Genome Biology | Volume 3 Issue 12

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	Volume 3 Issue 12
	Comment
	Comment Banana republic Gregory A Petsko Genome Biology 2002, 3:comment1016-comment1016.3 (26 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 'Banana republic' is a pejorative with a hundred-year old history. It's becoming less and less easy to argue that the term doesn't apply to biological research, and one of the biggest reasons is genomics.
	Review
	Protein family review The mitochondrial uncoupling proteins Amalia Ledesma, Mario de Lacoba, Eduardo Rial Genome Biology 2002, 3:reviews3015-reviews3015.9 (29 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The uncoupling proteins are transporters, present in the mitochondrial inner membrane, that mediate a regulated discharge of the proton gradient that is generated by the respiratory chain, to serve functions such as thermogenesis, maintenance of the redox balance, or reduction in the production of reactive oxygen species.
	Minireview New approaches to the study of developing wood Simon Turner Genome Biology 2002, 3:reviews1033-reviews1033.4 (15 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The study of single cells differentiating in vitro and collecting samples from across the region around the cambium of poplar trees have both revealed genes that have altered expression during xylem development.
	Minireview Glycan arrays for functional glycomics Kurt Drickamer, Maureen E Taylor Genome Biology 2002, 3:reviews1034-reviews1034.4 (27 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two recent papers describe how arrays of oligosaccharide and polysaccharide molecules can be used to investigate the interactions between carbohydrates and proteins more fully.
	Minireview RNAi hushes heterochromatin Julie M Bailis, Susan L Forsburg Genome Biology 2002, 3:reviews1035-reviews1035.4 (28 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work in the fission yeast Schizosaccharomyces pombe reveals that RNA is an integral component of silent heterochromatin.
	Report
	Paper report SAGE is better than dbEST Cathy Holding Genome Biology 2002, 3:reports0062 (22 November 2002) Abstract \| Full text \| Editor’s summary The more data compiled from serial analysis of gene expression experiments, the more novel genes are likely to be found, in contrast to the situation with expressed sequence tags.
	Paper report Proteomics of radiation resistance Wim D'Haeze Genome Biology 2002, 3:reports0061 (27 November 2002) Abstract \| Full text \| Editor’s summary An extensive proteome analysis will help understand how D. radiodurans survives under extreme conditions
	Paper report Family resemblances Wim D'Haeze Genome Biology 2002, 3:reports0063 (6 December 2002) Abstract \| Full text \| Editor’s summary The genome sequence of Brucella suis suggests that this animal pathogen may have evolved from a soil/plant-associated ancestor
	Paper report Xylella fastidiosa comparative genomics Wim D'Haeze Genome Biology 2002, 3:reports0064 (6 December 2002) Abstract \| Full text \| Editor’s summary Comparison of the genome sequences of Xylella fastidiosa strains reveals new drug targets
	Paper report Finding genes for nodulation Wim D'Haeze Genome Biology 2002, 3:reports0065 (6 December 2002) Abstract \| Full text \| Editor’s summary Characterization of nodule-specific genes in Medicago truncatula will enhance our understanding of nodule development
	Meeting report Whose genome is next? Danielle Kemmer, Andrew Fraser Genome Biology 2002, 3:reports4037-reports4037.3 (28 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the 14th Genome Sequencing and Analysis Conference, Boston, USA, 2-5 October 2002.
	Deposited research article MRD: a microsatellite repeats database for prokaryotic and eukaryotic genomes Subbaya Subramanian, Vamsi M Madgula, Ranjan George, Rakesh K Mishra, Madhusudhan W Pandit, Chandrashekar S Kumar, Lalji Singh Genome Biology 2002, 3:preprint0011-preprint0011.13 (13 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microsatellite repeats database (MRD) is a database system to access the microsatellite repeat information for eukaryotic genomes. Users can search for the repeat of interest and find its non-coding features and its abundance and distribution in the genome. The exact location of repeats with respect to genomic regions of interest whichever is applicable to the organism is highlighted.
