Brian Oliver, Ph.D.

Section Chief: Developmental Genomics Section​, Laboratory of Biochemistry & Genetics

Scientific Focus Areas: Computational Biology, Developmental Biology, Genetics and Genomics, Systems Biology, Stem Cell Biology

briano@niddk.nih.gov Add to Contacts

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Publications

A selection of recent and significant publications can be viewed below.

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Whole Animal Feeding FLat (WAFFL): a complete and comprehensive validation of a novel, high-throughput fly experimentation system.

Jaime MDLA, Salem GH, Martinez DJ, Karott S, Flores A, Palmer CD, Mahadevaraju S, Krynitsky J, Garmendia-Cedillos M, Anderson S, Harbison S, Pohida TJ, Ludington WB, Oliver B.

G3 (Bethesda) (2023 Mar 9) 13. Abstract/Full Text

Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes.

Raz AA, Vida GS, Stern SR, Mahadevaraju S, Fingerhut JM, Viveiros JM, Pal S, Grey JR, Grace MR, Berry CW, Li H, Janssens J, Saelens W, Shao Z, Hu C, Yamashita YM, Przytycka T, Oliver B, Brill JA, Krause H, Matunis EL, White-Cooper H, DiNardo S, Fuller MT.

Elife (2023 Feb 16) 12. Abstract/Full Text

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O'Brien LE, Dow JAT, FCA Consortium§, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP.

Science (2022 Mar 4) 375:eabk2432. Abstract/Full Text

Dynamic sex chromosome expression in Drosophila male germ cells.

Mahadevaraju S, Fear JM, Akeju M, Galletta BJ, Pinheiro MMLS, Avelino CC, Cabral-de-Mello DC, Conlon K, Dell'Orso S, Demere Z, Mansuria K, Mendonça CA, Palacios-Gimenez OM, Ross E, Savery M, Yu K, Smith HE, Sartorelli V, Yang H, Rusan NM, Vibranovski MD, Matunis E, Oliver B.

Nat Commun (2021 Feb 9) 12:892. Abstract/Full Text

Drosophila Heterochromatin Stabilization Requires the Zinc-Finger Protein Small Ovary.

Benner L, Castro EA, Whitworth C, Venken KJT, Yang H, Fang J, Oliver B, Cook KR, Lerit DA.

Genetics (2019 Nov) 213:877-895. Abstract/Full Text

Additional Publications

Correction to: DNA copy number evolution in Drosophila cell lines.

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, Przytycka TM, Gatti M, Oliver B, Graveley B, MacAlpine D.

Genome Biol (2019 Mar 11) 20:53. Abstract/Full Text

Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation.

Grobler Y, Yun CY, Kahler DJ, Bergman CM, Lee H, Oliver B, Lehmann R.

PLoS Pathog (2018 Nov) 14:e1007445. Abstract/Full Text

Non-canonical Drosophila X chromosome dosage compensation and repressive topologically associated domains.

Lee H, Oliver B.

Epigenetics Chromatin (2018 Oct 24) 11:62. Abstract/Full Text

Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements.

Chen ZX, Oliver B, Zhang YE, Gao G, Long M.

Genome Biol Evol (2017 Apr 1) 9:981-992. Abstract/Full Text

Microenvironmental Gene Expression Plasticity Among Individual Drosophila melanogaster.

Lin Y, Chen ZX, Oliver B, Harbison ST.

G3 (Bethesda) (2016 Dec 7) 6:4197-4210. Abstract/Full Text

A Class of Diacylglycerol Acyltransferase 1 Inhibitors Identified by a Combination of Phenotypic High-throughput Screening, Genomics, and Genetics.

Tschapalda K, Zhang YQ, Liu L, Golovnina K, Schlemper T, Eichmann TO, Lal-Nag M, Sreenivasan U, McLenithan J, Ziegler S, Sztalryd C, Lass A, Auld D, Oliver B, Waldmann H, Li Z, Shen M, Boxer MB, Beller M.

EBioMedicine (2016 Jun) 8:49-59. Abstract/Full Text

Sxl-Dependent, tra/tra2-Independent Alternative Splicing of the Drosophila melanogaster X-Linked Gene found in neurons.

