Susan Celniker - Publications

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112 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Langley S, Eng T, Wan KH, Herbert RA, Klein AP, Yoshikuni Y, Tringe SG, Brown JB, Celniker SE, Mortimer JC, Mukhopadhyay A. Complete Genome Sequence of sp. Strain 33MFTa1.1, Isolated from Roots. Microbiology Resource Announcements. 8. PMID 31515332 DOI: 10.1128/MRA.00432-19  0.44
2019 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 SE, Cherbas P, et al. Correction to: DNA copy number evolution in Drosophila cell lines. Genome Biology. 20: 53. PMID 30857560 DOI: 10.1186/s13059-019-1668-5  0.32
2018 Arbel H, Basu S, Fisher WW, Hammonds AS, Wan KH, Park S, Weiszmann R, Booth BW, Keranen SV, Henriquez C, Shams Solari O, Bickel PJ, Biggin MD, Celniker SE, Brown JB. Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. Proceedings of the National Academy of Sciences of the United States of America. PMID 30598455 DOI: 10.1073/pnas.1808833115  0.56
2018 Parra M, Booth BW, Weiszmann R, Yee BA, Yeo GW, Brown JB, Celniker SE, Conboy JG. An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys. Rna (New York, N.Y.). PMID 29959282 DOI: 10.1261/rna.066951.118  0.52
2018 Booth BW, McParland C, Beattie K, Fisher WW, Hammonds AS, Celniker SE, Frise E. OpenHiCAMM: High-Content Screening Software for Complex Microscope Imaging Workflows. Iscience. 2: 136-140. PMID 29888763 DOI: 10.1016/j.isci.2018.03.017  0.48
2017 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, ... ... Celniker SE, et al. The modERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics. PMID 29284660 DOI: 10.1534/genetics.117.300657  0.48
2017 Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE. Complete Genome Sequence of Acetobacter pomorum Oregon-R-modENCODE Strain BDGP5, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut. Genome Announcements. 5. PMID 29192079 DOI: 10.1128/genomeA.01333-17  0.48
2017 Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE. Complete Genome Sequence of Acetobacter tropicalis Oregon-R-modENCODE Strain BDGP1, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut. Genome Announcements. 5. PMID 29146844 DOI: 10.1128/genomeA.01020-17  0.48
2017 Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE. Complete Genome Sequence of Lactobacillus plantarum Oregon-R-modENCODE Strain BDGP2 Isolated from Drosophila melanogaster Gut. Genome Announcements. 5. PMID 29025953 DOI: 10.1128/genomeA.01155-17  0.48
2017 Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE. Complete Genome Sequence of Bacillus kochii Oregon-R-modENCODE Strain BDGP4, Isolated from Drosophila melanogaster Gut. Genome Announcements. 5. PMID 28983001 DOI: 10.1128/genomeA.01074-17  0.48
2017 Wan KH, Yu C, Park S, Hammonds AS, Booth BW, Celniker SE. Complete Genome Sequence of Enterococcus durans Oregon-R-modENCODE Strain BDGP3, a Lactic Acid Bacterium Found in the Drosophila melanogaster Gut. Genome Announcements. 5. PMID 28982997 DOI: 10.1128/genomeA.01041-17  0.48
2016 Snijders AM, Langley SA, Kim YM, Brislawn CJ, Noecker C, Zink EM, Fansler SJ, Casey CP, Miller DR, Huang Y, Karpen GH, Celniker SE, Brown JB, Borenstein E, Jansson JK, et al. Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nature Microbiology. 2: 16221. PMID 27892936 DOI: 10.1038/nmicrobiol.2016.221  0.44
2016 Wu S, Joseph A, Hammonds AS, Celniker SE, Yu B, Frise E. Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks. Proceedings of the National Academy of Sciences of the United States of America. PMID 27071099 DOI: 10.1073/pnas.1521171113  1
2015 Mao JH, Langley SA, Huang Y, Hang M, Bouchard KE, Celniker SE, Brown JB, Jansson JK, Karpen GH, Snijders AM. Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice. Scientific Reports. 5: 16247. PMID 26548763 DOI: 10.1038/srep16247  1
