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Program in Quantitative and Computational Biology

Director

Coleen T. Murphy

Executive Committee

Peter Andolfatto, Ecology and Evolutionary Biology, Lewis-Sigler Institute for Integrative Genomics

Coleen T. Murphy, Molecular Biology, Lewis-Sigler Institute for Integrative Genomics

Joshua D. Rabinowitz, Chemistry, Lewis-Sigler Institute for Integrative Genomics

Joshua W. Shaevitz, Physics, Lewis-Sigler Institute for Integrative Genomics

Olga G. Troyanskaya, Computer Science, Lewis-Sigler Institute for Integrative Genomics

Eric F. Wieschaus, Molecular Biology, Lewis-Sigler Institute for Integrative Genomics


The Program in Quantitative and Computational Biology is offered by the Lewis-Sigler Institute for Integrative Genomics and its affiliated departments. It is designed for students with a strong interest in multidisciplinary and systems-level approaches to understanding molecular, cellular, and organismal behavior. The curriculum introduces students to experimental and analytic techniques for acquisition of large-scale quantitative observations, and the interpretation of such data in the context of appropriate models. Strong emphasis is placed on using global genome-wide measurements (e.g., microarray gene expression, sequence, phenotype) to understand physiological and evolutionary processes.

Examples of ongoing research include organizational principles of metabolic networks, quantitative modeling of cell-biological processes, mapping the genetic basis of complex bacterial behavior, comparative genomics analysis of regulatory networks, the genetic basis of quantitative phenotypic variation, and genomic plasticity and mechanisms of phenotypic adaptation.

At the core of the curriculum is independent research initiated in the fall of junior year, in which students participate in the design, execution, and analysis of experiments in a host laboratory of their choice. The required courses provide a strong background in modern methodologies in data analysis, interpretation, and modeling. A certificate in quantitative and computational biology is awarded to students who successfully complete the program requirements.

Admission to the Program

Students are admitted to the program after they have chosen a concentration and consulted with the program committee in May of their sophomore year. The program committee will also assist students in selecting a laboratory for their junior independent and thesis work. Admission requires the completion of prerequisites listed below. Electives are chosen in consultation with the adviser.

There are two possible tracks for entry into the QCB certificate program:

1. Integrated Science ISC 231-234

2. All of the following courses:

  •  COS 126 or higher
  •  MOL 215
  •  One year of physics as a Princeton undergraduate (PHY 103-104 or higher)
  •  One year of chemistry as a Princeton undergraduate (CHM 201-202 or higher)
  •  One 200-level math course or higher
  •  One semester of statistics: ORF 245, MOL/EEB 355 or higher (but not PSY 251)

Applications for program admission, including the Research Lab form, must be submitted by May 31 of sophomore year and should include the following information: prerequisite courses, plans for courses in the junior and senior years, and independent work plans. Admission decisions are made by June 30.

Program of Study

1. QCB 302 Research Topics in QCB (taken in the fall of junior year)

2. Three electives from the course list below (Additional courses may be taken as electives with approval from the Director):

  •   PHY 209 Computational Physics Seminar
  •   PHY 412 Biological Physics
  •   MAT/APC 321 Numerical Methods
  •   QCB 511 Modeling Tools for Cell and Developmental Biology
  •   MOL/COS/QCB 455 Introduction to Genomics and Computational Molecular Biology
  •   MOL 515 Method and Logic in Quantitative Biology
  •   MOL/COS 557 Analysis & Visualization of Large-Scale Genomic Data Sets
  •   CBE 433 Mechanics/Dynamics of Soft Living Matter
  •   CBE/MAT481 Introduction to Nonlinear Dynamics
  •   CBE 440 The Physical Basis of Human Disease
  •   CHM 440 Drug Discovery in the Genomics Era
  •   NEU 408 Cellular and Systems Neuroscience

3. Junior and senior independent work must have significant overlap with areas in quantitative and computational biology.

A minimum of a B average in program courses and junior and senior independent work is required for successful completion of the program. Program courses cannot be taken pass/D/fail.

Certificate of Proficiency

Students who fulfill the requirements of the program receive a certificate of proficiency in quantitative and computational biology upon graduation. Students who pursue a certificate in quantitative and computational biology may not also receive a certificate in biophysics.

Note: Students in the Classes of 2015, and 2016, are subject to the requirements that are stated in the 2013-14 Undergraduate Announcement.


