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
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