Ph.D. Program Requirements

See QCB Student Handbook on QCB homepage for program details.  

  • Three core courses 
    1. QCB 515 Method and Logic in Quantitative Biology
    2. QCB 535 Biological networks across scales : Open problems and research methods of systems biology
    3. COS/QCB 551 Introduction to Genomics and Computational Molecular Biology
  • Two elective courses from the lists below, including at least one from the Quantitative course list
  • 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 

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

QCB 535: Biological networks across scales: Open problems and research methods of systems biology 

This Special Topics Quantitative and Computational Biology Course comprises five units, each presenting a different level of biological organization. Unit 1 focuses on the regulation of single genes and gene networks. Unit 2 discusses enzyme networks in metabolism and protein-protein interaction networks that control intracellular processes. Unit 3 focuses on cell-cell communication within adult and developing tissues. Unit 4 is on control systems that coordinate tissues in growing and aging organisms. Unit 5 is on networks of organisms, connecting with ideas from genetics, biochemistry, and physiology. Course details: QCB 535

COS/QCB 551: Introduction to Genomics and Computational Molecular Biology 

This interdisciplinary course provides a broad overview of computational and experimental approaches to decipher genomes and characterize molecular systems. We focus on methods for analyzing "omics" data, such as genome and protein sequences, gene expression, proteomics and molecular interaction networks. We cover algorithms used in computational biology, key statistical concepts (e.g., basic probability distributions, significance testing, multiple hypothesis correction, data evaluation), and machine learning methods which have been applied to biological problems (e.g., hidden Markov models, clustering, classification techniques). Course details: COS/QCB 551

QCB Graduate Colloquium 

QCB students are required to attend our QCB Graduate Colloquium during the spring term and all students will give a short research presentation for their peers. The series will end with first-years giving short talks on the research conducted during one of their rotations. Schedules will be made during the fall term for the upcoming spring. 

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 

• CBE 517 Soft Matter Mechanics Fundamentals & Applications 

• CHM 503/CBE 524/MSE 514 Introduction to Statistical Mechanics 

• CHM 515 Biophysical Chemistry I 

• CHM 516 Biophysical Chemistry II 

• 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 

• ELE 535 Machine Learning and Pattern Recognition 

• MAE 567/CBE 568 Crowd Control: Understanding and Manipulating Collective Behaviors and Swarm Dynamics 

• MAE 550/MSE 560 - Lessons from Biology for Engineering Tiny Devices 

• MAT 586/APC 511/MOL 511/QCB 513 Computational Methods in Cryo-Electron Microscopy 

• MOL 518 Quantitative Methods in Cell and Molecular Biology 

• MSE 504/CHM 560/PHY 512/CBE 520 Monte Carlo and Molecular Dynamics Simulation in Statistical Physics & Materials Science 

• NEU 437/537 Computational Neuroscience 

• NEU 501 Cellular and Circuits Neuroscience 

• NEU 560 Statistical Modeling and Analysis of Neural Data 

• ORF 524 Statistical Theory and Methods

• PHY 561/2 Biophysics

• QCB 505/PHY 555 Topics in Biophysics and Quantitative Biology 

• QCB 508 Foundations of Statistical Genomics 

Biological Courses (must take at least one)

• CHM 403 Advanced Organic Chemistry 

• CHM/QCB 541 Chemical Biology II 

• EEB 504 Fundamental Concepts in Ecology, Evolution, and Behavior II  

• EEB 507 Recent Research in Population Biology (note: need permission from EEB department to enroll)

• MAE 566 Biomechanics and Biomaterials: From Cells to Organisms 

- MAE 567/CBE 568 Crowd Control: Understanding and Manipulating Collective Behaviors and Swarm Dynamics

• MOL 504 Cellular Biochemistry 

• MOL 506 Cell Biology and Development 

• MOL 518 Quantitative Methods in Cell and Molecular Biology 

• MOL 521 - Systems Microbiology and Immunology (half-term course)

• MOL 523 Molecular Basis of Cancer 

• MOL 559 Viruses: Strategy & Tactics 

• QCB 490 Molecular Mechanisms of Longevity

-  QCB 535 Biological networks across scales: Open problems and research methods of systems biology

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.