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51.

1080
Accesses

Research   Open Access Highly Accessed

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.

1072
Accesses

Review   Subscription

Studying the microbiology of the indoor environment

Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study

53.

1037
Accesses

Research   Open Access Highly Accessed

A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response

Scott Schwartz, Iddo Friedberg, Ivan V Ivanov, Laurie A Davidson, Jennifer S Goldsby, David B Dahl, Damir Herman, Mei Wang, Sharon M Donovan, Robert S Chapkin Genome Biology 2012, 13:r32 (30 April 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota

54.

1004
Accesses

Comment   Free Highly Accessed

Sequestration: inadvertently killing biomedical research to score political points

Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013)

Abstract | Full text | PDF | PubMed | 1 comment |  Editor’s summary

Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction

55.

988
Accesses

Research   Open Access Highly Accessed

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

56.

976
Accesses

Method   Open Access Highly Accessed

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.

971
Accesses

Method   Open Access Highly Accessed

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

58.

960
Accesses

Research   Open Access Highly Accessed

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.

59.

956
Accesses

Research   Open Access Highly Accessed

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 Burglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Soon 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 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

60.

955
Accesses

Method   Open Access Highly Accessed

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

61.

948
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.

62.

946
Accesses

Method   Open Access Highly Accessed

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

63.

927
Accesses

Research   Open Access

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

64.

886
Accesses

Software   Open Access Highly Accessed

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.

65.

890
Accesses

Method   Open Access Highly Accessed

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

66.

880
Accesses

Software   Open Access Highly Accessed

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.

67.

879
Accesses

Research   Open Access Highly Accessed

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

68.

876
Accesses

Research highlight   Subscription Highly Accessed

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

69.

857
Accesses

Research   Open Access Highly Accessed

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

70.

827
Accesses

Correspondence   Free Highly Accessed

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.

71.

819
Accesses

Research   Open Access Highly Accessed

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Daniel P Melters, Keith R Bradnam, Hugh A Young, Natalie Telis, Michael R May, J GRAHAM Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank, Jose Fernando 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

72.

814
Accesses

Research   Open Access Highly Accessed

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

73.

803
Accesses

Research   Open Access Highly Accessed

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

74.

797
Accesses

Method   Open Access Highly Accessed

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.

785
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

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