Training in Systems Biology

Systems Biology Graduate Program

Our program trains students from diverse disciplinary backgrounds in the cutting-edge research techniques that comprise the interdisciplinary research of modern cell and computational biology. Students receive rigorous cross training in areas of mathematical, physical, and computational sciences and biology. Systems Biology students take courses, attend seminars and work on interdisciplinary research projects to broaden and strengthen their abilities to do quantitative cell biology research. The Systems Biology area of concentration is based within the Richard D. Berlin Center for Cell Analysis and Modeling at UConn Health.

FAQ about Systems Biology training:

Graduate Students


    • Portrait of Siyu Sun

      Siyu Sun

      Advisor
      Michael J. Guertin
      Education
      BS — SUNY Stony Brook; MS — New York University
      About
      Siyu Sun is a 2nd year PhD student at UConn Health. Before joining UConn Health,
      Siyu worked on a project focused on topoisomerases I/II’s role in regulating chromosome
      structure and transcription repression dosage compensation. Her current research focuses
      on ER-mediated transcriptional regulation through advanced sequencing techniques and
      bioinformatic analysis.

  • Portrait of Rudradeep Mukherjee

    Rudradeep Mukherjee

    Advisor
    Michael J. Guertin
    Education
    BE — Computer Science, BIT Mesra, Ranchi; MSc — Neuroscience, NBRC, Gurgaon
    About
    Rudradeep Mukherjee worked for some years as a software engineer. During M.Sc. he studied
    resting state networks of individuals with autism by using a maximum entropy model on fMRI data.
    He is currently interested in understanding transcriptional roles of Twist family of factors.
    In his free time, he reads about the history of science, follows Japanese manga and jogs during
    the beautiful summer evenings.
  • Portrait Photo Jinhong Dong

    Jinhong Dong

    Advisor
    Michael J. Guertin
    Education
    BA — Carleton College
    About
    After doing metagenomics research sparked an interest in bioinformatics, Jinhong is now focused on analyzing DNA- and RNA- sequencing data to gain a better understanding of the mechanisms of transcription regulation and initiation.
  • Portrait Photo Edwin Moses Appiah

    Edwin Moses Appiah

    Advisor
    Eran Agmon
    Education
    BSc. — Agricultural Biotechnology; Mphil.— Biodata Analytics and Computational Genomics (KNUST, Ghana)
    About
    Edwin is a first year Biomedical Science PhD student. Before joining the UConn health, Edwin worked on how the gastric microbiome influences gastric carcinogenesis focusing on bacterial diversity, co-occurrence patterns and predictive models. Currently, Edwin works on microbiome at the Agmon lab at CCAM with special focus on building multi-scale computational models for the gut microbiome.
  • Portrait photo Neyamat Khan

    Neyamat Khan Tanvir

    Advisor
    Eran Agmon
    Education
    BSc. and MSc. — Biotechnology and Genetic Engineering at Jahangirnagar University, Dhaka, Bangladesh
    About
    Before joining the graduate program (Ph.D. in Biomedical Science) at UConn Health, Neyamat Khan worked on the whole-genome sequencing and comparative analysis of Citrobacter werkmanii strain NIB003, uncovering unique tRNA-binding domains and N⁶-adenine DNA methylases with implications for virulence and pathogenesis. He now models community dynamic flux-balance analysis (cdFBA) in the Vivarium Python framework to investigate metabolic cross-feeding and diauxic shifts in microbial communities. Outside the lab, he enjoys hiking, follows international soccer(EPL,Laliga), delights in thoughtful discussions on life’s philosophical dimensions.
  • Portrait photo Rashmi Kaldera Dissasekara

    Rashmi Kaldera Dissasekara

    Advisor
    Eran Agmon
    Education
    BSc. — Biochemistry and Molecular Biology, University of Colombo, Sri Lanka
    About
    Before joining the PhD program at UConn Health, I worked on determining the structural dynamics of GPCRs using both experimental and computational approaches. Now I am interested in building muti-scale models that incorporate cellular to population level dynamics which can be used for useful scientific predictions. Outside of the lab, I enjoy taking a walk during warm weather or reading a good book at home with a warm cup of tea.
  • Portrait photo Maya Abdalla

    Maya Abdalla

    Advisor
    Eran Agmon
    Education
    BSc. Biology, Minors in Data Analytics and Public Health — Emmanuel College, Boston
    About
    Maya is a first year Biomedical Science PhD student. Before joining UConn, Maya worked as a research assistant in the Division of Pulmonary and Critical Care at Brigham and Women’s Hospital, where she managed and analyzed CT scans and imaging data for participants in the Framingham Heart Study. She previously participated in the Harvard T.H. Chan School of Public Health Summer Program in Biostatistics and Computational Biology, where she developed a SNP scoring algorithm based on the 1000 Genomes Project under the mentorship of Dr. Rafael Irizarry—an experience that sparked her passion for data science and computational biology. Currently she has joined the Agmon Lab, where she focuses on multiscale modeling and programming using the Vivarium framework. Outside of the lab, Maya enjoys cooking, traveling, and watching basketball.
  • Portrait photo Karen Osei-Boamah