	Deposited research article Osprey: A Network Visualization System Bobby-Joe Breitkreutz, Chris Stark, Mike Tyers Genome Biology 2002, 3:preprint0012-preprint0012.6 (21 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A software platform called Osprey has been developed for visualization and manipulation of complex interaction networks
	Deposited research article The GRID: The General Repository for Interaction Datasets Bobby-Joe Breitkreutz, Chris Stark, Mike Tyers Genome Biology 2002, 3:preprint0013-preprint0013.5 (21 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A relational database, called the General Repository for Interaction Datasets (The GRID) has been developed to archive and display physical, genetic and functional interactions.
	Research news Radish correlations and constraints Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021202-01 (2 December 2002) Abstract \| Full text \| Editor’s summary Analysis of radish populations reveals the genetic mechanisms that generate and maintain genetic correlations between phenotypic traits.
	Research news Blocking myostatin Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021203-01 (3 December 2002) Abstract \| Full text \| Editor’s summary Antibodies against myostatin improve the condition of a mouse model of muscular dystrophy.
	Research news Old flies Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021204-01 (4 December 2002) Abstract \| Full text \| Editor’s summary Histone deacetylases and caloric restriction contribute to longevity in Drosophila.
	Research news Public mouse sequence published Tabitha M Powledge Genome Biology 2002, 3:spotlight-20021205-01 (5 December 2002) Abstract \| Full text \| Editor’s summary With publication of the mouse genome sequence come tantalizing glimpses of its huge importance.
	Research news The mouse genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021205-02 (5 December 2002) Abstract \| Full text \| Editor’s summary An international collaborative consortium has generated a high-quality draft sequence of the mouse genome.
	Research news Staking claims Peg Brickley Genome Biology 2002, 3:spotlight-20021205-04 (5 December 2002) Abstract \| Full text \| Editor’s summary Public mouse sequence will cool the already waning gene patent frenzy.
	Research news The mammalian transcriptome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021205-01 (5 December 2002) Abstract \| Full text \| Editor’s summary Over 60,000 full-length mRNA transcripts from the mouse genome have been cloned and characterised.
	Research news Synteny on chromosome 21 Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021206-01 (6 December 2002) Abstract \| Full text \| Editor’s summary Comparison of human and mouse sequences identifies a large number of conserved blocks on human chromosome 21.
	Research news Imprinting and methylation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021209-01 (9 December 2002) Abstract \| Full text \| Editor’s summary The zinc-finger protein CTCF regulates differential methylation and the action of an imprinting control region.
	Research news Metastatic signature Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021210-01 (10 December 2002) Abstract \| Full text \| Editor’s summary A set of 17 genes can distinguish between metastatic and primary tumors.
	Research news Complexity's finest Brendan Maher Genome Biology 2002, 3:spotlight-20021211-01 (11 December 2002) Abstract \| Full text \| Editor’s summary Conference on modeling the neuron demonstrates multiple levels of difficulty.
	Research news The benefits of sex Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021212-01 (12 December 2002) Abstract \| Full text \| Editor’s summary Sex may offer an evolutionary advantage by increasing the speed of adaptation.
	Research news Gene clusters in the fly genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021213-01 (13 December 2002) Abstract \| Full text \| Editor’s summary Testis-specific genes in Drosophila are often located in genomic clusters.
	Research news Ascidian genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021217-01 (17 December 2002) Abstract \| Full text \| Editor’s summary The draft sequence of a sea squirt genome sheds light on vertebrate evolution.
	Research news The heart of the matter Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021218-01 (18 December 2002) Abstract \| Full text \| Editor’s summary Heart surgery in zebrafish induces cardiomyocyte proliferation and heart regeneration.
	Research news Pest management by transgene Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021220-01 (20 December 2002) Abstract \| Full text \| Editor’s summary A dominant embryonic lethality transgene system can create sterile insects for biological pest control.
