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Data Science investigators

Ivet Bahar

Ivet Bahar

412-624-7615 bahar@ccbb.pitt.edu 3058 Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh PA
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Riyue Bao

Riyue Bao

412-623-0021 baor@upmc.edu UPMC Cancer Pavilion, 1A
5150 Centre Ave.
Pittsburgh PA
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Michael Becich

Michael Becich

becich@pitt.edu 5607 Baum Boulevard
Room 521
Pittsburgh PA
Research Interests and Keywords
  • Translational bioinformatics
  • oncology informatics
  • tissue banking and pathology informatics
  • prostate tumor cell biology
  • research resource development
  • content-based image retrieval and digital libraries
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Panagiotis Benos

Panagiotis Benos

412-648-3315 benos@pitt.edu Department of Computational and Systems Biology
Biomedical Science Tower 3, Suite 3064 3501 Fifth Avenue
Pittsburgh PA
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Carlos Camacho

Carlos Camacho

412-648-7776 ccamacho@pitt.edu University of Pittsburgh, Room 3077
3501 Fifth Avenue
Pittsburgh PA
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Uma Chandran

Uma Chandran

chandranur@upmc.edu Room 513
5607 Baum Boulevard
Pittsburgh PA
Research Interests and Keywords
  • Bioinformatics
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Chakra Chennubhotla

Chakra Chennubhotla

412-648-7794 chakracs@pitt.edu Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh
3501 Fifth Avenue, Suite 3081, Biomedical Science Tower 3 (BST3)
Pittsburgh PA
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Madhavi Ganapathiraju

Madhavi Ganapathiraju

412-648-9331 madhavi@pitt.edu 5607 Baum Boulevard
Room 522
Pittsburgh PA
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Adrian Lee

Adrian Lee

412-641-7557 leeav@upmc.edu The Assembly
5051 Centre Ave
Pittsburgh PA
Summary

The goal of the Lee laboratory is translational breast cancer research. The laboratory has two main areas of focus. The first involves targeting the insulin-like growth factor pathway in breast cancer. A major emphasis is upon the downstream signaling intermediates the insulin receptor substrates (IRSs) analyzing interactions with steroid hormone receptors (ER and PR), role in normal mouse mammary gland development, mechanisms of transformation of mammary epithelial cells in vitro and in mouse models, and roles in human breast cancer. The second area of research is studies on tumor heterogeneity and molecular changes during progression, with a particular focus on DNA and RNA structural rearrangements. The laboratory participated in the first comprehensive report of structural rearrangements in a breast cancer cell line (MCF7) and reported on a novel massively parallel fosmid-based mate-pair assay for determining structural rearrangements. This work focuses on different tumor areas, or tumors from different parts of the body (obtained via rapid autopsy) to identify novel changes that may offer therapeutic insight. In addition, the University of Pittsburgh is the largest contributor of tissue to The Cancer Genome Atlas (TCGA), and many results are validated in these index cases.

Research Interests and Keywords
  • Breast cancer
  • steroid receptors
  • growth factor signaling
  • estrogen receptor
  • progesterone receptor
  • insulin-like growth factor
  • tumor heterogeneity
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Steffi Oesterreich

Steffi Oesterreich

oesterreichs@upmc.edu The Assembly
5051 Centre Ave
Pittsburgh PA
Summary

The main interest of Dr. Oesterreich's laboratory is to further our understanding of hormone action in women's cancers (including both breast and ovarian cancers), with the ultimate goal to use this knowledge for improved diagnosis and endocrine treatment. These studies include many aspects of translational breast cancer research utilizing basic biochemistry, molecular and cell biology, and cell lines, mouse models and clinical samples. Over the last few years, Dr. Oesterreich has developed a strong research interest in in situ and invasive lobular disease, the second most common yet understudied histological subtype of breast cancer. In her role as Director of Education at the Women's Cancer Research Center, Dr. Oesterreich is also very interested in providing outstanding training opportunities to the next generation of women's cancer researchers.