2015 Stoiber MH, Olson S, May GE, Duff MO, Manent J, Obar R, Guruharsha K, Artavanis-Tsakonas S, Brown JB, Graveley BR, Celniker SE. Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila. Genome Research. PMID 26294687 DOI: 10.1101/gr.182675.114  1
2015 Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Celniker SE, Graveley BR, Brenner SE. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Research. PMID 26294686 DOI: 10.1101/gr.192518.115  1
2015 Brown JB, Celniker SE. Lessons from modENCODE. Annual Review of Genomics and Human Genetics. PMID 26133010 DOI: 10.1146/annurev-genom-090413-025448  1
2015 Duff MO, Olson S, Wei X, Garrett SC, Osman A, Bolisetty M, Plocik A, Celniker SE, Graveley BR. Genome-wide identification of zero nucleotide recursive splicing in Drosophila. Nature. 521: 376-9. PMID 25970244 DOI: 10.1038/nature14475  1
2015 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, ... ... Celniker SE, et al. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Research. 25: 445-58. PMID 25589440 DOI: 10.1101/gr.185579.114  1
2014 Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM. Long-read, whole-genome shotgun sequence data for five model organisms. Scientific Data. 1: 140045. PMID 25977796 DOI: 10.1038/sdata.2014.45  1
2014 Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker SE, Graveley BR, Lai EC. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Reports. 9: 1966-80. PMID 25544350 DOI: 10.1016/j.celrep.2014.10.062  1
2014 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 SE, Cherbas P, et al. DNA copy number evolution in Drosophila cell lines. Genome Biology. 15: R70. PMID 25262759 DOI: 10.1186/gb-2014-15-8-r70  1
2014 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. Transcription factor networks in Drosophila melanogaster. Cell Reports. 8: 2031-43. PMID 25242320 DOI: 10.1016/j.celrep.2014.08.038  1
2014 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, ... ... Celniker SE, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/nature13424  0.48
2014 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, ... ... Celniker SE, et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research. 24: 1209-23. PMID 24985915 DOI: 10.1101/gr.159384.113  0.76
2014 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, ... ... Celniker SE, et al. Diversity and dynamics of the Drosophila transcriptome. Nature. 512: 393-9. PMID 24670639 DOI: 10.1038/nature12962  1
2014 Boley N, Wan KH, Bickel PJ, Celniker SE. Navigating and mining modENCODE data. Methods (San Diego, Calif.). 68: 38-47. PMID 24636835 DOI: 10.1016/j.ymeth.2014.03.007  1
2014 Boley N, Stoiber MH, Booth BW, Wan KH, Hoskins RA, Bickel PJ, Celniker SE, Brown JB. Genome-guided transcript assembly by integrative analysis of RNA sequence data. Nature Biotechnology. 32: 341-6. PMID 24633242 DOI: 10.1038/nbt.2850  1
2013 Hammonds AS, Bristow CA, Fisher WW, Weiszmann R, Wu S, Hartenstein V, Kellis M, Yu B, Frise E, Celniker SE. Spatial expression of transcription factors in Drosophila embryonic organ development. Genome Biology. 14: R140. PMID 24359758 DOI: 10.1186/gb-2013-14-12-r140  1
2013 Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. Plos Genetics. 9: e1003571. PMID 23935523 DOI: 10.1371/journal.pgen.1003571  1
2013 Özkan E, Carrillo RA, Eastman CL, Weiszmann R, Waghray D, Johnson KG, Zinn K, Celniker SE, Garcia KC. An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell. 154: 228-39. PMID 23827685 DOI: 10.1016/j.cell.2013.06.006  1
2013 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, et al. Global analysis of Drosophila Cysâ‚‚-Hisâ‚‚ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Research. 23: 928-40. PMID 23471540 DOI: 10.1101/gr.151472.112  1
2013 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, et al. Errata to Global patterns of tissue-specific alternative polyadenylation in drosophila [Cell Reports, 1 (2012) 277-289] Cell Reports. 3: 969. DOI: 10.1016/j.celrep.2013.03.022  1