Courses


ISC 231 An Integrated, Quantitative Introduction to the Natural Sciences I (also CHM 231/COS 231/MOL 231/PHY 231)   Fall STL

An integrated, mathematically and computationally sophisticated introduction to physics and chemistry and molecular biology. Alternative to the combination of PHY 105-106, CHM 201-202, MOL 214-215 and COS126. Students must enroll in ISC231 and ISC232 in the fall and ISC233 and ISC234 in the spring. Prerequisites: familiarity with calculus at the level of MAT 103-104 or Advanced Placement Calculus BC, solid high school physics and chemistry courses. Five lectures, one three-hour laboratory, one three-hour computational laboratory, one evening problem session. T. Gregor, P. Debenedetti, E. Wieschaus

ISC 232 An Integrated, Quantitative Introduction to the Natural Sciences I (also CHM 232/COS 232/MOL 232/PHY 232)   Fall QR

An integrated, mathematically and computationally sophisticated introduction to physics and chemistry and molecular biology. Alternative to the combination of PHY 105-106, CHM 201-202, MOL 214-215 and COS126. Students must enroll in ISC231 and ISC232 in the fall and ISC233 and ISC234 in the spring. Prerequisites: familiarity with the calculus at the level of MAT 103-104 or Advanced Placement Calculus BC, solid high school physics and chemistry courses. Five lectures, one three-hour laboratory, one three-hour computational laboratory, one evening problem session. T. Gregor, P. Debenedetti, E. Wieschaus

ISC 233 An Integrated, Quantitative Introduction to the Natural Sciences II (also CHM 233/COS 233/MOL 233/PHY 233)   Spring STL

An integrated, mathematically and computationally sophisticated introduction to physics, chemistry and molecular biology. Alternative to the combination of PHY 105-106, CHM 201-202, MOL 214-215, and COS126. Students must enroll in ISC231 and ISC232 in the fall and ISC233 and ISC234 in the spring. Prerequisites: familiarity with the calculus at the level of MAT 103-104 or Advanced Placement Calculus BC, solid high school physics and chemistry courses. Five lectures, one three-hour laboratory, one three-hour computational laboratory, one evening problem session. J. Shaevitz, O. Troyanskaya, H. Yang

ISC 234 An Integrated, Quantitative Introduction to the Natural Sciences II (also CHM 234/COS 234/MOL 234/PHY 234)   Spring

An integrated, mathematically and computationally sophisticated introduction to physics, chemistry, and molecular biology. Alternative to the combination of PHY 105-106, CHM 201-202, MOL 214-215 and COS126. Students must enroll in ISC231 and ISC232 in the fall and ISC233 and ISC234 in the spring. Prerequisites: familiarity with the calculus at the level of MAT 103-104 or Advanced Placement Calculus BC, solid high school physics and chemistry courses. Five lectures, one three-hour laboratory, one three-hour computational laboratory, one evening problem session. J. Shaevitz, O. Troyanskaya, H. Yang

ISC 235 An Integrated, Quantitative Introduction to the Natural Sciences III (also CHM 235/COS 235/MOL 235/PHY 235)   Spring

An integrated, mathematically and computationally sophisticated introduction to biochemistry, neurobiology, genetics, genomics, and evolution. For the 2014-15 AY, students must enroll in ISC236 in the fall and ISC235 in the spring. Prerequisites: ISC231-234 or equivalent preparation (MOL214, COS126, CHM 201-202 or 203-204, PHY 103-104 or 105-106) or by permission from the instructor. Two lectures, one precept, one evening problem session. J. Rabinowitz, M. Murthy

ISC 236 An Integrated, Quantitative Introduction to the Natural Sciences IV (also CHM 236/COS 236/MOL 236/PHY 236)   Fall

An integrated, mathematically and computationally sophisticated introduction to biochemistry, neurobiology, genetics, genomics, and evolution. For the 2014-15 AY, students must enroll in ISC236 in the fall and ISC235 in the spring. Prerequisites: ISC231-234 or equivalent preparation (MOL214, COS126, CHM 201-202 or 203-204, PHY 103-104 or 105-106) or by permission from the instructor. Two lectures, one precept, one evening problem session. P. Andolfatto, E. Wieschaus

QCB 301 Experimental Project Laboratory in Quantitative and Computational Biology (also MOL 301)   Not offered this year STL

An intensive double-credit course focusing on state-of-the-art experimental design and practice in quantitative biology. Emphasis is placed on functional genomics using global genome-wide measurements (e.g., microarray gene expression, sequence, phenotype) to understand physiological and evolutionary processes. Begins with a short introduction to technology and principles, followed by the design and execution of independent projects done by pairs of students in collaboration, with the continuing guidance and advice of the teaching staff. Prerequisites: ISC 231-234 and ISC 235-236. Four three-hour laboratories. Staff

QCB 302 Research Topics in QCB   Fall STN

Junior independent research projects will be discussed in order to provide guidance and feedback. We will emphasize critical thinking about experiments and large dataset analysis along with the ability to clearly communicate one's research. Students will present background research and progress reports. Written work will consist of an NSF-style proposal and an NIH-style grant proposal/research paper. Students must choose research labs in the spring of their sophomore year and be engaged in the research from the start of the fall term. Prerequisites: ISC231-234 and ISC235-236, or equivalent preparation. M. Noyes, C. Murphy, N. Wingreen

QCB 455 Introduction to Genomics and Computational Molecular Biology (also MOL 455/COS 455)   Fall QR

Introduction to computational and genomic approaches used to study molecular systems. Topics include computational approaches to sequence similarity and alignment, phylogenetic inference, gene expression analysis, structure prediction, comparative genome analysis, and high-throughput technologies for mapping genetic networks. Two lectures, one preceptorial. M. Singh