S E Celniker

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. ncbi request reprint The Drosophila genome
    S E Celniker
    Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Curr Opin Genet Dev 10:612-6. 2000
  2. ncbi request reprint The Drosophila melanogaster genome
    Susan E Celniker
    Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Annu Rev Genomics Hum Genet 4:89-117. 2003
  3. pmc Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R61. 2004
  4. pmc Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome
    Casey M Bergman
    Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0086. 2002
  5. pmc Global analysis of patterns of gene expression during Drosophila embryogenesis
    Pavel Tomancak
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 8:R145. 2007
  6. ncbi request reprint Chromatin looping mediates boundary element promoter interactions
    Susan E Celniker
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioessays 29:7-10. 2007
  7. pmc Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence
    Susan E Celniker
    Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0079. 2002
  8. ncbi request reprint A BAC-based physical map of the major autosomes of Drosophila melanogaster
    R A Hoskins
    Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 287:2271-4. 2000
  9. pmc Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
    Sima Misra
    Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0083. 2002
  10. pmc Sequence finishing and mapping of Drosophila melanogaster heterochromatin
    Roger A Hoskins
    Department of Genome and Computational Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 316:1625-8. 2007

Detail Information

Publications41

  1. ncbi request reprint The Drosophila genome
    S E Celniker
    Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Curr Opin Genet Dev 10:612-6. 2000
    ..For the first time homologous recombination has been demonstrated in flies and targeted gene disruptions may not be far off...
  2. ncbi request reprint The Drosophila melanogaster genome
    Susan E Celniker
    Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Annu Rev Genomics Hum Genet 4:89-117. 2003
    ..We first review the current state of the Drosophila melanogaster genome sequence and its structural annotation and then briefly summarize some promising approaches that are being taken to achieve an initial functional annotation...
  3. pmc Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R61. 2004
    ..Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters...
  4. pmc Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome
    Casey M Bergman
    Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0086. 2002
    ..It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined...
  5. pmc Global analysis of patterns of gene expression during Drosophila embryogenesis
    Pavel Tomancak
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 8:R145. 2007
    ....
  6. ncbi request reprint Chromatin looping mediates boundary element promoter interactions
    Susan E Celniker
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioessays 29:7-10. 2007
    ..Specifically, they studied the function of a boundary element within the cis-regulatory region of the Abdominal-B (Abd-B) gene of Drosophila melanogaster...
  7. pmc Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence
    Susan E Celniker
    Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0079. 2002
    ....
  8. ncbi request reprint A BAC-based physical map of the major autosomes of Drosophila melanogaster
    R A Hoskins
    Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 287:2271-4. 2000
    ....
  9. pmc Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
    Sima Misra
    Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0083. 2002
    ....
  10. pmc Sequence finishing and mapping of Drosophila melanogaster heterochromatin
    Roger A Hoskins
    Department of Genome and Computational Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 316:1625-8. 2007
    ..The strategy we describe is also applicable to generating substantially more information about heterochromatin in other species, including humans...
  11. pmc A Drosophila full-length cDNA resource
    Mark Stapleton
    Berkeley Drosophila Genome Project Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0080. 2002
    ....
  12. pmc Heterochromatic sequences in a Drosophila whole-genome shotgun assembly
    Roger A Hoskins
    Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0085. 2002
    ..To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly...
  13. pmc Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP)
    Roger A Hoskins
    Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 33:e185. 2005
    ..Finally, we discuss the relative merits of directed cDNA library screening and RT-PCR approaches...
  14. pmc RNA editing in Drosophila melanogaster: New targets and functional consequences
    Mark Stapleton
    Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    RNA 12:1922-32. 2006
    ..Our results indicate that editing in Drosophila increases the diversity of the proteome, and does so in a manner that has direct functional consequences on protein function...
  15. pmc Complete sequence of the bithorax complex of Drosophila
    C H Martin
    Human Genome Center, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 92:8398-402. 1995
    ....
  16. pmc Identification of a Drosophila muscle development gene with structural homology to mammalian early growth response transcription factors
    J C Lee
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 92:10344-8. 1995
    ..The identification of sr as an egr gene and its pattern of expression suggest that it functions in muscle development via intercellular communication...
  17. pmc A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome
    Mark Yandell
    Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Proc Natl Acad Sci U S A 102:1566-71. 2005
    ..Although we cannot rule out the discovery of genes with unusual features that make them refractory to existing methods, our results suggest that the D. melanogaster genome contains approximately 14,000 protein-coding genes...
  18. doi request reprint Automating fruit fly Drosophila embryo injection for high throughput transgenic studies
    E Cornell
    Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Rev Sci Instrum 79:013705. 2008
    ....
  19. pmc Systematic determination of patterns of gene expression during Drosophila embryogenesis
    Pavel Tomancak
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0088. 2002