	Research news Improved purification for proteomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021223-01 (23 December 2002) Abstract \| Full text \| Editor’s summary Combining tagged tandem affinity purification with RNAi improves the purification of protein complexes in higher eukaryotes.
	Research news Estrogen receptor activity in vivo Jonathan Weitzman Genome Biology 2002, 3:spotlight-20021224-01 (24 December 2002) Abstract \| Full text \| Editor’s summary A luciferase reporter gene under the control of activated estrogen receptor reveals the dynamics of receptor activity in mice.
	Research
	Research Membrane-bound progesterone receptors contain a cytochrome b₅-like ligand-binding domain William Mifsud, Alex Bateman Genome Biology 2002, 3:research0068-research0068.5 (12 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Membrane-associated progesterone receptors are thought to mediate a number of rapid cellular effects not involving changes in gene expression. These receptors are here identified as distant homologs of cytochrome b₅.
	Research The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations A Krupa, N Srinivasan Genome Biology 2002, 3:research0066-research0066.14 (13 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. The expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations.
	Research Whole-genome analysis of animal A- and B-type cyclins Conrad A Nieduszynski, James Murray, Mark Carrington Genome Biology 2002, 3:research0070-research0070.8 (15 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Multiple A- and B-type cyclins have been identified in animals, but their study is complicated by varying degrees of functional redundancy. A single functional A-type cyclin gene was found in invertebrates and two were found in vertebrates. The number and relationship of B-type cyclins varies between Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens but all contain at least one cyclin B1-like gene and a cyclin B3 gene.
	Research Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments Jeffrey P Townsend, Daniel L Hartl Genome Biology 2002, 3:research0071-research0071.16 (20 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many methodologies of microarray analysis discard the quantitative results inherent in cDNA microarray comparisons or cannot be flexibly applied to multifactorial experimental design. A quantitative Bayesian framework is presented that can be used to analyze normalized microarray data in which any number of treatments, genotypes, or developmental states are studied using a continuous chain of comparisons.
	Research Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data Céline Becquet, Sylvain Blachon, Baptiste Jeudy, Jean-Francois Boulicaut, Olivier Gandrillon Genome Biology 2002, 3:research0067-research0067.16 (21 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The association-rules discovery (ARD) technique has yet to be applied to gene-expression data analysis. To validate the technique it was applied to freely available human serial analysis of gene expression (SAGE) data. ARD is shown to be complementary to existing gene-expression clustering techniques.
	Research Identification and utilization of arbitrary correlations in models of recombination signal sequences Lindsay G Cowell, Marco Davila, Thomas B Kepler, Garnett Kelsoe Genome Biology 2002, 3:research0072-research0072.20 (21 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites. Current approaches sometimes perform poorly when positions in the site do not independently affect protein binding. A statistical technique has been devloped for modeling the correlation structure in variable DNA sequence sites.
	Research Supervised clustering of genes Marcel Dettling, Peter Bühlmann Genome Biology 2002, 3:research0069-research0069.15 (25 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We focus on microarray data where experiments monitor gene expression in different tissues and where each experiment is equipped with an additional response variable such as a cancer type. A new method is presented for finding groups of genes by directly incorporating the response variables into the grouping process, yielding a supervised clustering algorithm for genes.
	Research A strategy for oligonucleotide microarray probe reduction Alena A Antipova, Pablo Tamayo, Todd R Golub Genome Biology 2002, 3:research0073-research0073.4 (25 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes required for each gene, a systematic approach to choosing the most representative probes is needed. A generalizable empiric method is presented for reducing the number of probes per gene while maximizing the fidelity to the original array design.
	Research Heart-specific genes revealed by expressed sequence tag (EST) sampling Karine Mégy, Stéphane Audic, Jean-Michel Claverie Genome Biology 2002, 3:research0074-research0074.11 (25 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cardiovascular diseases are the primary cause of death worldwide; the identification of genes specifically expressed in the heart is thus of major biomedical interest. A list of genes specifically expressed in the human heart are presented, one of which is a candidate for a bleeding disorder.
