Stuart M. Brown

Biosketch / Results /

Stuart M. Brown, Ph.D.

Associate Professor; Dir of the Sequencing Informatics Group of CHIBI; Oper Dir Best Prac Integrative Svc Core CHIBI; Dir Resh Computing Resource & Biofrmatics
Department of Cell Biology (Cell Biology)

Contact Info

227 East 30th Street
Center for Health Informatics and Bioinformatics Floor 7 Room 747
Translational Research Building
New York, NY 10016


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— Dr. Brown was a Postdoctoral Fellow in Plant Molecular Biology and the University of Manitoba and subsequently a Research Scientist at the USDA-ARS Plant Genetics Resources Unit in Griffin, GA, PostDoctoral Training
1992 — Cornell University, Graduate Education

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Research Summary

Bioinformatics is a rapidly growing area that addresses the use of computers for the acquisition, management, and analysis of biological information. The explosion of interest in bioinformatics in the past few years has been driven by the tremendous growth of DNA sequencing technology. Investigators use sequencing techniques for a variety of genomics applications but requrie bioinformatics skills to support this work.

I act as bioinformatics consultant for NYU Medical Center, collaborating as needed on a wide range of research projects. The extent of these collaborations ranges from a few consultation meetings to co-investigator on NIH grants. I am currently working on projects that include metagenomics (Human Microbiome Project), the genetic variation in the malaria parasite, and analysis of RNA-seq data from a variety of clinical and basic science research projects. Other projects that I have recently worked on include discovery of antigens using a pattern based search of complete genome sequences, Search for bacterial genes linked to severe dental caries, and an evolutionary analysis of the mammalian glucosidase gene family.

Research Interests


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All data from NYU Health Sciences Library Faculty Bibliography — -


Identification of a Face Enhancer Reveals Direct Regulation of LIM homeobox 8 (Lhx8) by Wingless-Int (WNT)/beta-catenin Signaling
Landin Malt, Andre; Cesario, Jeffry M; Tang, Zuojian; Brown, Stuart; Jeong, Juhee
2014 Sep;:108-108, Journal of biological chemistry
— id: 1173362, year: 2014, vol: , page: 108, stat: Journal Article,

Global reprogramming of the cellular translational landscape facilitates cytomegalovirus replication
McKinney, Caleb; Zavadil, Jiri; Bianco, Christopher; Shiflett, Lora; Brown, Stuart; Mohr, Ian
2014 Jan;6(1):9-17, Cell reports
— id: 759792, year: 2014, vol: 6, page: 9, stat: Journal Article,

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells
Murtha, Matthew; Tokcaer-Keskin, Zeynep; Tang, Zuojian; Strino, Francesco; Chen, Xi; Wang, Yatong; Xi, Xiangmei; Basilico, Claudio; Brown, Stuart; Bonneau, Richard; Kluger, Yuval; Dailey, Lisa
2014 May;11(5):559-565, Nature methods
— id: 970072, year: 2014, vol: 11, page: 559, stat: Journal Article,

Increased risk of hepatic decompensation and hepatocellular carcinoma in HIV/HCV-co-infected patients compared to HCV-mono-infected patients despite combination antiretroviral therapy
Lo, Re V; Tate, J; Kallan, M; Lim, J; Goetz, M; Klein, M; Rimland, D; Rodriguez-Barradas, M; Butt, A; Gibert, C; Brown, S; Kostman, J; Strom, B; Reddy, R; Justice, A; Localio, R
2012 24 Oct 2012;15:47-47, Journal of the International AIDS Society
— id: 688362, year: 2012, vol: 15, page: 47, stat: Journal Article,

Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia
Ntziachristos, Panagiotis; Tsirigos, Aristotelis; Vlierberghe, Pieter Van; Nedjic, Jelena; Trimarchi, Thomas; Flaherty, Maria Sol; Ferres-Marco, Dolors; da Ros, Vanina; Tang, Zuojian; Siegle, Jasmin; Asp, Patrik; Hadler, Michael; Rigo, Isaura; Keersmaecker, Kim De; Patel, Jay; Huynh, Tien; Utro, Filippo; Poglio, Sandrine; Samon, Jeremy B; Paietta, Elisabeth; Racevskis, Janis; Rowe, Jacob M; Rabadan, Raul; Levine, Ross L; Brown, Stuart; Pflumio, Francoise; Dominguez, Maria; Ferrando, Adolfo; Aifantis, Iannis
2012 ;18(2):298-301, Nature medicine
— id: 158681, year: 2012, vol: 18, page: 298, stat: Journal Article,

