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	1. 215096 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-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.
	2. 151138 Accesses	Comment 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.
	3. 110443 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.
	4. 88049 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.
	5. 73026 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.
	6. 71879 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.
	7. 70621 Accesses	Method Differential expression analysis for sequence count data Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
	8. 61899 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-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.
	9. 58388 Accesses	Method 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
	10. 58218 Accesses	Review 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.
	11. 54941 Accesses	Research The human olfactory receptor repertoire Sergey Zozulya, Fernando Echeverri, Trieu Nguyen Genome Biology 2001, 2:research0018-research0018.12 (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.
	12. 51396 Accesses	Method Model-based Analysis of ChIP-Seq (MACS) Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu Genome Biology 2008, 9:R137 (17 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MACS performs model-based analysis of ChIP-Seq data generated by short read sequencers.
	13. 49925 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.
	14. 48119 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-research0003.21 (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.
	15. 45474 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.
	16. 45022 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:research0084-0084.20 (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.
	17. 45003 Accesses	Review A tale of histone modifications Patrick A Grant Genome Biology 2001, 2:reviews0003-reviews0003.6 (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.
	18. 43790 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.
	19. 43460 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.
	20. 43038 Accesses	Protein family review Fibroblast growth factors David M Ornitz, Nobuyuki Itoh Genome Biology 2001, 2:reviews3005-reviews3005.12 (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.
	21. 42781 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.
	22. 41227 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.
	23. 39444 Accesses	Method Improving RNA-Seq expression estimates by correcting for fragment bias Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extension to Cufflinks corrects bias in RNA-seq datasets
	24. 38514 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.
	25. 38389 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-research0004.13 (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.
	26. 37885 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. 37083 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. 36973 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. 37323 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. 36445 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. 36303 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. 35435 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. 35384 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. 35306 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. 34939 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. 34750 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. 34728 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. 34712 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. 34428 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. 34196 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. 34125 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. 33811 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. 33629 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. 32986 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. 32709 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. 32378 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. 32226 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. 31900 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. 31994 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. 31113 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
	51. 30669 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.
	52. 30613 Accesses	Opinion 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.
	53. 30119 Accesses	Method 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
	54. 30089 Accesses	Software BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data Lao H Saal, Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, Åke Borg, Carsten Peterson Genome Biology 2002, 3:software0003-software0003.6 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their extracted data matrices, and information about the physical array, the features and reporter molecules. We present a web-based customizable bioinformatics solution called BioArray Software Environment (BASE) for the management and analysis of all areas of microarray experimentation. All software necessary to run a local server is freely available.
	55. 29868 Accesses	Research An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Jennifer L Reed, Thuy D Vo, Christophe H Schilling, Bernhard O Palsson Genome Biology 2003, 4:R54 (28 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-scale metabolic model of E. coli has been reconstructed, including 904 genes and 931 unique biochemical reactions, which gives a more complete and chemically accurate description of E. coli metabolism than previous models.
	56. 29742 Accesses	Software 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.
	57. 29602 Accesses	Research Accuracy and quality of massively parallel DNA pyrosequencing Susan M Huse, Julie A Huber, Hilary G Morrison, Mitchell L Sogin, David Welch Genome Biology 2007, 8:R143 (20 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Error rates were estimated for the Roche GS20 massively parallel pyrosequencing system, and several factors were identified that can be used to remove low-quality reads, improving the accuracy to 99.75% or better.
	58. 29013 Accesses	Review Untranslated regions of mRNAs Flavio Mignone, Carmela Gissi, Sabino Liuni, Graziano Pesole Genome Biology 2002, 3:reviews0004-reviews0004.10 (28 February 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression is finely regulated at the post-transcriptional level. Features of the untranslated regions of mRNAs that control their translation, degradation and localization include stem-loop structures, upstream initiation codons and open reading frames, internal ribosome entry sites and various cis-acting elements that are bound by RNA-binding proteins.
	59. 28741 Accesses	Software 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.
	60. 28610 Accesses	Review The SET-domain protein superfamily: protein lysine methyltransferases Shane C Dillon, Xing Zhang, Raymond C Trievel, Xiaodong Cheng Genome Biology 2005, 6:227 (2 August 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The SET-domain protein methyltransferase superfamily includes all but one of the proteins known to methylate histones on lysine. Histone methylation is important in the regulation of chromatin and gene expression.
