Department of Genetics, University of Pennsylvania

Preprints

Kalita CA, Moyerbrailean GA, Brown CD, Wen X, Luca F, Pique-Regi R. QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays. BioRxiv. Cold Spring Harbor Labs Journals, Page: 105627, January 2017.
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Aguet F, Brown AA, Castel S, Davis JR, Mohammadi P, Segre AV, Zappala Z, Abell NS, Fresard L, Gamazon ER, Gelfand E, Gloudemans MJ, He Y, Hormozdiari F, Li X, Li X, Liu B, Garrido-Martin D, Ongen H, Palowitch JJ, Park Y, Peterson CB, Quon G, Ripke S, Shabalin AA, Shimko TC, Strober BJ, Sullivan TJ, Teran NA, Tsang EK, Zhang H, Zhou Y, Battle A, Bustamonte CD, Cox NJ, Engelhardt BE, Eskin E, Getz G, Kellis M, Li G, MacArthur DG, Nobel AB, Sabbati C, Wen X, Wright FA, GTEx Consortium, Lappalainen T, Ardlie KG, Dermitzakis ET, Brown CD, Montgomery SB. Local genetic effects on gene expression across 44 human tissues. BioRxiv. Cold Spring Harbor Labs Journals, Page: 074450, September 2016.
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Jo B, He Y, Strober BJ, Parsana P, Aguet F, Brown AA, Castel SE, Gamazon ER, Gewirtz A, Gliner G, Han B, He AZ, Kang EY, McDowell IC, Li X, Mohammadi P, Peterson CB, Quon G, Saha A, Segre AV, Sul JH, Sullivan TJ, Ardlie KG, Brown CD, Conrad DF, Cox NJ, Dermitzakis ET, Eskin E, Kellis M, Lappalainen T, Sabatti C, Engelhardt BE, Battle A, GTEx Consortium. Distant regulatory effects of genetic variation in multiple human tissues. BioRxiv. Cold Spring Harbor Labs Journals, Page: 074419, September 2016.
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Trizzino M, Park Y, Holsbach-Beltrame M, Aracena K, Mika K, Caliskan M, Perry GH, Lynch VJ, Brown CD. Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape. BioRxiv. Cold Spring Harbor Labs Journals, Page: 083980, October 2016.
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Publications

