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Program in Quantitative and Computational Biology

Director

David Botstein

Acting Director

Coleen T. Murphy (spring)

Executive Committee

David Botstein, Molecular Biology, Lewis-Sigler Institute for Integrative Genomics 

Simon A. Levin, Ecology and Evolutionary Biology

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

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

Mark D. Rose, Molecular Biology 

Joshua W. Shaevitz, Physics, 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 the project lab (QCB 301), a double-credit course taken during the fall of junior year, in which students participate in the design, execution, and analysis of experiments. The required courses provide a strong background in modern methodologies in data analysis, interpretation, and modeling. Courses are chosen with the help of advisers in molecular biology, ecology and evolutionary biology, physics, chemistry, computer science, and other related departments. 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. The course of study is structured upon department concentration, plus junior and senior independent work in genomics or quantitative and computational biology. Electives are chosen in consultation with the adviser.

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

1. For those students who have completed the integrated science curriculum ISC/CHM/COS/MOL/PHY 231-234 during their freshman year and ISC/CHM/COS/MOL/PHY 235-236 during their sophomore year. (See Integrated Science Curriculum below.)

2. For those students who have not taken the integrated science series, the following courses are the minimum that must be completed before the end of their sophomore year:

COS 126 or higher
MOL 342
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 year of mathematics as a Princeton undergraduate

Applications for program admission 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 301 Experimental Project Laboratory in Quantitative and Computational Biology (taken in the fall of junior year)

2. MOL/COS 455 Introduction to Genomics and Computational Molecular Biology

3. Senior thesis with a strong component of quantitative and computational analysis

Molecular biology concentrators will be required to take eight departmentals:

1. MOL 350 Laboratory in Molecular Biology (taken in spring of sophomore year)

2. MOL 348 Cell and Developmental Biology

3. MOL/COS 455 Introduction to Genomics and Computational Molecular Biology

4. QCB 301 Experimental Project Laboratory in Quantitative and Computational Biology (would count as two departmentals)

5. Three other science or math courses (Students are strongly encouraged to take APC/MOL 360 Biological Dynamics or EEB 355 Introduction to Biostatistics.)

6. Molecular biology concentrators will do a quantitative or computationally oriented junior paper in the spring of their junior year.

7. Seniors will choose a thesis project under the broad umbrella of quantitative or computational biology and with a faculty member and project approved by the QCB program committee.

8. For students who enter the program without taking the integrated science courses, it is expected that many will also take organic chemistry (CHM 301-302 or CHM 303-304), as well as biochemistry (MOL 345). These will also fulfill the MOL departmental requirement.

Physics concentrators may take half a semester of MOL 350 Laboratory in Molecular Biology and half a semester of PHY 311-312 Experimental Physics in the spring of their junior year. One junior paper and the senior thesis should be QCB related. The normal sequence of required courses in physics can be shifted to accommodate the QCB junior project lab.

Computer science concentrators are required to take eight computer science departmentals. The junior paper and senior thesis must be QCB related. Students interested in the QCB certificate should speak with Professor Mona Singh as early as possible to plan their course of study.

Chemistry concentrators are required to take four 300-, 400-, or 500-level courses in chemistry (at least one term each of organic, physical, inorganic, and experimental chemistry) plus four science cognates at the 300, 400, or 500 level. MOL 350 Laboratory in Molecular Biology can be substituted for CHM 371 Experimental Chemistry. One junior paper and the senior thesis should be QCB related.

Ecology and evolutionary biology concentrators are required to take eight EEB departmentals, at least five of which must normally be upper-level EEB or MOL courses. One junior paper and the senior thesis should be QCB related.

Students interested in a B.S.E. degree should contact Associate Dean Peter Bogucki in the School of Engineering and Applied Science for general information and electrical engineering concentrators should contact Professor Antoine Kahn.

Junior and Senior Independent Work. Junior and senior independent work should be arranged with the help of the program director and committee and supervised by the faculty in the various home departments. The senior thesis should make significant use of computational or quantitative methods.

Administrative Details. 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.

