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	26. 37863 Accesses	Method Consensus clustering and functional interpretation of gene-expression data Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel Martin, Christine Orengo, Xiaohui Liu, Paul Kellam Genome Biology 2004, 5:R94 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Consensus clustering, a new method for analyzing microarray data that takes a consensus set of clusters from various algorithms, is shown to perform better than individual methods alone.
	27. 36967 Accesses	Research 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
	28. 36938 Accesses	Research MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype Cherie Blenkiron, Leonard D Goldstein, Natalie P Thorne, Inmaculada Spiteri, Suet-Feung Chin, Mark J Dunning, Nuno L Barbosa-Morais, Andrew E Teschendorff, Andrew R Green, Ian O Ellis, Simon Tavaré, Carlos Caldas, Eric A Miska Genome Biology 2007, 8:R214 (8 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Integrated analysis of miRNA expression and genomic changes in human breast tumors allows the classification of tumor subtypes.
	29. 37304 Accesses	Review An overview of the structures of protein-DNA complexes Nicholas M Luscombe, Susan E Austin, Helen M Berman, Janet M Thornton Genome Biology 2000, 1:reviews001-reviews001.37 (9 June 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes.
	30. 36376 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
	31. 36288 Accesses	Method Relations in biomedical ontologies Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector, Cornelius Rosse Genome Biology 2005, 6:R46 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation.
	32. 35429 Accesses	Review Evolution of mammalian genome organization inferred from comparative gene mapping William J Murphy, Roscoe Stanyon, Stephen J O'Brien Genome Biology 2001, 2:reviews0005-reviews0005.8 (5 June 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genome analyses, including chromosome painting in over 40 diverse mammalian species, ordered gene maps from several representatives of different mammalian and vertebrate orders, and large-scale sequencing of the human and mouse genomes are beginning to provide insight into the rates and patterns of chromosomal evolution on a whole-genome scale, as well as into the forces that have sculpted the genomes of extant mammalian species.
	33. 35296 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.
	34. 35278 Accesses	Correspondence Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns Rie Takahashi, Jeffrey H Miller Genome Biology 2007, 8:405 (3 May 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How to make music from the genome.
	35. 34912 Accesses	Comment A day in the life of a genome biologist in the not-too-distant future Gregory A Petsko Genome Biology 2007, 8:104 (29 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A look into the future of a biologist: daily activities governed by presidential mandates and acts.
	36. 34723 Accesses	Protein family review The Rab GTPase family Harald Stenmark, Vesa M Olkkonen Genome Biology 2001, 2:reviews3007-reviews3007.7 (27 April 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Rab family of small GTPases are central regulators of vesicle budding, motility and fusion. The GTP-bound forms of the proteins interact with a range of specific effector proteins, which play central roles in different stages of vesicular transport events.
	37. 34693 Accesses	Deposited research article DAVID: Database for Annotation, Visualization, and Integrated Discovery Glynn Dennis, Brad T Sherman, Douglas A Hosack, Jun Yang, Wei Gao, H Clifford Lane, Richard A Lempicki Genome Biology 2003, 4:P3 (3 April 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Functional annotation of differentially expressed genes is a necessary and critical step in the analysis of microarray data. Database for Annotation, Visualization, and Integrated Discovery (DAVID) provides querybased access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information.
	38. 34675 Accesses	Software 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.
	39. 34413 Accesses	Research Design and implementation of microarray gene expression markup language (MAGE-ML) Paul T Spellman, Michael Miller, Jason Stewart, Charles Troup, Ugis Sarkans, Steve Chervitz, Derek Bernhart, Gavin Sherlock, Catherine Ball, Marc Lepage, Marcin Swiatek, WL Marks, Jason Goncalves, Scott Markel, Daniel Iordan, Mohammadreza Shojatalab, Angel Pizarro, Joe White, Robert Hubley, Eric Deutsch, Martin Senger, Bruce J Aronow, Alan Robinson, Doug Bassett, Christian J Stoeckert, Alvis Brazma Genome Biology 2002, 3:research0046-research0046.9 (23 August 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.
