Course Offerings (GSAS Bulletin)

Core courses selected for the Program in Computational Biology are assembled from participating home departments to provide students with an interdisciplinary approach to science. Students are also required to take elective courses to complete 72 points of credit. Additional information on courses may be accessed through the Web sites of individual home departments.

COMPUTATIONAL BIOLOGY

Computational Biology Student Seminar
G24.2300  Identical to G25.2200. Offered each term for the first two years of the computational biology doctoral program. Course content varies from semester to semester depending on instructor. Prerequisite: enrollment in the computational biology doctoral program or instructor’s approval. 2 points.

The many concerted initiatives in genomics, like sequencing various organisms, identifying genes in humans and analogues in other species, determining variations (polymorphisms) in human genes related to disease, and designing drugs for specific gene products, have immense ramifications on every aspect of our lives—from health to technology to law. Though progress appears to have been revolutionary in the past decade, such developments have evolved from foundations laid by many pioneers in the biochemical sciences and allied fields. This seminar introduces students to emerging disciplines that helped establish the field of computational biology through lectures and readings from the scientific literature, both technical (journal articles) and general (books about science and scientists). It seeks to both familiarize students with the field’s evolution, as well as help students develop a critical eye for conducting research in the field. The course presentations and readings from the sciences and the arts expose students to the roots of such scientific endeavors of our 21st century and the complex web of scientific discovery, including the personal dimensions in research and the mixture of serendipitous and systematic progress.

BASIC MEDICAL SCIENCES

Foundations of Cell and Molecular Biology I, II
G16.2001, G16.2002  I offered every fall; II offered every spring. Prerequisites: basic biochemistry and cell biology. Lecture and conference. Borowiec and staff. 6 points per term.

Intensive, two-semester advanced course. Provides a broad overview of nucleic acid and protein metabolism and function. The fall semester covers DNA metabolism, including DNA replication, repair, and recombination; chromatin structure; RNA transcription and processing; and translation control mechanisms. The spring semester covers various aspects of cell biology, signal transduction, and genetics. Topics include biogenesis of cellular membranes; vesicular transport; the cytoskeleton; cell differentiation and development; concepts in receptor signaling; and genetics of model organisms. Each semester consists of two or three modules that differ somewhat in organization, including the number of required lectures. Each module places significant emphasis on student-led discussions. The reading of primary research articles is heavily stressed. Grades are assigned on the basis of examination, essay, and discussion scores.

COMPUTER SCIENCE

Fundamental Algorithms
G22.1170  Prerequisite: at least one year’s experience with a high-level language such as Pascal, C, C++, or Java; knowledge of assembly language; and familiarity with recursive programming methods and with data structures (arrays, pointers, stacks, queues, linked lists, binary trees). 3 points.

Reviews a number of important algorithms, with emphasis on correctness and efficiency: solving recurrence equations; sorting algorithms; selection; binary search; hashing; binary search trees and balanced-tree strategies; tree traversal; partitioning; graphs; spanning trees; shortest paths; connectivity; depth first search; breadth first search. Dynamic programming, divide and conquer.

Programming Languages
G22.2110 3 points.
Design and use of mainstream programming languages: naming, scoping, type models, control structures, procedural abstractions, modularization. Implementation issues and runtime organization. Languages studied include Ada, C, C++, Java, LISP, ML, and Python. Extensive programming exercises in various languages.

Special Topics in Computer Science
G22.3033  Prerequisites vary according to topic. 3 points.
Topics vary each semester.

Honors Programming Languages
G22.3110  Prerequisite: permission of the instructor. 4 points.
In-depth examination of the four major categories of programming languages: imperative, object-oriented, functional, and logic languages. The specific languages covered include Ada, C++, LISP, ML, Prolog, and SETL. Fundamental issues of programming languages, such as type systems, scoping, concurrency, modularization, control flow, and semantics, are discussed.

