Latino Studies at New York University

Doctor of Philosophy Program in Computational Biology

A total of 72 points of credit is required for the Ph.D. program. Of these, a minimum of 39-43 points (depending on home department) is acquired through formal courses, while the remainder is from a mixture of laboratory rotations (or comparable), colloquia, independent study, and research. Salient requirements are

  1. Four semesters of the COB Research Seminar course (see description below).
  2. Required courses specific to the student’s home department (see descriptions below).
  3. Two crossover biological or computational courses depending on the area that is complementary to the student’s home department (see descriptions of representative courses below).
  4. Two elective courses (see descriptions of representative courses below).
  5. Two semesters of laboratory rotations or an equivalent experience.
  6. An ethics course.
  7. Four semesters of participation in the COB Colloquium/Student Seminar, including the presentation of a public seminar.
  8. Research and other credits to complete 72 points of credit to suit each student’s need.
  9. Ph.D. qualifying examination in the second year.
  10. Defense of dissertation.

GENERAL PROGRAM FEATURES

  1. Interdisciplinary training through flexible and background-tailored tracks.
  2. Dual mentors, a research adviser from a student’s home department, and a crossover mentor from a partner department other than the student’s home department. The crossover adviser will provide guidance from “the other side of the divide” (quantitative/computational vs. life sciences).
  3. Competitive stipend and benefits.
  4. Summer internship opportunities in industry, academia, government, and international laboratories.
  5. Learning environments and activities that promote interdisciplinary interactions and broader collaborations within and outside New York University, NYU School of Medicine–Sackler Institute, and Mount Sinai School of Medicine.
  6. Mentoring and career development activities.
  7. Interactive COB seminars, laboratory rotations, or independent study.

AREAS OF DISSERTATION RESEARCH

COB students are exposed to a wide variety of working scientists whose research spans the spectrum of cutting-edge problems at the intersection of biology and computational methods, including

  1. Macromolecular modeling: Macro-molecular algorithms and simulations; structure, dynamics, and function of biomolecules (interactions among biomolecules and with drugs and carcinogens).
  2. Computational genomics and proteomics: Structural, functional, and comparative genomics; regulatory, metabolic, signal transduction, and protein-protein interaction networks analyses.
  3. Bioinformatics data mining and systems biology: Methodologies including supervised, semisupervised, and unsupervised approaches for analyzing data generated from genomic, epigenomic, transcriptomic, proteomic, metabolo-mic, sequencing, and imaging technologies. Development and applications of advanced database systems for biological and medical datasets. Biological sequence analysis including whole-genome alignment, ortholog-detection, and phylogeny and motif detection. Integration of large-scale, heterogeneous genomics and proteomics data with ontologies and input from other biological repositories for inferring systems biology modules.
  4. Translational bioinformatics: This field is emerging as an essential subfield of clinical and translational science and can be expected to play a major role in day-to-day clinical practice, making it a common tool in predictive and personalized biomedicine. NYU and its collaborative clinical institutions ser-vice a very large and heterogeneous population. At the same time, the University has been involved in basic science research in computational and systems biology and biotechnology. This unique combination allows Ph.D. students to be involved in systematic and integrative large-scale studies that require bioinformatics specialization.
  5. Physiological and biophysical modeling: Cellular function, signal transduction pathways, neuronal networks, and cardiovascular and other systems.
  6. Methods in cellular and biomedical imaging: Computerized tomography (CT scanning), nuclear magnetic resonance spectroscopy and magnetic resonance imaging, ultrasound imaging, inverse problems, and image reconstruction in microscopy.

UNIQUE INTERDISCIPLINARY FEATURES OF THE CURRICULUM

COB Research Seminar: The four-semester COB Research Seminar course is a distinctive educational experience. Because of the fluid and multifaceted nature of contemporary computational biology, this course is flexible in structure and adaptive in its content. Each of the four semesters contains two to four modules, each focusing on one of the key research themes of the program (see above). To build an in-depth understanding of the topic, the modules begin with reading/discussion of an introductory-level article on a cutting-edge topic featuring an integrated look at the basic biological/chemical/ neural and computational concepts underlying the topic, followed by more advanced research reading and discussion. These fundamental concepts and computational methodologies may recur across research themes. Consideration of such commonalities is used to develop a rich understanding of the breadth of computational biology.

Crossover Courses: Students are required to take two courses from partner departments other than their own home department. These crossover courses are intended to broaden the interdisciplinary training of COB students.

Laboratory Rotations and Faculty-Guided Independent Study: Rotations provide a firsthand experience with cutting-edge research in computational biology and a way for students to identify faculty with whom they may wish to work on their dissertation. Partner departments that do not offer laboratory rotations attain the same goal with independent study credits focused on cutting-edge topics relevant to computational biology. These rotations/guided studies provide a direct experience of ongoing research in computational biology.

COB Colloquium/Student Seminar: The COB Colloquium series comprises approximately seven 90-minute presentations per semester by COB faculty, COB students, and invited external speakers. Each speaker provides an article title (either upon which the presentation is based or a background article) that COB students are required to read prior to the colloquium. In addition, the speaker is paired with a host. The one-hour presentation is followed by a half-hour discussion among the students and the speaker, coordinated by the speaker’s host. The colloquium provides COB students with a survey of research across the COB program and in the broader community.