Open Positions

Postdoctoral Position in Disease Modeling

Applications are invited for a two-year postdoctoral position in disease modeling, with Helen Moore, PhD in the Laboratory of Systems Medicine, University of Florida. Start date will be September 6, 2022 or later.

This is an opportunity to learn biology and advanced modeling methods, and to prepare for a faculty position in academia or for a modeling and simulation scientist position in the biopharma industry. Work on a project that can directly impact patients’ lives. Write manuscripts and contribute to grant proposals. Train with an award-winning teacher and mentor, who has spent 12 years in academia and 15 years in industry. Join a diverse group in a supportive department. Live in Gainesville, FL, a vibrant university town with a low cost of living and year-round access to nature and outdoor activities.

In this project, we will create and analyze a mathematical model for alpha-1 antitrypsin deficiency (AATD). AATD is a rare disease that is caused by an inherited genetic mutation. We will be closely collaborating with Mark Brantly, MD, who is a world expert in AATD and who initiated this project. Disease knowledge, data, and additional mentoring will be provided by Dr. Brantly and members of his lab. Project plans include literature searches, model development, calibration to data, model validation, sensitivity analysis, and optimal control. Promising model predictions will be tested by our experimental collaborators.

Preferred qualifications:

  • PhD in engineering, applied mathematics, mathematics, or similar fields by start date
  • experience with:
    • ODE modeling of an in-host disease
    • fitting model parameters to data
    • programming in MATLAB
    • writing manuscripts
  • ability to collaborate and communicate with scientists in other fields
  • interest in applications to biology and diseases
  • interest in learning model validation, sensitivity analysis, optimal control

Applications should include:

  • cover letter/email
  • curriculum vitae, including contact information for 3 references
  • any relevant peer-reviewed publications and posters

Review of completed applications will begin immediately and will continue until the position is filled. For more information or to apply for this position, send an email to helen.moore@medicine.ufl.edu.

Women and members of underrepresented minority groups are especially encouraged to apply.

Postdoctoral Position in Computational Biological Modeling

Dr. T.J. Sego  is recruiting for one postdoctoral position in computational biological modeling. Dr. Sego’s research focuses on development of computational biological models, simulation methods and software, and their application to problems in epithelial tissue dynamics, respiratory disease and immune response. The postdoctoral position will develop quantitative biological models and apply them in simulations of dynamic microenvironments and heterogeneous tissues. The postdoctoral position is available immediately for a duration of one year and subject to annual renewal based on performance and availability of funds.

Position

The candidate will develop conceptual and quantitative models using existing biological knowledge, and implement those models in single-cell and multicellular contexts as executable software. Methodologies will include, but are not limited to, systems of ordinary differential equations, stochastic Boolean networks, multiscale and agent-based modeling.

The candidate will conceptualize, plan and execute projects aligned with overarching lab goals and lead development of resulting submissions to academic journals for scholarly publication. The candidate will also assist with development of journal submissions supporting collaborations as relevant to the candidate’s experience, expertise and interests.

Dr. Sego plans to submit applications for funding to support long-term research projects related to the position, and so the candidate will assist with, and eventually lead, developing, writing and submitting research proposals to agencies like National Institutes of Health and National Science Foundation. The candidate will work closely with, and receive training from, Dr. Sego as relevant to the candidate’s experience, professional development and career goals.

Requirements

The candidate will hold a Ph.D. in biology, mathematics, engineering or related field. The candidate will have experience in developing and applying ordinary differential equation and/or Boolean network models of biological systems as demonstrated by peer-reviewed publications. Experience implementing dynamical models in Python, C++ or a comparable programming is preferred but not required. The candidate will also have a working understanding of agent-based modeling principles and biophysical processes relevant to tissue microenvironments and intercellular interactions, such as diffusion. The candidate must have strong communication skills in the form of effective, engaging public speaking and clear, concise writing.

