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D. melanogaster Release 5 Genome

Drosophila Heterochromatin Genome Project

SNP Map

EST Sequencing

Drosophila Gene Collection

modENCODE

Expression Patterns

Gene Disruption Project

Universal Proteomics Resource

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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.

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Genomic Sequencing | Annotation | cDNAs & ESTs
Natural Transposable Elements | Gene Disruption
Comparative Genomics | SNP Map
Regulatory Regions | Gene Expression | Functional Genomics

Genomic Sequencing

• Sequence finishing and mapping of Drosophila melanogaster heterochromatin.
  Hoskins RA, Carlson JW, Kennedy C, Acevedo D, Evans-Holm M, Frise E, Wan KH, Park S, Mendez-Lago M, Rossi F, Villasante A, Dimitri P, Karpen GH, Celniker SE.
  Science. 2007 Jun 15;316(5831):1625-8.
  PMID: 17569867
  
• BAC clones generated from sheared DNA.
  Osoegawa K, Vessere GM, Li Shu C, Hoskins RA, Abad JP, de Pablos B, Villasante A, de Jong PJ.
  Genomics. 2007 Feb;89(2):291-9. Epub 2006 Nov 13.
  PMID: 17098394

• 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

• Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?
  Carvalho AB, Vibranovski MD, Carlson JW, Celniker SE, Hoskins RA, Rubin GM, Sutton GG, Adams MD, Myers EW, Clark AG.
  Genetica. 2003 Mar;117(2-3):227-37.
  PMID: 12723702
  
• Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
  Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL Jr, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M.
  Genome Res. 2007 Dec;17(12):1823-36. Epub 2007 Nov 7.
  PMID: 17989253
  

• 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

• Curated table Fly, worm and yeast genes that are similar to human disease genes.

• Updated Interpro domain analysis

• 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

Table of P insertions in the Adh region
Table of genes in the Adh region
Summary of inferred functions of 91 genes in the Adh region
Full text of the paper
Download entire paper in pdf format

• 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

• Identification and analysis of U5 snRNA variants in Drosophila.
  Chen L, Lullo DJ, Ma E, Celniker SE, Rio DC, Doudna JA.
  RNA. 2005 Oct;11(10):1473-7.
  PMID: 16199758
  
• High-throughput plasmid cDNA library screening.
  Wan KH, Yu C, George RA, Carlson JW, Hoskins RA, Svirskas R, Stapleton M, Celniker SE.
  Nat Protoc. 2006;1(2):624-32.
  PMID: 17406289
  

• 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

• Genomic organization of the Drosophila telomere retrotransposable elements.
  George JA, DeBaryshe PG, Traverse KL, Celniker SE, Pardue ML.
  Genome Res. 2006 Oct;16(10):1231-40. Epub 2006 Sep 8.
  PMID: 16963706
  
• Improved repeat identification and masking in Dipterans.
  Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH.
  Gene. 2007 Mar 1;389(1):1-9. Epub 2006 Oct 12.
  PMID: 17137733
  

• 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

• Sequence datasets

Gene Disruption

• The carnegie protein trap library: a versatile tool for Drosophila developmental studies.
  Buszczak M, Paterno S, Lighthouse D, Bachman J, Planck J, Owen S, Skora AD, Nystul TG, Ohlstein B, Allen A, Wilhelm JE, Murphy TD, Levis RW, Matunis E, Srivali N, Hoskins RA, Spradling AC.
  Genetics. 2007 Mar;175(3):1505-31. Epub 2006 Dec 28.
  PMID: 17194782
• Exploring strategies for protein trapping in Drosophila.
  Quiñones-Coello AT, Petrella LN, Ayers K, Melillo A, Mazzalupo S, Hudson AM, Wang S, Castiblanco C, Buszczak M, Hoskins RA, Cooley L.
  Genetics. 2007 Mar;175(3):1089-104. Epub 2006 Dec 18.
  PMID: 17179094
• Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development.
  Norga KK, Gurganus MC, Dilda CL, Yamamoto A, Lyman RF, Patel PH, Rubin GM, Hoskins RA, Mackay TF, Bellen HJ.
  Curr Biol. 2003 Aug 19;13(16):1388-96.
  PMID: 12932322

• 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.
  Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB.
  BMC Bioinformatics. 2004 Jan 21;5:6.
  PMID: 14736341
  
• Drosophila by the dozen.
  Celniker SE, Hoskins RA.
  Genome Biol. 2007;8(7):309. No abstract available.
  PMID: 17634150
  