Integrated Science Curriculum. Integrated science is a revolutionary new introductory science curriculum developed at Princeton, intended for students considering a career in science. By breaking down traditional disciplinary barriers, a series of courses taken in the freshman and sophomore years provides students with first-rate preparation for a major in any of the core scientific disciplines, and in such a way that helps retain the connections to the other disciplines. The curriculum is founded on the expectation that much of the most important science of the future, though based on the classical disciplines, will lie in areas that span two or more of them.

The integrated science sequence is suitable for any undergraduate considering concentrating in the sciences or engineering at Princeton. The core training is perfect preparation for a very broad range of careers, both within and outside science. The curriculum is especially valuable for students interested in bridging the traditional barriers between the biological and the physical sciences.

The integrated science sequence provides an alternative path into the Departments of Chemistry, Computer Science, Molecular Biology, and Physics. ISC/CHM/COS/MOL/PHY 231-234 (a double course) can be taken in the freshman year and ISC/CHM/COS/MOL/PHY 235-236 can be taken in the sophomore year. These courses can be substituted for CHM 203-204, PHY 103-104 or 105-106, and COS 126 in the freshman year and MOL 214, 342, and 345 in the sophomore year.


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, drawing on examples from biological systems. Alternative to the combination of PHY 105-106, CHM 201-202, and COS 126. Students must enroll in 231 and 232 in the fall and 233 and 234 in the spring. Five lectures, one three-hour laboratory, one three-hour computational laboratory, one evening problem session. Prerequisites: familiarity with the calculus at the level of MAT 103-104 or Advanced Placement Calculus BC, solid high school physics and chemistry courses. W. Bialek, D. Botstein, P. Debenedetti

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, drawing on examples from biological systems. Alternative to the combination of PHY 105-106, CHM 201-202, and COS 126. Students must enroll in 231 and 232 in the fall and 233 and 234 in the spring. Five lectures, one three-hour laboratory, one three-hour computational laboratory, one evening problem session. Prerequisites: familiarity with the calculus at the level of MAT 103-104 or Advanced Placement Calculus BC, solid high school physics and chemistry courses. W. Bialek, D. Botstein, P. Debenedetti

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 and chemistry, drawing on examples from biological systems. Alternative to the combination of PHY 105-106, CHM 201-202, and COS 126. Students must enroll in 231 and 232 in the fall and 233 and 234 in the spring. Five lectures, one three-hour laboratory, one three-hour computational laboratory, one evening problem session. Prerequisites: familiarity with the calculus at the level of MAT 103-104 or Advanced Placement Calculus BC, solid high school physics and chemistry courses. J. Shaevitz, O. Troyanskaya

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 and chemistry, drawing on examples from biological systems. Alternative to the combination of PHY 105-106, CHM 201-202, and COS 126. Students must enroll in 231 and 232 in the fall and 233 and 234 in the spring. Five lectures, one three-hour laboratory, one three-hour computational laboratory, one evening problem session. Prerequisites: familiarity with the calculus at the level of MAT 103-104 or Advanced Placement Calculus BC, solid high school physics and chemistry courses. J. Shaevitz, O. Troyanskaya

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

An integrated, mathematically and computationally sophisticated introduction to biochemistry, molecular biology, genetics, genomics, and evolution. Students must enroll in 235 in the fall and 236 in the spring. Two lectures, one preceptorial, one evening problem session. Prerequisites: 231-234 or equivalent preparation (MOL 214, COS 126, CHM 201-202 or 203-204, PHY 103-104 or 105-106) or by permission of the instructor. D. Botstein, M. Llinás, M. Semmelhack

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

An integrated, mathematically and computationally sophisticated introduction to biochemistry, molecular biology, genetics, genomics, and evolution. Students must enroll in 235 in the fall and 236 in the spring. Three lectures, one preceptorial, one evening problem session. Prerequisites: 231-234 or equivalent preparation (MOL 214, COS 126, CHM 201-202 or 203-204, PHY 103-104 or 105-106) or by permission of the instructor. D. Botstein, M. Murthy, E. Wieschaus

QCB 301 Experimental Project Laboratory in Quantitative and Computational Biology (also MOL 301)   Fall 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. D. Botstein