2012 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. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 109: 21330-5. PMID 23236164 DOI: 10.1073/pnas.1209589110  1
2012 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, et al. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Reports. 1: 277-89. PMID 22685694 DOI: 10.1016/j.celrep.2012.01.001  1
2011 Hens K, Feuz JD, Isakova A, Iagovitina A, Massouras A, Bryois J, Callaerts P, Celniker SE, Deplancke B. Automated protein-DNA interaction screening of Drosophila regulatory elements. Nature Methods. 8: 1065-70. PMID 22037703 DOI: 10.1038/nmeth.1763  1
2011 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, ... ... Celniker SE, et al. A protein complex network of Drosophila melanogaster. Cell. 147: 690-703. PMID 22036573 DOI: 10.1016/j.cell.2011.08.047  1
2011 Atanesyan L, Günther V, Celniker SE, Georgiev O, Schaffner W. Characterization of MtnE, the fifth metallothionein member in Drosophila. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 16: 1047-56. PMID 21870250 DOI: 10.1007/s00775-011-0825-4  1
2011 Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biology. 12: R43. PMID 21569360 DOI: 10.1186/gb-2011-12-5-r43  1
2011 Yu C, Wan KH, Hammonds AS, Stapleton M, Carlson JW, Celniker SE. Development of expression-ready constructs for generation of proteomic libraries. Methods in Molecular Biology (Clifton, N.J.). 723: 257-72. PMID 21370071 DOI: 10.1007/978-1-61779-043-0_17  1
2011 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, ... ... Celniker SE, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. PMID 21179090 DOI: 10.1038/nature09715  1
2011 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, ... ... Celniker SE, et al. The transcriptional diversity of 25 Drosophila cell lines. Genome Research. 21: 301-14. PMID 21177962 DOI: 10.1101/gr.112961.110  1
2011 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, ... ... Celniker SE, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Research. 21: 182-92. PMID 21177961 DOI: 10.1101/gr.112466.110  1
2010 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, ... ... Celniker SE, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/science.1198374  0.44
2010 Hoang ML, Tan FJ, Lai DC, Celniker SE, Hoskins RA, Dunham MJ, Zheng Y, Koshland D. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination. Plos Genetics. 6: e1001228. PMID 21151956 DOI: 10.1371/journal.pgen.1001228  1
2010 Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. Plos Biology. 8. PMID 20808951 DOI: 10.1371/journal.pbio.1000456  1
2010 Frise E, Hammonds AS, Celniker SE. Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Molecular Systems Biology. 6: 345. PMID 20087342 DOI: 10.1038/msb.2009.102  1
2009 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. Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. Plos Genetics. 5: e1000709. PMID 19893611 DOI: 10.1371/journal.pgen.1000709  1
2009 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, et al. Unlocking the secrets of the genome. Nature. 459: 927-30. PMID 19536255 DOI: 10.1038/459927a  1
2009 Weiszmann R, Hammonds AS, Celniker SE. Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos. Nature Protocols. 4: 605-18. PMID 19360017 DOI: 10.1038/nprot.2009.55  1
2008 Morrison HA, Dionne H, Rusten TE, Brech A, Fisher WW, Pfeiffer BD, Celniker SE, Stenmark H, Bilder D. Regulation of early endosomal entry by the Drosophila tumor suppressors Rabenosyn and Vps45. Molecular Biology of the Cell. 19: 4167-76. PMID 18685079 DOI: 10.1091/mbc.E08-07-0716  1
2008 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, et al. Tools for neuroanatomy and neurogenetics in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 105: 9715-20. PMID 18621688 DOI: 10.1073/pnas.0803697105  1
2008 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, et al. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 133: 364-74. PMID 18423206 DOI: 10.1016/j.cell.2008.01.053  1
