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Department of Biological Engineering

BE Graduate Studies in Applied Biosciences

The Applied Biosciences Track is intended for students seeking Ph.D. thesis research involving the application of quantitative scientific approaches to the solution of biological and biomedical problems. Following completion of the required core subjects in the Applied Biosciences Track, students may focus or specialize in several areas, including molecular and systems toxicology and pharmacology and molecular and systems bacterial pathogenesis.

Students in the Applied Biosciences Track are eligible for support from the National Institute of Environmental Health Sciences Training Grant in Toxicology and are often involved with research projects in several Centers and Divisions affiliated with BE, including the Center for Environmental Health Sciences, the Division of Comparative Medicine, the Biotechnology Process Engineering Center, the Biomedical Engineering Center, and the BioImaging Center.

Research Specializations

Fellowships & Grants


The Doctor of Philosophy (Ph.D.) and Doctor of Science (Sc.D.) require:

  1. successful completion of course requirements,
  2. satisfactory performance on the comprehensive written and oral qualifying examinations,
  3. participation as a Teaching Assistant for at least one term, and
  4. execution and defense of a thesis based on original research.

A written exam is taken at the end of the first year (following completion of the core curriculum below), and an oral Qualifying Exam is taken during the second year. The oral exam serves as Thesis proposal. Following successful completion of the Exams, the student is expected to present to a Thesis Committee a minimum of two research Progress Reports before defending the Thesis. Completion of the doctoral requirements typically requires 5-6 years from date of entry.

Requirements for the Applied Biosciences Ph.D. Track

Entrance Requirements

Physics (2 semesters); Calculus (2 semesters); Organic Chemistry (2 semesters); Biochemistry (1 semester); Physical Chemistry or Biophysics or Engineering (1 semester); Cellular or Molecular Biology or Genetics (1 semester)

Required Core Subjects

During their first year, students engage in a unified curriculum of three core subjects, in which quantitative basic science is applied to problems in biology and human disease:

  • 20.420 Bimolecular Kinetics & Cellular Dynamics
  • 20.440 Analysis of Biological Networks
  • 20.450 Molecular and Cellular Pathophysiology

Elective Subjects

To enhance depth and breadth, the core subjects are supplemented by electives in science and /or engineering. Four elective subjects are chosen by the student in consultation with the advisor. The goal is to find MIT subjects that best fit a student's thesis research project and career objectives. Elective subject in three categories are acceptable upon approval by advisor and, for the subjects not listed here, the BE Graduate Program Chair:

1.  Biological Engineering — one subject

To provide breadth in biological engineering, at least one graduate-level course beyond the Core Classes must be selected from the following group:

  • 20.201 Mechanisms of Drug Actions
  • 20.410 Molecular/Cell Tissue Biomechanics
  • 20.415 Physical Biology
  • 20.430 Fields, Forces, and Flows in Biological Systems
  • 20.463 Biomaterials Science and Engineering
  • 20.490 Computational & Systems Biology

2.  Engineering/Science — one subject

To provide breadth in engineering or science, at least one graduate-level subject approved by the BE Graduate Committee Chair or Co-Chair must be selected.

3.  Biological Science — two subjects

To provide a firm foundation in modern biol¬ogy, the student will be expected to have biochemistry and cell biology as pre requisites and then select two graduate-level subjects in biological science. If cell biology has not been previously taken, it must be selected as one of these two graduate-level subjects. If biochemistry has not been previously taken, it must be taken as a remedial undergraduate subject before selecting the two graduate-level courses.

Specialization in Molecular and Systems Toxicology and Pharmacology

The Biological Engineering offers a graduate program leading to the degree of Ph.D. in Applied Biosciences with specialization in Molecular and Systems Toxicology and Pharmacology. For decades, scientists at MIT have harnessed chemical, genetic, biological, and epidemiological tools to make fundamental advances in public health and the chemotherapy of human diseases. For example, research done by toxicologists at MIT contributed to the identification of aflatoxin as a potent food carcinogen and to the elucidation of its role as a major risk factor for liver cancer globally. Based on this research, public health programs have been developed to combat contamination of food by aflatoxin. These programs have contributed to significant reduction of the impacts of aflatoxin exposure, and it is expected that minimization of exposure will in turn result in far fewer cases of liver cancer in populations of the developing world. Scientists at MIT have always taken a multidisciplinary approach to solving real world problems in toxicology and pharmacology. Today, this group of researchers has joined forces with engineers to expand even further the repertoire of tools available to do effective research that will improve public health and disease treatment.

Teaching and research in toxicology and pharmacology focus on understanding the interactions of organisms with chemical, biological, and physical agents. One goal here is to study how exogenous and endogenous agents induce toxicity and cause disease in humans. A second goal is to establish the molecular mechanisms of drug actions, with the longer term aim of developing improved therapeutics. The program is interdisciplinary in nature and interacts with other programs and departments that have an interest in human pathophysiology, molecular pharmacology, and environmental health. Many of the research activities are coordinated through the Center for Environmental Health Sciences at MIT, the nucleus of which is comprised of Biological Engineering faculty. Areas of research specialization include studies in environmental carcinogenesis and epidemiology; development of molecular methods for direct measurement of mutations in humans; metabolism of foreign compounds; genetic toxicology; the molecular aspects and dosimetry of interactions between mutagens and carcinogens with nucleic acids and proteins; molecular mechanisms of DNA damage and repair; design and mechanisms of action of chemotherapeutic agents; molecular mechanisms of carcinogenesis; cell physiology; and molecular and pathologic interactions between infectious microbial agents and carcinogens.

The core curriculum in the Applied Biosciences track provides rigorous training in the basic sciences, with particular emphasis on biochemistry, molecular biology, genetics, and pathophysiology. Students wishing to specialize in molecular and systems toxicology and pharmacology must then enroll in three elective subjects:

  • BE.201 Systems Toxicology and Pharmacology
  • BE.202 Animal Models in Toxicology and Pharmacology
  • BE.213 DNA Damage, Repair and Mutagenesis

Students specializing in molecular and systems toxicology and pharmacology are eligible for support by the National Institute of Environmental Health Sciences Toxicology Training Grant.

Specialization in Molecular and Systems Bacterial Pathogenesis

Biological Engineering offers a graduate program leading to the degree of Ph.D. or Sc.D. in Applied Biosciences with specialization in molecular and systems bacterial pathogenesis. There is growing interest in understanding the fundamental mechanisms by which bacterial pathogens and their toxins cause disease. In Biological Engineering, a multidisciplinary approach is being used to apply novel instrumentation and computational tools to elucidating these mechanisms quantitatively. Research in this area is critical for the development of rational strategies for the prevention and treatment of infectious diseases worldwide. Work being done today by scientists and engineers at MIT will impact the quality of life of individuals in the developed world as well as in the developing world in the near future.

Teaching and research in bacterial pathogenesis focus on cross-talk between pathogens and hosts. Traditional methods of investigating the role of individual virulence determinants have given way to systems pathogenesis, which involves signaling networks, genomics, proteomics, and glycomics. Many of these activities are coordinated through the Center for Environmental Health Sciences and the Division of Comparative Medicine at MIT. Areas of research specialization include emerging infectious diseases and biodefense; innate and adaptive immune responses to pathogens; microbial ecology of infectious diseases; as well as chronic infection, inflammation, and cancer risk.


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