    Karen Osei-Boamah

    Advisor
    Pedro Mendes
    Education
    BS — Biology & Biochemistry, Xavier University of Louisiana
    About
    Before UConn Health, Karen worked on characterizing DNA mismatch repair variants in S. cerevisiae. She is now focused on making models on intracellular iron regulation and metabolism. In her free time, Karen enjoys trying out different cuisines and local eateries across the Northeast.

Postdoctoral Fellows


  • Portrait photo Arnab Mutsuddy

    Arnab Mutsuddy

    Advisor
    Eran Agmon
    Education
    PhD in Chemical Engineering — Clemson University, South Carolina, United States; BS in Chemical Engineering — BUET, Dhaka, Bangladesh
    About
    In my PhD, my work was primarily focused on the application of single cell pharmacodynamic modeling as a tool to predict drug response for cancer cell lines. As a postdoctoral fellow at the Agmon Lab, I am currently working towards the implementation of simulation-based inference methodology for the discovery of unknown gene functions in E. coli.
  • Portrait photo Tasnif Rahman

    Tasnif Rahman

    Advisor
    Eran Agmon
    Education
    PhD in Biomedical Engineering — Rensselaer Polytechnic Institute under Dr. Leo Wan (2024); B.S. in Medical Microbiology and Bacteriology — University of South Florida (2018)
    About
    Tasnif is a postdoc working on developing multi-scale computational models of bacterial communities and their interactions with host tissues. His PhD training at the Rensselaer Polytechnic Institute was in tissue engineering and computational biomechanics, and his thesis work involved creating multicellular mechanical models to study symmetry breaking in tissue and organ morphogenesis. He looks forward to developing his computational skills is excited about revisiting his expertise in bacteriology developed during his undergraduate studies in Microbiology. Outside of the lab, Tasnif enjoys video games, basketball and dance music!
  • Portrait photo Milda Stanislauska

    Milda Stanislauskas

    Advisor
    Abhijit Deb Roy
    Education
    PhD — UConn Health; BA/MA — Hunter College
    About
    Before joining the graduate program at UConn Health, Milda worked at a skin disease research center studying Merkel cells, which are mechanoreceptive cells responsible for sensing light touch. Her research interests include how cells sense physical cues from the external environment and convert them into chemical signals, and how these signals affect various cellular processes, and disease pathogenesis.
UConn Undergraduate Student Trainees
Name Year Advisor Project
Shreedula Balakrishnan 2022 Vera‑Licone Working on tumor reversion in leukemia using computational biology.
Grace Curley‑Holmes 2021 Mayer / Machida Working on SH2 domain mapping
Noah Liguori‑Bills, Google Summer of Code Student 2021 Blinov Development of the ModelBricks website.
Nathan Schaumburger 2021 Blinov Model of aging phenotypes.
Amy Flis 2020 Wu
Chandrika Dhavala 2020 Blinov Visualization of rule‑based model.
Jennifer Kim 2020 Mendes Identification of chaos in nonlinear models using global optimization in COPASI.
Maria Menoutis, HRP Intern 2019 Loew Rules that govern the assembly of molecular machines.
Alexa Monroe 2019 Yan
Gavin Till 2018 Mayer Developing mathematical models to explore how membrane receptor clustering regulates signaling pathways.
Alumni – Postdoctoral Fellows
Name Year Advisor Current Position
Sulagna Das 2014 Yu Tenure‑track faculty position at Emory University
Alumni – Undergraduate Students
Name Year Advisor Program Current Position
Nathan Schaumburger, UConn 2022 Blinov PhD Biomedical Science Program, Summer Rotation PhD Candidate, Biomedical Sciences, Harvard
Daniel Fairchild, UConn 2021 Acker PhD Biomedical Science Program, Summer Rotation PhD Candidate, Biomedical Sciences, UConn Health
Devin Kot‑Thompson, UConn 2021 Acker Health Research Program (HRP) Completing B.S. in Biomedical Engineering
Morgan Neydorff, UConn 2020 Acker Health Research Program (HRP) Graduated, B.S. in Biomedical Engineering
Google Summer of Code Students
Name Year Advisor School
Sahil Jha 2020 Blinov Amity University, India
Saksham Raghuvanshi 2020 Blinov J.S.S. Academy of Technical Education, India
Nikita Mahoviya 2021 Blinov and Cowan National Institute of Technology Hamirpur (H.P.), India
Noah Liguori‑Bills 2021 Blinov UConn, Storrs, CT