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1.

Research   Open Access Highly Accessed

Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system

Stephen E Von Stetina, Joseph D Watson, Rebecca M Fox, Kellen L Olszewski, W Clay Spencer, Peter J Roy, David M Miller Genome Biology 2007, 8:R135 (5 July 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A novel strategy for profiling Caenorhabditis elegans cells identifies transcripts highly enriched in either the embryonic or larval C. elegans nervous system, including 19 conserved transcripts of unknown function that are also expressed in the mammalian brain.

2.

Method   Open Access Highly Accessed

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb Genome Biology 2011, 12:R67 (25 July 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq

3.

Comment   Free Highly Accessed

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.

4.

Research   Open Access Highly Accessed

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman Genome Biology 2002, 3:research0034-research0034.11 (18 June 2002)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment |  Editor’s summary

Using real-time reverse transcription PCR ten housekeeping genes from different abundance and functional classes in various human tissues were evaluated. The conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested.

5.

Research   Open Access Highly Accessed

Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes

Sandip Paul, Sumit K Bag, Sabyasachi Das, Eric T Harvill, Chitra Dutta Genome Biology 2008, 9:R70 (9 April 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A comparative genomic and proteomic study of halophilic and non-halophilic prokaryotes identifies specific genomic and proteomic features typical of halophilic species that are independent from genomic GC-content and taxonomic position.

6.

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.

7.

Review   Free Highly Accessed

From RNA-seq reads to differential expression results

Alicia Oshlack, Mark D Robinson, Matthew D Young Genome Biology 2010, 11:220 (22 December 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.

8.

Opinion   Free Highly Accessed

Bioinformatics: alive and kicking

Lincoln D Stein Genome Biology 2008, 9:114 (17 December 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Bioinformatics is alive and well in 2008 concludes Lincoln Stein, despite his earlier prediction of its imminent demise.

9.

Software   Open Access Highly Accessed

CellProfiler: image analysis software for identifying and quantifying cell phenotypes

Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Kang, Ola Friman, David A Guertin, Joo Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini Genome Biology 2006, 7:R100 (31 October 2006)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

CellProfiler, the first free, open-source system for flexible and high-throughput cell image analysis is described.

10.

Software   Open Access Highly Accessed

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R25 (4 March 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.

11.

Method   Open Access Highly Accessed

A scaling normalization method for differential expression analysis of RNA-seq data

Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A novel and empirical method for normalization of RNA-seq data is presented

12.

Comment   Free Highly Accessed

Having an impact (factor)

Gregory A Petsko Genome Biology 2008, 9:107 (29 July 2008)

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

A recently departed genome biologist discusses the impact factor of his life with St Peter at the Pearly Gates.

13.

Editorial   Free

Editor's note

Genome Biology 2000, 1:comment0002-comment0002.2 (13 October 2000)

Full text |  Editor’s summary

The fourth issue of GenomeBiology sees the launch of two new article types, the protein family review and the tutorial.

14.

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.

15.

Software   Open Access Highly Accessed

Searching for SNPs with cloud computing

Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.

16.

Research   Open Access Highly Accessed

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen Genome Biology 2009, 10:R80 (23 July 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions.

17.

Software   Open Access Highly Accessed

Calling on a million minds for community annotation in WikiProteins

Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert-Jan van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Jimmy Wales, Gerard Meijssen, Erik Moeller, Peter Roes, Katy Borner, Amos Bairoch Genome Biology 2008, 9:R89 (28 May 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

WikiProteins is a novel tool that allows community annotation in an open access, wiki-based system.

18.

Research   Open Access Highly Accessed

A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans

Anna C Need, Dalia Kasperavičiūtė, Elizabeth T Cirulli, David B Goldstein Genome Biology 2009, 10:R7 (22 January 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

A principal components analysis of genomic information showed that individuals with full Jewish ancestry formed a clearly distinct cluster from those individuals with no Jewish ancestry.

19.

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

20.

Research   Open Access Highly Accessed

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting

Andrew J Pask, Anthony T Papenfuss, Eleanor I Ager, Kaighin A McColl, Terence P Speed, Marilyn B Renfree Genome Biology 2009, 10:R1 (2 January 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Comparisons between the platypus and eutherian mammalian genomes provides new insights into how epigenetic imprinting may have evolved in mammalian genomes.

21.

