BDGP Resources

BDGP Publications

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.

modENCODE | Functional Genomics Genomic Sequencing | Annotation | cDNAs & ESTs Natural Transposable Elements | Drosophila Gene Disruption Project Comparative Genomics | SNP Map Regulatory Regions | Gene Expression | Control of Gene Expression Tools and Protocols for Drosophila Studies

modENCODE

• Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation. Westholm, J.O. Miura, P. Olson, S., Shenker, S., Joseph, B., Sanfilippo, P. Celniker, SE., Graveley, B.R., Lai EC. Cell Reports 2014 DOI: http://dx.doi.org/10.1016/j.celrep.2014.10.062
• The Comparative ENCODE RNA Resource Reveals Conserved Principles of Transcription. Gerstein MR, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier LW, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach RK, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Green P, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJP, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen R, Ladewig E, Lagarde J, Lai EC, Leng J, Lu ZJ, MacCoss M, May G, McWhirter RD, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip KY, Zaleski C, Zhang Y, Zheng H, Brenner SE*, Graveley BR*, Celniker SE*, Gingeras TR*, Waterston RH*. Nature. 2014. (*co-senior authors) PMCID:PMC4155737
• Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Chen Z-X, Sturgill D, Qu C, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki D, FitzGerald P, Artieri C, Atallah J, Barmina O, Brown JB, Blankenburg K, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kovar C, Lee S, Li M, Malley J, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Pu L-L, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner C, Worley KC, Wu Y-Q, Zou X, Cherbas P, Kellis M, Eisen M, Piano F, Kionte K, Fitch D, Sternberg P, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs R, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S. Genome Res (2014) 24(7):1209-23. PMCID: PMC4079975
• DNA copy number evolution in Drosophila modENCODE cell lines. Lee H, McManus CJ, Cho D-Y, Eaton ML, Renda F, Somma MP, Cherbas L, May G, Powell SK, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, Przytycka TM, Gatti M, Oliver B, Graveley BR, MacAlpine D. Genome Biol. 5(8):R70 2014 PMID: 25262759.
• Genome-guided transcript assembly by integrative analysis of RNA sequence data. Boley N, Stoiber MH, Booth BW, Wan K, Hoskins RA, Bickel PJ*, Celniker SE*, Brown BJ*. Nat. Biotechnol. 2014 Apr; 32(4):341-6. PMCID:PMC4037530
• Navigating and mining modENCODE data. Boley N, Wan KH, Bickel PJ, Celniker SE. Methods. 2014;68(1):38-47. PMID: 24636835.
• Diversity and dynamics of the Drosophila transcriptome. Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Weng J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandeza J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR*, Celniker SE*. Nature. 2014 512(7515):393-9. PMID:24670639 (*co-senior authors)
• Global patterns of tissue-specific alternative polyadenylation in Drosophila. Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE*, Graveley BR*, Lai EC*. Cell Rep. 2012 1:277-89. PMID:22685694 (*co-corresponding authors)
• Genome-wide analysis of promoter architecture in Drosophila melanogaster. Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE. Genome Res. 2011 Feb;21(2):182-92. PMID: 21177961
• The transcriptional diversity of 25 Drosophila cell lines. Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P. Genome Res. 2011 Feb;21(2):301-14. PMID: 21177962
• The developmental transcriptome of Drosophila melanogaster. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. Nature. 2010 Dec 22. PMID: 21179090
• Identification of functional elements and regulatory circuits by Drosophila modENCODE. modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Science. 2010 Dec 24;330(6012):1787-97. PMID: 21177974
• Unlocking the secrets of the genome. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium. Nature. 2009 Jun 18;459(7249):927-30. PMID: 19536255

Functional Genomics

• Transcription Factor Networks in Drosophila melanogaster. Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S. Cell Rep. 2014 Sep 17. pii: S2211-1247(14)00714-1
• An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Özkan E, Carrillo RA, Eastman CL, Weiszmann R, Waghray D, Johnson KG, Zinn K, Celniker SE, Garcia KC. Cell. 154:228-39 PMC3756661
• A protein complex network of Drosophila melanogaster. Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi SP, Celniker SE, Obar RA, Artavanis-Tsakonas S. Cell. 2011 Oct 28;147(3):690-703. PMID: 22036573
• Development of expression-ready constructs for generation of proteomic libraries. Yu C, Wan KH, Hammonds AS, Stapleton M, Carlson JW, Celniker SE. Methods Mol Biol. 2011;723:257-72. PMID: 21370071
• A molecularly defined duplication set for the X chromosome of Drosophila melanogaster. Venken KJ, Popodi E, Holtzman SL, Schulze KL, Park S, Carlson JW, Hoskins RA, Bellen HJ, Kaufman TC. Genetics. 2010 Dec;186(4):1111-25. PMID: 20876565
• Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Venken KJ, Carlson JW, Schulze KL, Pan H, He Y, Spokony R, Wan KH, Koriabine M, de Jong PJ, White KP, Bellen HJ, Hoskins RA. Nature Methods. 2009 Jun;6(6):431-4. PMID: 19465919
• 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
• 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
• 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

Genomic Sequencing

• The Release 6 reference sequence of the Drosophila melanogaster genome. Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE. Genome Res. 2015 Jan 14. pii: gr.185579.114. [Epub ahead of print]

• Characterization of MtnE, the fifth metallothionein member in Drosophila. Atanesyan L, Günther V, Celniker SE, Georgiev O, Schaffner W. J Biol Inorg Chem. 2011. 16(7):1047-56. Epub 2011 Aug 26.

