Postdoctoral Fellow, Software Engineer, or PhD student in online simulation and visualization

About the Karr Lab

Despite the explosion of experimental data, we do not understand the details of how phenotype arises from genotype and the environment. We are developing whole-cell computational models which comprehensively predict how cell behavior emerges from the molecular level by representing all of the biochemical activity inside cells. Our goal is to use whole-cell models to transform bioengineering and medicine into rigorous, quantitative disciplines. For example, we believe that whole-cell models could enable bioengineers to design microbial genomes for a variety of industrial applications, as well as enable physicians to tailor medical therapy to individual patients. Our research is highly interdisciplinary, involving systems biology, genomics, bioinformatics, data integration, parallel simulation, optimization, software engineering, and data visualization, and highly team-oriented.

About the Institute for Genomics & Multiscale Biology and the Icahn School of Medicine at Mount Sinai

The Icahn Institute for Genomics & Multiscale Biology is a leader in basic and translational genomic and computational biology research. The institute's multidisciplinary researchers bring state-of-the-art genomic technologies together with advanced computational analyses to discover new disease mechanisms, develop new diagnostics, and identify new drug targets. The institute is a highly collaborative and interdisciplinary environment. Please see the institute's website for more information.

The Icahn School of Medicine at Mount Sinai is a world leader in translational medicine. The school's multidisciplinary research institutes foster collaboration along a seamless continuum from the laboratory to patient care. State-of-the-art laboratories support groundbreaking research, and abundant clinical venues offer superb patient care and training.


To help enable whole-cell models, the candidate will help develop new tools for simulating models and visualizing simulation results online. This will include developing a universal systems biology simulator that is capable of executing a wide range of simulations including steady-state, logical, deterministic kinetic, stochastic kinetic, and spatial simulations; a repository for simulation results; a system for large-scale analysis of simulation results; and tools for visually analyzing simulation results in the context of biologically intuitive diagrams. Importantly, all of these tools will be web-based to enable researchers to collaboratively build and simulate models, as well as to enable journal reviewers and readers to simulate reported models. The candidate will work with our team at Mount Sinai, as well as with our collaborators at the University of Washington (Herbert Sauro and John Gennari ), the University of Connecticut Health Center (Ion Moraru , Jim Schaff , and Michael Blinov ), and the University of Auckland (David Nickerson ) and our partner journals. The candidate would also have many opportunities to work with our team to build and analyze models.

Desired skills/experience

Whole-cell modeling is a highly interdisciplinary problem. Consequently, we're looking for team members with a broad range of skills and experience. The ideal candidate has the following skills. Applicants with related experience are also encouraged to apply.

  • BS, MS, or PhD in computer science, applied math, or a related field;
  • Strong experience in modeling, software engineering, and/or visualization;
  • Deep commitment to innovation and desire to tackle the most challenging problems;
  • Abilities to solve challenging problems by thinking creatively, integrating diverse concepts, and pushing through barriers;
  • Passion for transforming bioengineering and medicine;
  • Excellent oral and written communication skills; and
  • Abilities to work independently and within a team.

Career development, recreation, benefits, and compensation

The Karr Lab and Mount Sinai offer numerous opportunities for career development, as well as competitive benefits. Compensation will be commensurate with experience and education. Please see the links below for more information.

  • Staff
    • Benefits
    • Recreation
  • Postdoctoral scholars
    • Career development
    • Benefits
    • Subsidized housing
    • Recreation
    • Office of Postdoctoral Affairs
  • Graduate students
    • PhD and MS programs
    • Student organizations
    • Recreation
    • Subsidized housing

How to apply

Postdoctoral fellows and staff: Please email Jonathan a cover letter and CV.

Graduate students: Please email Jonathan a cover letter and CV, as well as apply to one of Mount Sinai's MS, MD, or PhD programs . PhD applications are due December 1 each year to start the following September.

Undergraduate students: Exceptional undergraduate students should email Jonathan a cover letter and CV and, if eligible, apply to the Mount Sinai Summer Undergraduate Research Program , the Systems Biology Center New York Summer Undergraduate Research Program , or the Mount Sinai Student Research Program .

High school students: Exceptional high school students should email Jonathan a cover letter and CV and, if eligible, apply to the Mount Sinai Student Research Program .

Mount Sinai Medical Center is an equal opportunity/affirmative action employer.

More information

Please contact Jonathan Karr .