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76.

785
Accesses

Research   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Free Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Free Highly Accessed

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   Subscription Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Subscription Highly Accessed

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   Free Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Free Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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.

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