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We request that you please cite the BDGP in any publications based on the use of BDGP data or techniques. Please use the accession number, authors, and appropriate paper for the given projects. See How to Cite BDGP data for more information.
Genomic Sequencing | Annotation | cDNAs & ESTs
Natural Transposable Elements | Gene Disruption
Comparative Genomics | SNP Map
Regulatory Regions | Gene Expression

Genomic Sequencing

  • The Drosophila melanogaster genome
    S.E. Celniker and G.M. Rubin
    Annual Reviews of Genomics and Human Genetics (2003) 4:89-117

  • Finishing a whole genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence
    S.E. Celniker, D.A. Wheeler, B. Kronmiller, J.W. Carlson, A. Halpern, S. Patel, M. Adams, M. Champe, S.P. Dugan, E. Frise, A. Hodgson , R.A. George, R.A. Hoskins, T. Laverty, D.M. Muzny, C.R. Nelson, J.M. Pacleb, S. Park, B.D. Pfeiffer, S. Richards, E.J. Sodergren, R. Svirskas, P.E. Tabor, K. Wan, M. Stapleton, G.G. Sutton, C. Venter, G. Weinstock, S.E. Scherer, E.W. Myers, R.A. Gibbs and G.M. Rubin
    Genome Biology (2002) 3(12):research0079.1-0079.14
    Download entire paper in pdf format

  • Heterochromatic sequences in a Drosophila whole genome shotgun assembly
    R.A. Hoskins, C.D. Smith, J.W. Carlson, A.B. Carvalho, A. Halpern, J.S. Kaminker, C. Kennedy, C.J. Mungall, B.A. Sullivan, G.G. Sutton, J.C. Yasuhara, B.T. Wakimoto, E.W. Myers, S.E. Celniker, G.M. Rubin and G.H. Karpen
    Genome Biology (2002) 3(12):research0085.1-0085.16
    Download entire paper in pdf format

  • The Genome Sequence of Drosophila melanogaster
    M.D. Adams, S.E. Celniker, R.A. Holt, C.A. Evans, J.D. Gocayne et. al.
    Science (2000) 287:2185-2195

  • A BAC-based Physical Map of the Major Autosomes of Drosophila melanogaster
    R.A. Hoskins, C.R. Nelson, B.P. Berman, T.R. Laverty, R.A. George et al.
    Science (2000) 287:2271-2274

  • A Brief History of Drosophila's Contributions to Genome Research
    G.M. Rubin and E.B. Lewis
    Science (2000) 287:2216-2218

  • Around the Genomes: The Drosophila Genome Project
    G.M. Rubin
    Genome Research (1996) 6:71-79

  • The Role of the Genome Project in Determining Gene Function: Insights from Model Organisms
    G.L.G. Miklos and G.M. Rubin
    Cell (1996) 86:521-529

  • A P1-Based Physical Map of the Drosophila Euchromatic Genome
    W. Kimmerly et al.
    Genome Research (1996) 6:414-430

    Annotation

  • Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster
    J. Tupy*, A.M. Bailey*, G. Dailey, M. Evans-Holm, C.W. Siebel, S.Misra, S.E. Celniker, and G.M. Rubin
    *These authors contributed equally to this work.
    PNAS (2005) 102(15):5495-5500
    Download entire paper in pdf format

  • A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome
    M. Yandell*, A.M. Bailey*, S. Misra*, S. Shu, C. Wiel, M. Evans-Holm, S.E. Celniker, G.M. Rubin
    *These authors contributed equally to this work.
    PNAS (2005) 102(5):1566-1571
    Download entire paper in pdf format

  • An integrated computational pipeline and database to support whole-genome sequence annotation
    C.J. Mungall, S. Misra, B.P. Berman, J. Carlson, E. Frise, N. Harris, B. Marshall, S. Shu, J.S. Kaminker, S.E. Prochnik, C.D. Smith, E. Smith, J.L. Tupy, C. Wiel, G.M. Rubin and S.E. Lewis
    Genome Biology (2002) 3(12):research0081.1-0081.11
    Download entire paper in pdf format

  • Apollo: a sequence annotation editor
    S.E. Lewis, S.M.J. Searle, N. Harris, M. Gibson, V. Iyer, J. Richter, C. Wiel, L. Bayraktaroglu, E. Birney, M.A. Crosby, J.S. Kaminker, B.B. Matthews, S.E. Prochnik, C.D. Smith, J.L. Tupy, G.M. Rubin, S. Misra, C.J. Mungall and M.E. Clamp
    Genome Biology (2002) 3(12):research0082.1-0082.14
    Download entire paper in pdf format

  • Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
    S. Misra, M.A. Crosby, C.J. Mungall, B.B. Matthews, K.S. Campbell, P. Hradecky, Y. Huang, J.S. Kaminker, G.H. Millburn, S.E. Prochnik, C.D. Smith, J.L. Tupy, E.J. Whitfield, L. Bayraktaroglu, B.P. Berman, B.R. Bettencourt, S.E. Celniker, A.D.N.J. de Grey, R.A. Drysdale, N.L. Harris, J. Richter, S. Russo, A.J. Schroeder, S.Q. Shu, M. Stapleton, C. Yamada, M. Ashburner, W.M. Gelbart, G.M. Rubin and S.E. Lewis
    Genome Biology (2002) 3(12):research0083.1-0083.22
    Download entire paper in pdf format

  • Comparative Genomics of the Eukaryotes
    G.M. Rubin, M.D. Yandell, J.R. Wortman, G.L.G. Miklos, C.R. Nelson et. al.
    Science (2000) 287:2204-2215
  • An exploration of the sequence of a 2.9-megabase region of the genome of Drosophila melanogaster - The'Adh' region.
    M. Ashburner, S. Misra, J. Roote, S. Lewis, R. Blazej et al.
    Genetics (2000) 153:179-219
  • Genome Annotation Assessment in Drosophila melanogaster.
    M.G. Reese, G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril and S.E. Lewis
    Genome Research (2000) 10:483-501

  • BioViews: Java-Based Tools for Genomic Data Visualization
    G.A. Helt, S. Lewis, A.E. Loraine and G.M. Rubin
    Genome Research (1998) 8:291-305

    cDNAs & ESTs

  • RNA editing in Drosophila melanogaster: New targets and functional consequences
    Stapleton M, Carlson JW, Celniker SE
    RNA 2006 Nov;12(11):1922-32. Epub 2006 Oct 3.

  • Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP)
    R.A. Hoskins, M. Stapleton, R.A. George, C. Yu, K.H. Wan, J.W. Carlson and S.E. Celniker
    Nucleic Acids Research 2005, 33(21):e185
    Download entire paper in pdf format

  • A Drosophila full-length cDNA resource
    M. Stapleton, J. Carlson, P. Brokstein, C. Yu, M. Champe, R. George, H. Guarin, B. Kronmiller, J. Pacleb, S. Park, K. Wan, G.M. Rubin and S.E. Celniker
    Genome Biology 2002, 3(12):research0080.1-0080.8
    Download entire paper in pdf format

  • The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes
    M. Stapleton, G. Liao, P. Brokstein, L. Hong, P. Carninci, T. Shiraki, Y. Hayashizaki, M. Champe, J. Pacleb, K. Wan, C. Yu, J. Carlson, R. George, S. Celniker, and G.M. Rubin
    Genome Research (2002) 12(8):1294-1300

  • A Drosophila Complementary DNA Resource
    G.M. Rubin, L. Hong, P. Brokstein, M. Evans-Holm, E. Frise, M. Stapleton and D.A. Harvey
    Science (2000) 287:2222-2224

  • A High Throughput Screen to Identify Novel Secreted and Transmembrane Proteins Involved in Drosophila Embryogenesis
    C.C. Kopczynski, J.N. Noordermeer, T.L. Serano, W.Y. Chen, J.D. Pendleton, S. Lewis, C.S. Goodman and G.M. Rubin
    Proc Natl Acad Sci U S A (1998) 95:9973-9978

    Natural Transposable Elements

  • The transposable elements of the Drosophila melanogaster euchromatin - a genomics perspective
    J.S. Kaminker, C.M. Bergman, B. Kronmiller, J. Carlson, R. Svirskas, S. Patel, E. Frise, D.A. Wheeler, S.E. Lewis, G.M. Rubin, M. Ashburner and S.E. Celniker
    Genome Biology (2002) 3(12):research0084.1-0084.20
    Download entire paper in pdf format
    Gene Disruption

  • The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes
    Bellen, H.J., Levis, R.W., Liao, G., He, Y., Carlson, J.W., Tsang, G., Evans-Holm, M., Hiesinger, P.R., Schulze, K.L., Rubin, G.M., Hoskins, R.A., and Spradling, A.C.
    Genetics (2004) 167:761-781

  • Insertion Site Preferences of the P Transposable Element in Drosophila Melanogaster
    G. Liao, E.J. Rehm and G.M. Rubin
    Proc Natl Acad Sci U S A (2000) 97:3347-3351

  • The BDGP Gene Disruption Project: Single P Element Insertions Mutating 25% of Vital Drosophila Genes.
    A.C. Spradling, D. Stern, A. Beaton, E.J. Rhem, T. Laverty, N. Mozden, S. Misra and G.M. Rubin
    Genetics (1999) 153:135-177

  • Systematic Gain-of-Function Genetics in Drosophila.
    P. Rorth, K. Szabo, A. Bailey, T. Laverty, J. Rehm, G.M Rubin, K. Weigmann, M. Milan, V. Benes, W. Ansorge and S.M. Cohen
    Development (1998) 125:1049-1057

