Brian Oliver

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc FlyGEM, a full transcriptome array platform for the Drosophila community
    Rick Johnston
    Incyte Genomics, Palo Alto, CA 94304, USA
    Genome Biol 5:R19. 2004
  2. pmc Germline-dependent gene expression in distant non-gonadal somatic tissues of Drosophila
    Michael J Parisi
    Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
    BMC Genomics 11:346. 2010
  3. pmc How many genes in a genome?
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, 50 South Dr, Bethesda, MD 20892 8028, USA
    Genome Biol 5:204. 2003
  4. pmc Gene expression neighborhoods
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Biol 1:4. 2002
  5. ncbi request reprint Fly factory
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda Maryland, 20892 USA
    Genome Res 12:1017-8. 2002
  6. ncbi request reprint Battle of the Xs
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 8028, USA
    Bioessays 26:543-8. 2004
  7. pmc Lipid profiles of female and male Drosophila
    Michael Parisi
    Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, 50 South Drive, Bethesda MD 20892, USA
    BMC Res Notes 4:198. 2011
  8. pmc A non-random walk through the genome
    Brian Oliver
    National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    Genome Biol 6:214. 2005
  9. ncbi request reprint Suppression of distinct ovo phenotypes in the Drosophila female germline by maleless- and Sex-lethal
    B Oliver
    Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    Dev Genet 23:335-46. 1998
  10. pmc Sex, dose, and equality
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Biol 5:e340. 2007

Detail Information

Publications49

  1. pmc FlyGEM, a full transcriptome array platform for the Drosophila community
    Rick Johnston
    Incyte Genomics, Palo Alto, CA 94304, USA
    Genome Biol 5:R19. 2004
    ..The array gene list has been extensively annotated and linked-out to other databases. Incyte and the NIH have made the platform available to the community via academic microarray facilities selected by an NIH committee...
  2. pmc Germline-dependent gene expression in distant non-gonadal somatic tissues of Drosophila
    Michael J Parisi
    Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
    BMC Genomics 11:346. 2010
    ..We know little about the coordinated regulation of gene expression patterns in distant somatic tissues that support the developmental cost of gamete production...
  3. pmc How many genes in a genome?
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, 50 South Dr, Bethesda, MD 20892 8028, USA
    Genome Biol 5:204. 2003
    ..A recent study has added perhaps 2,000 genes to the predicted total, and raises a number of questions about how genome annotation data should be stored and presented...
  4. pmc Gene expression neighborhoods
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Biol 1:4. 2002
    ..The finding that neighboring eukaryotic genes are often expressed in similar patterns suggests the involvement of chromatin domains in the control of genes within a genomic neighborhood...
  5. ncbi request reprint Fly factory
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda Maryland, 20892 USA
    Genome Res 12:1017-8. 2002
  6. ncbi request reprint Battle of the Xs
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 8028, USA
    Bioessays 26:543-8. 2004
    ..Recent microarray work in Drosophila and C. elegans clearly shows the opposite. Why is the X chromosome a highly disfavored location for genes with male-biased expression in these animals?..
  7. pmc Lipid profiles of female and male Drosophila
    Michael Parisi
    Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, 50 South Drive, Bethesda MD 20892, USA
    BMC Res Notes 4:198. 2011
    ..abstract:..
  8. pmc A non-random walk through the genome
    Brian Oliver
    National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    Genome Biol 6:214. 2005
    ..It seems probable that this organization is related to chromatin and the structure of the nucleus...
  9. ncbi request reprint Suppression of distinct ovo phenotypes in the Drosophila female germline by maleless- and Sex-lethal
    B Oliver
    Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    Dev Genet 23:335-46. 1998
    ..Thus, ovo+ is required for at least two distinct functions, one involving mle+, and one mediated by Sxl+ gene products. The existence of ovo+ functions independent of mle+ and Sxl+ is likely...
  10. pmc Sex, dose, and equality
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Biol 5:e340. 2007
  11. pmc Drosophila melanogaster, two years into the post-genomic era
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Biol 3:REPORTS4021. 2002
    ..A report on the 43rd Drosophila Research Conference held in San Diego, USA, 10-14 April 2002...
  12. pmc A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults
    Michael Parisi
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    Genome Biol 5:R40. 2004
    ..Sexual dimorphism results in the formation of two types of individuals with specialized reproductive roles and is most evident in the germ cells and gonads...
  13. pmc Core promoter sequences contribute to ovo-B regulation in the Drosophila melanogaster germline
    Beata Bielinska
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
    Genetics 169:161-72. 2005
    ..This idea is further supported by the evolutionarily conserved organization of OVO binding sites at or near the start sites of ovo loci in other flies...
  14. pmc Paucity of genes on the Drosophila X chromosome showing male-biased expression
    Michael Parisi
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892 8028, USA
    Science 299:697-700. 2003
    ..These data indicate that the X chromosome is a disfavored location for genes selectively expressed in males...