Ko YA, Yi H, Qiu C, Huang S, Park J, Ledo N, Köttgen A, Li H, Rader DJ, Pack MA, Brown CD, Susztak K. Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease. Am J Hum Genet. 2017 Jun 1;100(6):940-953.
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Pashos EE, Park Y, Wang X, Raghavan A, Yang W, Abbey D, Peters DT, Arbelaez J, Hernandez M, Kuperwasser N, Li W, Lian Z, Liu Y, Lv W, Lytle-Gabbin SL, Marchadier DH, Rogov P, Shi J, Slovik KJ, Stylianou IM, Wang L, Yan R, Zhang X, Kathiresan S, Duncan SA, Mikkelsen TS, Morrisey EE, Rader DJ, Brown CD, Musunuru K. Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci. Cell Stem Cell. 2017 Apr 6;20(4):558-570.e10.
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Stricker TP, Brown CD, Bandlamudi C, McNerney M, Kittler R, Montoya, Peterson A, Grossman R, White KP. Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression. PLoS Genetics 13(3): e1006589, March 2017.
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Ji X, Kember RL, Brown CD, Bućan M. Increased burden of deleterious variants in essential genes in autism spectrum disorder. Proceedings of the National Academy of Sciences 113(52): 201613195, December 2016.
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Khetarpal SA, Schjoldager KT, Christoffersen C, Raghavan A, Edmondson AC, Reutter HM, Ahmed B, Ouazzani R, Peloso GM, Vitali C, Zhao W, Hanasoge Somasundara AM, Millar JS, Park Y, Fernando G, Livanov V, Choi S, Noé E, Patel P, Ho SP, Myocardial Infarction Exome Sequencing Study, Kirchgessner TG, Wandall HH, Hansen L, Bennett EP, Vakhrushev SY, Saleheen D, Kathiresan S, Brown CD, Jamra RA, LeGuern E, Clausen H, Rader DJ. Loss of Function of GALNT2 Lowers High-Density Lipoproteins in Humans, Nonhuman Primates, and Rodents. Cell Metabolism 24(2): 234-245, August 2016.
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C Gao, I C McDowell, S Zhao, C D Brown, B E Engelhardt. Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering. PLOS Computational Biology 12(7), July 2016.
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Jha AR, Zhou D, Brown CD, Kreitman M, Haddad GG, White KP. Shared genetic signals of hypoxia adaptation in Drosophila and in high-altitude human populations. Molecular biology and evolution 33(2): 501, February 2016.
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Jha AR, Miles CM, Lippert NR, Brown CD, White KP, Kreitman M. Whole-genome resequencing of experimental populations reveals polygenic basis of egg-size variation in Drosophila melanogaster. Molecular biology and evolution 32(10): 2616-2632, October 2015.
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Yoo EJ, Brown CD, Tsai YC, Cooke NE, Liebhaber SA. Autonomous actions of the human growth hormone long-range enhancer. Nucleic acids research 43(4): gkv093, February 2015.
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Seiwert TY, Zuo X, Keck MK, Khattri A, Pedamallu CS, Stricker T, Brown CD, Pugh TJ, Stojanov P, Cho J, Lawrence MS, Getz G, Brägelmann J, DeBoer R, Weichselbaum RR, Langerman A, Portugal L, Blair E, Stenson K, Lingen MW, Cohen EE, Vokes EE, White KP, Hammerman PS. Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas. Clinical Cancer Research 21(3): 632-641, February 2015.
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Keck MK, Zuo Z, Khattri A, Stricker TP, Brown CD, Imanguli M, Rieke D, Endhardt K, Fang P, Brägelmann J, DeBoer R, El-Dinali M, Aktolga S, Lei Z, Tan P, Rozen SG, Salgia R, Weichselbaum RR, Lingen MW, Story MD, Ang KK, Cohen EE, White KP, Vokes EE, Seiwert TY. Integrative Analysis of Head and Neck Cancer Identifies Two Biologically Distinct HPV and Three Non-HPV Subtypes. Clinical Cancer Research 21(4): 870-881, February 2015.
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Guo C, Ludvik AE, Arlotto ME, Hayes MG, Armstrong LL, Scholtens DM, Brown CD, Newgard CB, Becker TC, Layden BT, Lowe WL, Reddy TE. Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1. Nature communications 4(6): 609, February 2015.
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Ferrara AM, Pappa T, Fu J, Brown CD, Peterson A, Moeller LC, Wyne K, White KP, Pluzhnikov A, Trubetskoy V, Nobrega M, Weiss RE, Dumitrescu AM, Refetoff S. A novel mechanism of inherited TBG deficiency: mutation in a liver specific enhancer. J Clin Endocrinol Metab. 2014 Oct 31:jc20143490.
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Khattri A, Zuo Z, Brägelmann J, Keck MK, El Dinali M, Brown CD, Stricker T, Munagala A, Cohen EE, Lingen MW, White KP, Vokes EE, Seiwert TY. Rare occurrence of EGFRvIII deletion in head and neck squamous cell carcinoma. Oral Oncol. 2015 Jan;51(1):53-8. doi: 10.1016/j.oraloncology.2014.08.014.
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Hause RJ, Stark AL, Antao NN, Gorsic LK, Chung SH, Brown CD, Wong SS, Gill DF, Myers JL, To LA, White KP, Dolan ME, Jones RB. Identification and Validation of Genetic Variants that Influence Transcription Factor and Cell Signaling Protein Levels. Am J Hum Genet 95, 1–15, August 7, 2014.
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Seiwert TY, Zuo Z, Keck MK, Khattri A, Pedamallu CS, Stricker TP, Brown CD, Pugh TJ, Stojanov P, Cho J, Lawrence M, Getz G, Bragelmann J, DeBoer R, Weichselbaum RR, Langerman A, Portugal LD, Blair EA, Stenson KM, Lingen MW, Cohen EE, Vokes EE, White KP, Hammerman PS. Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas. Clin Cancer Res. 2014 Jul 23. pii: clincanres.3310.2013
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McNerney ME, Brown CD, Peterson AL, Banerjee M, Larson RA, Anastasi J, Le Beau MM, White KP. The spectrum of somatic mutations in high-risk acute myeloid leukaemia with -7/del(7q). Br J Haematol. 2014 Jun 13. PMID: 24931631
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VanderWeele, D, Brown CD, Taxy J, Gillard M, Hatcher D, Westin T, Stadler W, White KP. Low grade prostate cancer diverges early from high grade and metastatic disease. Cancer Science. 2014 May 31. PMID: 24890684
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Georgi B, Craig D, Kember RL, Liu W, Lindquist I, Nasser S, Brown C, Egeland JA, Paul SM, Bućan M. Genomic view of bipolar disorder revealed by whole genome sequencing in a genetic isolate. PLoS Genet. 2014 Mar 13;10(3):e1004229. PMID: 24625924.
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Mangravite LM*, Engelhardt BE*, Medina MW, Smith JD, Brown CD, Chasman DI, Mecham BH, Howie B, Shim H, Naidoo D, Feng Q, Rieder MJ, Chen YDI, Rotter JI, Ridker PM, Hopewell JC, Parish S, Armitage J, Collins R, Wilke RA, Nickerson DA, Stephens M, Krauss RM. A statin-dependent QTL for GATM expression is associated with statin-induced myopathy. Nature. 2013 Oct 17;502(7471):377-80.
html | pdf | The Scientist | GEO