Honors Analysis of Algorithms
G22.3520  Prerequisites: G22.1170 or one semester of undergraduate algorithms, and permission of the instructor. 4 points.
Design of algorithms and data structures. Review of searching, sorting, and fundamental graph algorithms. In-depth analysis of algorithmic complexity, including advanced topics on recurrence equations and NP-complete problems. Advanced topics on lower bounds, randomized algorithms, amortized algorithms, and data structure design as applied to union-find, pattern matching, polynomial arithmetic, network flow, and matching.

BIOLOGY

Bio Core 1: Molecules and Cells
G23.1001  4 points.
A survey of the major topics of up-to-date molecular and cellular biology starting with molecular structure and function of proteins and polynucleic acids and ending with cell division and apoptosis.

Bio Core 2: Genes, Systems, and Evolution
G23.1002  4 points.
A survey of the major topics of modern biology including genetics, systematics, genomics, systems biology, developmental genetics, plant biology, immunology, neurobiology, population genetics, evolution, and geobiology.

Bioinformatics and Genomes
G23.1127  Prerequisites: calculus I and II, demonstrated interest in computation, and permission of the instructor. Rajewsky. 4 points.
The recent explosion in the availability of genome-wide data such as whole genome sequences and microarray data led to a vast increase in bioinformatics research and tool development. Bioinformatics is becoming a cornerstone for modern biology, especially in fields such as genomics. It is thus crucial to understand the basic ideas and to learn fundamental bioinformatics techniques. The emphasis of this course is on developing not only an understanding of existing tools but also the programming and statistics skills that allow students to solve new problems in a creative way.

Genomics
G23.1128  Prerequisites:V23.0021-0022. Lecture. Piano. 4 points.
Introduction to genomic methods for acquiring and analyzing genomic DNA sequence. Topics: genomic approaches to determining gene function, including determining genome-wide expression patterns; the use of genomics for disease-gene discovery and epidemiology; the emerging fields of comparative genomics and proteomics; and applications of genomics to the pharmaceutical and agbiotech sectors. Throughout the course, the computational methods for analysis of genomic data is stressed.

Statistics in Biology
G23.2030  Prerequisites: college algebra and/or calculus. Lecture and laboratory. Tranchina. 4 points.
Advanced course on techniques of statistical analysis and experimental design that are useful in research and in the interpretation of biology literature. Principles of statistical inference, the design of experiments, and analysis of data are taught using examples drawn from the literature. Covers the use of common parametric and nonparametric distributions for the description of data and the testing of hypotheses.

CHEMISTRY

Biochemistry I, II
G25.1881, 1882  Identical to G23.1046, 1047. Prerequisites: V25.0243 and V25.0244, or equivalent courses in organic chemistry for G25.1881; G25.1881 for G25.1882. Kallenbach, staff. 4 points per term.

Two-semester course taught jointly by faculty from the Departments of Biology and Chemistry. Topics include organic and physical chemistry of proteins, lipids, carbohydrates, and nucleic acids; enzyme kinetics and mechanisms; membranes and transport; bioenergetics and intermediary metabolism; molecular genetics and regulation.

Statistical Mechanics
G25.2600  4 points.
Introduction to the fundamentals of statistical mechanics. Topics include classical mechanics in the Lagrangian and Hamiltonian formulations and its relation to classical statistical mechanics, phase space and partition functions, and the development of thermodynamics. Methods of molecular dynamics and Monte Carlo simulations are also discussed.

Biomolecular Modeling
G25.2601  Prerequisite: basic programming experience. 4 points.
Introduction to molecular modeling and simulation, including development of ab initio and semiempirical potentials, molecular mechanics, Monte Carlo simulations, and molecular dynamics simulations, both theory and practice.

MATHEMATICS

Numerical Methods
G63.2010, 2020  Identical to G22.2420, 2421. Corequisite: linear algebra.
Numerical linear algebra. Approximation theory. Quadrature rules and numerical integration. Non-linear equations and optimization. Ordinary differential equations. Elliptic equations. Iterative methods for large, sparse systems. Parabolic and hyperbolic equations.

Special Topics in Mathematical Physiology
G63.2855, 2856  Identical to G23.2855, 2856.
Recent topics: physiological control mechanisms; mathematical aspects of neurophysiology; mathematical aspects of visual physiology; mathematical models in cell physiology.