Thomas P Zwaka, MD, PhD
img_Thomas P Zwaka
PROFESSOR | Cell, Developmental & Regenerative Biology
Research Topics
Apoptosis/Cell Death, Cell Biology, Developmental Biology, Embryology, Epigenetics, Gene Regulation, Gene Therapy, Stem Cells, Tissue Engineering, Transcription Factors, Transcriptional Activation and Repression
Multi-Disciplinary Training Area
Development Regeneration and Stem Cells [DRS]
Cell competition: Protection of early embryogenesis and pluripotent stem cells against genetic parasites through a primitive immune system
Retrotransposons can seriously damage the genome of the nascent embryo and cause sporadic diseases and infertility. Here we will explore a new sensing mechanism that involves early embryonic cells “sniffing” one another for endogenous retroviruses and the removal of cells that failed to silence their genetic parasites. Our line of investigation will provide new targets for genetic diagnosis and interventions targeting pregnancy loss, birth defects and childlessness.
Quantum biology
In this project we explore non-classical (quantum physical) properties of early embryonic cells and neurons. The idea is that the current view that cells organize activities (like signal transduction or subcellular communication) via random walks among the staggering range of possibilities is incredibly unlikely. We propose instead a quantum mechanics-based relationship between molecular assemblies and elements of cell behavior. We are currently testing the prediction that cells harbor highly specialized structures that act in a quantum-computer like fashion to orchestrate cell function at a higher level.
Molecular control of stem cells
This project seeks to clarify the molecular function Ronin, a member of the THAP (Thanatos-associated domain-containing apoptosis-associated proteins) gene family, and its biochemical role in specific cell types as they change fates. We propose that Ronin (and other THAPs) mediate promoter-promoter interactions to regulate gene transcription in a cell type-specific manner.
Developing new models for Parkinson’s disease
We have discovered methods to enhance the self-organizing properties of differentiating pluripotent cells to promote the proper development of mid-brain structures. Ultimately, we are creating patient-specific ex vivo models of PD using the methods we are developing to generate midbrain organoids from patient iPSCs. This will allow us to get a handle on the factors relevant to each individual’s unique manifestation of the disease. We are also conducting parallel screens in this system for neuroprotective small molecules.

MD PhD, University of Ulm

Postdoctoral, University of Wisconsin, Madison


Selected Publications

SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Mehdi Bouhaddou, Ann Kathrin Reuschl, Benjamin J. Polacco, Lucy G. Thorne, Manisha R. Ummadi, Chengjin Ye, Romel Rosales, Adrian Pelin, Jyoti Batra, Gwendolyn M. Jang, Jiewei Xu, Jack M. Moen, Alicia L. Richards, Yuan Zhou, Bhavya Harjai, Erica Stevenson, Ajda Rojc, Roberta Ragazzini, Matthew V.X. Whelan, Wilhelm Furnon, Giuditta De Lorenzo, Vanessa Cowton, Abdullah M. Syed, Alison Ciling, Noa Deutsch, Daniel Pirak, Giulia Dowgier, Dejan Mesner, Jane L. Turner, Briana L. McGovern, M. Luis Rodriguez, Rocio Leiva-Rebollo, Alistair S. Dunham, Xiaofang Zhong, Manon Eckhardt, Andrea Fossati, Nicholas F. Liotta, Thomas Kehrer, Anastasija Cupic, Magdalena Rutkowska, Ignacio Mena, Sadaf Aslam, Alyssa Hoffert, Helene Foussard, Charles Ochieng’ Olwal, Weiqing Huang, Thomas Zwaka, John Pham, Molly Lyons, Laura Donohue, Aliesha Griffin, Rebecca Nugent, Kevin Holden, Robert Deans, Pablo Aviles, Jose A. Lopez-Martin, Jose M. Jimeno, Kirsten Obernier, Jacqueline M. Fabius, Margaret Soucheray, Ruth Hüttenhain, Irwin Jungreis, Manolis Kellis, Ignacia Echeverria, Kliment Verba, Paola Bonfanti, Pedro Beltrao, Roded Sharan, Jennifer A. Doudna, Luis Martinez-Sobrido, Arvind H. Patel, Massimo Palmarini, Lisa Miorin, Kris White, Danielle L. Swaney, Adolfo Garcia-Sastre, Clare Jolly, Lorena Zuliani-Alvarez, Greg J. Towers, Nevan J. Krogan. Cell

Regulatory architecture of housekeeping genes is driven by promoter assemblies. Mahesh Ramamoorthy, Xing Yin, Ran Brosh, Thomas P. Zwaka. Cell Reports

Bat pluripotent stem cells reveal unusual entanglement between host and viruses. Marion Déjosez, Arturo Marin, Graham M. Hughes, Ariadna E. Morales, Carlos Godoy-Parejo, Jonathan L. Gray, Yiren Qin, Arun A. Singh, Hui Xu, Javier Juste, Carlos Ibáñez, Kris M. White, Romel Rosales, Nancy J. Francoeur, Robert P. Sebra, Dominic Alcock, Thomas L. Volkert, Sébastien J. Puechmaille, Andrzej Pastusiak, Simon D.W. Frost, Michael Hiller, Richard A. Young, Emma C. Teeling, Adolfo García-Sastre, Thomas P. Zwaka. Cell

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Physicians and scientists on the faculty of the Icahn School of Medicine at Mount Sinai often interact with pharmaceutical, device and biotechnology companies to improve patient care, develop new therapies and achieve scientific breakthroughs. In order to promote an ethical and transparent environment for conducting research, providing clinical care and teaching, Mount Sinai requires that salaried faculty inform the School of their relationships with such companies.

Below are financial relationships with industry reported by Dr. Zwaka during 2022 and/or 2023. Please note that this information may differ from information posted on corporate sites due to timing or classification differences.

Company Founder:

  • Paratus Sciences


  • Paratus Sciences

Equity (Stock or stock options valued at greater than 5% ownership of a publicly traded company or equity of any value in a privately held company)

  • Paratus Sciences

Royalty Payments:

  • Paratus Sciences

Mount Sinai's faculty policies relating to faculty collaboration with industry are posted on our website. Patients may wish to ask their physician about the activities they perform for companies.