Gerald M Rubin

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. pmc Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs
    Eric C Lai
    Department of Molecular and Cell Biology Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720 3200, USA
    Genes Dev 19:1067-80. 2005
  5. 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
  6. pmc Computational identification of Drosophila microRNA genes
    Eric C Lai
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720, USA
    Genome Biol 4:R42. 2003
  7. ncbi request reprint The ubiquitin ligase Drosophila Mind bomb promotes Notch signaling by regulating the localization and activity of Serrate and Delta
    Eric C Lai
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, 545 Life Sciences Addition, University of California at Berkeley, Berkeley, CA 94720 3200, USA
    Development 132:2319-32. 2005
  8. pmc Refinement of tools for targeted gene expression in Drosophila
    Barret D Pfeiffer
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Genetics 186:735-55. 2010
  9. 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
  10. 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

Collaborators

Detail Information

Publications34

  1. 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...
  2. 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...
  3. 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...
  4. pmc Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs
    Eric C Lai
    Department of Molecular and Cell Biology Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720 3200, USA
    Genes Dev 19:1067-80. 2005
    ..Collectively, these data establish insights into miRNA target recognition and demonstrate that the Notch signaling pathway is a major target of miRNA-mediated regulation in Drosophila...
  5. 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...
  6. pmc Computational identification of Drosophila microRNA genes
    Eric C Lai
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720, USA
    Genome Biol 4:R42. 2003
    ..Second, miRNAs are usually highly conserved between the genomes of related species. Third, miRNAs display a characteristic pattern of evolutionary divergence...
  7. ncbi request reprint The ubiquitin ligase Drosophila Mind bomb promotes Notch signaling by regulating the localization and activity of Serrate and Delta
    Eric C Lai
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, 545 Life Sciences Addition, University of California at Berkeley, Berkeley, CA 94720 3200, USA
    Development 132:2319-32. 2005
    ..We conclude that ubiquitination of Delta and Serrate by Neuralized and D-mib is an obligate feature of DSL ligand activation throughout Drosophila development...
  8. pmc Refinement of tools for targeted gene expression in Drosophila
    Barret D Pfeiffer
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Genetics 186:735-55. 2010
    ..The increased strength and reliability of these optimized reagents overcome many of the previous limitations of these methods and will facilitate genetic manipulations of greater complexity and sophistication...
  9. 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...
  10. 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
    ....
  11. 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
    ....
  12. pmc The Drosophila synaptotagmin-like protein bitesize is required for growth and has mRNA localization sequences within its open reading frame
    Julia Serano
    Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3200, USA
    Proc Natl Acad Sci U S A 100:13368-73. 2003
    ..Thus, we have found that bitesize is a metazoan example of a transcript for which all identifiable mRNA localization sequences are contained within the protein-coding region...
  13. pmc Large-scale trends in the evolution of gene structures within 11 animal genomes
    Mark Yandell
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Comput Biol 2:e15. 2006
    ..This means that genome annotations can be used in new ways to inform, corroborate, and test conclusions drawn from comparative genomics analyses that are based upon protein and nucleotide sequence similarities...
  14. pmc A GAL4-driver line resource for Drosophila neurobiology
    Arnim Jenett
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Cell Rep 2:991-1001. 2012
    ..The set of DNA fragments, each driving a documented expression pattern, will facilitate the generation of additional constructs for manipulating neuronal function...
  15. pmc Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development
    A Aziz Aboobaker
    Department of Molecular and Cell Biology, University of California, Berkeley, 94720 3200, USA
    Proc Natl Acad Sci U S A 102:18017-22. 2005
    ..Intriguingly, the expression patterns of several fly miRNAs are analogous to those of their vertebrate counterparts, suggesting that these miRNAs may have ancient roles in animal patterning...
  16. pmc The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes
    Hugo J Bellen
    Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Genetics 167:761-81. 2004
    ..Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool...
  17. pmc Using translational enhancers to increase transgene expression in Drosophila
    Barret D Pfeiffer
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Proc Natl Acad Sci U S A 109:6626-31. 2012
    ....
  18. pmc Computational analysis of core promoters in the Drosophila genome
    Uwe Ohler
    Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0087. 2002
    ..Drosophila TSSs have generally been mapped by individual experiments; the low number of accurately mapped TSSs has limited analysis of promoter sequence motifs and the training of computational prediction tools...
  19. 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...
  20. 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...
  21. pmc Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes
    Eric C Lai
    Howard Hughes Medical Institute, University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, California 94720 3200, USA
    RNA 10:171-5. 2004
    ....
  22. pmc Global analyses of mRNA translational control during early Drosophila embryogenesis
    Xiaoli Qin
    Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Genome Biol 8:R63. 2007
    ..To understand post-transcriptional regulation during Drosophila early embryonic development, we used sucrose polysomal gradient analyses and GeneChip analysis to illustrate the translation profile of individual mRNAs...
  23. 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
    ....
  24. pmc ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos
    Robert W Williams
    Department of Molecular and Cell Biology and the Howard Hughes Medical Institute, University of California, Berkeley, CA 94720 3200, USA
    Proc Natl Acad Sci U S A 99:6889-94. 2002
    ..Furthermore, AGO1 is not required for siRNA production in vitro nor can the introduction of siRNA bypass AGO1 mutants in vivo. These data suggest that AGO1 functions downstream of siRNA production...
  25. 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...
  26. pmc Evidence for large domains of similarly expressed genes in the Drosophila genome
    Paul T Spellman
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3400, USA
    J Biol 1:5. 2002
    ..Regulation of sets of adjacent genes by mechanisms operating at the level of chromosomal domains has been demonstrated in a number of cases, but the fraction of genes in the genome subject to regulation at this level is unknown...
  27. pmc Multiple new site-specific recombinases for use in manipulating animal genomes
    Aljoscha Nern
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 2408, USA
    Proc Natl Acad Sci U S A 108:14198-203. 2011
    ..We also show that the KD and B3 recombinases are active in mice...
  28. 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
    ....
  29. pmc A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS
    Laurina Manning
    Institutes of Neuroscience and Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA
    Cell Rep 2:1002-13. 2012
    ....
  30. pmc The effort to make mosaic analysis a household tool
    Tian Xu
    Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
    Development 139:4501-3. 2012
    ..In 1990, we set out to improve the methods used to make genetic mosaics in Drosophila by taking advantage of recently developed approaches for genome engineering. These efforts led to the work described in our 1993 Development paper...
  31. 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...
  32. pmc The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes
    Mark Stapleton
    Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 12:1294-300. 2002
    ..This second release of the DGC (DGCr2) contains 5061 additional clones, extending the collection to 10,910 cDNAs representing >70% of the predicted genes in Drosophila...
  33. pmc The Ca(2+)-calmodulin-activated protein phosphatase calcineurin negatively regulates EGF receptor signaling in Drosophila development
    Kathleen M C Sullivan
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 3200, USA
    Genetics 161:183-93. 2002
    ..On the basis of our results, we propose that calcineurin, upon activation by Ca(2+)-calmodulin, cooperates with other factors to negatively regulate Egf receptor signaling at the level of sprouty and the GTPase-activating protein Gap1...
  34. ncbi request reprint Drosophila matrix metalloproteinases are required for tissue remodeling, but not embryonic development
    Andrea Page-McCaw
    Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Dev Cell 4:95-106. 2003
    ..Thus, MMPs are not required for Drosophila embryonic development, but, rather, for tissue remodeling...