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	76. 25041 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. 24725 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. 24629 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
	79. 24610 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.
	80. 24577 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. 24415 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. 24169 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. 24163 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. 23615 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. 23435 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. 23378 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.
	87. 23352 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.
	88. 23327 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. 23191 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. 23173 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.
	91. 23148 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.
	92. 23036 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
	93. 23000 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.
	94. 22958 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
	95. 22949 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.
	96. 22740 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. 22720 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. 22571 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. 22547 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. 22427 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.