Trends and developments in bioinformatics in 2010: prospects and perspectives
Aliferis, C F; Alekseyenko, A V; Aphinyanaphongs, Y; Brown, S; Fenyo, D; Fu, L; Shen, S; Statnikov, A; Wang, J
2011 ;6(1):146-155, Yearbook of medical informatics
— id: 174460, year: 2011, vol: 6, page: 146, stat: Journal Article,

A Molecular Epidemiological Study of var Gene Diversity to Characterize the Reservoir of Plasmodium falciparum in Humans in Africa
Chen, Donald S; Barry, Alyssa E; Leliwa-Sytek, Aleksandra; Smith, Terry-Ann; Peterson, Ingrid; Brown, Stuart M; Migot-Nabias, Florence; Deloron, Philippe; Kortok, Moses M; Marsh, Kevin; Daily, Johanna P; Ndiaye, Daouda; Sarr, Ousmane; Mboup, Souleymane; Day, Karen P
2011 ;6(2):e16629-e16629, PLoS one
— id: 124110, year: 2011, vol: 6, page: e16629, stat: Journal Article,

Effects of Nickel Treatment on H3K4 Trimethylation and Gene Expression
Tchou-Wong, Kam-Meng; Kiok, Kathrin; Tang, Zuojian; Kluz, Thomas; Arita, Adriana; Smith, Phillip R; Brown, Stuart; Costa, Max
2011 ;6(3):e17728-e17728, PLoS one
— id: 130306, year: 2011, vol: 6, page: e17728, stat: Journal Article,

Constitutive mTORC1 activation by a herpesvirus Akt surrogate stimulates mRNA translation and viral replication
Chuluunbaatar, Uyanga; Roller, Richard; Feldman, Morris E; Brown, Stuart; Shokat, Kevan M; Mohr, Ian
2010 Dec 1;24(23):2627-2639, Genes & development
— id: 114863, year: 2010, vol: 24, page: 2627, stat: Journal Article,

Diversity of 16S rRNA genes within individual prokaryotic genomes
Pei, Anna Y; Oberdorf, William E; Nossa, Carlos W; Agarwal, Ankush; Chokshi, Pooja; Gerz, Erika A; Jin, Zhida; Lee, Peng; Yang, Liying; Poles, Michael; Brown, Stuart M; Sotero, Steven; Desantis, Todd; Brodie, Eoin; Nelson, Karen; Pei, Zhiheng
2010 Jun;76(12):3886-3897, Applied & environmental microbiology
— id: 156291, year: 2010, vol: 76, page: 3886, stat: Journal Article,

Targeted deletion of the genes encoding NTH1 and NEIL1 DNA N-glycosylases reveals the existence of novel carcinogenic oxidative damage to DNA
Chan, Michael K; Ocampo-Hafalla, Maria T; Vartanian, Vladimir; Jaruga, Pawel; Kirkali, Guldal; Koenig, Karen L; Brown, Stuart; Lloyd, R Stephen; Dizdaroglu, Miral; Teebor, George W
2009 Jul 4;8(7):786-794, DNA repair (Amsterdam)
— id: 100475, year: 2009, vol: 8, page: 786, stat: Journal Article,

Geographic population structure of the immune evasion (var) genes of Plasmodium falciparum
Barry, AE; Smith, TA; Chen, D; Sytek, AL; Imrie, H; Tavul, L; Migot-Nabias, F; Brown, SM; Deloron, P; Daily, J; Marsh, K; McVean, G; Day, KP
2008 JAN ;38(1):S38-S39, International journal for parasitology
— id: 76166, year: 2008, vol: 38, page: S38, stat: Journal Article,

