Research Topics
Genomes and GenesSpecies | S E CelnikerSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
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Publications
The Drosophila genomeS 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...- The Drosophila melanogaster genomeSusan 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... - Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscuraBenjamin 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... - Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genomeCasey M Bergman
Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
Genome Biol 3:RESEARCH0086. 2002..Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone... - Global analysis of patterns of gene expression during Drosophila embryogenesisPavel Tomancak
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
Genome Biol 8:R145. 2007.... - Chromatin looping mediates boundary element promoter interactionsSusan 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... - Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequenceSusan E Celniker
Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Genome Biol 3:RESEARCH0079. 2002.... - A BAC-based physical map of the major autosomes of Drosophila melanogasterR A Hoskins
Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Science 287:2271-4. 2000.... - Annotation of the Drosophila melanogaster euchromatic genome: a systematic reviewSima Misra
Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
Genome Biol 3:RESEARCH0083. 2002.... - Sequence finishing and mapping of Drosophila melanogaster heterochromatinRoger 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... - A Drosophila full-length cDNA resourceMark Stapleton
Berkeley Drosophila Genome Project Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Genome Biol 3:RESEARCH0080. 2002.... - Heterochromatic sequences in a Drosophila whole-genome shotgun assemblyRoger 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... - 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... - RNA editing in Drosophila melanogaster: New targets and functional consequencesMark 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... - Complete sequence of the bithorax complex of DrosophilaC H Martin
Human Genome Center, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 92:8398-402. 1995.... - Identification of a Drosophila muscle development gene with structural homology to mammalian early growth response transcription factorsJ 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... - A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genomeMark 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... - Automating fruit fly Drosophila embryo injection for high throughput transgenic studiesE Cornell
Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
Rev Sci Instrum 79:013705. 2008.... - Systematic determination of patterns of gene expression during Drosophila embryogenesisPavel 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..Systematic analysis of rigorously annotated patterns of gene expression will complement and extend the types of analyses carried out using expression microarrays... - Regulation of early endosomal entry by the Drosophila tumor suppressors Rabenosyn and Vps45Holly 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... - Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genomeBenjamin 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... - Identification of putative noncoding polyadenylated transcripts in Drosophila melanogasterJonathan 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... - Systematic image-driven analysis of the spatial Drosophila embryonic expression landscapeErwin 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... - Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancerYinghui 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... - Benchmarking tools for the alignment of functional noncoding DNADaniel 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... - Transcription factors bind thousands of active and inactive regions in the Drosophila blastodermXiao Yong Li
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
PLoS Biol 6:e27. 2008.... - Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenesMichele 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... - Tools for neuroanatomy and neurogenetics in DrosophilaBarret 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... - Improved repeat identification and masking in DipteransChristopher D Smith
Department of Biology, San Francisco State University, San Francisco, CA, United States
Gene 389:1-9. 2007.... - The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspectiveJoshua 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... - Discovery of functional elements in 12 Drosophila genomes using evolutionary signaturesAlexander 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... - Evolution of genes and genomes on the Drosophila phylogenyAndrew 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... - Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomesMichael 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... - 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... - 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 intronStephanie 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... - Evolution of the homeobox complex in the DipteraEdward B Lewis
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
Curr Biol 13:R587-8. 2003 - Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resourceVolker 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... - Posterior patterning genes and the identification of a unique body region in the brine shrimp Artemia franciscanaTijana 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... - Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogasterCasey M Bergman
Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
Bioinformatics 21:1747-9. 2005..AVAILABILITY: http://www.flyreg.org/ CONTACT: cbergman@gen.cam.ac.uk... - Genomic organization of the Drosophila telomere retrotransposable elementsJanet A George
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 16:1231-40. 2006.... - Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomeraseAlfredo 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...