Uma Chandran, PhD, MSIS

Room 513
5607 Baum Boulevard
Phone: 
412-648-9326
Admin Support: 

Dr. Chandran's Summary of Research

Cancer Bioinformatics Services

Health Sciences Core Research Facilities

Biography:

I have extensive experience in both bench research and bioinformatics and co-direct the Cancer Bioinformatics Service (CBS), a translational core service at the University of Pittsburgh Cancer Institute. CBS is an interdisciplinary collaboration between my core team, the Department of Biomedical Informatics faculty, UPCI, the Institute for Personalized Medicine, the Pittsburgh Supercomputing Center and the University of Pittsburgh's Simulation and Modeling Center. The CBS aims are to 1) provide data analysis, 2) develop high performance computing (HPC) infrastructure and 3) develop research databases to integrate clinical and genomic data for biomarker discovery. I have deep experience working with all genomic platforms and applications including next generation sequencing (NGS) based RNA Seq, Whole Exome Seq (WXS) and Whole Genome Seq (WGS). I have also performed integrative analysis across multiple platforms and from large consortia datasets such as The Cancer Genome Atlas (TCGA) project. I am a key member of several data science projects in DBMI including the Pittsburgh Genome Resource Repository (PGRR), a regulatory, hardware and software infrastructure for TCGA data and the PACURE projects in breast and lung cancers. CBS supports all CCCG's disease specific programs and has performed somatic variant analysis in melanoma, lung, mesothelioma and renal cell cancers, copy number analysis to understand the differences and similarities between pediatric gliomas to adult gliomas, and RNA seq expression and integrative analysis of TCGA breast tumor samples. My team of analysts and I also support non-cancer genomic studies including development of methods for de novo transcriptome assembly. The combination of experience in bench science and bioinformatics allows me to not only provide data analysis services but also biological insight into the results of high throughput data such as integrative analysis of ChIP Seq and RNA seq data. We have partnered closely with the PSC and SaM to develop the HPC infrastructure to meet the computational demands of next generation sequencing analysis and have been awarded NSF's XSEDE award for computation and storage. With this team approach to bioinformatics, I have built a shared resource which can quickly meet the bioinformatics requirements of rapidly changing genomics landscape and a computing infrastructure which scales easily to terabytes of data.

Research Interests:
Genomic data mining
Next Generation Sequencing data analysis
Integrative analysis of The Cancer Genome Atlas Project (TCGA)
Development of computing infrastructure for large genomics datasets
Academic Appointments: 
12/2015 - present
Research Associate Professor, Department of Biomedical Informatics, University of Pittsburgh
12/2015 - present  
Co-director, Cancer Bioinformatics Services, UPCI, University of Pittsburgh
Director, Genomics Analysis Core (GAC), University of Pittsburgh
Grants & Contracts: 
02/1/2016 - 01/31/2017
NIH 5R01HD072189
Molecular Bases Committing Primate Spermatogonia to a Pathway of Differentiation
Role: Co-Investigator
06/1/2015 - 05/31/2018
PA DOH SAP4100070287
Big Data for Better Health (BD4BH) in Pennsylvania
Role: Co-Investigator
07/15/2013 - 06/30/2017
NIH 5R01DK099320
Regulation of HNF4 in Hepatic Failure in Cirrhosis
Role: Co-Investigator
07/1/2006 - 06/30/2018
NIH P50 CA121973
Spore in Skin Cancer
Role: Co-Investigator
09/1/1998 - 01/31/2017
NIH 5R01NS037704
Molecular Markers as Predictors of Outcome in Gliomas
Role: Research Associate
09/10/1997 - 07/31/2020
NIH/NCI 2P30CA047904
Cancer Center Support (CCSG)
Role: Core Lead
12/18/1996 - 02/28/2019
NIH 5R01CA186780
Roles of EAF2 in Androgen Action in the Prostate
Role: Co-Investigator
Teaching Activities: 
2013 - present   Intro to Bioinformatics
03/2007 - present   Introduction to Microarray Analysis
07/2002 - present   Introduction to Bioinformatics to Pathology Residents
Service Activities: 
Department
present Training Program Member, Training Program Committee
Other
present Reviewer, Pathology Informatics
present

Reviewer, AMIA conference on Translational Bioinformatics

Presentations: 
- Chandran U, Chakka A. Variant Analysis for Cancer Genomics. Presented at: AACR. San Diego, CA.
- Chandran U. PGRR - Intro to the Cancer Genome Atlas. Presented at: UPCI Annual Retreat 2014 2014 Jun 18 - 19. University of Pittsburgh Greensburg.
- Chandran U. The Cancer Genome Atlas. Presented at: Magee Women's Research Institute Annual Retreat 2013 Nov 15 - 16. Nemacolin Woods, PA.
- Chandran U. Bioinformatics - Practical Applications in Pathology. Presented at: APIII 2010 2010 Sep 19 - 22. Boston, MA.
Peer-reviewed Publications: 
44
Publications

Chandran UR, Lyons-Weiler J, Sciulli C, Monzon FA. Informatics requirements of a high throughput genomics laboratory. AMIA Summit on Translational Bioinformatics. 2008;(0).

