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Celniker, Susan

Title
InstitutionLawrence Berkeley National Lab
DepartmentBiological Systems & Eng
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/486-6258
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker S, White KP, Ma L, Gerstein M, Reinke V, Waterston RH. The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics. 2018 Mar; 208(3):937-949. PMID: 29284660.
      View in: PubMed
    2. Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker S. Complete Genome Sequence of Acetobacter pomorum Oregon-R-modENCODE Strain BDGP5, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut. Genome Announc. 2017 Nov 30; 5(48). PMID: 29192079.
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    3. Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker S. Complete Genome Sequence of Acetobacter tropicalis Oregon-R-modENCODE Strain BDGP1, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut. Genome Announc. 2017 Nov 16; 5(46). PMID: 29146844.
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    4. Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker S. Complete Genome Sequence of Lactobacillus plantarum Oregon-R-modENCODE Strain BDGP2 Isolated from Drosophila melanogaster Gut. Genome Announc. 2017 Oct 12; 5(41). PMID: 29025953.
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    5. Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker S. Complete Genome Sequence of Bacillus kochii Oregon-R-modENCODE Strain BDGP4, Isolated from Drosophila melanogaster Gut. Genome Announc. 2017 Oct 05; 5(40). PMID: 28983001.
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    6. Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker S. Complete Genome Sequence of Enterococcus durans Oregon-R-modENCODE Strain BDGP3, a Lactic Acid Bacterium Found in the Drosophila melanogaster Gut. Genome Announc. 2017 Oct 05; 5(40). PMID: 28982997.
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    7. Celniker S. Susan Celniker: Foundational Resources To Study a Dynamic Genome. Genetics. 2016 11; 204(3):845-848. PMID: 28114099.
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    8. Wu S, Joseph A, Hammonds AS, Celniker S, Yu B, Frise E. Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks. Proc Natl Acad Sci U S A. 2016 Apr 19; 113(16):4290-5. PMID: 27071099; PMCID: PMC4843452 [Available on 10/19/16].
    9. Stoiber M, Celniker S, Cherbas L, Brown B, Cherbas P. Diverse Hormone Response Networks in 41 Independent Drosophila Cell Lines. G3 (Bethesda). 2016 Jan 15; 6(3):683-94. PMID: 26772746; PMCID: PMC4777130.
    10. Mao JH, Langley SA, Huang Y, Hang M, Bouchard KE, Celniker S, Brown JB, Jansson JK, Karpen GH, Snijders AM. Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice. Sci Rep. 2015 Nov 09; 5:16247. PMID: 26548763; PMCID: PMC4637864.
    11. Stoiber MH, Olson S, May GE, Duff MO, Manent J, Obar R, Guruharsha KG, Bickel PJ, Artavanis-Tsakonas S, Brown JB, Graveley BR, Celniker S. Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila. Genome Res. 2015 Nov; 25(11):1692-702. PMID: 26294687; PMCID: PMC4617965.
    12. Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Booth BW, Celniker S, Graveley BR, Brenner SE. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Res. 2015 Nov; 25(11):1771-80. PMID: 26294686; PMCID: PMC4617972.
    13. Brown JB, Celniker S. Lessons from modENCODE. Annu Rev Genomics Hum Genet. 2015; 16:31-53. PMID: 26133010.
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    14. Duff MO, Olson S, Wei X, Garrett SC, Osman A, Bolisetty M, Plocik A, Celniker S, Graveley BR. Genome-wide identification of zero nucleotide recursive splicing in Drosophila. Nature. 2015 May 21; 521(7552):376-9. PMID: 25970244; PMCID: PMC4529404.
    15. 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 S. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015 Mar; 25(3):445-58. PMID: 25589440; PMCID: PMC4352887.
    16. Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker S, Graveley BR, Lai EC. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep. 2014 Dec 11; 9(5):1966-1980. PMID: 25544350.
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    17. Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker S, Phillippy AM, Bergman CM, Landolin JM. Long-read, whole-genome shotgun sequence data for five model organisms. Sci Data. 2014; 1:140045. PMID: 25977796; PMCID: PMC4365909.
    18. Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker S, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S. Transcription factor networks in Drosophila melanogaster. Cell Rep. 2014 Sep 25; 8(6):2031-2043. PMID: 25242320; PMCID: PMC4403667.
    19. Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, 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, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, 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 K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker S, Gingeras TR, Waterston R. Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512(7515):445-8. PMID: 25164755.