Sun X, Yang H, Sturgill D, Oliver B, Rabinow L, Samson ML.

G3 (Bethesda) (2015 Oct 28) 5:2865-74. Abstract/Full Text

X Chromosome and Autosome Dosage Responses in Drosophila melanogaster Heads.

Chen ZX, Oliver B.

G3 (Bethesda) (2015 Apr 7) 5:1057-63. Abstract/Full Text

Diversity and dynamics of the Drosophila transcriptome.

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, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE.

Nature (2014 Aug 28) 512:393-9. Abstract/Full Text

Comparative analysis of the transcriptome across distant species.

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, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.

Nature (2014 Aug 28) 512:445-8. Abstract/Full Text

DNA copy number evolution in Drosophila cell lines.

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, Przytycka TM, Gatti M, Oliver B, Graveley B, MacAlpine D.

Genome Biol (2014 Aug 28) 15:R70. Abstract/Full Text

Transcriptional effects of gene dose reduction.

Chen ZX, Golovnina K, Sultana H, Kumar S, Oliver B.

Biol Sex Differ (2014 Mar 3) 5:5. Abstract/Full Text

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

Sturgill D, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.

BMC Bioinformatics (2013 Nov 9) 14:320. Abstract/Full Text

Simplification and desexualization of gene expression in self-fertile nematodes.

Thomas CG, Li R, Smith HE, Woodruff GC, Oliver B, Haag ES.

Curr Biol (2012 Nov 20) 22:2167-72. Abstract/Full Text

Genomics of sex determination in Drosophila.

Clough E, Oliver B.

Brief Funct Genomics (2012 Sep) 11:387-94. Abstract/Full Text

Mediation of Drosophila autosomal dosage effects and compensation by network interactions.

Malone JH, Cho DY, Mattiuzzo NR, Artieri CG, Jiang L, Dale RK, Smith HE, McDaniel J, Munro S, Salit M, Andrews J, Przytycka TM, Oliver B.

Genome Biol (2012 Apr 24) 13:r28. Abstract/Full Text

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.

Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM.

Nat Genet (2011 Oct 23) 43:1179-85. Abstract/Full Text

Synthetic spike-in standards for RNA-seq experiments.

Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B.

Genome Res (2011 Sep) 21:1543-51. Abstract/Full Text

Lipid profiles of female and male Drosophila.

Parisi M, Li R, Oliver B.

BMC Res Notes (2011 Jun 15) 4:198. Abstract/Full Text

Microarrays, deep sequencing and the true measure of the transcriptome.

Malone JH, Oliver B.

BMC Biol (2011 May 31) 9:34. Abstract/Full Text

The developmental transcriptome of Drosophila melanogaster.

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, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE.

Nature (2011 Mar 24) 471:473-9. Abstract/Full Text

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, 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, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science (2010 Dec 24) 330:1787-97. Abstract/Full Text

Transcriptional regulation by CHIP/LDB complexes.

Bronstein R, Levkovitz L, Yosef N, Yanku M, Ruppin E, Sharan R, Westphal H, Oliver B, Segal D.

PLoS Genet (2010 Aug 12) 6:e1001063. Abstract/Full Text

Germline-dependent gene expression in distant non-gonadal somatic tissues of Drosophila.

Parisi MJ, Gupta V, Sturgill D, Warren JT, Jallon JM, Malone JH, Zhang Y, Gilbert LI, Oliver B.

BMC Genomics (2010 Jun 1) 11:346. Abstract/Full Text

Expression in aneuploid Drosophila S2 cells.

Zhang Y, Malone JH, Powell SK, Periwal V, Spana E, Macalpine DM, Oliver B.

PLoS Biol (2010 Feb 23) 8:e1000320. Abstract/Full Text

COPI complex is a regulator of lipid homeostasis.

Beller M, Sztalryd C, Southall N, Bell M, Jäckle H, Auld DS, Oliver B.

PLoS Biol (2008 Nov 25) 6:e292. Abstract/Full Text

Evolution of protein-coding genes in Drosophila.

Larracuente AM, Sackton TB, Greenberg AJ, Wong A, Singh ND, Sturgill D, Zhang Y, Oliver B, Clark AG.

