Brian Oliver, Ph.D.

Photo of Dr. Brian Oliver
Scientific Focus Areas: Computational Biology, Developmental Biology, Genetics and Genomics

Publications

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

Select Publications

Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster.
Lee H, Cho DY, Whitworth C, Eisman R, Phelps M, Roote J, Kaufman T, Cook K, Russell S, Przytycka T, Oliver B.
PLoS Genet (2016 Sep) 12:e1006295. Abstract/Full Text
Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes.
Clough E, Jimenez E, Kim YA, Whitworth C, Neville MC, Hempel LU, Pavlou HJ, Chen ZX, Sturgill D, Dale RK, Smith HE, Przytycka TM, Goodwin SF, Van Doren M, Oliver B.
Dev Cell (2014 Dec 22) 31:761-73. Abstract/Full Text
Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster.
Lin Y, Golovnina K, Chen ZX, Lee HN, Negron YL, Sultana H, Oliver B, Harbison ST.
BMC Genomics (2016 Jan 5) 17:28. Abstract/Full Text
Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S.
Genome Res (2014 Jul) 24:1209-23. Abstract/Full Text
Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults.
Yang H, Basquin D, Pauli D, Oliver B.
BMC Genomics (2017 May 18) 18:384. Abstract/Full Text

Additional Publications

Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila.
Wang Y, Cho DY, Lee H, Fear J, Oliver B, Przytycka TM.
Nat Commun (2018 Oct 3) 9:4061. Abstract/Full Text
Dosage-Dependent Expression Variation Suppressed on the Drosophila Male X Chromosome.
Lee H, Cho DY, Wojtowicz D, Harbison ST, Russell S, Oliver B, Przytycka TM.
G3 (Bethesda) (2018 Feb 2) 8:587-598. 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