  15. pmc Global analysis of X-chromosome dosage compensation
    Vaijayanti Gupta
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Biol 5:3. 2006
    ..Male germ cells lack MSL complexes, indicating that either germline X-chromosome dosage compensation is MSL-independent, or that germ cells do not carry out dosage compensation...
  16. pmc Expression in aneuploid Drosophila S2 cells
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Biol 8:e1000320. 2010
    ..Our data indicate that expression dosage compensation dampens the effect of altered DNA copy number genome-wide. For the X chromosome, compensation includes fixed and dose-dependent components...
  17. pmc Sex-specific DoublesexM expression in subsets of Drosophila somatic gonad cells
    Leonie U Hempel
    Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, 50 South Drive, Bethesda MD 20892 USA
    BMC Dev Biol 7:113. 2007
    ..The male-specific DSXM represses genes involved in female development and activates genes involved in male development. Spatial and temporal control of dsx during embryogenesis is not well documented...
  18. pmc Demasculinization of X chromosomes in the Drosophila genus
    David Sturgill
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda Maryland 20892, USA
    Nature 450:238-41. 2007
    ....
  19. pmc Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)
    David Sturgill
    National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
    BMC Bioinformatics 14:320. 2013
    ..However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment...
  20. pmc Drosophila mojoless, a retroposed GSK-3, has functionally diverged to acquire an essential role in male fertility
    Rasika Kalamegham
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
    Mol Biol Evol 24:732-42. 2007
    ..We postulate that mjl has undergone functional diversification and is now under stabilizing selection in the Drosophila genus...
  21. pmc Constraint and turnover in sex-biased gene expression in the genus Drosophila
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
    Nature 450:233-7. 2007
    ..This higher divergence and turnover of genes with male-biased expression may be due to high transcription rates in the male germline, greater functional pleiotropy of genes expressed in females, and/or sexual competition...
  22. pmc COPI complex is a regulator of lipid homeostasis
    Mathias Beller
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Biol 6:e292. 2008
    ..These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets...
  23. pmc An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure?
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 8028, USA
    BMC Genomics 11:6. 2010
    ..The evolution of this system could result in neutral X chromatin changes that will be apparent in females...
  24. ncbi request reprint Drosophila OVO regulates ovarian tumor transcription by binding unusually near the transcription start site
    J Lu
    Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 2715, USA
    Development 128:1671-86. 2001
    ..These data unambiguously identify otu as a direct OVO target gene and raise the tantalizing possibility that an OVO site, at the location normally occupied by basal components, functions as part of a specialized core promoter...
  25. ncbi request reprint Drosophila OVO zinc-finger protein regulates ovo and ovarian tumor target promoters
    J Lu
    The Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda Maryland 20892, USA
    Dev Genes Evol 208:213-22. 1998
    ..Our observation that two strong OVO-binding sites are at the initiator of the TATA-less ovo-B and ovarian tumor promoters raises the possibility that OVO proteins influence the nucleation of transcriptional pre-initiation complexes...
  26. pmc Mediation of Drosophila autosomal dosage effects and compensation by network interactions
    John H Malone
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA
    Genome Biol 13:r28. 2012
    ..While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering in expression networks...
  27. pmc Sex determination signals control ovo-B transcription in Drosophila melanogaster germ cells
    Justen Andrews
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genetics 160:537-45. 2002
    ..Thus, while somatic inductive signals and chromosome karyotype have overlapping regulatory influences, a 2X karyotype is a critical germline autonomous determinant of ovo-B function in the germline...
  28. ncbi request reprint Drosophila microarray platforms
    Vaijayanti Gupta
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive Diseases and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20895, USA
    Brief Funct Genomic Proteomic 2:97-105. 2003
    ..Currently, researchers are using three main Drosophila array platform types, with elements composed of cDNA amplicons, oligonucleotides (short and long) or genomic amplicons. This paper provides a broad overview of these platforms...
  29. pmc The genomic 'inner fish' and a regulatory enigma in the vertebrates
    John Malone
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
    J Biol 8:32. 2009
    ..It reveals a core set of genes with similar tissue-expression patterns yet no common regulatory signatures--a gene-expression paradox...
  30. doi request reprint Drosophila germline sex determination: integration of germline autonomous cues and somatic signals
    Leonie U Hempel
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
    Curr Top Dev Biol 83:109-50. 2008
    ..A critical role of the germline sex determination pathway may therefore be to ensure the proper receipt and processing of signals from the niche...
  31. ncbi request reprint OVO transcription factors function antagonistically in the Drosophila female germline
    J Andrews
    Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda MD, USA
    Development 127:881-92. 2000
    ..Our data indicate that tight regulation of antagonistic OVO-B and OVO-A isoforms is critical for germline formation and differentiation...
