Uma Chandran

  • Research Associate Professor, Department of Biomedical Informatics

 A. Personal Statement 

I co-direct the Cancer Bioinformatics Service (CBS), a highly utilized shared resource providing bioinformatics support for the University of Pittsburgh Cancer Institute (UPCI)’s CCSG disease-focused research programs. CBS, which received an exceptional rating in the 2015 CCSG renewal provides data analysis, high performance computing and specialized databases for cancer genomics. I have deep experience working with all aspects of genomics data, and have analyzed data from all Next Generation Sequencing (NGS) platforms including RNA Seq, Whole Exome Seq (WXS) andWhole Genome Seq (WGS), have performed integrative analysis across multiple platforms and from large consortia datasets such as TCGA, and am a key member of the Pittsburgh Genome Resource Repository (PGRR), a regulatory, hardware and software local infrastructure for TCGA data. CBS is an interdisciplinary service with collaborations 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.With this team approach to bioinformatics, I have built a shared resource which can quickly meet the bioinformatics requirements of the rapidly changing genomics landscape, and a computing infrastructure which scales easily to terabytes of data. With my combination of bench experience and applied bioinformatics, I bring unique strengths to genomics analysis and look forward to expanding CBS’s expertise in emerging platforms, new infrastructure projects and research informatics based data warehouse for cancer biomarker discovery.

1. Concha-Benavente F, Srivastava RM, Trivedi S, Lei Y, Chandran U, Seethala RR, Freeman GJ, Ferris RL. Identification of the Cell-Intrinsic and -Extrinsic Pathways Downstream of EGFR and IFNy That Induce PD-L1 Expression in Head and Neck Cancer. Cancer Res. 2016 Mar 1;76(5):1031-43. doi: 10.1158/0008-5472.CAN-15-2001.  PMID:26676749. PMCID: PMC4775348.

2. Manohar R, Li Y, Fohrer H, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E. Identification of a candidate stem cell in human gallbladder. Stem Cell Res. 2015 May;14(3):258-69. Epub 2015 Feb 7. PMID: 25765520. PMCID: PMC4439375.

3. Mao P, Joshi K, Li J, Kim SH, Li P, Santana-Santos L, Luthra S, Chandran UR, Benos PV, Smith L, Wang M, Hu B, Cheng SY, Sobol RW, Nakano I. Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3. Proceedings of the National Academy of Sciences of the United States of America. 2013 May 21; 110 (21):8644-9. PMCID: PMC3666732

4. Li J, Luthra S, Wang XH, Chandran UR, Sobol RW. Transcriptional profiling reveals elevated Sox2 in DNA polymerase ß null mouse embryonic fibroblasts. American journal of cancer research. 2012; 2 (6):699-713. PMCID: PMC3512183

B. Positions and Honors 

Positions and Employment

09/1991 - 08/1998        Senior Research Associate, Biological Sciences,
                                     University of Pittsburgh, Pittsburgh, PA 

11/1998 - 12/1999        Application Developer, Computerm Corporation,
                                     Pittsburgh, PA 

05/2000 - 12/2000        Scientific Curator, Proteome Inc., Beverly, MA 

05/2000 - 12/2000        Scientific Consultant, MSA Corporation, Pittsburgh, PA 

07/2006 - 06/2007        Systems Programmer, Biomedical Informatics,
                                     University of Pittsburgh, Pittsburgh, PA 

07/2007 - Present        Research Associate, Biomedical Informatics, University
                                    of Pittsburgh, Pittsburgh, PA 

09/1/2004 - Present     Co-Director, Cancer Bioinformatics Services,
                                     Biomedical Informatics, University of Pittsburgh Cancer
                                     Institute, Pittsburgh, PA 

12/1/2015 - Present     Research Associate Professor, Department of Biomedical
                                     Informatics, University of Pittsburgh, Pittsburgh, PA 

Other Experience and Professional Memberships

09/2001 - Present         Member, Association of Pathology Informatics 

05/15/2015 - Present    Member, American Medical Informatics Association 

05/15/2015 - Present    Member, Association of Biomolecular Resource Facilities 


1996 - 1996                   Endocrine Society Travel Award to present at the 10th International
                                      Congress of Endocrinology, San Francisco, CA 

1992 - 1994                   National Research Service Award (NRSA) IF32HDO7593-01A1 

1991 - 1992                   Post-Doctoral Fellowship in Reproductive Physiology, Institutional
                                      National Research Service Award (NRSA) IT32HD)7332 - Center for
                                      Reproductive Physiology, School of Medicine, University of Pittsburgh,
                                      Pittsburgh, PA 