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    20. Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen 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, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker S. Diversity and dynamics of the Drosophila transcriptome. Nature. 2014 Aug 28; 512(7515):393-9. PMID: 24670639.
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    21. Lee H, McManus CJ, Cho DY, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker S, Cherbas P, Przytycka TM, Gatti M, Oliver B, Graveley B, MacAlpine D. DNA copy number evolution in Drosophila cell lines. Genome Biol. 2014 Aug 28; 15(8):R70. PMID: 25262759; PMCID: PMC4289277.
    22. Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker S, Oliver B, Richards S. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul; 24(7):1209-23. PMID: 24985915.
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    23. Boley N, Stoiber MH, Booth BW, Wan KH, Hoskins RA, Bickel PJ, Celniker S, Brown JB. Genome-guided transcript assembly by integrative analysis of RNA sequence data. Nat Biotechnol. 2014 Apr; 32(4):341-6. PMID: 24633242; PMCID: PMC4037530.
    24. Boley N, Wan KH, Bickel PJ, Celniker S. Navigating and mining modENCODE data. Methods. 2014 Jun 15; 68(1):38-47. PMID: 24636835; PMCID: PMC4857704.
    25. Hammonds AS, Bristow CA, Fisher WW, Weiszmann R, Wu S, Hartenstein V, Kellis M, Yu B, Frise E, Celniker S. Spatial expression of transcription factors in Drosophila embryonic organ development. Genome Biol. 2013 Dec 20; 14(12):R140. PMID: 24359758; PMCID: PMC4053779.
    26. Cheng Q, Kazemian M, Pham H, Blatti C, Celniker S, Wolfe SA, Brodsky MH, Sinha S. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genet. 2013; 9(8):e1003571. PMID: 23935523; PMCID: PMC3731213.
    27. Özkan E, Carrillo RA, Eastman CL, Weiszmann R, Waghray D, Johnson KG, Zinn K, Celniker S, Garcia KC. An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell. 2013 Jul 03; 154(1):228-39. PMID: 23827685; PMCID: PMC3756661.
    28. 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 S, Sinha S, Stormo GD, Brodsky MH, Wolfe SA. Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res. 2013 Jun; 23(6):928-40. PMID: 23471540; PMCID: PMC3668361.
    29. 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 S. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21330-5. PMID: 23236164; PMCID: PMC3535648.
    30. 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 S, Graveley BR, Lai EC. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep. 2012 Mar 29; 1(3):277-89. PMID: 22685694; PMCID: PMC3368434.
    31. Hens K, Feuz JD, Isakova A, Iagovitina A, Massouras A, Bryois J, Callaerts P, Celniker S, Deplancke B. Automated protein-DNA interaction screening of Drosophila regulatory elements. Nat Methods. 2011 Oct 30; 8(12):1065-70. PMID: 22037703; PMCID: PMC3929264.
    32. 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 S, Obar RA, Artavanis-Tsakonas S. A protein complex network of Drosophila melanogaster. Cell. 2011 Oct 28; 147(3):690-703. PMID: 22036573; PMCID: PMC3319048.
    33. Atanesyan L, Günther V, Celniker S, Georgiev O, Schaffner W. Characterization of MtnE, the fifth metallothionein member in Drosophila. J Biol Inorg Chem. 2011 Oct; 16(7):1047-56. PMID: 21870250.
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    34. Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker S, Biggin MD, Stamatoyannopoulos JA. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011; 12(5):R43. PMID: 21569360; PMCID: PMC3219966.
    35. Yu C, Wan KH, Hammonds AS, Stapleton M, Carlson JW, Celniker S. Development of expression-ready constructs for generation of proteomic libraries. Methods Mol Biol. 2011; 723:257-72. PMID: 21370071.
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    36. 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 S. The developmental transcriptome of Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):473-9. PMID: 21179090.
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    37. 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 S. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011 Feb; 21(2):182-92. PMID: 21177961; PMCID: PMC3032922.
    38. 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 S, Gingeras TR, Cherbas P. The transcriptional diversity of 25 Drosophila cell lines. Genome Res. 2011 Feb; 21(2):301-14. PMID: 21177962; PMCID: PMC3032933.
    39. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974.
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    40. Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker S, Kumar S, Wolfe SA, Brodsky MH, Sinha S. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol. 2010 Aug 17; 8(8). PMID: 20808951; PMCID: PMC2923081.
    41. Frise E, Hammonds AS, Celniker S. Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Mol Syst Biol. 2010; 6:345. PMID: 20087342; PMCID: PMC2824522.