	Research Identification of frequent cytogenetic aberrations in hepatocellular carcinoma using gene-expression microarray data Joseph J Crawley, Kyle A Furge Genome Biology 2002, 3:research0075-research0075.8 (25 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using comparative genomic microarray analysis (CGMA), 104 hepatocellular carcinoma (HCC) gene-expression microarray profiles were analyzed. CGMA identified 13 regions of frequent cytogenetic change in the HCC samples (+lq, -4q, +6p, -8p, +8q, -13q, -16q, -17p, +17q, +20q) three three of which have not been previously identified
	Research Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales Bruno Dombrecht, Kathleen Marchal, Jos Vanderleyden, Jan Michiels Genome Biology 2002, 3:research0076-research0076.11 (26 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two complete rhizobial genomes (Mesorhizobium loti, Sinorhizobium meliloti) and four symbiotic regions (Rhizobium etli, Rhizobium sp. NGR234, Bradyrhizobium japonicum, M. loti) were screened for the presence of highly conserved RpoN-binding sites. The methodology used to predict RpoN-binding sites proved highly effective as nearly all known RpoN-controlled genes were identified.
	Research JEvTrace: refinement and variations of the evolutionary trace in JAVA Marcin P Joachimiak, Fred E Cohen Genome Biology 2002, 3:research0077-research0077.12 (26 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Protein families and phylogeny represent complex data with statistical outliers and special cases. The JEvTrace implementation of the evolutionary trace method in a JAVA graphical interface allows detailed mining and graphical visualization of evolutionary sequence relationships.
	Research In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases Kriste E Marshall, Elizabeth L Godden, Fan Yang, Sonya Burgers, Kari J Buck, James M Sikela Genome Biology 2002, 3:research0078-research0078.9 (27 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The identification of genes underlying complex traits has been aided by quantitative trait locus (QTL) mapping approaches, which in turn have benefited from advances in mammalian genome research. Most recently, whole-genome draft sequences and assemblies have been generated for mouse strains that have been used for a large fraction of QTL mapping studies. It has been shown here that strain-specific mouse genome sequence databases can be used as part of a high-throughput pipeline for the in silico discovery of gene-coding variations within murine QTLs.
	Research Computational analysis of core promoters in the Drosophila genome Uwe Ohler, Guo-chun Liao, Heinrich Niemann, Gerald M Rubin Genome Biology 2002, 3:research0087-0087.12 (20 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Candidate transcription start sites have been identified for about 2,000 Drosophila genes by aligning 5' expressed sequence tags (ESTs) from cap-trapped cDNA libraries to the genome. Examination of the sequences flanking these candidate transcription start sites revealed the presence of well-known core promoter motifs such as the TATA box, the initiator and the downstream promoter element (DPE).
	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.
	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.
	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.
	Research Systematic determination of patterns of gene expression during Drosophila embryogenesis Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2002, 3:research0088-0088.14 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos.
	Research Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0086-0086.20 (30 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons.
	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.
	Research Heterochromatic sequences in a Drosophila whole-genome shotgun assembly Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo Carvalho, Aaron Halpern, Joshua S Kaminker, Cameron Kennedy, Chris J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M Rubin, Gary H Karpen Genome Biology 2002, 3:research0085-0085.16 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Fluorescence in situ hybridization was used to correlate the genomic sequence with the cytogenetic map; the annotated euchromatic sequence extends into the centric heterochromatin on each chromosome arm.
	Software An integrated computational pipeline and database to support whole-genome sequence annotation CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin, SE Lewis Genome Biology 2002, 3:research0081-0081.11 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In the course of annotating the Drosophila melanogaster genome sequence, several new open-source software tools and a database schema to support large-scale genome annotation were developed and integrated in to a reusable software system for whole-genome annotation.
