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Eytan Ruppin, M.D., Ph.D.

  • Center for Cancer Research
  • National Cancer Institute
Senior Investigator
Head, Computational Precision Oncology Section

RESEARCH SUMMARY

My research is focused on multi-disciplinary algorithmic computationally driven analysis of large-scale biomedical omics and clinical data, with an emphasis on AI and machine / deep learning approaches. Overall, it centered on three main aims: (1) development of next generation precision oncology approaches, (2) the computational study of immunotherapy response and (3) collaborative multiomics studies of cancer development and treatment. The first two aims are primarily initiated and driven by my lab, and the third one is co-driven in a collaborative nature. 

Areas of Expertise

Big Data Analysis
Machine Learning
Genome-Scale Metabolic Modeling
Genetic Interactions In Cancer

Publications

Selected Recent Publications

PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors

Sanju Sinha, Rahulsimham Vegesna, Sumit Mukherjee, Ashwin V. Kammula, Saugato Rahman Dhruba, Wei Wu, D. Lucas Kerr, Nishanth Ulhas Nair, Matthew G. Jones, Nir Yosef, Oleg V. Stroganov, Ivan Grishagin, Kenneth D. Aldape, Collin M. Blakely, Peng Jiang, Craig J. Thomas, Cyril H. Benes, Trever G. Bivona, Alejandro A. Schäffer & Eytan Ruppin
Nature Cancer. 2024.
Full-Text Article
[ Journal Article ]

Prediction of DNA methylation-based tumor types from histopathology in central nervous system tumors with deep learning

Danh-Tai Hoang, Eldad D. Shulman, Rust Turakulov, Zied Abdullaev, Omkar Singh, Emma M. Campagnolo, H. Lalchungnunga, Eric A. Stone, MacLean P. Nasrallah, Eytan Ruppin* & Kenneth Aldape* (*corresponding last author)
Nature Medicine. 2024.
Full-Text Article
[ Journal Article ]

LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features

Tian-Gen Chang, Yingying Cao, Hannah J. Sfreddo, Saugato Rahman Dhruba, Se-Hoon Lee, Cristina Valero, Seong-Keun Yoo, Diego Chowell, Luc G. T. Morris* & Eytan Ruppin* (*corresponding last author)
Nature Cancer. 2024.
Full-Text Article
[ Journal Article ]

A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics

Danh-Tai Hoang*, Gal Dinstag, Eldad D. Shulman, Leandro C. Hermida, Doreen S. Ben-Zvi, Efrat Elis, Katherine Caley, Stephen-John Sammut, Sanju Sinha, Neelam Sinha, Christopher H. Dampier, Chani Stossel, Tejas Patil, Arun Rajan, Wiem Lassoued, Julius Strauss, Shania Bailey, Clint Allen, Jason Redman, Tuvik Beker, Peng Jiang, Talia Golan, Scott Wilkinson, Adam G. Sowalsky, Sharon R. Pine, Carlos Caldas, James L. Gulley, Kenneth Aldape, Ranit Aharonov, Eric A. Stone* & Eytan Ruppin* (*corresponding last author)
Nature Cancer. 2024.
Full-Text Article
[ Journal Article ]

Synthetic lethality-mediated precision oncology via the tumor transcriptome

Joo Sang Lee, Nishanth Ulhas Nair, Gal Dinstag, Lesley Chapman, Youngmin Chung, Kun Wang, Sanju Sinha, Hongui Cha, Dasol Kim, Alexander V Schperberg, Ajay Srinivasan, Vladimir Lazar, Eitan Rubin, Sohyun Hwang, Raanan Berger, Tuvik Beker, Ze'ev Ronai, Sridhar Hannenhalli, Mark R Gilbert, Razelle Kurzrock, Se-Hoon Lee, Kenneth Aldape, Eytan Ruppin
Cell. 2021. [ Journal Article ]

Job Vacancies

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Team

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Postdoctoral Visiting Fellow
Tiangen Chang, Ph.D
Predoctoral Fellow (CRTA)
Sanna Madan, BSc.
STAFF SCIENTIST
Tai Hoang, Ph.D.
Postdoctoral Fellow (Visiting)
Binbin Wang, Ph.D.
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Postdoctoral Fellow
Saugato Rahman Dhruba, Ph.D.
Special Volunteer
Matt Nagy, BSc.
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POSTDOCTORAL FELLOW (VISITING)
Yingying Cao, Ph.D
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POSTDOCTORAL FELLOW (CRTA)
Yael Schmidt, Ph.D
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PREDOCTORAL FELLOW(CRTA)
Neel SanJay Sanghvi, M.S.
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POSTDOCTORAL FELLOW
Eldad Shulman, PH.D.
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POSTDOCTORAL FELLOW
Sumit Mukherjee, PH.D.
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POST-BACCALAUREATE, CRTA
Emma Campagnolo, B.S.
PREDOCOTORAL FELLOW (VISITING)
Shai Dulberg, B.S.
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POST DOCTORAL FELLOW (VISITING)
Sumeet Patiyal, Ph.D.,
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POST DOCTORAL FELLOW (VISITING)
Ranjan Barman, PHD
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Ph.D., POSTDOCTORAL FELLOW (VISITING)
Thomas Cantore, Ph.D.
POSTDOCTORAL FELLOW (VISITING)
Sumona Biswas, Ph.D.
PREDOCTORAL FELLOW (CRTA)
Amos Stemmer, M.D.