    42. Ho MC, Johnsen H, Goetz SE, Schiller BJ, Bae E, Tran DA, Shur AS, Allen JM, Rau C, Bender W, Fisher WW, Celniker S, Drewell RA. Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. PLoS Genet. 2009 Nov; 5(11):e1000709. PMID: 19893611; PMCID: PMC2763271.
    43. Celniker S, 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. Unlocking the secrets of the genome. Nature. 2009 Jun 18; 459(7249):927-30. PMID: 19536255; PMCID: PMC2843545.
    44. Weiszmann R, Hammonds AS, Celniker S. Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos. Nat Protoc. 2009; 4(5):605-18. PMID: 19360017; PMCID: PMC2780369.
    45. Morrison HA, Dionne H, Rusten TE, Brech A, Fisher WW, Pfeiffer BD, Celniker S, Stenmark H, Bilder D. Regulation of early endosomal entry by the Drosophila tumor suppressors Rabenosyn and Vps45. Mol Biol Cell. 2008 Oct; 19(10):4167-76. PMID: 18685079; PMCID: PMC2555928.
    46. 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 S, Rubin GM. Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9715-20. PMID: 18621688; PMCID: PMC2447866.
    47. 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. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008 Apr 18; 133(2):364-74. PMID: 18423206.
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    48. Markstein M, Pitsouli C, Villalta C, Celniker S, Perrimon N. Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat Genet. 2008 Apr; 40(4):476-83. PMID: 18311141; PMCID: PMC2330261.
    49. 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 S, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008 Feb; 6(2):e27. PMID: 18271625; PMCID: PMC2235902.
    50. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 08; 450(7167):219-32. PMID: 17994088; PMCID: PMC2474711.
    51. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 08; 450(7167):203-18. PMID: 17994087.
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    52. Villasante A, Abad JP, Planelló R, Méndez-Lago M, Celniker S, de Pablos B. Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase. Genome Res. 2007 Dec; 17(12):1909-18. PMID: 17989257; PMCID: PMC2099598.
    53. 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, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker S, Gelbart WM, Kellis M. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res. 2007 Dec; 17(12):1823-36. PMID: 17989253; PMCID: PMC2099591.
    54. Hudson SG, Garrett MJ, Carlson JW, Micklem G, Celniker S, Goldstein ES, Newfeld SJ. 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. Genetics. 2007 Nov; 177(3):1349-61. PMID: 18039871; PMCID: PMC2147949.
    55. 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 S, Mills GB, Huntsman DG, Gray JW. Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer. Clin Cancer Res. 2007 Oct 01; 13(19):5745-55. PMID: 17908964.
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    56. 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 S. Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science. 2007 Jun 15; 316(5831):1625-8. PMID: 17569867; PMCID: PMC2825053.
    57. Celniker S, Hoskins RA. Drosophila by the dozen. Genome Biol. 2007; 8(7):309. PMID: 17634150; PMCID: PMC2323228.
    58. Celniker S, Drewell RA. Chromatin looping mediates boundary element promoter interactions. Bioessays. 2007 Jan; 29(1):7-10. PMID: 17187351.
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    59. Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker S, Rubin GM. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2007; 8(7):R145. PMID: 17645804; PMCID: PMC2323238.
    60. Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker S, Myers EW, Karpen GH. Improved repeat identification and masking in Dipterans. Gene. 2007 Mar 01; 389(1):1-9. PMID: 17137733; PMCID: PMC1945102.
    61. Stapleton M, Carlson JW, Celniker S. RNA editing in Drosophila melanogaster: New targets and functional consequences. RNA. 2006 Nov; 12(11):1922-32. PMID: 17018572; PMCID: PMC1624909.
    62. George JA, DeBaryshe PG, Traverse KL, Celniker S, Pardue ML. Genomic organization of the Drosophila telomere retrotransposable elements. Genome Res. 2006 Oct; 16(10):1231-40. PMID: 16963706; PMCID: PMC1581432.
    63. Wan KH, Yu C, George RA, Carlson JW, Hoskins RA, Svirskas R, Stapleton M, Celniker S. High-throughput plasmid cDNA library screening. Nat Protoc. 2006; 1(2):624-32. PMID: 17406289.
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    64. Hoskins RA, Stapleton M, George RA, Yu C, Wan KH, Carlson JW, Celniker S. Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP). Nucleic Acids Res. 2005 Dec 02; 33(21):e185. PMID: 16326860; PMCID: PMC1301602.