	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.

	Volume 3 Issue 12
	Comment
	Comment Banana republic Gregory A Petsko Genome Biology 2002, 3:comment1016-comment1016.3 (26 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 'Banana republic' is a pejorative with a hundred-year old history. It's becoming less and less easy to argue that the term doesn't apply to biological research, and one of the biggest reasons is genomics.
	Review
	Protein family review The mitochondrial uncoupling proteins Amalia Ledesma, Mario de Lacoba, Eduardo Rial Genome Biology 2002, 3:reviews3015-reviews3015.9 (29 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The uncoupling proteins are transporters, present in the mitochondrial inner membrane, that mediate a regulated discharge of the proton gradient that is generated by the respiratory chain, to serve functions such as thermogenesis, maintenance of the redox balance, or reduction in the production of reactive oxygen species.
	Minireview New approaches to the study of developing wood Simon Turner Genome Biology 2002, 3:reviews1033-reviews1033.4 (15 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The study of single cells differentiating in vitro and collecting samples from across the region around the cambium of poplar trees have both revealed genes that have altered expression during xylem development.
	Minireview Glycan arrays for functional glycomics Kurt Drickamer, Maureen E Taylor Genome Biology 2002, 3:reviews1034-reviews1034.4 (27 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two recent papers describe how arrays of oligosaccharide and polysaccharide molecules can be used to investigate the interactions between carbohydrates and proteins more fully.
	Minireview RNAi hushes heterochromatin Julie M Bailis, Susan L Forsburg Genome Biology 2002, 3:reviews1035-reviews1035.4 (28 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work in the fission yeast Schizosaccharomyces pombe reveals that RNA is an integral component of silent heterochromatin.
	Report
	Paper report SAGE is better than dbEST Cathy Holding Genome Biology 2002, 3:reports0062 (22 November 2002) Abstract \| Full text \| Editor’s summary The more data compiled from serial analysis of gene expression experiments, the more novel genes are likely to be found, in contrast to the situation with expressed sequence tags.
	Paper report Proteomics of radiation resistance Wim D'Haeze Genome Biology 2002, 3:reports0061 (27 November 2002) Abstract \| Full text \| Editor’s summary An extensive proteome analysis will help understand how D. radiodurans survives under extreme conditions
	Paper report Family resemblances Wim D'Haeze Genome Biology 2002, 3:reports0063 (6 December 2002) Abstract \| Full text \| Editor’s summary The genome sequence of Brucella suis suggests that this animal pathogen may have evolved from a soil/plant-associated ancestor
	Paper report Xylella fastidiosa comparative genomics Wim D'Haeze Genome Biology 2002, 3:reports0064 (6 December 2002) Abstract \| Full text \| Editor’s summary Comparison of the genome sequences of Xylella fastidiosa strains reveals new drug targets
	Paper report Finding genes for nodulation Wim D'Haeze Genome Biology 2002, 3:reports0065 (6 December 2002) Abstract \| Full text \| Editor’s summary Characterization of nodule-specific genes in Medicago truncatula will enhance our understanding of nodule development
	Meeting report Whose genome is next? Danielle Kemmer, Andrew Fraser Genome Biology 2002, 3:reports4037-reports4037.3 (28 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the 14th Genome Sequencing and Analysis Conference, Boston, USA, 2-5 October 2002.
	Deposited research article MRD: a microsatellite repeats database for prokaryotic and eukaryotic genomes Subbaya Subramanian, Vamsi M Madgula, Ranjan George, Rakesh K Mishra, Madhusudhan W Pandit, Chandrashekar S Kumar, Lalji Singh Genome Biology 2002, 3:preprint0011-preprint0011.13 (13 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microsatellite repeats database (MRD) is a database system to access the microsatellite repeat information for eukaryotic genomes. Users can search for the repeat of interest and find its non-coding features and its abundance and distribution in the genome. The exact location of repeats with respect to genomic regions of interest whichever is applicable to the organism is highlighted.