	40. 34180 Accesses	Method MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data Scott W Doniger, Nathan Salomonis, Kam D Dahlquist, Karen Vranizan, Steven C Lawlor, Bruce R Conklin Genome Biology 2003, 4:R7 (6 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP.
	41. 34093 Accesses	Protein family review Cytochromes P450: a success story Danièle Werck-Reichhart, René Feyereisen Genome Biology 2000, 1:reviews3003-reviews3003.9 (8 December 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cytochrome P450 proteins are enzymes that function in diverse pathways, from carbon source assimilation to hormone biosynthesis. In all P450s, heme is bound in a structurally conserved protein core, allowing them to catalyze regioselective and stereoselective oxidation of hydrocarbons.
	42. 33789 Accesses	Software Apollo: a sequence annotation editor SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall, ME Clamp Genome Biology 2002, 3:research0082-0082.14 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Apollo was developed to enable curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome.
	43. 33578 Accesses	Review 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.
	44. 32949 Accesses	Research Social regulation of gene expression in human leukocytes Steve W Cole, Louise C Hawkley, Jesusa M Arevalo, Caroline Y Sung, Robert M Rose, John T Cacioppo Genome Biology 2007, 8:R189 (13 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of differentially expressed in circulating leukocytes from people who chronically experienced high versus low levels of subjective social isolation (loneliness) revealed over-expression of some anti-inflammatory genes and under-expression of some pro-inflammatory genes.
	45. 32686 Accesses	Software GoMiner: a resource for biological interpretation of genomic and proteomic data Barry R Zeeberg, Weimin Feng, Geoffrey Wang, May D Wang, Anthony T Fojo, Margot Sunshine, Sudarshan Narasimhan, David W Kane, William C Reinhold, Samir Lababidi, Kimberly J Bussey, Joseph Riss, J Barrett, John N Weinstein Genome Biology 2003, 4:R28 (25 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GoMiner, a program package that organizes lists of 'interesting' genes for biological interpretation in the context of the Gene Ontology, has been developed.
	46. 32370 Accesses	Research A DNA microarray survey of gene expression in normal human tissues Radha Shyamsundar, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, Jonathan R Pollack Genome Biology 2005, 6:R22 (14 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic survey of gene expression in 115 human tissue samples using cDNA microarrays provides a dataset that can be used as a baseline for comparison with expression in diseased tissue.
	47. 32199 Accesses	Research Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation Lorenzo F Sempere, Sarah Freemantle, Ian Pitha-Rowe, Eric Moss, Ethan Dmitrovsky, Victor Ambros Genome Biology 2004, 5:R13 (16 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Northern blot analysis of 119 previously reported microRNAs in adult organs from mouse and human identified a subset of brain-expressed miRNAs whose expression behavior is conserved in both mouse and human differentiating neurons, implicating these microRNAs in mammalian neuronal development or function
	48. 31872 Accesses	Review Exploring prokaryotic diversity in the genomic era Philip Hugenholtz Genome Biology 2002, 3:reviews0003-reviews0003.8 (29 January 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	49. 31972 Accesses	Review An overview of the potassium channel family Christopher Miller Genome Biology 2000, 1:reviews0004-reviews0004.5 (13 October 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potassium channels, tetrameric integral membrane proteins that form aqueous pores through which K⁺ can flow, are found in virtually all organisms; the genomes of humans, Drosophila, and Caenorhabditis elegans contain 30-100 K⁺ channel genes each. The structure of a bacterial K⁺ channel, sequence comparisons with other channels and electrophysiological measurements have enabled conclusions about the mechanism of gating and ion flow to be drawn for many other channels.
	50. 30947 Accesses	Method Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke Genome Biology 2011, 12:R18 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The optimization of PCR amplification steps in Illumina libraries significantly reduces sequencing bias