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	51. 988 Accesses	Research DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes Dvir Aran, Sivan Sabato, Asaf Hellman Genome Biology 2013, 14:R21 (12 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers
	52. 984 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
	53. 933 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 \| Provisional 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
	54. 933 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
	55. 931 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
	56. 929 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
	57. 912 Accesses	Research Analysis of variation at transcription factor binding sites in Drosophila and humans Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, Ewan Birney Genome Biology 2012, 13:R49 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription factor binding site variability in fly and human provides evidence for a buffering phenomenon
	58. 908 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.
	59. 905 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.
	60. 892 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. 859 Accesses	Research RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grutzner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
	62. 855 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
	63. 857 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
	64. 846 Accesses	Correspondence Do-it-yourself genetic testing Steven L Salzberg, Mihaela Pertea Genome Biology 2010, 11:404 (7 October 2010) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary How to test your BRCA status and why we need to prepare for the personal genomics age.
	65. 837 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
	66. 830 Accesses	Research Transposable elements reveal a stem cell-specific class of long noncoding RNAs David Kelley, John Rinn Genome Biology 2012, 13:R107 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A characterization of the transposable element content of human lincRNAs to resolve the evolutionary origins of lincRNAs in the human genome
	67. 827 Accesses	Research Retrotransposition of gene transcripts leads to structural variation in mammalian genomes Adam D Ewing, Tracy J Ballinger, Dent Earl, Broad Institute Genome Sequencing and Analysis Program and Platform, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
	68. 821 Accesses	Method High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord Genome Biology 2011, 12:R104 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
	69. 820 Accesses	Software Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team Genome Biology 2010, 11:R86 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy computing platform allows researchers to share data and data analysis workflows, facilitating easily reproducible analyses.
	70. 806 Accesses	Research Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution Daniël P Melters, Keith R Bradnam, Hugh A Young, Natalie Telis, Michael R May, J Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank, José Garcia, Joseph L DeRisi, Timothy Smith, Christian Tobias, Jeffrey Ross-Ibarra, Ian Korf, Simon WL Chan Genome Biology 2013, 14:R10 (30 January 2013) Abstract \| Provisional PDF \| PubMed \| F1000 Biology \| Editor’s summary An analysis of centromere tandem repeats in 282 species reveals similar modes of evolution despite the lack of sequence conservation
	71. 811 Accesses	Software Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult, Joel L Sussman Genome Biology 2008, 9:R121 (3 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Proteopedia is an interactive wiki-style web resource that presents 3D structural and functional information in a user-friendly manner and allows real-time community annotation.
	72. 808 Accesses	Research highlight A CRISPR way to engineer the human genome Sivaprakash Ramalingam, Narayana Annaluru, Srinivasan Chandrasegaran Genome Biology 2013, 14:107 (26 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Srinivasan Chandrasegaran and colleagues explain how recent advances in mammalian genome engineering exploit the natural properties of the bacterial CRISPR system
	73. 805 Accesses	Research Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Bürglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang, Peter Hegemann, Hillel Fromm, Didier Raoult, Gilbert Greub, Diego Miranda-Saavedra, Nansheng Chen, Piers Nash et al. Genome Biology 2013, 14:R11 (1 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
	74. 775 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.
	75. 766 Accesses	Research Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells Deborah A Sanders, Caryn S Ross-Innes, Dario Beraldi, Jason S Carroll, Shankar Balasubramanian Genome Biology 2013, 14:R6 (24 January 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Binding sites for FOXM1 are mapped in breast cancer cell lines with and without estrogen receptor