Brown CD, Mangravite LM, Engelhardt BE. Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs. PLoS Genetics. 2013 9(8): e1003649.
html | pdf | arXiv | Haldane's Sieve

Brägelmann J, Dagogo-Jack I, El Dinali M, Stricker T, Brown CD, Zuo Z, Khattri A, Keck M, McNerney ME, Longnecker R, Bieging K, Kocherginsky M, Alexander K, Salgia R, Lingen MW, Vokes EE, White KP, Cohen EE, Seiwert TY. Oral cavity tumors in younger patients show a poor prognosis and do not contain viral RNA. Oral Oncology. 2013 Mar 9. PMID: 23490885
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Jiang Z, Xia F, Johnson K, Brown CD, Bartom E, Tuteja JH, Stevens R, Grossman R, Brumin M, White KP, Ghanim M. Comparison of the Genome Sequences of “Candidatus Portiera aleyrodidarum” Primary Endosymbionts of the Whitefly Bemisia tabaci B and Q Biotypes. Applied and Environmental Microbiology. 2013 Mar. PMID: 23315735
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McNerney ME, Brown CD, Wang X, Bartom ET, Karmakar S, Bandlamudi C, Yu S, Ko J, Sandall BP, Stricker T, Anastasi J, Grossman RL, Cunningham JM, Le Beau MM, White KP. CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia. Blood. 2013 Feb 7. PMID: 23212519
html | pdf | Blood editorial | Science Life | Cover Image

