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

Day RS, McDade K, Grover H, Luthra S, Chandran U, Lisovich A. Bioinformatic Data Integration to Assess Data Preprocessing. In: Proceedings of the AMIA Joint Summit on Translational Science; 2012 Mar 19-21; San Francisco, CA.

McDade K, Day RS, Chandran U, Lisovich A. Optimal Probeset Filtering Using Proteomic-Transcriptomic Correlations. In: Proceedings of the AMIA Joint Summit on Translational Science; 2012 Mar 19-21; San Francisco, CA.

Krill-Burger JM, Lyons MA, Kelly LA, Sciulli CM, Petrosko P, Chandran UR, Kubal MD, Bastacky SI, Parwani AV, Dhir R, LaFramboise WA. Renal cell neoplasms contain shared tumor type-specific copy number variations. Am J Pathol. 2012 Jun; 180(6):2427-39. PMID: 22483639. PMCID: PMC3378847. doi: 10.1016/j.ajpath.2012.01.044

Boyd LB, Hunicke-Smith SP, Stafford GA, Freund ET, Ehlman M, Chandran U, Dennis R, Fernandez AT, Goldstein S, Steffen D, Tycko B, Klemm JD. The caBIG® Life Science Business Architecture Model. Bioinformatics. 2011 May 15; 27(10):1429-35. Epub 2011 Mar 29. PMID: 21450709. PMCID: PMC3087952. doi: 10.1093/bioinformatics/btr141.

Bartholow TL, Chandran UR, Becich MJ, Parwani AV. Immunohistochemical profiles of claudin-3 in primary and metastatic prostatic adenocarcinoma. Diagn Pathol. 2011 Jan 21;6:12. PMID: 21255442. PMCID: PMC3033791. doi: 10.1186/1746-1596-6-12

Bartholow TL, Chandran UR, Becich MJ, Parwani AV. Immunohistochemical staining of radixin and moesin in prostatic adenocarcinoma. BMC Clin Pathol. 2011 Jan 14;11:1. PMID: 21235778 PMCID: PMC3029218 doi: 10.1186/1472-6890-11-1

Maxwell GL, Hood BL, Day R, Chandran U, Kirchner D, Kolli VS, Bateman NW, Allard J, Miller C, Sun M, Flint MS, Zahn C, Oliver J, Banerjee S, Litzi T, Parwani A, Sandburg G, Rose S, Becich MJ, Berchuck A, Kohn E, Risinger JI, Conrads TP. Proteomic analysis of stage I endometrial cancer tissue: identification of proteins associated with oxidative processes and inflammation. Gynecologic oncology. 2011 Jun 1; 121 (3):586-94. Epub 2011 Apr 1. PMID: 21458040. doi: 10.1016/j.ygyno.2011.02.031

Bartholow TL, Becich MJ, Chandran UR, Parwani AV. Immunohistochemical staining of slit2 in primary and metastatic prostatic adenocarcinoma. Translational oncology. 2011 Oct; 4(5):314-20. PMID: 21966548. PMCID: PMC3162306

Manohar R, Komori J, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E. Identification and expansion of a unique stem cell population from adult mouse gallbladder. Hepatology. 2011 Nov; 54(5):1830-41. PMID: 21793026. PMCID: PMC3205206 doi: 10.1002/hep.24568

Day RS, McDade KK, Chandran UR, Lisovich A, Conrads TP, Hood BL, Kolli VS, Kirchner D, Litzi T, Maxwell GL. (2011). Identifier mapping performance for integrating transcriptomics and proteomics experimental results. BMC Bioinformatics, 12, 213. http://doi.org/10.1186/1471-2105-12-213 PMID: 21619611 PMCID: PMC3124437

Lisovich A, Chandran UR, Lyons-Weiler MA, LaFramboise WA, Brown AR, Jakacki RI, Pollack IF, Sobol RW. (2011). A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples. BMC Medical Genomics, 4, 14. http://doi.org/10.1186/1755-8794-4-14 PMID: 21269491 PMCID: PMC3041647

Chang G, Xu S, Dhir R, Chandran U, O'Keefe DS, Greenberg NM, Gingrich JR. Hypoexpression and epigenetic regulation of candidate tumor suppressor gene CADM-2 in human prostate cancer. Clin Cancer Res. 2010 Nov 15; 16(22):5390-401. Epub 2010 Nov 9. PMID: 21062931. PMCID: PMC3541035. doi: 10.1158/1078-0432.CCR-10-1461.

AEscamilla-Hernandez, R., Little-Ihrig, L., Orwig, K. E., Yue, J., Chandran, U., & Zeleznik, A. J. (2008). Constitutively Active Protein Kinase A Qualitatively Mimics the Effects of Follicle-Stimulating Hormone on Granulosa Cell Differentiation. Molecular Endocrinology, 22(8), 1842–1852. http://doi.org/10.1210/me.2008-0103 PMID: 18535249 PMCID: PMC2725770

Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP, Parwani AV, Sciulli CM, Li J, Chandran UR, Bastacky SI, Dhir R. Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Modern Pathology : An Official JouCopyrnal of The United States and Canadian Academy of Pathology, Inc. 2008 May;21(5):599-608.  PMID: 18246049 DOI: 10.1038/modpathol.2008.20

Yin M, Bastacky S, Chandran U, Becich MJ, Dhir R. Prevalence of incidental prostate cancer in the general population: a study of healthy organ donors. The Journal of Urology. 2008 Mar;179(3):892-5; discussion 895. PMID: 18207193 DOI: 10.1016/j.juro.2007.10.057

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