	61. 28543 Accesses	Research Annotation of the Drosophila melanogaster euchromatic genome: a systematic review Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis et al. Genome Biology 2002, 3:research0083-0083.22 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.
	62. 27460 Accesses	Method POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer Christopher Lausted, Timothy Dahl, Charles Warren, Kimberly King, Kimberly Smith, Michael Johnson, Ramsey Saleem, John Aitchison, Lee Hood, Stephen R Lasky Genome Biology 2004, 5:R58 (27 July 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An open-source inkjet arrayer is described here capable of rapidly producing sets of unique 9,800-feature arrays.
	63. 27101 Accesses	Method How biologically relevant are interaction-based modules in protein networks? Juan F Poyatos, Laurence D Hurst Genome Biology 2004, 5:R93 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors present a method to identify modules within protein-interaction networks. Phylogenetic profiles are used to determine the biological relevance of the modules.
	64. 27087 Accesses	Software 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.
	65. 26892 Accesses	Method 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
	66. 26825 Accesses	Minireview The origin and early evolution of mitochondria Michael W Gray, Gertraud Burger, B Franz Lang Genome Biology 2001, 2:reviews1018-reviews1018.5 (5 June 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial (specifically a-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome.
	67. 26245 Accesses	Research Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants Peter M Palenchar, Andrei Kouranov, Laurence V Lejay, Gloria M Coruzzi Genome Biology 2004, 5:R91 (29 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis and the 'InterAct class' method were used to study interactions between carbon and nitrogen signaling in Arabidopsis.
	68. 26078 Accesses	Research A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale Genome Biology 2004, 5:R7 (15 January 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes.
	69. 25974 Accesses	Method 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.
	70. 25662 Accesses	Research Computational prediction of human metabolic pathways from the complete human genome Pedro Romero, Jonathan Wagg, Michelle L Green, Dale Kaiser, Markus Krummenacker, Peter D Karp Genome Biology 2004, 6:R2 (22 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computation pathway analysis of the human genome is presented that assigns enzymes encoded by the genome to predicted metabolic pathways. This analysis provides a genome-based view of human nutrition.
	71. 25373 Accesses	Method 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
	72. 25322 Accesses	Protein family review The F-box protein family Edward T Kipreos, Michele Pagano Genome Biology 2000, 1:reviews3002-reviews3002.7 (10 November 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary F-box proteins were first described as components of ubiquitin ligase complexes, but have more recently been found to be involved in a variety of cellular functions, including in the kinetochore and in translational elongation.
	73. 25276 Accesses	Method Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen Genome Biology 2009, 10:R79 (22 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A set of methods is presented for normalization, quantification of noise and co-expression analysis for gene expression studies using deep sequencing.
	74. 25137 Accesses	Research 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.
	75. 25126 Accesses	Research Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset Sung E Choe, Michael Boutros, Alan M Michelson, George M Church, Marc S Halfon Genome Biology 2005, 6:R16 (28 January 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A 'spike-in' experiment for Affymetrix GeneChips is described that provides a defined dataset of 3,860 RNA species. A 'best route' combination of analysis methods is presented which allows detection of approximately 70% of true positives before reaching a 10% false discovery rate.
	76. 24912 Accesses	Research Functional analysis of transcription factor binding sites in human promoters Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Aldred, Nathan D Trinklein, Richard M Myers, Zhiping Weng Genome Biology 2012, 13:R50 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary TFBSs are predicted from ENCODE data, and experiments in four cell lines find 70% to be functional
	77. 24689 Accesses	Software Identifying biological themes within lists of genes with EASE Douglas A Hosack, Glynn Dennis, Brad T Sherman, H Lane, Richard A Lempicki Genome Biology 2003, 4:R70 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data.
	78. 24587 Accesses	Research Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans Ravi S Kamath, Maruxa Martinez-Campos, Peder Zipperlen, Andrew G Fraser, Julie Ahringer Genome Biology 2000, 2:research0002-research0002.10 (20 December 2000) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNAi can be achieved by feeding worms Escherichia coli expressing dousble-stranded RNA corresponding to a specific gene. An optimized feeding method is presented that results in phenotypes at least as strong as those produced by direct injection of RNA for embryonic lethal genes, and stronger for genes with post-embryonic phenotypes.