• Phylogenetic and genomewide analyses suggest a functional relationship between kayak, the Drosophila fos homolog, and fig, a predicted protein phosphatase 2c nested within a kayak intron.
  Hudson SG, Garrett MJ, Carlson JW, Micklem G, Celniker SE, Goldstein ES, Newfeld SJ.
  Genetics. 2007 Nov;177(3):1349-61.
  PMID: 18039871
  
• Evolution of genes and genomes on the Drosophila phylogeny.
  Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.
  Nature. 2007 Nov 8;450(7167):203-18.
  PMID: 17994087
  
• Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
  Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M.
  Nature. 2007 Nov 8;450(7167):219-32.
  PMID: 17994088
  
• Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase.
  Villasante A, Abad JP, Planelló R, Méndez-Lago M, Celniker SE, de Pablos B.
  Genome Res. 2007 Dec;17(12):1909-18. Epub 2007 Nov 7.
  PMID: 17989257
  
• A BAC-based physical map of the Drosophila buzzatii genome.
  González J, Nefedov M, Bosdet I, Casals F, Calvete O, Delprat A, Shin H, Chiu R, Mathewson C, Wye N, Hoskins RA, Schein JE, de Jong P, Ruiz A.
  Genome Res. 2005 Jun;15(6):885-92.
  PMID: 15930498
  

• 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

• Web companion

• 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. Rincon-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

• Sequence datasets

• 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

• Curated table Fly, worm and yeast genes that are similar to human disease genes.

• Updated Interpro domain analysis

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

• Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
  Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE.
  Genome Biol. 2004;5(9):R61. Epub 2004 Aug 20.
  PMID: 15345045
  
• Chromatin looping mediates boundary element promoter interactions.
  Celniker SE, Drewell RA.
  Bioessays. 2007 Jan;29(1):7-10. Review.
  PMID: 17187351
  

• 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

• Web companion

• 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

• Posterior patterning genes and the identification of a unique body region in the brine shrimp Artemia franciscana.
  Copf T, Rabet N, Celniker SE, Averof M.
  Development. 2003 Dec;130(24):5915-27. Epub 2003 Oct 15.
  PMID: 14561635
  
• Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource.
  Hollich V, Johnson E, Furlong EE, Beckmann B, Carlson J, Celniker SE, Hoheisel JD.
  Biotechniques. 2004 Aug;37(2):282-4.
  PMID: 15335221
  
• Global analysis of patterns of gene expression during Drosophila embryogenesis.
  Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM.
  Genome Biol. 2007;8(7):R145.
  PMID: 17645804
  

• Global analyses of mRNA translational control during early Drosophila Embryogenesis
  X. Qin, S. Ahn, T.P. Speed, G.M. Rubin
  Genome Biology In Press
  Supplemental datasets

• 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

Functional Genomics

• P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogaster.
  Venken KJ, He Y, Hoskins RA, Bellen HJ.
  Science. 2006 Dec 15;314(5806):1747-51. Epub 2006 Nov 30.
  PMID: 17138868
• Thirty-one flavors of Drosophila rab proteins. Zhang J, Schulze KL, Hiesinger PR, Suyama K, Wang S, Fish M, Acar M, Hoskins RA, Bellen HJ, Scott MP.
  Genetics. 2007 Jun;176(2):1307-22. Epub 2007 Apr 3.
  PMID: 17409086
• Automating fruit fly Drosophila embryo injection for high throughput transgenic studies.
  Li XY, Macarthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD.
  Cornell E, Fisher WW, Nordmeyer R, Yegian D, Dong M, Biggin MD, Celniker SE, Jin J.
  Rev Sci Instrum. 2008 Jan;79(1):013705.
  PMID: 18248037

Unclassified

• Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer.
  Guan Y, Kuo WL, Stilwell JL, Takano H, Lapuk AV, Fridlyand J, Mao JH, Yu M, Miller MA, Santos JL, Kalloger SE, Carlson JW, Ginzinger DG, Celniker SE, Mills GB, Huntsman DG, Gray JW.
  Clin Cancer Res. 2007 Oct 1;13(19):5745-55.
  PMID: 17908964
  
• In memoriam: Edward B. Lewis (1918-2004).
  Duncan I, Celniker SE.
  Dev Cell. 2004 Oct;7(4):487-9. No abstract available.
  PMID: 15469837
  

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