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	51. 30675 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. 30659 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. 30176 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. 30097 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. 29893 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. 29796 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. 29640 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. 29035 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. 28780 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. 28637 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. 28562 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. 27477 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. 27161 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.
	64. 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.
	65. 26934 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. 26838 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. 26246 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. 26093 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. 26037 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. 25682 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. 25430 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. 25338 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. 25296 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. 25160 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. 25145 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.