2008 Markstein M, Pitsouli C, Villalta C, Celniker SE, Perrimon N. Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nature Genetics. 40: 476-83. PMID 18311141 DOI: 10.1038/ng.101  1
2008 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, ... ... Celniker SE, et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. Plos Biology. 6: e27. PMID 18271625 DOI: 10.1371/journal.pbio.0060027  1
2008 Cornell E, Fisher WW, Nordmeyer R, Yegian D, Dong M, Biggin MD, Celniker SE, Jin J. Automating fruit fly Drosophila embryo injection for high throughput transgenic studies. The Review of Scientific Instruments. 79: 013705. PMID 18248037 DOI: 10.1063/1.2827516  1
2008 Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Hou CC, Ogawa N, Inwood W, Sementchenko V, Beaton A, ... ... Celniker SE, et al. Correction: Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm (PLoS Biology (2008) 6,2 (e27) DOI: 10.1371/journal.pbio.0060027) Plos Biology. 6: 1600. DOI: 10.1371/journal.pbio.0060190  1
2007 Hudson SG, Garrett MJ, Carlson JW, Micklem G, Celniker SE, 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. 177: 1349-61. PMID 18039871 DOI: 10.1534/genetics.107.071670  1
2007 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, ... ... Celniker SE, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/nature06340  1
2007 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, ... ... Celniker SE, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/nature06341  1
2007 Villasante A, Abad JP, Planelló R, Méndez-Lago M, Celniker SE, de Pablos B. Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase. Genome Research. 17: 1909-18. PMID 17989257 DOI: 10.1101/gr.6365107  1
2007 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, ... ... Celniker SE, et al. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Research. 17: 1823-36. PMID 17989253 DOI: 10.1101/gr.6679507  1
2007 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, et al. Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 13: 5745-55. PMID 17908964 DOI: 10.1158/1078-0432.CCR-06-2882  1
2007 Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biology. 8: R145. PMID 17645804 DOI: 10.1186/gb-2007-8-7-r145  1
2007 Celniker SE, Hoskins RA. Drosophila by the dozen. Genome Biology. 8: 309. PMID 17634150 DOI: 10.1186/gb-2007-8-7-309  1
2007 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. Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science (New York, N.Y.). 316: 1625-8. PMID 17569867 DOI: 10.1126/science.1139816  1
2007 Celniker SE, Drewell RA. Chromatin looping mediates boundary element promoter interactions. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 29: 7-10. PMID 17187351 DOI: 10.1002/bies.20520  1
2007 Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH. Improved repeat identification and masking in Dipterans. Gene. 389: 1-9. PMID 17137733 DOI: 10.1016/j.gene.2006.09.011  1
2007 Celniker SE, Lewis EB. Molecular basis of transabdominal - A sexually dimorphic mutant of the bithorax complex of Drosophila Genes, Development, and Cancer: the Life and Work of Edward B. Lewis. 383-391. DOI: 10.1007/978-1-4020-6345-9_17  1
2007 Harmon CL, Ahammad P, Hammonds A, Weiszmann R, Celniker SE, Sastry SS, Rubin GM. Comparative analysis of spatial patterns of gene expression in Drosophila melanogaster imaginal discs Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4453: 533-547.  1
2006 Wan KH, Yu C, George RA, Carlson JW, Hoskins RA, Svirskas R, Stapleton M, Celniker SE. High-throughput plasmid cDNA library screening. Nature Protocols. 1: 624-32. PMID 17406289 DOI: 10.1038/nprot.2006.90  1
2006 Stapleton M, Carlson JW, Celniker SE. RNA editing in Drosophila melanogaster: New targets and functional consequences. Rna (New York, N.Y.). 12: 1922-32. PMID 17018572 DOI: 10.1261/rna.254306  1
2006 George JA, DeBaryshe PG, Traverse KL, Celniker SE, Pardue ML. Genomic organization of the Drosophila telomere retrotransposable elements. Genome Research. 16: 1231-40. PMID 16963706 DOI: 10.1101/gr.5348806  1
