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	1. 136610 Accesses	Research 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 (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.
	2. 57959 Accesses	Method Bioconductor: open software development for computational biology and bioinformatics Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang Genome Biology 2004, 5:R80 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.
	3. 46380 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 (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.
	4. 45953 Accesses	Research The human olfactory receptor repertoire Sergey Zozulya, Fernando Echeverri, Trieu Nguyen Genome Biology 2001, 2:research0018 (1 June 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification and cloning of 347 putative human full-length odorant receptor genes is an important initial step in understanding receptor-ligand specificity and combinatorial encoding of odorant stimuli in human olfaction.
	5. 40715 Accesses	Research Deciphering cellular states of innate tumor drug responses Esther Graudens, Virginie Boulanger, Cindy Mollard, Régine Mariage-Samson, Xavier Barlet, Guilaine Grémy, Christine Couillault, Malika Lajémi, Dominique Piatier-Tonneau, Patrick Zaborski, Eric Eveno, Charles Auffray, Sandrine Imbeaud Genome Biology 2006, 7:R19 (15 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nearly 700 genes were identified that are differently expressed between tumors of patients with colorectal cancer who subsequently responded well to combined chemotherapy and those of patients who were resistant to the therapy.
	6. 39703 Accesses	Research Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli Brian J Peter, Javier Arsuaga, Adam M Breier, Arkady B Khodursky, Patrick O Brown, Nicholas R Cozzarelli Genome Biology 2004, 5:R87 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Microarray analysis shows that transcription of 306 E. Coli genes is affected by changes in the level of chromosome supercoiling, suggesting that supercoiling transmits regulatory signals from the environment to many cellular pathways.
	7. 39503 Accesses	Research 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy, Louis Staudt, Wing C Chan, David Botstein, Patrick Brown Genome Biology 2000, 1:research0003 (4 August 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A statistical method called 'gene shaving' can be used to analyze data from large gene expression studies. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene expression measurements made on samples from patients with diffuse large B-cell lymphoma were analyzed using the gene shaving method. A small cluster of genes whose expression is highly predictive of survival was identified.
	8. 39041 Accesses	Software 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.
	9. 37090 Accesses	Research MicroRNA targets in Drosophila Anton J Enright, Bino John, Ulrike Gaul, Thomas Tuschl, Chris Sander, Debora S Marks Genome Biology 2003, 5:R1 (12 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A computational method for whole-genome prediction of microRNA target genes is presented. Application of this method to the Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known microRNAs.
	10. 35749 Accesses	Software GOToolBox: functional analysis of gene datasets based on Gene Ontology David Martin, Christine Brun, Elisabeth Remy, Pierre Mouren, Denis Thieffry, Bernard Jacq Genome Biology 2004, 5:R101 (26 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tools are presented to identify Gene Ontology terms that are over- or under-represented in a dataset, to cluster genes by function and to find genes with similar annotations.
	11. 34766 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.
	12. 33075 Accesses	Research Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions Brian B Haab, Maitreya J Dunham, Patrick O Brown Genome Biology 2001, 2:research0004 (22 January 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is described for printing protein microarrays and using them in a comparative fluorescence assay to measure the abundance of specific proteins in complex solutions. Antigens or antibodies were spotted onto the arrays, and accurate measurements of their cognate ligands were made at concentrations of 1.6 μg/ml or below. Some antibody-antigen pairs allowed detection of the cognate ligands at absolute concentrations below 1 ng/ml and partial concentrations of less than 1 part in 10⁶, sensitivities sufficient for measurement of many clinically important proteins in patient blood samples.
	13. 33061 Accesses	Research 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.
	14. 32792 Accesses	Research *The transposable elements of the Drosophila melanogaster* euchromatin: a genomics perspective** Joshua S Kaminker, Casey M Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A Wheeler, Suzanna E Lewis, Gerald M Rubin, Michael Ashburner, Susan E Celniker Genome Biology 2002, 3:research0084 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using Release 3 of the euchromatic genomic sequence of Drosophila melanogaster, 85 known and eight novel families of transposable element have been identified, varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence.
	15. 32515 Accesses	Review A tale of histone modifications Patrick A Grant Genome Biology 2001, 2:reviews0003 (5 April 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The modification of chromatin structure is important for a number of nuclear functions, exemplified by the regulation of transcription. This review discusses recent studies of covalent histone modifications and the enzymatic machines that generate them.
	16. 32391 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 (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.
	17. 31948 Accesses	Review Statistical tests for differential expression in cDNA microarray experiments Xiangqin Cui, Gary A Churchill Genome Biology 2003, 4:210 (17 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The simplest statistical method for extracting biological information from microarray data is the t test. Analysis of variance (ANOVA) and the mixed ANOVA model are general and powerful approaches for more complex microarray experiments.
	18. 31252 Accesses	Software 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.
	19. 30252 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 (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.
	20. 30191 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 (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.
	21. 28705 Accesses	Protein family review Fibroblast growth factors David M Ornitz, Nobuyuki Itoh Genome Biology 2001, 2:reviews3005 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fibroblast growth factors (FGFs) are a large family of peptide growth factors that require heparan sulfate to activate their tyrosine kinase receptors. They have diverse roles in development, regulating proliferation, migration and differentiation. In adult animals, FGFs are important for homeostasis and tissue repair.
	22. 28645 Accesses	Research Microarray analysis of microRNA expression in the developing mammalian brain Eric A Miska, Ezequiel Alvarez-Saavedra, Matthew Townsend, Akira Yoshii, Nenad Šestan, Pasko Rakic, Martha Constantine-Paton, H Robert Horvitz Genome Biology 2004, 5:R68 (31 August 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microarray technology suitable for analyzing the expression of microRNAs and of other small RNAs was used to determine the microRNA expression profile during mouse-brain development and observed a temporal wave of gene expression of sequential classes of microRNAs.
	23. 28356 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.
	24. 28125 Accesses	Research *A Drosophila* protein-interaction map centered on cell-cycle regulators** Clement A Stanyon, Guozhen Liu, Bernardo A Mangiola, Nishi Patel, Loic Giot, Bing Kuang, Huamei Zhang, Jinhui Zhong, Russell L Finley Genome Biology 2004, 5:R96 (26 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Drosophila protein-protein interaction map was constructed using the LexA system, complementing a previous map using the GAL4 system and adding many new interactions.
	25. 27708 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.