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	76. 785 Accesses	Research Whole-genome reconstruction and mutational signatures in gastric cancer Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Zang, Fei Yao, Pierre-Étienne Jacques, Audrey SM Teo, Ioana Cutcutache, Zhenshui Zhang, Wah Lee, Yee Sia, Song Gao, Pramila N Ariyaratne, Andrea Ho, Xing Woo, Lavanya Veeravali, Choon Ong, Niantao Deng, Kartiki V Desai, Chiea Khor, Martin L Hibberd, Atif Shahab, Jaideepraj Rao, Mengchu Wu, Ming Teh, Feng Zhu, Sze Chin, Brendan Pang, Jimmy BY So, Guillaume Bourque et al. Genome Biology 2012, 13:R115 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer.
	77. 774 Accesses	Method CGAL: computing genome assembly likelihoods Atif Rahman, Lior Pachter Genome Biology 2013, 14:R8 (29 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A likelihood based approach for better estimation of genome assembly quality
	78. 768 Accesses	Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
	79. 760 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
	80. 731 Accesses	Opinion Categorization of humans in biomedical research: genes, race and disease Neil Risch, Esteban Burchard, Elad Ziv, Hua Tang Genome Biology 2002, 3:comment2007-comment2007.12 (1 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A debate has arisen regarding the validity of racial/ethnic categories for biomedical and genetic research. An epidemiologic perspective on the issue of human categorization in biomedical and genetic research strongly supports the continued use of self-identified race and ethnicity.
	81. 729 Accesses	Research Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies Masayuki Sugawara, Brendan Epstein, Brian Badgley, Tatsuya Unno, Lei Xu, Jennifer Reese, Prasad Gyaneshwar, Roxanne Denny, Joann Mudge, Arvind K Bharti, Andrew D Farmer, Gregory D May, Jimmy E Woodward, Claudine Medigue, David Vallenet, Aurelie Lajus, Zoe Rouy, Betsy Martinez-Vaz, Peter Tiffin, Nevin D Young, Michael J Sadowsky Genome Biology 2013, 14:R17 (20 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Sequencing the genomes of 48 strains of Sinorhizobium reveals a large heterogeneity in strategies for colonization in this family
	82. 730 Accesses	Research Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice Falk Hildebrand, Thi Nguyen, Brigitta Brinkman, Roberto Yunta, Benedicte Cauwe, Peter Vandenabeele, Adrian Liston, Jeroen Raes Genome Biology 2013, 14:R4 (24 January 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study finds that enterotypes are not only present in mice, but also similar to those in humans
	83. 723 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
	84. 718 Accesses	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.
	85. 713 Accesses	Opinion The birth of the Epitranscriptome: deciphering the function of RNA modifications Yogesh Saletore, Kate Meyer, Jonas Korlach, Igor D Vilfan, Samie Jaffrey, Christopher E Mason Genome Biology 2012, 13:175 (31 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary First came genomics, and then epigenomics. But is epitranscriptomics the future? A picture is emerging of RNA methylation's functional importance
	86. 711 Accesses	Research Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer Genome Biology 2013, 14:R14 (15 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
	87. 703 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
	88. 707 Accesses	Comment A 10-step guide to party conversation for bioinformaticians Alicia Oshlack Genome Biology 2013, 14:104 (29 January 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Alicia Oshlack's 10-step guide to party conversation for bioinformaticians
	89. 697 Accesses	Review Overview of the voltage-gated sodium channel family Frank H Yu, William A Catterall Genome Biology 2003, 4:207 (24 February 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Different sodium channels have remarkably similar functional properties, but small changes in sodium-channel function are biologically relevant, as underscored by mutations that cause several human diseases of hyperexcitability.
	90. 692 Accesses	Research Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King Genome Biology 2013, 14:R15 (18 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity
	91. 689 Accesses	Research Accelerated exon evolution within primate segmental duplications Belen Lorente-Galdos, Jonathan Bleyhl, Gabriel Santpere, Laura Vives, Oscar Ramírez, Jessica Hernandez, Roger Anglada, Gregory M Cooper, Arcadi Navarro, Evan E Eichler, Tomas Marques-Bonet Genome Biology 2013, 14:R9 (29 January 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study looks at segmental duplication genes in humans and macaques to elucidate exon evolution in primates
	92. 686 Accesses	Research Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers Alayne L Brunner, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West Genome Biology 2012, 13:R75 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs
	93. 672 Accesses	Research Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 Seth Frietze, Rui Wang, Lijing Yao, Yu Tak, Zhenqing Ye, Malaina Gaddis, Heather Witt, Peggy J Farnham, Victor X Jin Genome Biology 2012, 13:R52 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcription factor TCF7L2 can be tethered to the genome by GATA3, and therefore can target sites lacking its own motif
	94. 666 Accesses	Method Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina Leslie Genome Biology 2010, 11:R90 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary mirSVR is a method for miRNA target prediction that, unusually, takes into account non-canonical binding sequences and non-conserved sites
	95. 666 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
	96. 659 Accesses	Method Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition Andrew Adey, Hilary G Morrison, Asan, Xu Xun, Jacob O Kitzman, Emily H Turner, Bethany Stackhouse, Alexandra P MacKenzie, Nicholas C Caruccio, Xiuqing Zhang, Jay Shendure Genome Biology 2010, 11:R119 (8 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protocols for rapid, low-input sequencing library construction without clean up.
	97. 665 Accesses	Software ggbio: an R package for extending the grammar of graphics for genomic data Tengfei Yin, Dianne Cook, Michael Lawrence Genome Biology 2012, 13:R77 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent, robust and versatile software tool for visualizing genomic data
	98. 653 Accesses	Open letter Genome sequencing of the important oilseed crop Sesamum indicum L Haiyang Zhang, Hongmei Miao, Lei Wang, Lingbo Qu, Hongyan Liu, Qiang Wang, Meiwang Yue Genome Biology 2013, 14:401 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sesame Genome Working Group describe the project for sequencing the sesame genome
	99. 651 Accesses	Research Biogeography of the ecosystems of the healthy human body Yanjiao Zhou, Hongyu Gao, Kathie A Mihindukulasuriya, Patricio S La Rosa, Kristine M Wylie, Tatiana Vishnivetskaya, Mircea Podar, Barb Warner, Phillip I Tarr, David E Nelson, J Fortenberry, Martin J Holland, Sarah E Burr, William D Shannon, Erica Sodergren, George M Weinstock Genome Biology 2013, 14:R1 (14 January 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary As part of the Human Microbiome Project, taxonomic analyses were performed on the bacteria from 22 body sites on 279 subjects
	100. 651 Accesses	Software DAVID: Database for Annotation, Visualization, and Integrated Discovery Glynn Dennis, Brad T Sherman, Douglas A Hosack, Jun Yang, Wei Gao, H Lane, Richard A Lempicki Genome Biology 2003, 4:R60 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DAVID, a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries, has been described and will assist in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.