    ..Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription...
  20. pmc Regulation of early endosomal entry by the Drosophila tumor suppressors Rabenosyn and Vps45
    Holly A Morrison
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Mol Biol Cell 19:4167-76. 2008
    ..This work represents the first characterization of a Rab5 effector as a tumor suppressor, and it provides in vivo evidence for a Rbsn-Vps45 complex on early endosomes that links Rab5 to the SNARE fusion machinery...
  21. pmc Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:757-62. 2002
    ..We tested one of the newly identified clusters, mapping upstream of the gap gene giant (gt), and show that it acts as an enhancer that recapitulates the posterior expression pattern of gt...
  22. pmc Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster
    Jonathan L Tupy
    Berkeley Drosophila Genome Project and Department of Genome Sciences, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64 121, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:5495-500. 2005
    ..We show that the expression of many of these transcripts is conserved in other Drosophila species, indicating that they have important biological functions...
  23. pmc Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape
    Erwin Frise
    Department of Genome Dynamics, Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Mol Syst Biol 6:345. 2010
    ..The known genes suggest developmental roles for the clusters, and identification of related patterns predicts requirements for co-occurring biological functions...
  24. ncbi request reprint Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer
    Yinghui Guan
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Clin Cancer Res 13:5745-55. 2007
    ..This study was designed to elucidate the role of amplification at 8q24 in the pathophysiology of ovarian and breast cancer because increased copy number at this locus is one of the most frequent genomic abnormalities in these cancers...
  25. pmc Benchmarking tools for the alignment of functional noncoding DNA
    Daniel A Pollard
    Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 5:6. 2004
    ..For noncoding sequences, where such independent validation is lacking, simulation provides an effective means to generate "correct" alignments with which to benchmark alignment tools...
  26. pmc Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
    Xiao Yong Li
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS Biol 6:e27. 2008
    ....
  27. pmc Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes
    Michele Markstein
    Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 40:476-83. 2008
    ..The generality of our approach makes it adaptable to other model systems to identify and modify loci for optimal transgene expression...
  28. pmc Tools for neuroanatomy and neurogenetics in Drosophila
    Barret D Pfeiffer
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn VA 20147, USA
    Proc Natl Acad Sci U S A 105:9715-20. 2008
    ..We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain...
  29. pmc Improved repeat identification and masking in Dipterans
    Christopher D Smith
    Department of Biology, San Francisco State University, San Francisco, CA, United States
    Gene 389:1-9. 2007
    ....
  30. pmc The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective
    Joshua S Kaminker
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Genome Biol 3:RESEARCH0084. 2002
    ..We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species...
  31. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander Stark
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Nature 450:219-32. 2007
    ..We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies...
  32. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  33. pmc Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
    Michael F Lin
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Genome Res 17:1823-36. 2007
    ..These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied as Drosophila melanogaster...
  34. ncbi request reprint Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?
    A Bernardo Carvalho
    Departamento de Genetica, Universidade Federal do Rio de Janeiro, Caixa Postal 68011 CEP 21944 970, Rio de Janeiro, Brazil
    Genetica 117:227-37. 2003
    ..It appears much more hopeful than anyone would have imagined that whole genome shotgun assemblies can recover the great bulk of even heterochromatic genes...
  35. pmc 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
    Stephanie G Hudson
    School of Life Sciences, Arizona State University, Tempe, Arizona 85287 4501, USA
    Genetics 177:1349-61. 2007
    ..Overall, our phylogenetic and genomewide analyses suggest that the nested arrangement of kay and fig may be due to a functional relationship between them...
  36. ncbi request reprint Evolution of the homeobox complex in the Diptera
    Edward B Lewis
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Curr Biol 13:R587-8. 2003
  37. ncbi request reprint Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource
    Volker Hollich
    Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Biotechniques 37:282-4. 2004
    ..2% of chromosomal arm 2R, 79.0% of 2L, 89.6% of 3R, and 80.5% of chromosome 4. In total, the 25,135 clones represent 76.7 Mb--equivalent to about 67% of the genome--and would be suitable for producing a microarray on a single slide...
  38. ncbi request reprint Posterior patterning genes and the identification of a unique body region in the brine shrimp Artemia franciscana
    Tijana Copf
    Institute of Molecular Biology and Biotechnology IMBB FORTH Vouton, 71110 Iraklio Crete, Greece
    Development 130:5915-27. 2003
    ..We argue that these segments constitute a unique body region that bears no obvious homology to previously characterised domains of Hox gene activity...
  39. ncbi request reprint Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
    Casey M Bergman
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
    Bioinformatics 21:1747-9. 2005
    ....
  40. pmc Genomic organization of the Drosophila telomere retrotransposable elements
    Janet A George
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 16:1231-40. 2006
    ....
  41. pmc Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase
    Alfredo Villasante
    Centro de Biologia Molecular Severo Ochoa, Cantoblanco, 28049 Madrid, Spain
    Genome Res 17:1909-18. 2007
    ..Our results suggest that an existing non-LTR retrotransposon was recruited to perform the cellular function of telomere maintenance...