Trends Genet (2008 Mar) 24:114-23. Abstract/Full Text

Drosophila germline sex determination: integration of germline autonomous cues and somatic signals.

Hempel LU, Kalamegham R, Smith JE 3rd, Oliver B.

Curr Top Dev Biol (2008) 83:109-50. Abstract/Full Text

Molecular pathology of the MEN1 gene.

Agarwal SK, Lee Burns A, Sukhodolets KE, Kennedy PA, Obungu VH, Hickman AB, Mullendore ME, Whitten I, Skarulis MC, Simonds WF, Mateo C, Crabtree JS, Scacheri PC, Ji Y, Novotny EA, Garrett-Beal L, Ward JM, Libutti SK, Richard Alexander H, Cerrato A, Parisi MJ, Santa Anna-A S, Oliver B, Chandrasekharappa SC, Collins FS, Spiegel AM, Marx SJ.

Ann N Y Acad Sci (2004 Apr) 1014:189-98. Abstract/Full Text

Paucity of genes on the Drosophila X chromosome showing male-biased expression.

Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, Andrews J, Eastman S, Oliver B.

Science (2003 Jan 31) 299:697-700. Abstract/Full Text

Drosophila OVO zinc-finger protein regulates ovo and ovarian tumor target promoters.

Lü J, Andrews J, Pauli D, Oliver B.

Dev Genes Evol (1998 Jun) 208:213-22. Abstract/Full Text

Multiple developmental requirements of noisette, the Drosophila homolog of the U2 snRNP-associated polypeptide SP3a60.

Meyer V, Oliver B, Pauli D.

Mol Cell Biol (1998 Apr) 18:1835-43. Abstract/Full Text

New AUG initiation codons in a long 5' UTR create four dominant negative alleles of the Drosophila C2H2 zinc-finger gene ovo.

Andrews J, Levenson I, Oliver B.

Dev Genes Evol (1998 Jan) 207:482-7. Abstract/Full Text

Suppression of distinct ovo phenotypes in the Drosophila female germline by maleless- and Sex-lethal.

Oliver B, Pauli D.

Dev Genet (1998) 23:335-46. Abstract/Full Text

Identification of regions interacting with ovoD mutations: potential new genes involved in germline sex determination or differentiation in Drosophila melanogaster.

Pauli D, Oliver B, Mahowald AP.

Genetics (1995 Feb) 139:713-32. Abstract/Full Text

Function of Drosophila ovo+ in germ-line sex determination depends on X-chromosome number.

Oliver B, Singer J, Laget V, Pennetta G, Pauli D.

Development (1994 Nov) 120:3185-95. Abstract/Full Text

Evidence for sex transformation of germline cells in ovarian tumor mutants of Drosophila.

Wei G, Oliver B, Pauli D, Mahowald AP.

Dev Biol (1994 Jan) 161:318-20. Abstract/Full Text

Sex-lethal, master and slave: a hierarchy of germ-line sex determination in Drosophila.

Oliver B, Kim YJ, Baker BS.

Development (1993 Nov) 119:897-908. Abstract/Full Text

The role of the ovarian tumor locus in Drosophila melanogaster germ line sex determination.

Pauli D, Oliver B, Mahowald AP.

Development (1993 Sep) 119:123-34. Abstract/Full Text

Gonadal dysgenesis reveals sexual dimorphism in the embryonic germline of Drosophila.

Wei G, Oliver B, Mahowald AP.

Genetics (1991 Sep) 129:203-10. Abstract/Full Text

Genetic evidence that the ovo locus is involved in Drosophila germ line sex determination.

Oliver B, Pauli D, Mahowald AP.

Genetics (1990 Jul) 125:535-50. Abstract/Full Text

Genetic evidence that the sans fille locus is involved in Drosophila sex determination.

Oliver B, Perrimon N, Mahowald AP.

Genetics (1988 Sep) 120:159-71. Abstract/Full Text

The ovo locus is required for sex-specific germ line maintenance in Drosophila.

Oliver B, Perrimon N, Mahowald AP.

Genes Dev (1987 Nov) 1:913-23. Abstract/Full Text