Open letter   Free Highly Accessed

The ethics of characterizing difference: guiding principles on using racial categories in human genetics

Sandra Lee, Joanna Mountain, Barbara Koenig, Russ Altman, Melissa Brown, Albert Camarillo, Luca Cavalli-Sforza, Mildred Cho, Jennifer Eberhardt, Marcus Feldman, Richard Ford, Henry Greely, Roy King, Hazel Markus, Debra Satz, Matthew Snipp, Claude Steele, Peter Underhill Genome Biology 2008, 9:404 (15 July 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment |  Editor’s summary

We are a multidisciplinary group of Stanford faculty who propose ten principles to guide the use of racial and ethnic categories when characterizing group differences in research into human genetic variation.

22.

Protein family review   Free

The 14-3-3s

Robert J Ferl, Michael S Manak, Matthew F Reyes Genome Biology 2002, 3:reviews3010-reviews3010.7 (27 June 2002)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The major native forms of 14-3-3s are homo- and hetero-dimers, the biological functions of which are to interact physically with specific client proteins and thereby effect a change in the client. As a result, 14-3-3s are involved in a vast array of processes such as the response to stress, cell-cycle control, and apoptosis, serving as adapters, activators, and repressors. There are currently 133 full-length sequences available.

23.

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.

24.

Research   Open Access Highly Accessed

Metabolic changes in schizophrenia and human brain evolution

Philipp Khaitovich, Helen E Lockstone, Matthew T Wayland, Tsz M Tsang, Samantha D Jayatilaka, Arfu J Guo, Jie Zhou, Mehmet Somel, Laura W Harris, Elaine Holmes, Svante Pääbo, Sabine Bahn Genome Biology 2008, 9:R124 (5 August 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Human cognitive evolution involved genes implicated in energy metabolism and energy-expensive brain functions that are also altered in schizophrenia, suggesting that human brains may have reached their metabolic limit, with schizophrenia as a costly by-product.

25.

Method   Open Access Highly Accessed

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones Genome Biology 2009, 10:R94 (11 September 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A method for de novo assembly of a eukaryotic genome using Illumina, 454 and Sanger generated sequence data

26.

Research   Open Access Highly Accessed

Community-wide analysis of microbial genome sequence signatures

Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton, Jillian F Banfield Genome Biology 2009, 10:R85 (21 August 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members.

27.

Method   Open Access Highly Accessed

Genome-wide prediction of transcription factor binding sites using an integrated model

Kyoung-Jae Won, Bing Ren, Wei Wang Genome Biology 2010, 11:R7 (22 January 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A new approach for genome-wide transcription factor binding site prediction is presented that integrates sequence and chromatin modification data.

28.

Research   Open Access Highly Accessed

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.

29.

Method   Open Access Highly Accessed

Sniper: improved SNP discovery by multiply mapping deep sequenced reads

Daniel F Simola, Junhyong Kim Genome Biology 2011, 12:R55 (20 June 2011)

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

A method for improved SNP discovery in next-generation sequencing data

30.

Method   Open Access Highly Accessed

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

Desmond S Lun, Ashley Sherrid, Brian Weiner, David R Sherman, James E Galagan Genome Biology 2009, 10:R142 (22 December 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

CSdeconv is a novel method for determining the location of transcription factor binding from ChIP-seq data that discriminates closely-spaced sites.

31.

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

32.

Research   Open Access Highly Accessed

Implications for health and disease in the genetic signature of the Ashkenazi Jewish population

Saurav Guha, Jeffrey A Rosenfeld, Anil K Malhotra, Annette T Lee, Peter K Gregersen, John M Kane, Itsik Pe'er, Ariel Darvasi, Todd Lencz Genome Biology 2012, 13:R2 (25 January 2012)

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

A population-specific genetic signature, derived from a large genotyping study, helps explain why some diseases are overrepresented in the Ashkenazi population

33.

Research   Open Access Highly Accessed

Proteomic analysis of the secretome of Leishmania donovani

J Maxwell Silverman, Simon K Chan, Dale P Robinson, Dennis M Dwyer, Devki Nandan, Leonard J Foster, Neil E Reiner Genome Biology 2008, 9:R35 (18 February 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Analysis of Leishmania-conditioned medium resulted in the identification of 151 proteins apparently secreted by the parasitic protozoan Leishmania donovani and suggested a vesicle-based secretion system.

34.

