Ph.D. Program Requirements

See QCB Student Handbook on QCB homepage for program details.  

  • Two core courses (both courses are required)
    1. QCB 515
    2. COS/QCB 551
  • Three additional courses from the lists below, including at least one each from the Quantitative and Biological course lists.
  • Course in Responsible Conduct of Research: QCB 501: Topics in Ethics in Science
  • Participation in our QCB Graduate Colloquium
  • Research rotations (three required)
  • General exam (January of second year)
  • Two semesters of teaching (usually in fourth year of study)
  • Annual thesis committee meetings
  • Dissertation defense

The course of study for each student must be approved by the Director of Graduate Studies in the beginning of their first year, and course substitutions are possible with the permission of the DGS.

QCB 515: Method and Logic in Quantitative Biology (offered in fall term)

Close reading of published papers illustrating the principles, achievements, and difficulties that lie at the interface of theory and experiment in biology. Two important papers, read in advance by all students, will be considered each week; the emphasis will be on discussion with students as opposed to formal lectures. Topics include: cooperativity, robust adaptation, kinetic proofreading, sequence analysis, clustering, phylogenetics, analysis of fluctuations, and maximum likelihood methods. A general tutorial on Matlab and specific tutorials for the four homework assignments will be available. Course details: QCB 515

COS/QCB 551: Introduction to Genomics and Computational Molecular Biology (offered in fall term)

Introduction to basic computational methods used for problems arising in molecular biology, genomics, and proteomics. We also discuss the basic biology of the genome and experimental methods used to probe its function. Topics include computational approaches to: sequence similarity and alignment, phylogenic inference, gene recognition, gene expression analysis, structure prediction, population and comparative genomics. Course details: COS/QCB 551

QCB Graduate Colloquium 

QCB students are required to attend our QCB Graduate Colloquium during the academic year.  First, third, and fourth year students will present their research to their peers over the fall and spring semesters.  Schedules will be made during the summer for the upcoming academic year. 

QCB 501: Topics in Ethics in Science

Discussion and evaluation of the role professional researchers play in dealing with the reporting of research, responsible authorship, human and animal studies, misconduct and fraud in science, intellectual property, and professional conduct in scientific relationships. Participants are expected to read the materials and cases prior to each meeting. Successful completion is based on regular attendance and active participation in discussion. This half-term course is designed to satisfy federal funding agencies' requirements for training in the ethical practice of scientists. Required for graduate students and post-docs.

Quantitative Courses (must take at least one)

APC 524 /MAE 506/AST 506 Software Engineering for Scientific Computing (offered fall 2020-21)

CBE 517 Soft Matter Mechanics Fundamentals & Applications (offered fall 2020-21)

CHM 503/CBE 524/MSE 514 Introduction to Statistical Mechanics (offered fall 2020-21)

CHM 515 Biophysical Chemistry I (offered fall 2020-21)

CHM 516 Biophysical Chemistry II (last offered spring 2019-20)

CHM 542 Principles of Macromolecular Structure: Protein Folding, Structure, and Design

COS 511 Theoretical Machine Learning

COS 524/COS 424 Fundamentals of Machine Learning

COS 597D Advanced Topics in Computer Science: Advanced Computational Genomics

COS 597F Advanced Topics in Computer Sci: Computational Biology of Single Cells (offered fall 2020-21)

ELE 535 Machine Learning and Pattern Recognition (offered fall 2020-21)

MAE 567/CBE 568 Crowd Control: Understanding and Manipulating Collective Behaviors and Swarm Dynamics (offered fall 2020)

MAE 550/MSE 560 - Lessons from Biology for Engineering Tiny Devices (last offered spring 2019-20)

MAT 586/APC 511/MOL 511/QCB 513 Computational Methods in Cryo-Electron Microscopy (last offered spring 2019-20)

MOL 518 Quantitative Methods in Cell and Molecular Biology (last offered spring 2019-20)

MSE 504/CHM 560/PHY 512/CBE 520 Monte Carlo and Molecular Dynamics Simulation in Statistical Physics & Materials Science (last offered spring 2019-20)

NEU 437/537 Computational Neuroscience (last offered spring 2019-20)

NEU 501 Cellular and Circuits Neuroscience (offered fall 2020-21)

NEU 560 Statistical Modeling and Analysis of Neural Data (offered fall 2020-21)

 ORF 524 Statistical Theory and Methods

PHY 561/2 Biophysics (offered spring 2019-20) 

QCB 505/PHY 555 Topics in Biophysics and Quantitative Biology (offered in fall term)

QCB 508 Foundations of Statistical Genomics (offered in spring term)

Biological Courses (must take at least one)

CHM 403 Advanced Organic Chemistry (offered fall 2020-21)

CHM/QCB 541 Chemical Biology II (last offered spring 2019-20)  

EEB 504 Fundamental Concepts in Ecology, Evolution, and Behavior II  (offered fall 2020-21)

EEB 507 Recent Research in Population Biology (offered fall 2020-21)

MAE 566 Biomechanics and Biomaterials: From Cells to Organisms (last offered spring 2019-20)

MOL 504 Cellular Biochemistry (offered fall 2020-21)

MOL 506 Cell Biology and Development (offered fall 2020-21) 

MOL 518 Quantitative Methods in Cell and Molecular Biology (last offered spring 2019-20)

MOL 521 - Systems Microbiology and Immunology (offered fall 2020-21; half-term course)

MOL 523 Molecular Basis of Cancer (last offered spring 2018-19)  

MOL 559 Viruses: Strategy & Tactics (offered fall 2020-21)

QCB 490 Molecular Mechanisms of Longevity (offered in spring term)

Selected undergraduate courses of interest
(note: these do not count towards course requirements)

APC 350 Introduction in Differential Equations  

COS 226 Algorithms and Data Structures

  COS 343 Algorithms for Computational Biology 

EEB 324 Theoretical Ecology

MOL/QCB 485 Mathematical Models in Biology

ORF 309/MAT 380 Probability and Stochastic Systems

QCB 302 Research Topics in QCB


 Please visit Course Offerings for to see the most up-to-date course information.