Gene expression profiles of bronchoalveolar cells in pulmonary TB
Raju, Bindu; Hoshino, Yoshihiko; Belitskaya-Levy, Ilana; Dawson, Rod; Ress, Stanley; Gold, Jeffrey A; Condos, Rany; Pine, Richard; Brown, Stuart; Nolan, Anna; Rom, William N; Weiden, Michael D
2008 Jan;88(1):39-51, Tuberculosis (Edinburgh, Scotland)
— id: 74211, year: 2008, vol: 88, page: 39, stat: Journal Article,

Genetic classification of severe early childhood caries by use of subtracted DNA fragments from Streptococcus mutans
Saxena, Deepak; Caufield, Page W; Li, Yihong; Brown, Stuart; Song, Jinmei; Norman, Robert
2008 Sep;46(9):2868-2873, Journal of clinical microbiology
— id: 156784, year: 2008, vol: 46, page: 2868, stat: Journal Article,

Population genomics of the immune evasion (var) genes of Plasmodium falciparum
Barry, Alyssa E; Leliwa-Sytek, Aleksandra; Tavul, Livingston; Imrie, Heather; Migot-Nabias, Florence; Brown, Stuart M; McVean, Gilean A V; Day, Karen P
2007 Mar;3(3):e34-e34, PLoS pathogens
— id: 96299, year: 2007, vol: 3, page: e34, stat: Journal Article,

TBLR1 regulates the expression of nuclear hormone receptor co-repressors
Zhang, Xin-Min; Chang, Qing; Zeng, Lin; Gu, Judy; Brown, Stuart; Basch, Ross S
2006 ;7:31-31, BMC cell biology
— id: 68630, year: 2006, vol: 7, page: 31, stat: Journal Article,

Selection and validation of differentially expressed genes in head and neck cancer
Kuriakose, M A; Chen, W T; He, Z M; Sikora, A G; Zhang, P; Zhang, Z Y; Qiu, W L; Hsu, D F; McMunn-Coffran, C; Brown, S M; Elango, E M; Delacure, M D; Chen, F A
2004 Jun;61(11):1372-1383, Cellular & molecular life sciences: CMLS
— id: 44893, year: 2004, vol: 61, page: 1372, stat: Journal Article,

Aerosolized gamma interferon (IFN-gamma) induces expression of the genes encoding the IFN-gamma-inducible 10-kilodalton protein but not inducible nitric oxide synthase in the lung during tuberculosis
Raju, Bindu; Hoshino, Yoshihiko; Kuwabara, Kenichi; Belitskaya, Ilana; Prabhakar, Savita; Canova, Antony; Gold, Jeffrey A; Condos, Rany; Pine, Richard I; Brown, Stuart; Rom, William N; Weiden, Michael D
2004 Mar;72(3):1275-1283, Infection & immunity
— id: 42241, year: 2004, vol: 72, page: 1275, stat: Journal Article,

Transcriptome of axenic liver stages of Plasmodium yoelii
Wang, Qian; Brown, Stuart; Roos, David S; Nussenzweig, Victor; Bhanot, Purnima
2004 Sep;137(1):161-168, Molecular & biochemical parasitology
— id: 48869, year: 2004, vol: 137, page: 161, stat: Journal Article,

Bioinformatics becomes respectable
Brown, Stuart M
2003 Jun;34(6):1124-1127, Biotechniques
— id: 39192, year: 2003, vol: 34, page: 1124, stat: Journal Article,

Essentials of medical genomics
Brown, Stuart M; Hay, John G; Ostrer, Harry
Hoboken NJ : Wiley-Liss, 2003,
— id: 899, year: 2003, vol: , page: , stat: ,

Infectivity-associated changes in the transcriptional repertoire of the malaria parasite sporozoite stage
Matuschewski, Kai; Ross, Jessica; Brown, Stuart M; Kaiser, Karine; Nussenzweig, Victor; Kappe, Stefan H I
2002 Nov 1;277(44):41948-41953, Journal of biological chemistry
— id: 39415, year: 2002, vol: 277, page: 41948, stat: Journal Article,

Genomics-based identification of self-ligands with T cell receptor-specific biological activity
Santori, Fabio R; Brown, Stuart M; Vukmanovic, Stanislav
2002 Dec;190(4):146-160, Immunological reviews
— id: 34692, year: 2002, vol: 190, page: 146, stat: Journal Article,