2005 Hoskins RA, Stapleton M, George RA, Yu C, Wan KH, Carlson JW, Celniker SE. Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP). Nucleic Acids Research. 33: e185. PMID 16326860 DOI: 10.1093/nar/gni184  1
2005 Tupy JL, Bailey AM, Dailey G, Evans-Holm M, Siebel CW, Misra S, Celniker SE, Rubin GM. Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 102: 5495-500. PMID 15809421 DOI: 10.1073/pnas.0501422102  1
2005 Yandell M, Bailey AM, Misra S, Shu S, Wiel C, Evans-Holm M, Celniker SE, Rubin GM. A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proceedings of the National Academy of Sciences of the United States of America. 102: 1566-71. PMID 15668397 DOI: 10.1073/pnas.0409421102  1
2005 Bergman CM, Carlson JW, Celniker SE. Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics (Oxford, England). 21: 1747-9. PMID 15572468 DOI: 10.1093/bioinformatics/bti173  1
2004 Duncan I, Celniker SE. In memoriam: Edward B. Lewis (1918-2004). Developmental Cell. 7: 487-9. PMID 15469837 DOI: 10.1016/j.devcel.2004.09.005  1
2004 Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biology. 5: R61. PMID 15345045 DOI: 10.1186/gb-2004-5-9-r61  1
2004 Hollich V, Johnson E, Furlong EE, Beckmann B, Carlson J, Celniker SE, Hoheisel JD. Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource. Biotechniques. 37: 282-4. PMID 15335221  1
2004 Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Correction: Benchmarking tools for the alignment of functional noncoding DNA. Bmc Bioinformatics. 5: 73. PMID 15186509 DOI: 10.1186/1471-2105-5-73  1
2004 Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. Bmc Bioinformatics. 5: 6. PMID 14736341 DOI: 10.1186/1471-2105-5-6  1
2003 Copf T, Rabet N, Celniker SE, Averof M. Posterior patterning genes and the identification of a unique body region in the brine shrimp Artemia franciscana. Development (Cambridge, England). 130: 5915-27. PMID 14561635 DOI: 10.1242/dev.00835  1
2003 Celniker SE, Rubin GM. The Drosophila melanogaster genome. Annual Review of Genomics and Human Genetics. 4: 89-117. PMID 14527298 DOI: 10.1146/annurev.genom.4.070802.110323  1
2003 Lewis EB, Pfeiffer BD, Mathog DR, Celniker SE. Evolution of the homeobox complex in the Diptera. Current Biology : Cb. 13: R587-8. PMID 12906807 DOI: 10.1007/978-1-4020-6345-9_20  1
2003 Carvalho AB, Vibranovski MD, Carlson JW, Celniker SE, 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. 117: 227-37. PMID 12723702 DOI: 10.1023/A:1022900313650  1
2002 Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GM. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biology. 3: RESEARCH0088. PMID 12537577  1
2002 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, ... ... Celniker SE, et al. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biology. 3: RESEARCH0086. PMID 12537575  1
2002 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 SE, Rubin GM, et al. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biology. 3: RESEARCH0085. PMID 12537574  1
2002 Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biology. 3: RESEARCH0084. PMID 12537573  1
2002 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, ... ... Celniker SE, et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biology. 3: RESEARCH0083. PMID 12537572  1
2002 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 SE. A Drosophila full-length cDNA resource. Genome Biology. 3: RESEARCH0080. PMID 12537569  1
2002 Celniker SE, 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, et al. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biology. 3: RESEARCH0079. PMID 12537568  1
2002 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 Research. 12: 1294-300. PMID 12176937 DOI: 10.1101/gr.269102  1
2002 Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, 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. Proceedings of the National Academy of Sciences of the United States of America. 99: 757-62. PMID 11805330 DOI: 10.1073/pnas.231608898  1
