Postdoctoral Fellows, Software Engineers, or PhD students in data integration, online simulation, and/or visualization

About the Karr Lab

Despite the explosion of data, we do not understand the details of how phenotype arises from genotype and the environment. We are developing whole-cell computational models which aim to 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, 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, numerical simulation, software engineering, and data visualization, and team-oriented.

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

The Karr Lab is a member of the Icahn Institute for Genomics & Multiscale Biology at the Icahn School of Medicine at Mount Sinai . The Icahn Institute aims to bring genomic technologies together with computational analyses to discover new disease mechanisms, develop new diagnostics, and identify new drug targets. The institute is a collaborative and interdisciplinary environment.

The Icahn School of Medicine at Mount Sinai is a superb environment for translational research and training. The school's multidisciplinary research institutes foster seamless collaboration with clinicians.

Responsibilities

To help enable whole-cell models, the scientists/engineers will develop new tools for systematically, scalably, and collaboratively building, simulating, and analyzing models of individual cells. In addition to accelerating cell modeling, these tools will help journal reviewers and readers explore reported models. Examples of tools that the scientists/engineers would develop include

  • An integrated database of biochemical and genomic data for cell modeling;
  • Tools for discoverying relevant data for modeling specific organisms and environmental conditions;
  • A framework for scalably designing models from large datasets;
  • A simulation web service that can simulate any cell model including steady-state, logical, deterministic, stochastic, and spatial models;
  • A database for simulation results;
  • Tools for mining large-scale simulation results; and
  • Web-based tools for interactively analyzing models of simulation results.

The scientists/engineers will be part of the new NIH-funded Center for Reproducible Biomedical Modeling which aims to develop a platform for systematically building and simulating models of cells. The center is a collaboration with Herbert Sauro and John Gennari at the University of Washington, Ion Moraru and Michael Blinov at the University of Connecticut Health Center, and David Nickerson at the University of Auckland. The scientists/engineers would have opportunities to work with our collaborators, as well as work with our team to build and analyze models.

Desired skills/experience

Whole-cell modeling is highly interdisciplinary. Consequently, we're looking for team members with a broad range of relevant skills and experience.

  • Passion for transforming bioengineering and medicine through modeling;
  • Desire to tackle challenging problems;
  • Commitment to innovation;
  • Abilities to think creatively, integrate diverse concepts, and push past barriers;
  • Knowledge of molecular cell biology;
  • Experience in software engineering;
  • Excellent oral and written communication skills;
  • Abilities to work independently and within a team; and
  • BS, MS, or PhD in computer science, applied math, or a related field.

Career development, recreation, benefits, and compensation

Mount Sinai offers numerous opportunities for career development, as well as competitive benefits. Compensation will be commensurate with experience. Please see the links below for more information.

  • Staff
    • Benefits
    • Recreation programs
  • Postdoctoral scholars
    • Career development programs
    • Benefits
    • Subsidized housing
    • Recreation programs
  • Graduate students
    • PhD programs
    • Student organizations
    • Recreation programs
    • Subsidized housing

How to apply

Postdoctoral fellows and staff: Email a cover letter and CV to Jonathan .

Graduate students: Email a cover letter and CV to Jonathan , and apply to one of Mount Sinai's graduate programs . PhD applications are due December 1 each year to start the following September.

Undergraduate students: Email a cover letter and CV to Jonathan and, if eligible, apply to the Mount Sinai Summer Undergraduate Research Program .

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

More information

Please contact Jonathan .