Research   Open Access Highly Accessed

Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity

Corneliu Henegar, Joan Tordjman, Vincent Achard, Danièle Lacasa, Isabelle Cremer, Michèle Guerre-Millo, Christine Poitou, Arnaud Basdevant, Vladimir Stich, Nathalie Viguerie, Dominique Langin, Pierre Bedossa, Jean-Daniel Zucker, Karine Clement Genome Biology 2008, 9:R14 (21 January 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Analysis of the transcriptomic signature of white adipose tissue in obese human subjects revealed increased interstitial fibrosis and an infiltration of inflammatory cells into the tissue.

35.

Software   Open Access Highly Accessed

Constructing a fish metabolic network model

Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The first genome-wide fish metabolic model, MetaFishNet, is presented.

36.

Research   Open Access Highly Accessed

The draft genome and transcriptome of Cannabis sativa

Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment | F1000 Biology |  Editor’s summary

The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity

37.

Software   Open Access Highly Accessed

PyCogent: a toolkit for making sense from sequence

Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying, Gavin A Huttley Genome Biology 2007, 8:R171 (21 August 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The COmparative GENomic Toolkit, a framework for probabilistic analyses of biological sequences, devising workflows and generating publication quality graphics, has been implemented in Python.

38.

Research   Open Access Highly Accessed

Many LINE1 elements contribute to the transcriptome of human somatic cells

Sanjida H Rangwala, Lili Zhang, Haig H Kazazian Genome Biology 2009, 10:R100 (22 September 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Over 600 LINE 1 elements are shown to be transcribed in humans; 400 of these are full-length elements in the reference genome.

39.

Research   Open Access Highly Accessed

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium

Richard A Stabler, Miao He, Lisa Dawson, Melissa Martin, Esmeralda Valiente, Craig Corton, Trevor D Lawley, Mohammed Sebaihia, Michael A Quail, Graham Rose, Dale N Gerding, Maryse Gibert, Michel R Popoff, Julian Parkhill, Gordon Dougan, Brendan W Wren Genome Biology 2009, 10:R102 (25 September 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A genome comparison of non-epidemic and epidemic strains of Clostridium difficile reveals gene gains that could explain how a hypervirulent strain has emerged

40.

Method   Open Access Highly Accessed

Closing gaps in the human genome using sequencing by synthesis

Manuel Garber, Michael C Zody, Harindra M Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2009, 10:R60 (2 June 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A novel method for closing non-structural gaps in the human genome assembly using 454 sequencing is presented here.

41.

Review   Free Highly Accessed

The case for cloud computing in genome informatics

Lincoln D Stein Genome Biology 2010, 11:207 (5 May 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 3 comments |  Editor’s summary

With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics.

42.

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

43.

Review   Free Highly Accessed

Genetic determinants of phenotypic diversity in humans

Nazli G Rahim, Olivier Harismendy, Eric J Topol, Kelly A Frazer Genome Biology 2008, 9:215 (24 April 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

New techniques are enabling the identification of genetic variants underlying complex diseases and phenotypic traits.

44.

Method   Open Access Highly Accessed

A simple, fast, and accurate method of phylogenomic inference

Martin Wu, Jonathan A Eisen Genome Biology 2008, 9:R151 (13 October 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

An automated pipeline for phylogenomic analysis (AMPHORA) is presented that overcomes existing limits to large-scale protein phylogenetic inference.

45.

Research   Open Access Highly Accessed

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

Christophe Dessimoz, Manuel Gil Genome Biology 2010, 11:R37 (6 April 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Tree-based tests of alignment methods enable the evaluation of the effect of gap placement on the inference of phylogenetic relationships.

46.

Method   Open Access Highly Accessed

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network

Alexey V Antonov, Sabine Dietmann, Hans W Mewes Genome Biology 2008, 9:R179 (18 December 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A web-based tool for interpretation of experimentally-derived gene lists that provides global models uniting genes from different metabolic pathways.

47.

Research   Open Access Highly Accessed

Preferential regulation of duplicated genes by microRNAs in mammals

Jingjing Li, Gabriel Musso, Zhaolei Zhang Genome Biology 2008, 9:R132 (26 August 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Analysis of duplicate genes and predicted microRNA targets in human and mouse shows that microRNAs are important in how the regulatory patterns of mammalian paralogs have evolved.

48.

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

49.

Method   Open Access Highly Accessed

Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing

Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer Genome Biology 2011, 12:R124 (20 December 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples

50.

Research   Open Access Highly Accessed

Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases

Monika Ray, Jianhua Ruan, Weixiong Zhang Genome Biology 2008, 9:R148 (8 October 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Analysis of microarray data reveals extensive links between Alzheimer’s disease and cardiovascular diseases.

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