Rare, structurally homologous self-peptides promote thymocyte positive selection
Santori, Fabio R; Kieper, William C; Brown, Stuart M; Lu, Yun; Neubert, Thomas A; Johnson, Kenneth L; Naylor, Stephen; Vukmanovic, Stanislav; Hogquist, Kristin A; Jameson, Stephen C
2002 Aug;17(2):131-142, Immunity
— id: 32496, year: 2002, vol: 17, page: 131, stat: Journal Article,

Definitive Identification of Mammalian 5-Hydroxymethyluracil DNA N-Glycosylase Activity as SMUG1
Boorstein RJ; Cummings A Jr; Marenstein DR; Chan MK; Ma Y; Neubert TA; Brown SM; Teebor GW
2001 Nov 9;276(45):41991-41997, Journal of biological chemistry
— id: 23928, year: 2001, vol: 276, page: 41991, stat: Journal Article,

Exploring the transcriptome of the malaria sporozoite stage
Kappe SH; Gardner MJ; Brown SM; Ross J; Matuschewski K; Ribeiro JM; Adams JH; Quackenbush J; Cho J; Carucci DJ; Hoffman SL; Nussenzweig V
2001 Aug 14;98(17):9895-9900, Proceedings of the National Academy of Sciences of the United States of America
— id: 25508, year: 2001, vol: 98, page: 9895, stat: Journal Article,

Cutting Edge: Positive Selection Induced by a Self-Peptide with TCR Antagonist Activity
Santori FR; Brown SM; Lu Y; Neubert TA; Vukmanovic S
2001 Dec 1;167(11):6092-6095, Journal of immunology (1950)
— id: 23925, year: 2001, vol: 167, page: 6092, stat: Journal Article,

Squamous cell carcinoma of the nail bed: is finger predominance another clue to etiology? A report of 5 cases
Zabawski, E J Jr; Washak, R V; Cohen, J B; Cockerell, C J; Brown, S M
2001 Jan;67(1):59-64, Cutis
— id: 123719, year: 2001, vol: 67, page: 59, stat: Journal Article,

Get your bioinformatics on the Web!
Brown SM
2000 Feb;28(2):244-246, Biotechniques
— id: 11829, year: 2000, vol: 28, page: 244, stat: Journal Article,

Be alert: free sequence alerting services
Brown, S M
2000 Dec;29(6):1210-1212, Biotechniques
— id: 111700, year: 2000, vol: 29, page: 1210, stat: Journal Article,

Dealing with Genome Project data
Brown SM
1999 ;26(2):266-26?, Biotechniques
— id: 8125, year: 1999, vol: 26, page: 266, stat: Journal Article,

Phylogenetics on the Web
Brown SM
1999 Dec;27(6):1146-1148, Biotechniques
— id: 11869, year: 1999, vol: 27, page: 1146, stat: Journal Article,

Snapping up SNPs
Brown SM
1999 Jun;26(6):'437'-'445', Biotechniques
— id: 6141, year: 1999, vol: 26, page: '437', stat: Journal Article,

Analyzing protein families and domains on the Web
Brown SM
1998 Oct;25(4):596-598, Biotechniques
— id: 7307, year: 1998, vol: 25, page: 596, stat: Journal Article,

Sequence similarity searches on the World Wide Web
Brown SM
1998 Feb;24(2):248-250, Biotechniques
— id: 7514, year: 1998, vol: 24, page: 248, stat: Journal Article,

Advanced similarity searches on the Web: Gapped BLAST, PSI-BLAST, FASTA 3.0 and INCA
Brown, SM
1998 AUG ;25(2):214-+, Biotechniques
— id: 53395, year: 1998, vol: 25, page: 214, stat: Journal Article,

Sequence alignment on the Web
Brown, SM
1998 JUN ;24(6):944-+, Biotechniques
— id: 53436, year: 1998, vol: 24, page: 944, stat: Journal Article,

Biologists and mathematicians: bridging the chasm
Brown SM
1997 May;13(5):173-173, Trends in genetics
— id: 7126, year: 1997, vol: 13, page: 173, stat: Journal Article,