Chiosea S, Jelezcova E, Chandran U, Luo J, Mantha G, Sobol RW, Dacic S. Overexpression of Dicer in precursor lesions of lung adenocarcinoma. Cancer research. 2007 Mar 1;67(5):2345-50. PMID: 17332367 DOI: 10.1158/0008-5472.CAN-06-3533

Kelavkar UP, Harya NS, Hutzley J, Bacich DJ, Monzon FA, Chandran U, Dhir R, O'Keefe DS. DNA methylation paradigm shift: 15-lipoxygenase-1 upregulation in prostatic intraepithelial neoplasia and prostate cancer by atypical promoter hypermethylation. Prostaglandins & other lipid mediators. 2007 Jan;82(1):185-97. PMID: 17164146 DOI: 10.1016/j.prostaglandins.2006.05.015

Chandran UR, Ma C, Dhir R, Bisceglia M, Lyons-Weiler J, Liang W, Michalopoulos GK, Becich MJ, Monzon FA. Gene expression profiles of metastatic prostate cancer reveals disregulation of specific molecular pathways. BMC Cancer. 2007;7(0):64. PMID: 17430594 PMCID: PMC1865555

Chiosea S, Jelezcova E, Chandran U, Acquafondata M, McHale T, Sobol RW, Dhir R. Up-regulation of dicer, a component of the MicroRNA machinery, in prostate adenocarcinoma. The American journal of pathology. 2006 Nov;169(5):1812-20. PMID 17071602 PMCID: PMC1780192

Shah UZ, Dhir R, Gollin SM, Chandran UR, Lewis D, Acquafondata M, Pflug BR. Fatty Acid Synthase Gene Expression Amplification in Prostate Adenocarcinoma. Hum Pathol. 2006;4(0):401-409.

Kelavkar, U., Lin, Y., Landsittel, D., Chandran, U., & Dhir, R. (2006). The yin and yang of 15-lipoxygenase-1 and delta-desaturases: Dietary omega-6 linoleic acid metabolic pathway in prostate. Journal of Carcinogenesis, 5, 9. http://doi.org/10.1186/1477-3163-5-9 PMID: 16566819 PMCID: PMC1440856

Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer cell. 2005 Nov;8(5):393-406. PMID: 16286247

Chandran, U. R., Dhir, R., Ma, C., Michalopoulos, G., Becich, M., & Gilbertson, J. (2005). Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer, 5, 45. http://doi.org/10.1186/1471-2407-5-45 PMID: 15892885 PMCID: PMC1173092

Chandran U, Monzon FA, Becich MJ, Gilbertson J. A new pathology biomarker laboratory. Proc. Medinfo. (CD). 2004;(0):1546.

Chandran UR, Warren BS, Baumann CT, Hager GL, DeFranco DB. The glucocorticoid receptor is tethered to DNA-bound Oct-1 at the mouse GnRH distal negative glucocorticoid response element. J. Biol. Chem. 1999;274(0):2372-2378. PMID: 9891005

Chandran UR, DeFranco DB. Regulation of gonadotropin-releasing hormone gene transcription. Behavioural Brain Research. 1999;105(0):29-36. PMID: 10553688

Attardi B, Tsujii T, Friedman R, Zeng Z, Roberts JL, Dellovade T, Pfaff D, Chandran UR, DeFranco DB. Glucocorticoid repression of gonadotropin-releasing hormone gene expression and secretion in morphologically distinct subpopulations of GT1-7 cells. Mol. Cell. Endocrinol. 1997;131(0):241-255. PMID: 9296383

Chandran UR, Attardi B, Friedman R, Zheng ZW, Roberts JL, DeFranco DB. Glucocorticoid repression of the mouse gonadotropin-releasing hormone gene is mediated by promoter elements that are recognized by heteromeric complexes containing glucocorticoid receptor. J. Biol. Chem.. 1996;271(0):20412-20420. PMID: 8702778

DeFranco DB, Madan AP, Tang Y, Chandran UR, Xiao N, Yang J. Nucleocytoplasmic shuttling of steroid receptors. In Vitamins and Hormones. Academic Press. 1994;51(0):315-338. PMID: 7483326

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