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    Celniker, Susan

    Title
    SchoolLawrence Berkeley National Lab
    DepartmentBiological Systems & Eng
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-6258
    vCardDownload vCard

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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. Snijders AM, Langley SA, Kim YM, Brislawn CJ, Noecker C, Zink EM, Fansler SJ, Casey CP, Miller DR, Huang Y, Karpen GH, Celniker S, Brown JB, Borenstein E, Jansson JK, Metz TO, Mao JH. Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nat Microbiol. 2016 Nov 28; 2:16221. PMID: 27892936.
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      2. Celniker S. Susan Celniker: Foundational Resources To Study a Dynamic Genome. Genetics. 2016 Nov; 204(3):845-848. PMID: 28114099.
        View in: PubMed
      3. 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].
      4. 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.
      5. 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.
      6. 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.
      7. 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.
      8. Brown JB, Celniker S. Lessons from modENCODE. Annu Rev Genomics Hum Genet. 2015; 16:31-53. PMID: 26133010.
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      9. 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.
      10. 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.
      11. 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):1966-80. PMID: 25544350; PMCID: PMC4279448.
      12. 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.
      13. 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):2031-43. PMID: 25242320; PMCID: PMC4403667.
      14. 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.
      15. 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; PMCID: PMC4152413.
      16. 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; PMCID: PMC4155737.
      17. 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; PMCID: PMC4079975.
      18. 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.
      19. 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.
      20. 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.
      21. 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.
      22. 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.
      23. 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.
      24. 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.
      25. 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.
      26. 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.
      27. 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.
      28. 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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      29. 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.
      30. 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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      31. 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.
      32. 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.
      33. 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 S, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974; PMCID: PMC3192495.
      34. 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; PMCID: PMC3075879.
      35. 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.
      36. 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.
      37. 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.
      38. 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.
      39. 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.
      40. 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.
      41. 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.
      42. 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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      43. 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.
      44. 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.
      45. Cornell E, Fisher WW, Nordmeyer R, Yegian D, Dong M, Biggin MD, Celniker S, Jin J. Automating fruit fly Drosophila embryo injection for high throughput transgenic studies. Rev Sci Instrum. 2008 Jan; 79(1):013705. PMID: 18248037.
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      46. 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 S, 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, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 08; 450(7167):203-18. PMID: 17994087.
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      47. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, 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 S, Gelbart WM, Kellis M. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 08; 450(7167):219-32. PMID: 17994088; PMCID: PMC2474711.
      48. 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.
      49. 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.
      50. 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.
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