	79. 24579 Accesses	Method Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts Joshua Z Levin, Michael F Berger, Xian Adiconis, Peter Rogov, Alexandre Melnikov, Timothy Fennell, Chad Nusbaum, Levi A Garraway, Andreas Gnirke Genome Biology 2009, 10:R115 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Combining next-generation sequencing with capture of sequences from a relevant subset of a transcriptome produces an enhanced view of this subset
	80. 24530 Accesses	Software Cloud-scale RNA-sequencing differential expression analysis with Myrna Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
	81. 24402 Accesses	Research Computational identification of Drosophila microRNA genes Eric C Lai, Pavel Tomancak, Robert W Williams, Gerald M Rubin Genome Biology 2003, 4:R42 (30 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An informatic procedure has been used to analyze the euchromatic sequences of Drosophila melanogaster and D. pseudoobscura for conserved sequences that adopt an extended stem-loop structure and display other characteristics of known miRNAs.
	82. 24137 Accesses	Minireview Endogenous retroviruses in the human genome sequence David J Griffiths Genome Biology 2001, 2:reviews1017-reviews1017.5 (5 June 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human genome contains many endogenous retroviral sequences, and these have been suggested to play important roles in a number of physiological and pathological processes. Can the draft human genome sequences help us to define the role of these elements more closely?
	83. 24081 Accesses	Research A human functional protein interaction network and its application to cancer data analysis Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.
	84. 23606 Accesses	Correspondence Orthologs and paralogs - we need to get it right Roy A Jensen Genome Biology 2001, 2:interactions1002-interactions1002.3 (3 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Homologuephobia, by Gregory A Petsko, Genome Biology 2001 2:comment1002.1-1002.2, to An apology for orthologs - or brave new memes by Eugene V Koonin, Genome Biology 2001, 2:comment1005.1-1005.2, and to Can sequence determine function? by John A Gerlt and Patricia C Babbitt, Genome Biology 2000, 1:reviews0005.1-0005.10.
	85. 23423 Accesses	Research A Drosophila full-length cDNA resource Mark Stapleton, Joe Carlson, Peter Brokstein, Charles Yu, Mark Champe, Reed George, Hannibal Guarin, Brent Kronmiller, Joanne Pacleb, Soo Park, Ken Wan, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0080-0080.8 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-quality full-insert sequence for 8,921 putative full-length cDNA clones in the Drosophila Gene Collection has been generated and compared to the annotated Release 3 genomic sequence. More than 5,300 cDNAs have been identifieed that contain a complete and accurate protein-coding sequence, corresponding to at least one splice form for 40% of the predicted D. melanogaster genes.
	86. 23339 Accesses	Tutorial Having a BLAST with bioinformatics (and avoiding BLASTphemy) Alexander Pertsemlidis, John W Fondon Genome Biology 2001, 2:reviews2002-reviews2002.10 (27 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the principles, workings, applications and potential pitfalls of BLAST, focusing on the implementation developed at the National Center for Biotechnology Information.
	87. 23335 Accesses	Research Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets Xiu-Jie Wang, José L Reyes, Nam-Hai Chua, Terry Gaasterland Genome Biology 2004, 5:R65 (31 August 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Using bioinformatic methods, 83 novel Arabidopsis miRNAs have been predicted. Putative target mRNAs have been identified for most of the candidate genes.
	88. 23310 Accesses	Research Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George, Roger A Hoskins, Todd Laverty, Donna M Muzny, Catherine R Nelson, Joanne M Pacleb, Soo Park, Barret D Pfeiffer, Stephen Richards, Erica J Sodergren, Robert Svirskas, Paul E Tabor, Kenneth Wan, Mark Stapleton, Granger G Sutton, Craig Venter, George Weinstock, Steven E Scherer, Eugene W Myers, Richard A Gibbs, Gerald M Rubin et al. Genome Biology 2002, 3:research0079-0079.14 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Drosophila melanogaster genome was the first metazoan genome to be sequenced by whole-genome shotgun. Now, the sequence has been finished in a process designed to close gaps, improve sequence quality and validate the assembly.