C. Contribution to Science 

1. From 2001 to 2005, I was a member of the Department of Pathology team, which participated in NCI’s Director Challenge for Molecular Reclassification of Cancer project on prostate cancer. This was one of the first projects to analyze cancer microarray data with large sample sizes. We were one of the first groups to demonstrate that tissue adjacent to prostate tumors, although appearing normal, express gene expression profiles resembling prostate cancers and also demonstrated distinct molecular changes in metastatic versus organ confined cancers. In collaboration with Arul Chinnaiyan’s group at the University of Michigan performed one of the first integrative studies examining protein and gene expression in prostate cancers.

a. 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; 7:64.
b. 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.
c. Chandran UR, Dhir R, Michalopoulos GK, Becich MJ, Gilbertson JR, Ma C. Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer. 2005; 45.

2. Since 2004, I have led the bioinformatics shared resource facility at the University of Pittsburgh Cancer Institute and have developed the Cancer Bioinformatics Services (CBS), a resource which provides data analysis, high performance computing (HPC) and specialized databases for cancer research. This highly utilized resource was ranked exceptional in the CCSG 2015 renewal and is utilized by the majority of CCSG research programs. I have co-authored 45 publications and the CBS shared resource model is a robust and scalable infrastructure which can support small studies to massively parallel big data sets. CBS is based on a highly collaborative team science approach consisting of faculty scientists, master’s level analysts, IT personnel, the Pittsburgh Supercomputing Center (PSC), University of Pittsburgh Center for Simulation and Modeling (SaM), the Institute for Personalized Medicine (IPM) and UPCI.

a. Sikora MJ, Cooper KL, Bahreini A, Luthra S, Wang G, Chandran UR, Davidson NE, Dabbs DJ, Welm AL, Oesterreich S. Invasive lobular carcinoma cell lines are characterized by unique estrogen-mediated gene expression patterns and altered tamoxifen response. Cancer Research. 2014 Mar 1; 74 (5):1463-74. PMCID: PMC3955299.
b. Krill-Burger JM, Lyons MA, Kelly LA, Sciulli CM, Petrosko P, Chandran UR, Kubal MD, Bastacky SI, Parwani AV, Dhir R, LaFramboiseWA. Renal cell neoplasms contain shared tumor type-specific copy number variations. The American journal of pathology. 2012 Jun; 180 (6):2427-39. PMCID: PMC3378847
c. Lisovich A, Chandran UR, Lyons-Weiler MA, LaFramboiseWA, Brown AR, Jakacki RI, Pollack IF, Sobol RW. A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples. BMC medical genomics. 2011; 4:14. PMCID: PMC3041647 

3. CBS’s efforts have expanded to include integrative proteomic and genomic platforms, integrative analysis across multiple TCGA platforms, survey of biomedical researchers to understand data analysis bottlenecks, and development of new resources to provide bioinformatics support. An example of such a resource is the Pittsburgh Genome Resource Repository (PGRR); led by Dr. Rebecca Jacobson, PGRR is an institution wide regulatory compliant, high performance infrastructure to locally store and analyze all levels and data types from TCGA. CBS is an integral part of this project and projects and provides expertise in all aspects of its implementation, from TCGA domain expertise to data analysis support.

a. Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS. Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PloS One. 2015; 10 (6):e0131166. PMCID: PMC4483235. doi: 10.1371/journal.pone.0131166
b. Liao S, Hartmaier RJ, McGuire KP, Puhalla SL, Luthra S, Chandran UR, Ma T, Bhargava R, Modugno F, Davidson NE, Benz S, Lee AV, Tseng GC, Oesterreich S. The molecular landscape of premenopausal breast cancer. Breast Cancer Research: BCR. 2015; 17:104. PMCID: PMC4531812. doi: 10.1186/s13058-015-0618-8
c. McDade KK, Chandran U, Day RS. Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Informatics. 2015; 14:149-61.
PMCID: PMC4686346. doi: 10.4137/CIN.S33076
d. Day RS, McDade KK, Chandran UR, Lisovich A, Conrads TP, Hood BL, Kolli VS, Kirchner D, Litzi T, Maxwell GL. Identifier mapping performance for integrating transcriptomics and proteomics experimental results. BMC bioinformatics. 2011; 12:213. PMCID: PMC3124437 

Complete List of Published Work in MyBibliography