing platforms for population targeted sequencing studies Olivier Harismendy, Pauline C Ng, Robert L Strausberg, Xiaoyun Wang, Timothy B Stockwell, Karen Y Beeson, Nicholas J Schork, Sarah S Murray, Eric J Topol, Samuel Levy, Kelly A Frazer Genome Biology 2009, 10:R32 (27 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Human sequence generated from three next-generation sequencing platforms reveals systematic variability in sequence coverage due to local sequence characteristics.
	61. 870 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
	62. 871 Accesses	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 \| F1000 Biology \| Editor’s summary The dynamism of microbiome populations is seen in daily samples from a landmark multi-body site, multi-individual study
	63. 864 Accesses	Method qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data Jan Hellemans, Geert Mortier, Anne De Paepe, Frank Speleman, Jo Vandesompele Genome Biology 2007, 8:R19 (9 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary qBase, a free program for the management and automated analysis of qPCR data, is described
	64. 838 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
	65. 839 Accesses	Research Systematic biases in DNA copy number originate from isolation procedures Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation
	66. 826 Accesses	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
	67. 821 Accesses	Method EMu: probabilistic inference of mutational processes and their localization in the cancer genome Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
	68. 816 Accesses	Research p53 induces transcriptional and translational programs to suppress cell proliferation and growth Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress
	69. 813 Accesses	Method Gene ontology analysis for RNA-seq: accounting for selection bias Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack Genome Biology 2010, 11:R14 (4 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq
	70. 814 Accesses	Method A novel and universal method for microRNA RT-qPCR data normalization Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele Genome Biology 2009, 10:R64 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The mean expression value: a new method for accurate and reliable normalization of microRNA expression data from RT-qPCR experiments.
	71. 792 Accesses	Method SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan, Xiangke Liao, Xiaoqian Zhu, Shaoliang Peng, Yingrui Li, Jun Wang, Guangwu Guo Genome Biology 2013, 14:R12 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements
	72. 793 Accesses	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 \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
	73. 789 Accesses	Research DNA binding specificities of the long zinc-finger recombination protein PRDM9 Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
	74. 791 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 \| Full text \| 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
	75. 787 Accesses	Research DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Jordana T Bell, Athma A Pai, Joseph K Pickrell, Daniel J Gaffney, Roger Pique-Regi, Jacob F Degner, Yoav Gilad, Jonathan K Pritchard Genome Biology 2011, 12:R10 (20 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Profiling lymphoblastoid cell lines from HapMap individuals reveals a significant genetic component for inter-individual DNA methylation and gene expression