	Deposited research article Osprey: A Network Visualization System Bobby-Joe Breitkreutz, Chris Stark, Mike Tyers Genome Biology 2002, 3:preprint0012-preprint0012.6 (21 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A software platform called Osprey has been developed for visualization and manipulation of complex interaction networks
	Deposited research article The GRID: The General Repository for Interaction Datasets Bobby-Joe Breitkreutz, Chris Stark, Mike Tyers Genome Biology 2002, 3:preprint0013-preprint0013.5 (21 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A relational database, called the General Repository for Interaction Datasets (The GRID) has been developed to archive and display physical, genetic and functional interactions.
	Research news Radish correlations and constraints Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021202-01 (2 December 2002) Abstract \| Full text \| Editor’s summary Analysis of radish populations reveals the genetic mechanisms that generate and maintain genetic correlations between phenotypic traits.
	Research news Blocking myostatin Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021203-01 (3 December 2002) Abstract \| Full text \| Editor’s summary Antibodies against myostatin improve the condition of a mouse model of muscular dystrophy.
	Research news Old flies Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021204-01 (4 December 2002) Abstract \| Full text \| Editor’s summary Histone deacetylases and caloric restriction contribute to longevity in Drosophila.
	Research news Public mouse sequence published Tabitha M Powledge Genome Biology 2002, 3:spotlight-20021205-01 (5 December 2002) Abstract \| Full text \| Editor’s summary With publication of the mouse genome sequence come tantalizing glimpses of its huge importance.
	Research news The mouse genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021205-02 (5 December 2002) Abstract \| Full text \| Editor’s summary An international collaborative consortium has generated a high-quality draft sequence of the mouse genome.
	Research news Staking claims Peg Brickley Genome Biology 2002, 3:spotlight-20021205-04 (5 December 2002) Abstract \| Full text \| Editor’s summary Public mouse sequence will cool the already waning gene patent frenzy.
	Research news The mammalian transcriptome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021205-01 (5 December 2002) Abstract \| Full text \| Editor’s summary Over 60,000 full-length mRNA transcripts from the mouse genome have been cloned and characterised.
	Research news Synteny on chromosome 21 Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021206-01 (6 December 2002) Abstract \| Full text \| Editor’s summary Comparison of human and mouse sequences identifies a large number of conserved blocks on human chromosome 21.
	Research news Imprinting and methylation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021209-01 (9 December 2002) Abstract \| Full text \| Editor’s summary The zinc-finger protein CTCF regulates differential methylation and the action of an imprinting control region.
	Research news Metastatic signature Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021210-01 (10 December 2002) Abstract \| Full text \| Editor’s summary A set of 17 genes can distinguish between metastatic and primary tumors.
	Research news Complexity's finest Brendan Maher Genome Biology 2002, 3:spotlight-20021211-01 (11 December 2002) Abstract \| Full text \| Editor’s summary Conference on modeling the neuron demonstrates multiple levels of difficulty.
	Research news The benefits of sex Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021212-01 (12 December 2002) Abstract \| Full text \| Editor’s summary Sex may offer an evolutionary advantage by increasing the speed of adaptation.
	Research news Gene clusters in the fly genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021213-01 (13 December 2002) Abstract \| Full text \| Editor’s summary Testis-specific genes in Drosophila are often located in genomic clusters.
	Research news Ascidian genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021217-01 (17 December 2002) Abstract \| Full text \| Editor’s summary The draft sequence of a sea squirt genome sheds light on vertebrate evolution.
	Research news The heart of the matter Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021218-01 (18 December 2002) Abstract \| Full text \| Editor’s summary Heart surgery in zebrafish induces cardiomyocyte proliferation and heart regeneration.
	Research news Pest management by transgene Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021220-01 (20 December 2002) Abstract \| Full text \| Editor’s summary A dominant embryonic lethality transgene system can create sterile insects for biological pest control.