  • Gene Disruptions Using P transposable elements: An integral component of the Drosophila genome project
    A.C. Spradling et al.
    Proc Natl Acad Sci U S A (1995) 92:10824-10830

    Comparative Genomics

  • Benchmarking tools for the alignment of functional noncoding DNA
    D.A. Pollard, C.M. Bergman, J. Stoye, S.E. Celniker, and M.B. Eisen
    BMC Bioinformatics (2004) 5:6
    Correction
    Download entire paper in pdf format
    Download correction in pdf format

  • Evolution of the homeobox complex in the Diptera
    E.B. Lewis, B.D. Pfeiffer, D.R. Mathog and S.E. Celniker
    Current Biology (2003) 13(15):R587-R588

  • Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome
    C.M. Bergman, B.D. Pfeiffer, D.E. Rincón-Limas, R.A. Hoskins, A. Gnirke, C.J. Mungall, A.M. Wang, B. Kronmiller, J. Pacleb, S. Park, M. Stapleton, K. Wan, R.A. George, P.J. de Jong, J. Botas, G.M. Rubin and S.E. Celniker
    Genome Biology (2002) 3(12):research0086.1-0086.20
    Download entire paper in pdf format
  • Comparative Genomics of the Eukaryotes
    G.M. Rubin, M.D. Yandell, J.R. Wortman, G.L.G. Miklos, C.R. Nelson et. al.
    Science (2000) 287:2204-2215


    Single Nucleotide Polymorphism Map

  • SNP Markers for Genetic Mapping in Drosophila melanogaster
    R.A. Hoskins, A.C. Phan, M. Naeemuddin, F.A. Mapa, D.A. Ruddy, J.J. Ryan, L.M. Young, T. Wells, C. Kopczynski and M.C. Ellis
    Genome Res. (2001) 11:1100-1113

  • Haplotype dimorphism in a SNP collection from Drosophila melanogaster
    K. Teeter, M. Naeemuddin, R. Gasperini, E. Zimmerman, K.P. White, R. Hoskins and G. Gibson
    J. Expt. Zoology (Mol. Dev. Evol.) (2000) 288(1): 63-75.

    Regulatory Regions

  • Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
    C.M. Bergman, J.W. Carlson, and S.E. Celniker
    Bioinformatics (2005) 21(8):1747-1749
    Download entire paper in pdf format

  • Computational analysis of core promoters in the Drosophila genome
    U. Ohler, G. Liao, H. Niemann and G.M. Rubin
    Genome Biology (2002) 3(12):research0087.1-0087.12
    Download entire paper in pdf format

  • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    B.P. Berman, Y. Nibu, B.D. Pfeiffer, P. Tomancak, S.E. Celniker, M. Levine, G.M. Rubin, M.B. Eisen
    Proc Natl Acad Sci U S A (2002) 99:757-762
    • HTML version of the article (must have access to PNAS website)
    • web companion and interactive version of the cis-analyst program.

    Gene Expression

  • Systematic determination of patterns of gene expression during Drosophila embryogenesis
    P. Tomancak, A. Beaton, R. Weiszmann, E. Kwan, S. Shu, S.E. Lewis, S. Richards, M. Ashburner, V. Hartenstein, S.E. Celniker and G.M. Rubin
    Genome Biology (2002) 3(12):research0088.1-0088.14
    Download entire paper in pdf format

  • Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays
    E. De Gregorio, P.T. Spellman, G.M. Rubin, and B. Lemaitre
    Proc Natl Acad Sci (2001) 98(22):12590-12595

    Relevant Publications from Other Laboratories

  • A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac
    Thibault, S.T., Singer, M.A., Miyazaki, W.Y., Milash, B., Dompe, N.A., Singh, C.M., Buchholz, R., Demsky, M., et al.
    Nat Genet (2004) 36:283-7

  • From Sequence to Chromosome: The Tip of the X Chromosome of D. melanogaster
    P.V. Benos, M.K. Gatt, M. Ashburner, L. Murphy, D. Harris, et al.
    Science (2000) 287: 2220-2222

  • A Whole-Genome Assembly of Drosophila
    E.W. Myers, G.G. Sutton, A.L. Delcher, I.M. Dew et al.
    Science (2000) 287:2196-2204

  • A Physical Map of the Polytenized Region (101EF-102F) of Chromosome 4 in Drosophila melanogaster
    J. Locke, L. Podemski, N. Aippersbach, H. Kemp, and R. Hodgetts
    Genetics (2000) 155:1175-1183

  • Characterization of bacteriophage P1 library containing inserts of Drosophila DNA of 75-100 kilobase pairs
    D.A. Smoller, D. Petrov and D.L. Hartl
    Chromosoma (1991) 100:487-94

    This page last updated on: 12/7/05
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