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

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 Research. 2016 Mar 1;76(5):1031-43. PMID:26676749.

Frahm KA, Peffer ME, Zhang JY, Luthra S, Chakka AB, Couger MB, Chandran UR, Monaghan AP, DeFranco DB. Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells. Molecular Endocrinology (Baltimore, Md.). 2016 Jan;30(1):144-54. PMID: 26606517

Gau DM, Lesnock JL, Hood BL, Bhargava R, Sun M, Darcy K, Luthra S, Chandran U, Conrads TP, Edwards RP, Kelley JL, Krivak TC, Roy P. (2015). BRCA1 deficiency in ovarian cancer is associated with alteration in expression of several key regulators of cell motility – A proteomics study. Cell Cycle, 14(12), 1884–1892. http://doi.org/10.1080/15384101.2015.1036203 PMID: 25927284 PMCID: PMC4614952

McDade KK, Chandran U, Day RS. Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Informatics, 2015. PMID: 26715829 PMCID: PMC4686346

McDade, K. K., Chandran, U., & Day, R. S. (2015). Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Informatics, 14, 149–161.  PMID: 26715829 PMCID: PMC4686346 DOI: 10.4137/CIN.S33076

Chandran, U. R., Luthra, S., Santana-Santos, L., Mao, P., Kim, S.-H., Minata, M., Li J, Benos PV, DeWang M, Hu B, Cheng SY, Nakano I, Sobol RW. (2015). Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells. Genomics Data, 5, 333–336. http://doi.org/10.1016/j.gdata.2015.07.007 PMID: 26251826 PMCID: PMC4523279

Manohar R, Li Y, Fohrer H, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E.  (2015). Identification of a candidate stem cell in human gallbladder. Stem Cell Research, 14(3), 258–269. http://doi.org/10.1016/j.scr.2014.12.003  PMID:  25765520 PMCID: PMC4439375

Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS. (2015). Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PLoS ONE, 10(6), e0131166. http://doi.org/10.1371/journal.pone.0131166 PMID: 26115441 PMCID: PMC4483235

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. (2015). The molecular landscape of premenopausal breast cancer. Breast Cancer Research : BCR, 17(1), 104. http://doi.org/10.1186/s13058-015-0618-8 PMID: 26251034 PMCID: PMC4531812

Sikora MJ, Cooper KL, Bahreini A, Luthra S, Wang G, Chandran UR, Davidson NE, Dabbs DJ, Welm AL, Oesterreich S. (2014). Invasive lobular carcinoma cell lines are characterized by unique estrogen-mediated gene expression patterns and altered tamoxifen response. Cancer Research, 74(5), 1463–1474. http://doi.org/10.1158/0008-5472.CAN-13-2779 PMID: 24425047 PMCID: PMC3955299

Risinger JI, Allard J, Chandran U, Day R, Chandramouli GV, Miller C, Zahn C, Oliver J, Litzi T, Marcus C, Dubil E, Byrd K, Cassablanca Y, Becich M, Berchuck A, Darcy KM, Hamilton CA, Conrads TP, Maxwell GL. Gene expression analysis of early stage endometrial cancers reveals unique transcripts associated with grade and histology but not depth of invasion. Front Oncol. 2013 Jun 17; 3:139. PMID: 23785665. PMCID: PMC3683664. doi: 10.3389/fonc.2013.00139

Maxwell GL, Allard J, Gadisetti CV, Litzi T, Casablanca Y, Chandran U, Darcy KM, Levine DA, Berchuck A, Hamilton CA, Conrads TP, Risinger JI. Transcript expression in endometrial cancers from Black and White patients. Gynecol Oncol. 2013 Jul; 130(1):169-73. PMID: 23603370. doi: 10.1016/j.ygyno.2013.04.017

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. Proc Natl Acad Sci U S A. 2013 May 21;110(21):8644-9. PMID: 23650391. PMCID: PMC3666732. doi: 10.1073/pnas.1221478110

LaFramboise WA, Dhir R, Kelly LA, Petrosko P, Krill-Burger JM, Sciulli CM, Lyons-Weiler MA, Chandran UR, Lomakin A, Masterson RV, Marroquin OC, Mulukutla SR, McNamara DM. Serum protein profiles predict coronary artery disease in symptomatic patients referred for coronary angiography. BMC Med. 2012 Dec 5; 10:157. PMID: 23216991. PMCID: PMC3566965. doi: 10.1186/1741-7015-10-157

Li J, Luthra S, Wang XH, Chandran UR, Sobol RW. Transcriptional profiling reveals elevated Sox2 in DNA polymerase ß null mouse embryonic fibroblasts. Am J Cancer Res. 2012; 2(6):699-713. Epub 2012 Nov 20. PMID: 23226616. PMCID: PMC3512183

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