	Research news Improved purification for proteomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20021223-01 (23 December 2002) Abstract \| Full text \| Editor’s summary Combining tagged tandem affinity purification with RNAi improves the purification of protein complexes in higher eukaryotes.
	Research news Estrogen receptor activity in vivo Jonathan Weitzman Genome Biology 2002, 3:spotlight-20021224-01 (24 December 2002) Abstract \| Full text \| Editor’s summary A luciferase reporter gene under the control of activated estrogen receptor reveals the dynamics of receptor activity in mice.
	Research
	Research Membrane-bound progesterone receptors contain a cytochrome b₅-like ligand-binding domain William Mifsud, Alex Bateman Genome Biology 2002, 3:research0068-research0068.5 (12 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Membrane-associated progesterone receptors are thought to mediate a number of rapid cellular effects not involving changes in gene expression. These receptors are here identified as distant homologs of cytochrome b₅.
	Research The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations A Krupa, N Srinivasan Genome Biology 2002, 3:research0066-research0066.14 (13 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. The expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations.
	Research Whole-genome analysis of animal A- and B-type cyclins Conrad A Nieduszynski, James Murray, Mark Carrington Genome Biology 2002, 3:research0070-research0070.8 (15 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Multiple A- and B-type cyclins have been identified in animals, but their study is complicated by varying degrees of functional redundancy. A single functional A-type cyclin gene was found in invertebrates and two were found in vertebrates. The number and relationship of B-type cyclins varies between Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens but all contain at least one cyclin B1-like gene and a cyclin B3 gene.
	Research Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments Jeffrey P Townsend, Daniel L Hartl Genome Biology 2002, 3:research0071-research0071.16 (20 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many methodologies of microarray analysis discard the quantitative results inherent in cDNA microarray comparisons or cannot be flexibly applied to multifactorial experimental design. A quantitative Bayesian framework is presented that can be used to analyze normalized microarray data in which any number of treatments, genotypes, or developmental states are studied using a continuous chain of comparisons.
	Research Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data Céline Becquet, Sylvain Blachon, Baptiste Jeudy, Jean-Francois Boulicaut, Olivier Gandrillon Genome Biology 2002, 3:research0067-research0067.16 (21 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The association-rules discovery (ARD) technique has yet to be applied to gene-expression data analysis. To validate the technique it was applied to freely available human serial analysis of gene expression (SAGE) data. ARD is shown to be complementary to existing gene-expression clustering techniques.
	Research Identification and utilization of arbitrary correlations in models of recombination signal sequences Lindsay G Cowell, Marco Davila, Thomas B Kepler, Garnett Kelsoe Genome Biology 2002, 3:research0072-research0072.20 (21 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites. Current approaches sometimes perform poorly when positions in the site do not independently affect protein binding. A statistical technique has been devloped for modeling the correlation structure in variable DNA sequence sites.
	Research Supervised clustering of genes Marcel Dettling, Peter Bühlmann Genome Biology 2002, 3:research0069-research0069.15 (25 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We focus on microarray data where experiments monitor gene expression in different tissues and where each experiment is equipped with an additional response variable such as a cancer type. A new method is presented for finding groups of genes by directly incorporating the response variables into the grouping process, yielding a supervised clustering algorithm for genes.
	Research A strategy for oligonucleotide microarray probe reduction Alena A Antipova, Pablo Tamayo, Todd R Golub Genome Biology 2002, 3:research0073-research0073.4 (25 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes required for each gene, a systematic approach to choosing the most representative probes is needed. A generalizable empiric method is presented for reducing the number of probes per gene while maximizing the fidelity to the original array design.
	Research Heart-specific genes revealed by expressed sequence tag (EST) sampling Karine Mégy, Stéphane Audic, Jean-Michel Claverie Genome Biology 2002, 3:research0074-research0074.11 (25 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cardiovascular diseases are the primary cause of death worldwide; the identification of genes specifically expressed in the heart is thus of major biomedical interest. A list of genes specifically expressed in the human heart are presented, one of which is a candidate for a bleeding disorder.