    65. Chen L, Lullo DJ, Ma E, Celniker S, Rio DC, Doudna JA. Identification and analysis of U5 snRNA variants in Drosophila. RNA. 2005 Oct; 11(10):1473-7. PMID: 16199758; PMCID: PMC1370830.
    66. Tupy JL, Bailey AM, Dailey G, Evans-Holm M, Siebel CW, Misra S, Celniker S, Rubin GM. Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2005 Apr 12; 102(15):5495-500. PMID: 15809421; PMCID: PMC555963.
    67. Yandell M, Bailey AM, Misra S, Shu S, Wiel C, Evans-Holm M, Celniker S, Rubin GM. A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A. 2005 Feb 01; 102(5):1566-71. PMID: 15668397; PMCID: PMC545494.
    68. Bergman CM, Carlson JW, Celniker S. Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics. 2005 Apr 15; 21(8):1747-9. PMID: 15572468.
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    69. Duncan I, Celniker S. In memoriam: Edward B. Lewis (1918-2004). Dev Cell. 2004 Oct; 7(4):487-9. PMID: 15469837.
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    70. Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker S. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 2004; 5(9):R61. PMID: 15345045; PMCID: PMC522868.
    71. Hollich V, Johnson E, Furlong EE, Beckmann B, Carlson J, Celniker S, Hoheisel JD. Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource. Biotechniques. 2004 Aug; 37(2):282-4. PMID: 15335221.
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    72. Pollard DA, Bergman CM, Stoye J, Celniker S, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics. 2004 Jan 21; 5:6. PMID: 14736341; PMCID: PMC344529.
    73. Copf T, Rabet N, Celniker S, Averof M. Posterior patterning genes and the identification of a unique body region in the brine shrimp Artemia franciscana. Development. 2003 Dec; 130(24):5915-27. PMID: 14561635.
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    74. Lewis EB, Pfeiffer BD, Mathog DR, Celniker S. Evolution of the homeobox complex in the Diptera. Curr Biol. 2003 Aug 05; 13(15):R587-8. PMID: 12906807.
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    75. Carvalho AB, Vibranovski MD, Carlson JW, Celniker S, Hoskins RA, Rubin GM, Sutton GG, Adams MD, Myers EW, Clark AG. Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go? Genetica. 2003 Mar; 117(2-3):227-37. PMID: 12723702.
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    76. Celniker S, Rubin GM. The Drosophila melanogaster genome. Annu Rev Genomics Hum Genet. 2003; 4:89-117. PMID: 14527298.
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    77. Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker S, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002; 3(12):RESEARCH0083. PMID: 12537572; PMCID: PMC151185.
    78. Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, Yasuhara JC, Wakimoto BT, Myers EW, Celniker S, Rubin GM, Karpen GH. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 2002; 3(12):RESEARCH0085. PMID: 12537574; PMCID: PMC151187.
    79. Bergman CM, Pfeiffer BD, Rincón-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, de Jong PJ, Botas J, Rubin GM, Celniker S. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol. 2002; 3(12):RESEARCH0086. PMID: 12537575; PMCID: PMC151188.
    80. Celniker S, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, Hodgson A, George RA, Hoskins RA, Laverty T, Muzny DM, Nelson CR, Pacleb JM, Park S, Pfeiffer BD, Richards S, Sodergren EJ, Svirskas R, Tabor PE, Wan K, Stapleton M, Sutton GG, Venter C, Weinstock G, Scherer SE, Myers EW, Gibbs RA, Rubin GM. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 2002; 3(12):RESEARCH0079. PMID: 12537568; PMCID: PMC151181.
    81. Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker S. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 2002; 3(12):RESEARCH0084. PMID: 12537573; PMCID: PMC151186.
    82. Stapleton M, Carlson J, Brokstein P, Yu C, Champe M, George R, Guarin H, Kronmiller B, Pacleb J, Park S, Wan K, Rubin GM, Celniker S. A Drosophila full-length cDNA resource. Genome Biol. 2002; 3(12):RESEARCH0080. PMID: 12537569; PMCID: PMC151182.
    83. Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker S, Rubin GM. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002; 3(12):RESEARCH0088. PMID: 12537577; PMCID: PMC151190.
    84. Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, Yu C, Carlson J, George R, Celniker S, Rubin GM. The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res. 2002 Aug; 12(8):1294-300. PMID: 12176937; PMCID: PMC186637.
    85. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker S, Levine M, Rubin GM, Eisen MB. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A. 2002 Jan 22; 99(2):757-62. PMID: 11805330; PMCID: PMC117378.
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