2000 Celniker SE. The Drosophila genome. Current Opinion in Genetics & Development. 10: 612-6. PMID 11088010 DOI: 10.1016/S0959-437X(00)00140-4  1
2000 Hoskins RA, Nelson CR, Berman BP, Laverty TR, George RA, Ciesiolka L, Naeemuddin M, Arenson AD, Durbin J, David RG, Tabor PE, Bailey MR, DeShazo DR, Catanese J, Mammoser A, ... ... Celniker SE, et al. A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science (New York, N.Y.). 287: 2271-4. PMID 10731150 DOI: 10.1126/science.287.5461.2271  1
2000 Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, ... ... Celniker SE, et al. Comparative genomics of the eukaryotes. Science (New York, N.Y.). 287: 2204-15. PMID 10731134 DOI: 10.1126/science.287.5461.2204  1
2000 Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, et al. The genome sequence of Drosophila melanogaster. Science (New York, N.Y.). 287: 2185-95. PMID 10731132 DOI: 10.1126/science.287.5461.2185  1
1999 Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, Hartzell G, Harvey D, Hong L, Houston K, Hoskins R, ... ... Celniker S, et al. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. Genetics. 153: 179-219. PMID 10471707  1
1996 Fernandes JJ, Celniker SE, VijayRaghavan K. Development of the indirect flight muscle attachment sites in Drosophila: role of the PS integrins and the stripe gene. Developmental Biology. 176: 166-84. PMID 8660859 DOI: 10.1006/dbio.1996.0125  1
1995 Lewis EB, Knafels JD, Mathog DR, Celniker SE. Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 92: 8403-7. PMID 7667302 DOI: 10.1007/978-1-4020-6345-9_18  1
1995 Martin CH, Mayeda CA, Davis CA, Ericsson CL, Knafels JD, Mathog DR, Celniker SE, Lewis EB, Palazzolo MJ. Complete sequence of the bithorax complex of Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 92: 8398-402. PMID 7667301 DOI: 10.1073/pnas.92.18.8398  1
1995 Lee JC, VijayRaghavan K, Celniker SE, Tanouye MA. Identification of a Drosophila muscle development gene with structural homology to mammalian early growth response transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 92: 10344-8. PMID 7479781 DOI: 10.1073/pnas.92.22.10344  1
1994 Fernandes J, Celniker SE, Lewis EB, VijayRaghavan K. Muscle development in the four-winged Drosophila and the role of the Ultrabithorax gene. Current Biology : Cb. 4: 957-64. PMID 7874495 DOI: 10.1016/S0960-9822(00)00219-0  1
1993 Celniker SE, Lewis EB. Molecular basis of transabdominal--a sexually dimorphic mutant of the bithorax complex of Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 90: 1566-70. PMID 8094560 DOI: 10.1073/pnas.90.4.1566  1
1990 Celniker SE, Sharma S, Keelan DJ, Lewis EB. The molecular genetics of the bithorax complex of Drosophila: cis-regulation in the Abdominal-B domain. The Embo Journal. 9: 4277-86. PMID 2265608  1
1989 Celniker SE, Keelan DJ, Lewis EB. The molecular genetics of the bithorax complex of Drosophila: characterization of the products of the Abdominal-B domain. Genes & Development. 3: 1424-36. PMID 2575066  1
1987 Celniker SE, Lewis EB. Transabdominal, a dominant mutant of the Bithorax Complex, produces a sexually dimorphic segmental transformation in Drosophila. Genes & Development. 1: 111-23. PMID 3678820 DOI: 10.1007/978-1-4020-6345-9_16  1
1985 Karch F, Weiffenbach B, Peifer M, Bender W, Duncan I, Celniker S, Crosby M, Lewis EB. The abdominal region of the bithorax complex. Cell. 43: 81-96. PMID 3935319 DOI: 10.1007/978-1-4020-6345-9_15  1
1984 Celniker SE, Sweder K, Srienc F, Bailey JE, Campbell JL. Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae. Molecular and Cellular Biology. 4: 2455-66. PMID 6392851  1
1982 Celniker SE, Campbell JL. Yeast DNA replication in vitro: initiation and elongation events mimic in vivo processes. Cell. 31: 201-13. PMID 6297748 DOI: 10.1016/0092-8674(82)90420-2  1
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