  32. ncbi request reprint New AUG initiation codons in a long 5' UTR create four dominant negative alleles of the Drosophila C2H2 zinc-finger gene ovo
    J Andrews
    Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
    Dev Genes Evol 207:482-7. 1998
    ..These data suggest that ovoD mutations result in inappropriate expression of OVO-A in the female germline...
  33. pmc Synthetic spike-in standards for RNA-seq experiments
    Lichun Jiang
    Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 21:1543-51. 2011
    ..These quality metrics facilitate comparable analysis across different samples, protocols, and platforms...
  34. pmc Comparative genomics of Drosophila and human core promoters
    Peter C FitzGerald
    Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Biol 7:R53. 2006
    ..We compare these results with those obtained for human promoters...
  35. pmc Microarrays, deep sequencing and the true measure of the transcriptome
    John H Malone
    Laboratory of Cellular and Developmental Biology, National Institute of Digestive, Diabetes, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Biol 9:34. 2011
    ..We conclude that microarrays remain useful and accurate tools for measuring expression levels, and RNA-Seq complements and extends microarray measurements...
  36. ncbi request reprint Genetic control of germline sexual dimorphism in Drosophila
    Brian Oliver
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Int Rev Cytol 219:1-60. 2002
    ..The integration of these two pathways is not yet clear...
  37. pmc Genetic interactions between Drosophila melanogaster menin and Jun/Fos
    Aniello Cerrato
    National Institute of Diabetes and Digestive and Kidney Diseases, Department of Health and Human Services, Bethesda, MD 20892, USA
    Dev Biol 298:59-70. 2006
    ..We observed complex genetic interactions between mnn1 and jun in different developmental settings. Our data support the idea that one function of menin is to modulate Jun activity in a manner dependent on the cellular context...
  38. ncbi request reprint Dosage compensation goes global
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Curr Opin Genet Dev 17:113-20. 2007
    ..These approaches have resolved old controversies, suggested new questions, and promise to give us a more clear and comprehensive understanding of an old problem in molecular and cell biology...
  39. pmc The sex chromosome that refused to die
    John H Malone
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    Bioessays 30:409-11. 2008
    ..melanogaster genome.1 These results show that variation on Y has an important influence on the deployment of the genome...
  40. ncbi request reprint Menin molecular interactions: insights into normal functions and tumorigenesis
    S K Agarwal
    National Institute of Diabetes and Digestive and Kidney Diseases NIH, 9000 Rockville Pike, Bethesda, MD 20892 1802, USA
    Horm Metab Res 37:369-74. 2005
    ..Inactivation of menin switches its JunD partner from a downstream action of growth suppression to growth promotion. This is a plausible mechanism for menin tumorigenesis...
  41. ncbi request reprint X for intersection: retrotransposition both on and off the X chromosome is more frequent
    Pavel P Khil
    Genetics and Biochemistry Branch and Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Trends Genet 21:3-7. 2005
    ..A new study addresses the differential distribution of retroposed genes in human and mouse genomes. Surprisingly, chromosome X is a major source and a preferred target for retrotransposition...
  42. ncbi request reprint Characterization of a MEN1 ortholog from Drosophila melanogaster
    S C Guru
    Genetics and Molecular Biology Branch, National Human Genome Research Institute, 49 Convent Drive, Bethesda, MD 20892, USA
    Gene 263:31-8. 2001
    ..The identification of the MEN1 ortholog from Drosophila melanogaster will provide an opportunity to utilize Drosophila genetics to enhance our understanding of the function of human menin...
  43. pmc Genomics of sex determination in Drosophila
    Emily Clough
    Section of Developmental Genomics and Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD 20892 8028, USA
    Brief Funct Genomics 11:387-94. 2012
    ..The current challenge is linking transcriptional profiles with the regulatory genes. This will be a complex synthesis, but the prospects for progress are outstanding...
  44. ncbi request reprint One hundred years of high-throughput Drosophila research
    Mathias Beller
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Chromosome Res 14:349-62. 2006
    ..Several high-throughput techniques and experimental strategies highlighting the unbiased and integrative nature of Drosophila research during the last century will be discussed...
  45. ncbi request reprint Functional conservation for lipid storage droplet association among Perilipin, ADRP, and TIP47 (PAT)-related proteins in mammals, Drosophila, and Dictyostelium
    Shinji Miura
    Membrane Regulation Section, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20992 8028, USA
    J Biol Chem 277:32253-7. 2002
    ....
  46. ncbi request reprint Comparative validation of the D. melanogaster modENCODE transcriptome annotation
    Zhen Xia Chen
    National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 24:1209-23. 2014
    ..We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community. ..
  47. doi request reprint Evolution of protein-coding genes in Drosophila
    Amanda M Larracuente
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Trends Genet 24:114-23. 2008
    ....
  48. 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...
  49. ncbi request reprint Tiling DNA microarrays for fly genome cartography
    Brian Oliver
    Nat Genet 38:1101-2. 2006