Gao W, Grossman R, Yu P, Brown CD, Slattery M, Ma L, White KP. Discovering Geometric Patterns in Genomic Data. ACM-BCB 2012.
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Hekman KE, Yu G*, Brown CD*, Zhu H, Du X, Gervin K, Undlien DE, Peterson A, Stevanin G, Clark HB, Pulst S, Bird T, White KP, Gomez CM. A Conserved eEF2 Coding Variant in SCA26 Leads to Loss of Translational Fidelity and Increased Susceptibility to Proteostatic Insult. Human Molecular Genetics. 2012 Sep 21. PMID:23001565.
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Doré LC, Chlon TM, Brown CD, White KP, Crispino JD. Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis. Blood. 2012 Apr 19;119(16):3724-33. PMID:22383799.
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Yong Tao, Jue Ruan, Shiou-Hwei Yeh, Xuemei Lu, Yu Wang, Weiwei Zhai, Jun Cai, Shaoping Ling, Qiang Gong, Zecheng Chong, Zhengzhong Qu, Qianqian Li, Jiang Liu, Jin Yang, Caihong Zheng, Changqing Zeng, Hurng-Yi Wang, Jing Zhang, Sheng-Han Wang, Lingtong Hao, Lili Dong, Wenjie Li, Min Sun, Wei Zou, Caixia Yu, Chaohua Li, Guojing Liu, Lan Jiang, Jin Xu, Huanwei Huang, Chunyan Li, Shuangli Mi, Bing Zhang, Baoxian Chen, Wenming Zhao, Songnian Hu, Shi-Mei Zhuang, Yang Shen, Suhua Shi, Brown CD, White KP, Ding-Shinn Chen, Pei-Jer Chen, Chung-I Wu. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):12042-7. PMID: 21730188.
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Innocenti F*, Cooper GM*, Stanaway IB, Gamazon ER, Smith JD, Mirkov S, Ramirez J, Liu W, Lin YS, Maloney C, Force Aldred S,Trinklein ND, Schuetz E, Nickerson DA, Thummel KE, Rieder MJ, Rettie AE, Ratain MJ, Cox NJ, Brown CD. Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genetics 2011 7(5): e1002078. PMID: 21637794
html | pdf | Merck GEO | UC GEO | UW GEO | eQTL Browser

Nègre N*, Brown CD*, Ma L*, Bristow CA*, Miller SW*, Wagner U*, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP. A cis-regulatory map of the Drosophila genome. Nature 2011 Mar 24;471(7339):527-31. PMID: 21430782
html | pdf | SOM | GEO | Data on modMine | News and Views | F1000

The modENCODE Consortium, et al. Identification of functional elements and regulatory circuits in Drosophila by large-scale data integration. Science 2010 Dec 24;330(6012):1787-97. PMID: 21177974
html | pdf | SOM | Web Companion | Science Perspective | Science Editorial | NRG Highlight

Nègre N*, Brown CD*, Shah P, Kheradpour P, Morrison CA, Henikoff JG, Feng X, Ahmad K, Russell S, White RAH, Stein L, Henikoff S, Kellis M, White KP. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genetics 2010 Jan 15; 6(1):e1000814. PMID: 20084099
html | pdf | Insulator beds | GEO | modENCODE data

Celniker SE, Dillon LAL, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH, modENCODE Consortium. Unlocking the Secrets of the Genome. Nature. 2009 Jun 18;459(7249):927-30. PMID: 19536255
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Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A, White KP. Analysis of Drosophila Segmentation Network Identifies a JNK Pathway Factor Overexpressed in Kidney Cancer. Science 2009 Feb 27;323(5918):1218-22. PMID: 19164706.
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Brown CD. Ph.D. Thesis, 2007, Stanford University
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Brown CD, Johnson DS, Sidow A. Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 2007 Sept 14, 317:1557-1560. PMID: 17872446
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Johnson DS, Davidson B, Brown CD, Smith WC, Sidow A. Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance. Genome Research 2004 Dec;14(12):2448-56. PMID: 15545496
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Commentary

Barsh GS, Bergman CM, Brown CD, Singh ND, Copenhaver GP. Bringing PLOS Genetics Editors to Preprint Servers. PLoS Genet. 2016 Dec 1;12(12):e1006448.
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Engelhardt BE, Brown CD. Diving deeper to predict noncoding sequence function. Nat Methods. 2015 Oct;12(10):925-6. doi: 10.1038/nmeth.3604.
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Cooper GM and Brown CD. Qualifying the relationship between sequence conservation and molecular function. Genome Research 2008 Feb, 18:201-205. PMID: 18245453
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*Denotes equal contributions