Environment

The University of Florida  is situated in beautiful Gainesville, FL, a thriving town with a low cost of living, outstanding community, access to numerous parks and recreational facilities, and year-round outdoor weather. As a member of the Laboratory for Systems Medicine , the candidate will work in a highly collaborative research environment that closely integrates quantitative, clinical and experimental research.

Applying

Applications should include a cover letter, updated curriculum vitae and contact information for three references. Relevant peer-reviewed publications by the applicant are welcome but not necessary. Review of completed applications will continue until the position is filled. The Laboratory from Systems Medicine is committed to increasing diversity, and especially welcomes applications from researchers who are members of underrepresented groups. For more information or to apply, please contact Dr. T.J. Sego, timothy.sego@ufl.edu.

Graduate Research Assistant in Localized Outcome Prediction

A Research Assistant is sought to work with Dr. Cory Brunson to develop a localized predictive modeling framework and its application to clinical risk assessment.

The RA will be responsible for the implementation of a new interpretable machine learning approach to modeling clinical risk. The approach combines aspects of case-based reasoning, nearest neighbors prediction, and penalized regression. The implementation will be done in Julia in order to leverage the category-theoretic functionality of the AlgebraicJulia package collection. Our primary research application is to predict clinical outcomes of COVID-19 infection and to identify key risk factors specific to well-defined subpopulations.

All applicants will be considered, and applications from historically underrepresented groups are especially encouraged. Relevant training or experience (e.g. public health, artificial intelligence, Julia) is helpful but not required.

The project is funded by a Precision Health pilot grant by the Clinical and Translational Science Institute and is a collaboration with computational mathematician James Fairbanks, hospitalist Osama Dasa, and mathematician Reinhard Laubenbacher. The position is classified as Other Personnel Services (OPS) at 1.0 Full-Time Equivalent (FTE) for 12 months. Funding is available as soon as the position can be filled. Interested graduate students are requested to email a CV with a statement of interest.

Faculty Positions in Computational Systems Medicine

The Department of Medicine at the University of Florida is expanding its research program in computational systems medicine with one position each at the tenured full, tenured associate, and tenure-track assistant professor level. These positions are research-focused, with modest teaching responsibilities. An internationally-recognized research program and demonstrated grant funding commensurate with seniority is expected.

All areas of research are being considered, with particular interest in the role of the immune system in a wide range of health conditions, such as respiratory diseases or cancer. Examples of current faculty research interests include multi-scale modeling of the immune response to respiratory infections, model-based control of microbial communities, ODE models of signaling pathways for tumor response to immunotherapy, and optimization of combination drug regimens.

We offer a highly collaborative research environment that closely integrates quantitative researchers with clinicians and experimentalists. The University of Florida is heavily engaged in a related initiative to build a strong research capability in artificial intelligence, including a partnership with Nvidia and the hire of 100 new faculty in this field. See this UF News item for more information.

The Laboratory for Systems Medicine is committed to increasing diversity, and especially welcomes applications from researchers who are members of underrepresented groups.

For more information, please contact Dr. Reinhard Laubenbacher, reinhard.laubenbacher@medicine.ufl.edu.

Additional Openings

The newly established Laboratory for Systems Medicine at University of Florida Health is focused on computational and mathematical approaches to human health. We have several immediate openings for faculty positions at all ranks, in both the research and tenure tracks.

We are looking for scientists who work well in an interdisciplinary environment, have an outstanding record and who have a strong track record or promise of extramural funding. While expertise in respiratory diseases and immunology are of particular interest, all aspects of human health, the basic science underpinning it, systems biology approaches, and a focus on computational and data science methodology will be seriously considered.

We are committed to creating an environment that supports diversity, collaboration, and interdisciplinarity. For inquiries, please contact Dr. Reinhard Laubenbacher, reinhard.laubenbacher@medicine.ufl.edu. We also have several research scientist and postdoctoral positions available for projects in computational systems biology, optimization, software development, bioinformatics, and biophysical modeling.