	89. 23179 Accesses	Protein family review Toll-like receptors: a family of pattern-recognition receptors in mammals Myriam A Armant, Matthew J Fenton Genome Biology 2002, 3:reviews3011-reviews3011.6 (29 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Toll-like receptors are a family of pattern-recognition receptors in mammals that can discriminate between chemically diverse classes of microbial products, including bacterial cell-wall components, and that can elicit pathogen-specific cellular immune responses. Toll-like receptors share characteristic features with the interleukin-1 and interleukin-18 cytokine receptors and these receptor classes activate similar signal-transduction pathways.
	90. 23125 Accesses	Research Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species Michael W Rey, Preethi Ramaiya, Beth A Nelson, Shari D Brody-Karpin, Elizabeth J Zaretsky, Maria Tang, Alfredo de Leon, Henry Xiang, Veronica Gusti, Ib Groth Clausen, Peter B Olsen, Michael D Rasmussen, Jens T Andersen, Per L Jørgensen, Thomas S Larsen, Alexei Sorokin, Alexander Bolotin, Alla Lapidus, Nathalie Galleron, S Dusko Ehrlich, Randy M Berka Genome Biology 2004, 5:r77 (13 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The complete sequence of the Bacillus licheniformis ATCC 14580 genome was determined, revealing 4,208 predicted protein-coding genes, 7 rRNA operons and 72 tRNA genes.
	91. 23099 Accesses	Method 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.
	92. 22964 Accesses	Method Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network Christine Brun, François Chevenet, David Martin, Jérôme Wojcik, Alain Guénoche, Bernard Jacq Genome Biology 2003, 5:R6 (15 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary PRODISTIN, a new computational method allowing the functional clustering of proteins on the basis of protein-protein interaction data. This method was used to classify 11% of the Saccharomyces cerevisiae proteome into several groups.
	93. 22960 Accesses	Research 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
	94. 22931 Accesses	Research Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes Qi Zhou, Jun Wang, Ling Huang, Wenhui Nie, Jinhuan Wang, Yan Liu, Xiangyi Zhao, Fengtang Yang, Wen Wang Genome Biology 2008, 9:R98 (14 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The nascent neo-sex chromosomes of black muntjacs show that regulatory mutations could accelerate the degeneration of the Y chromosome and contribute to the further evolution of dosage compensation.
	95. 22897 Accesses	Method EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield Genome Biology 2011, 12:R44 (19 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Reconstructing full length rRNA sequences from short reads to estimate microbial community structure
	96. 22695 Accesses	Method 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.
	97. 22674 Accesses	Method 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.
	98. 22551 Accesses	Research The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis Robert W Williams, Jing Gu, Shuhua Qi, Lu Lu Genome Biology 2001, 2:research0046-research0046.18 (22 October 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The density of typed microsatellite markers has been increased 2- to 5-fold in each of several major recombinant inbred sets of mice and consensus RI maps that integrate genotypes of approximately 1600 microsatellite loci assembled.
	99. 22520 Accesses	Research The genome of Rhizobium leguminosarum has recognizable core and accessory components J Peter W Young, Lisa C Crossman, Andrew WB Johnston, Nicholas R Thomson, Zara F Ghazoui, Katherine H Hull, Margaret Wexler, Andrew RJ Curson, Jonathan D Todd, Philip S Poole, Tim H Mauchline, Alison K East, Michael A Quail, Carol Churcher, Claire Arrowsmith, Inna Cherevach, Tracey Chillingworth, Kay Clarke, Ann Cronin, Paul Davis, Audrey Fraser, Zahra Hance, Heidi Hauser, Kay Jagels, Sharon Moule, Karen Mungall, Halina Norbertczak, Ester Rabbinowitsch, Mandy Sanders, Mark Simmonds, Sally Whitehead, Julian Parkhill et al. Genome Biology 2006, 7:R34 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the α-proteobacterial N2-fixing symbiont of legumes, Rhizobium leguminosarum, is described, revealing a 'core' and an 'accessory' component.
	100. 22385 Accesses	Research A whole-genome assembly of the domestic cow, Bos taurus Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke, Steven L Salzberg Genome Biology 2009, 10:R42 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A cow whole-genome assembly of 2.86 billion base pairs that closes gaps and corrects previously-described inversions and deletions as well as describing a portion of the Y chromosome.