Research Interests and Keywords
  • breast cancer
  • ovarian cancer
  • estrogen receptor
  • invasive lobular carcinoma
  • epigenetics
  • chromatin
  • coregulators
  • bone metastases
  • lobular carcinoma in situ
  • mutations
Read More about Steffi Oesterreich
Hatice Osmanbeyoglu

Hatice Osmanbeyoglu

412-623-7789 osmanbeyogluhu@pitt.edu UPMC Hillman Cancer Center Research Pavilion
Suite G27c, 5117 Centre Ave.
Pittsburgh PA
Research Interests and Keywords
  • Computational oncology
  • Cancer epigenetics
  • Omics approaches in immunology and immunotherapy
Read More about Hatice Osmanbeyoglu
Jonathan Silverstein

Jonathan Silverstein

412-624-8950 j.c.s@pitt.edu Department of Biomedical Informatics
Room 433, 5607 Baum Boulevard, Suite 500
Pittsburgh PA
Research Interests and Keywords
  • Clinical Informatics
  • Imaging/Visualization/Virtual Reality
  • Vocabularies
  • Virtual Organizations
  • Learning Health Systems
  • Oncology Informatics
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Xiaosong Wang

Xiaosong Wang

412-623-1587 xiaosongw@pitt.edu Hillman Cancer Center, Room G.5a
5117 Centre Ave.
Pittsburgh PA
Summary

The Cancer Genome Project Initiatives have generated a daunting amount of genomic and deep sequencing data for tens of thousands of human tumors. An overarching challenge of this post-genomic era is to identify and recognize the cancer drivers and targets from these big genomic data, especially those that can be therapeutically targeted to improve the clinical outcome. The mission of our lab is to apply a multiple disciplinary approach inclusive of integrative bioinformatics, cancer genetics, molecular cancer biology, and translational studies to identify driving genetic aberrations and appropriate cancer targets on the basis of deep sequencing and genomic profiling datasets. Our research projects are composed of both computational and laboratory components. Our dry lab researches focus on developing innovative and integrative computational technologies to discover causal genetic and epigenetic alternations, viable therapeutic targets, and predictive biomarkers in cancer. In particular, we have innovated a concept signature (ConSig) analysis that employs molecular fingerprints for high-throughput interpretation of the biological function of candidate targets in cancer (Nature biotech 2009). In addition, we have formulated a 'fusion breakpoint principle' that describes the intragenic copy number aberrations characteristic of recurrent gene fusions, thus enabling genome-wide detection of copy number breakpoints generating gene fusions. Based on these principles we further developed a powerful bioinformatics tool called 'Fusion Zoom' that identifies recurrent pathological gene fusions via integrative analyses of RNA sequencing, copy number, and gene concept datasets (Nature Commun 2014). Further, we have discovered the crucial application of ConSig analysis in revealing the primary oncogenes targeted by genomic amplifications, and developed a new integrative genomic analysis called 'ConSig-Amp' to detect viable cancer targets. Moreover we also developed an integrated computational-experimental approach called HEPA-PARSE for the genome-wide detection of clinically important tumor specific antigen (TSA) targets (Cancer Research 2012). Our wet lab researches focus on experimentally characterizing individual genetic and epigenetic aberrations in breast cancer such as recurrent gene fusions, genomic amplifications, and epimutations, as well as qualifying viable cancer targets and predictive biomarkers for the development of precision therapeutics in breast cancer. Our current disease focus is clinically intractable breast cancers, such as luminal B or basal-like tumors. In particular, by applying the FusionZoom analysis to the RNAseq and copy number data from The Cancer Genome Atlas, we have discovered a novel recurrent gene fusion involving the estrogen receptor gene in a subset of breast cancers. This fusion called ESR1-CCDC170 is preferentially present in 6-8% of luminal B tumors -- a more aggressive subtype of estrogen receptor positive breast cancer. To date, this is the first and most frequent gene fusion yet reported in this tumor entity (Nature Commun. 2014). We are now assessing the druggability of this fusion with the goal of developing effective targeted therapy against this genomic target. We expect that our new discoveries will yield novel insights into the recurring genetic abnormalities leading to breast cancer initiation, progression, and therapeutic resistance, and establish viable targets for effective intervention.

Research Interests and Keywords
  • Cancer genomics
  • integrative bioinformatics
  • cancer genetics
  • cancer cell biology
Read More about Xiaosong Wang

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