Photo of Eran Agmon, Ph.D.

Eran Agmon, Ph.D.

Assistant Professor
Center for Cell Analysis and Modeling
Department of Molecular Biology and Biophysics
Biomedical Engineering Department
Academic Office Location:
Center for Cell Analysis and Modeling
UConn Health
263 Farmington Avenue
Farmington, CT 06030-6406
Phone: 860-679-1452
Website(s):

Eran Agmon Lab

The Agmon Lab is focused on developing comprehensive, multi-scale models of cells – from their molecular underpinnings, to their integrated functions, to the organismic level with many heterogeneous cells interacting in a shared environment. Recent decades of biological research have generated abundant data on the composition, spatial organization, and dynamics of thousands of cell types; however, we need new tools that can transform this data into predictive models that can be used for scientific discovery. Rather than building isolated models that capture a narrow range of cellular behavior with a single class of representation, the next generation of computational models will combine multi-source and multi-level data with diverse, meaningful representations of biological mechanisms into integrative simulations. These simulations will be used to interpret the input datasets, make experimental predictions, identify medical solutions, and help us understand fundamental principles of biological organization.

Education
DegreeInstitutionMajor
Ph.D.Indiana UniversityInformatics and Computing, and Cognitive Science

Post-Graduate Training
TrainingInstitutionSpecialty
PostdoctoralColumbia UniversityDepartment of Biological Sciences
PostdoctoralStanford UniversityDepartment of Bioengineering

Awards
Name of Award/HonorAwarding Organization
Faculty FellowCenter for Chemical Currencies of a Microbial Planet

The Agmon lab takes a 2-pronged approach to modeling whole cells: 1) develop computational methods and software for combining multi-omics datasets and diverse models into multi-scale simulations, and 2) apply these tools to build integrative simulations of whole microbiomes, which span molecular to multi-cellular scales.


Research keywords: computational systems biology, multi-scale modeling and simulation, cell biology, machine learning, complex adaptive systems


 

Accepting Lab Rotation Students: Fall 2022, Winter 2022, Spring 2023, Summer 2023

Journal Articles

  • T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
    Hickey, John W; Haist, Maximillian; Horowitz, Nina; Caraccio, Chiara; Tan, Yuqi; Rech, Andrew J; Baertsch, Marc-Andrea; Rovira-Clavé, Xavier; Zhu, Bokai; Vazquez, Gustavo; Barlow, Graham; Agmon, Eran; Goltsev, Yury; Sunwoo, John B; Covert, Markus; Nolan, Garry P Cell reports 2023 Dec;42(12):113494
  • Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses.
    Skalnik, Christopher J; Cheah, Sean Y; Yang, Mica Y; Wolff, Mattheus B; Spangler, Ryan K; Talman, Lee; Morrison, Jerry H; Peirce, Shayn M; Agmon, Eran; Covert, Markus W PLoS computational biology 2023 Jun;19(6):e1011232
  • BioSimulators: a central registry of simulation engines and services for recommending specific tools.
    Shaikh, Bilal; Smith, Lucian P; Vasilescu, Dan; Marupilla, Gnaneswara; Wilson, Michael; Agmon, Eran; Agnew, Henry; Andrews, Steven S; Anwar, Azraf; Beber, Moritz E; Bergmann, Frank T; Brooks, David; Brusch, Lutz; Calzone, Laurence; Choi, Kiri; Cooper, Joshua; Detloff, John; Drawert, Brian; Dumontier, Michel; Ermentrout, G Bard; Faeder, James R; Freiburger, Andrew P; Fröhlich, Fabian; Funahashi, Akira; Garny, Alan; Gennari, John H; Gleeson, Padraig; Goelzer, Anne; Haiman, Zachary; Hasenauer, Jan; Hellerstein, Joseph L; Hermjakob, Henning; Hoops, Stefan; Ison, Jon C; Jahn, Diego; Jakubowski, Henry V; Jordan, Ryann; Kalaš, Matúš; König, Matthias; Liebermeister, Wolfram; Sheriff, Rahuman S Malik; Mandal, Synchon; McDougal, Robert; Medley, J Kyle; Mendes, Pedro; Müller, Robert; Myers, Chris J; Naldi, Aurelien; Nguyen, Tung V N; Nickerson, David P; Olivier, Brett G; Patoliya, Drashti; Paulevé, Loïc; Petzold, Linda R; Priya, Ankita; Rampadarath, Anand K; Rohwer, Johann M; Saglam, Ali S; Singh, Dilawar; Sinha, Ankur; Snoep, Jacky; Sorby, Hugh; Spangler, Ryan; Starruß, Jörn; Thomas, Payton J; van Niekerk, David; Weindl, Daniel; Zhang, Fengkai; Zhukova, Anna; Goldberg, Arthur P; Schaff, James C; Blinov, Michael L; Sauro, Herbert M; Moraru, Ion I; Karr, Jonathan R Nucleic acids research 2022 May;
  • Vivarium: an interface and engine for integrative multiscale modeling in computational biology.
    Agmon, Eran; Spangler, Ryan K; Skalnik, Christopher J; Poole, William; Peirce, Shayn M; Morrison, Jerry H; Covert, Markus W Bioinformatics (Oxford, England) 2022 Feb;
  • A forecast for large-scale, predictive biology: Lessons from meteorology.
    Covert, Markus W; Gillies, Taryn E; Kudo, Takamasa; Agmon, Eran Cell systems 2021 Jun;12(6):488-496
  • A Multi-Scale Approach to Modeling E. coli Chemotaxis.
    Agmon, Eran; Spangler, Ryan K Entropy (Basel, Switzerland) 2020 Sep;22(10):
  • Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation.
    Macklin, Derek N; Ahn-Horst, Travis A; Choi, Heejo; Ruggero, Nicholas A; Carrera, Javier; Mason, John C; Sun, Gwanggyu; Agmon, Eran; DeFelice, Mialy M; Maayan, Inbal; Lane, Keara; Spangler, Ryan K; Gillies, Taryn E; Paull, Morgan L; Akhter, Sajia; Bray, Samuel R; Weaver, Daniel S; Keseler, Ingrid M; Karp, Peter D; Morrison, Jerry H; Covert, Markus W Science (New York, N.Y.) 2020 Jul;369(6502):

Reviews

Title or AbstractTypeSponsor/EventDate/YearLocation
Integrative, multiscale modeling of cellular systemsTalkDARPA ARC - Discovering Unknown Function2023Boston, MA
Process Bigraph Schema: A Framework for Integrative, Multiscale ModelingTalkInternational Conference on Systems Biology2023Hartford, CT