• 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 Drosophila Genome. Celniker, S. Current Opinion in Genetics and Development. 2000. 10:612-16.

• 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

• Complete sequence of the bithorax complex of Drosophila. Martin CH, Mayeda CA, Davis CA, Ericsson CL, Knafels JD, Mathog DR, Celniker S, Lewis EB, Palazzolo MJ. Proc Natl Acad Sci U S A. 1995. 92(18):8398-402.

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

Drosophila Gene Disruption Project

• The Drosophila gene disruption project: progress using transposons with distinctive site-specificities. Bellen, H.J., R.W. Levis, Y. He, J.W. Carlson, M. Evans-Holm, E. Bae, J. Kim, A. Metaxakis, C. Savakis, K.L. Schulze, R.A. Hoskins and A.C. Spradling. Genetics 188(3):731-43. 2011. PMID: 21515576

• MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes. Venken, K.J.T., K.L. Schulze, N.A. Haelterman, H. Pan, Y. He, M. Evans-Holm, J.W. Carlson, R.W. Levis, A.C. Spradling, R.A. Hoskins and H.J. Bellen. Nat Methods 8(9):737-43. 2011.

• Drosophila P elements preferentially transpose to replication origins. Spradling, A.C., H.J. Bellen and R.A. Hoskins. Proc. Nat. Acad. Sci. U S A [Epub ahead of print, September 6, 2011] 2011. PMID: 21896744

• 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

• 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

• 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

• 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 diverse mechanisms underlying transcription factor-DNA occupancy. Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S. PLoS Genet. 9(8):e1003571

• Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA. Genome Res. 2013 23:928-40

• DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, Macarthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE. Proc Natl Acad Sci U S A. 2012 109:21330-5.

• Automated protein-DNA interaction screening of Drosophila regulatory elements. Hens K, Feuz JD, Isakova A, Iagovitina A, Massouras A, Bryois J, Callaerts P, Celniker SE, Deplancke B. Nat Methods 8(12):1065-70. doi:10.1038/nmeth.1763

• 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.

Tools and Protocols for Drosophila Studies

• Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos. Weiszmann R, Hammonds AS, Celniker SE. Nat Protoc. 2009. 4(5):605-18.
• Tools for neuroanatomy and neurogenetics in Drosophila. Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, Celniker SE, Rubin GM. Proc Natl Acad Sci USA. 2008. 105(28):9715-20.
• Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Markstein M, Pitsouli C, Villalta C, Celniker SE, Perrimon N. Nat Genet. 2008. 40(4):476-83.
• Automating fruit fly Drosophila embryo injection for high throughput transgenic studies. Cornell E, Fisher WW, Nordmeyer R, Yegian D, Dong M, Biggin MD, Celniker SE, Jin J. Rev Sci Instrum. 2008. 79(1):013705.

Gene Expression

• spatial expression of transcription factors in drosophila embryonic organ development. Hammonds AS, Bristow CA, Fisher WW, Weiszmann R, Wu S, Hartenstein V, Kellis M, Yu B, Frise E, Celniker SE. Genome Biol. 2013 Dec 20;14(12):R140. [Epub ahead of print].

• Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA. Genome Biol. 2011. 12(5):R43.

• Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Frise E, Hammonds AS, Celniker SE. Mol Syst Biol. 2010. 6:345. Epub 2010 Jan 19.

• Regulation of early endosomal entry by the Drosophila tumor suppressors Rabenosyn and Vps45. Morrison HA, Dionne H, Rusten TE, Brech A, Fisher WW, Pfeiffer BD, Celniker SE, Stenmark H, Bilder D. Mol Biol Cell 2008. 19(10):4167-76.

• A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Fowlkes CC, Hendriks CL, Keränen SV, Weber GH, Rübel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, Biggin MD, Eisen MB, Malik J. Cell 2008. 133(2):364-74.

• Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs. Harmon CL, Ahammad P, Hammonds A, Weiszmann R, Celniker SE, Sastry S, Rubin GM. RECOMB 2007. 2007:533-547.

• 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

• 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

• 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

• 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

Control of Gene Expression

• Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S. PLoS Biol. 2010. 8(8). pii: e1000456.
• Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. Ho MC, Johnsen H, Goetz SE, Schiller BJ, Bae E, Tran DA, Shur AS, Allen JM, Rau C, Bender W, Fisher WW, Celniker SE, Drewell RA. PLoS Genet. 2009. 5(11):e1000709.
• Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo 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. PLoS Biol. 2008. 6(2):e27.
• Exploiting transcriptional synergy to identify cis-regulatory modules in the Drosophila genome involved in axis formation. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker S, Levine M, Rubin GM, Eisen MB. Proc. Natl. Acad.Sci USA. 2001. 99:757-62.
• Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila. Lewis EB, Knafels JD, Mathog DR, Celniker S. Proc. Natl. Acad. Sci. 1995. 92: 8403-8407.

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

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