	Research Identification of frequent cytogenetic aberrations in hepatocellular carcinoma using gene-expression microarray data Joseph J Crawley, Kyle A Furge Genome Biology 2002, 3:research0075-research0075.8 (25 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using comparative genomic microarray analysis (CGMA), 104 hepatocellular carcinoma (HCC) gene-expression microarray profiles were analyzed. CGMA identified 13 regions of frequent cytogenetic change in the HCC samples (+lq, -4q, +6p, -8p, +8q, -13q, -16q, -17p, +17q, +20q) three three of which have not been previously identified
	Research Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales Bruno Dombrecht, Kathleen Marchal, Jos Vanderleyden, Jan Michiels Genome Biology 2002, 3:research0076-research0076.11 (26 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two complete rhizobial genomes (Mesorhizobium loti, Sinorhizobium meliloti) and four symbiotic regions (Rhizobium etli, Rhizobium sp. NGR234, Bradyrhizobium japonicum, M. loti) were screened for the presence of highly conserved RpoN-binding sites. The methodology used to predict RpoN-binding sites proved highly effective as nearly all known RpoN-controlled genes were identified.
	Research JEvTrace: refinement and variations of the evolutionary trace in JAVA Marcin P Joachimiak, Fred E Cohen Genome Biology 2002, 3:research0077-research0077.12 (26 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Protein families and phylogeny represent complex data with statistical outliers and special cases. The JEvTrace implementation of the evolutionary trace method in a JAVA graphical interface allows detailed mining and graphical visualization of evolutionary sequence relationships.
	Research In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases Kriste E Marshall, Elizabeth L Godden, Fan Yang, Sonya Burgers, Kari J Buck, James M Sikela Genome Biology 2002, 3:research0078-research0078.9 (27 November 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The identification of genes underlying complex traits has been aided by quantitative trait locus (QTL) mapping approaches, which in turn have benefited from advances in mammalian genome research. Most recently, whole-genome draft sequences and assemblies have been generated for mouse strains that have been used for a large fraction of QTL mapping studies. It has been shown here that strain-specific mouse genome sequence databases can be used as part of a high-throughput pipeline for the in silico discovery of gene-coding variations within murine QTLs.
	Research Computational analysis of core promoters in the Drosophila genome Uwe Ohler, Guo-chun Liao, Heinrich Niemann, Gerald M Rubin Genome Biology 2002, 3:research0087-0087.12 (20 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Candidate transcription start sites have been identified for about 2,000 Drosophila genes by aligning 5' expressed sequence tags (ESTs) from cap-trapped cDNA libraries to the genome. Examination of the sequences flanking these candidate transcription start sites revealed the presence of well-known core promoter motifs such as the TATA box, the initiator and the downstream promoter element (DPE).
	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.
	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.
	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.
	Research Systematic determination of patterns of gene expression during Drosophila embryogenesis Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2002, 3:research0088-0088.14 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos.
	Research Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0086-0086.20 (30 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons.
	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.
	Research Heterochromatic sequences in a Drosophila whole-genome shotgun assembly Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo Carvalho, Aaron Halpern, Joshua S Kaminker, Cameron Kennedy, Chris J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M Rubin, Gary H Karpen Genome Biology 2002, 3:research0085-0085.16 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Fluorescence in situ hybridization was used to correlate the genomic sequence with the cytogenetic map; the annotated euchromatic sequence extends into the centric heterochromatin on each chromosome arm.
	Software An integrated computational pipeline and database to support whole-genome sequence annotation CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin, SE Lewis Genome Biology 2002, 3:research0081-0081.11 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In the course of annotating the Drosophila melanogaster genome sequence, several new open-source software tools and a database schema to support large-scale genome annotation were developed and integrated in to a reusable software system for whole-genome annotation.
	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.

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