CLS Core Courses
To fulfill the 2 Core Courses, take two Core Courses from two different Core Areas.
Please see available Computational Life Science (CLS) Core Courses below. The two Core Courses MUST BE selected from two different Core Areas.
If two Core Courses are taken from the same area, only one of them will be counted.
BCHM 56100 – General Biochemistry I
This course provides upper-division undergraduate and graduate students with basic understanding of biochemical and structural properties of amino acids, nucleic acids, lipids, and carbohydrates. This course allows students to connect the relationship between structure and function of biomolecules. In addition, students learn to understand enzyme properties, enzyme mechanism of action, and enzyme regulation.
BCHM 56200 – General Biochemistry II
This course provides upper-division undergraduate and graduate students with an understanding of core metabolic pathways. Anabolic and catabolic processes of metabolic pathways are studied. Biochemical and structural knowledge is used to determine how enzymes and coenzymes are needed to regulate and control metabolic pathways.
BIOL 51700 - Molecular Biology: Proteins
Principles of protein three-dimensional architecture. The molecular and structural basis of protein folding, function, and evolution.
BIOL 54100 - Molecular Genetics of Bacteria
Advanced bacterial genetics, with emphasis on the use of genetics as a powerful and creative intellectual activity that enables us to discover biological functions and to construct new organisms by the manipulation of DNA. Major topics include: mutations, genetic selections, recombination, regulatory mechanisms, and genomic evolution.
BIOL 55001 - Eukaryotic Molecular Biology
This is a general survey course intended for advanced undergrads and beginning grad students. The course will draw upon examples from the plant, animal, and fungal kingdoms, and will familiarize students with the basic principles of molecular biology analyses as they apply to eukaryotic organisms. By the end of the course students should have knowledge of these molecular processes and should be able to design and analyze experiments dealing with these topics.
BIOL 58000 - Evolution
A study of evolution as a basic concept of the biological sciences; an examination of current methods of experimentation within the area, as well as evidences for the possible mechanisms of evolutionary change.
BME 69500 - Multi-Scale Modeling in Biological Systems
This course is designed primarily for specialized topic areas for which there is no specific course, workshop, or individual study plan, but having enough student interest to justify the formalized teaching of an advanced course. Permission of instructor required.
FS 59100 - Microbial Genomics and Metabolism
Specialized topics not covered in other courses will be offered as one-credit minicourses. Topics, requirements, and credits will be determined yearly. Permission of instructor required.
MCMP 57000 - Basic Principles of Chemical Action on Biological Systems
Detailed description of modern pharmacology with emphasis on the mechanism of drug action and approaches used to understand their therapeutic and toxic effects. Topics include receptor theory and signal transduction, pharmacokinetics and pharmacogenetics with emphasis on current concepts in molecular pharmacology. Permission of instructor required.
BIOL 59500- Practical Biocomputing
Special work, such as directed reading, independent study or research, supervised library, laboratory, or field work, or presentation of material not available in the formal courses of the department. The field in which work is offered will be indicated in the student’s record. Permission of instructor required.
CHM 69600 – Mathematical Methods for Chemists
Lectures on selected topics of current interest.
CNIT 55800 – Bioinformatics Computing and Systems Integration
This is a graduate-level course for students interested in the application of computational methods and information technology in the pharmaceutical, biotechnology, and life sciences arena. An overall understanding of information technology and systems is assumed, as well as an in-depth knowledge of one or more areas of information technology. Permission of instructor required.
CS 50100 – Computing for Science and Engineering
Computational concepts, tools, and skills for computational science and engineering scripting for numerical computing, scripting for file processing, high performance computing, and software development. Project may be required.
CS 51400 – Numerical Analysis
Alternative methods for solving nonlinear equations; linear difference equations, applications to solution of polynomial equations; differentiation and integration formulas; numerical solution of ordinary differential equations; roundoff error bounds.
CS 51500 – Numerical Linear Algebra
Direct and iterative solvers of dense and sparse linear systems of equations, numerical schemes for handling symmetric algebraic eigenvalue problems, and the singular-value decomposition and its applications in linear least squares problems.
CS 52500 – Parallel Computing
Parallel computing for science and engineering applications: parallel programming and performance evaluation, parallel libraries and problem-solving environments, models of parallel computing and run-time support systems, and selected applications.
CS 53000 – Introduction to Scientific Visualization
Teaches the fundamentals of scientific visualization and prepares students to apply these techniques in fields such as astronomy, biology, chemistry, engineering, and physics. Emphasis is on the representation of scalar, vector, and tensor fields; data sampling and resampling; and reconstruction using multivariate finite elements (surfaces, volumes, and surfaces on surfaces).
CS 54100 – Database Systems
Fundamentals for the logical design of database systems. The entity-relationship model, semantic model, relational model, hierarchical model, network model. Implementations of the models. Design theory for relational databases. Design of query languages and the use of semantics for query optimization. Design and verification of integrity assertions, and security. Introduction to intelligent query processing and database machines.
CS 57300 – Data Mining
Data Mining has emerged at the confluence of artificial intelligence, statistics, and databases as a technique for automatically discovering summary knowledge in large datasets. This course introduces students to the process and main techniques in data mining, including classification, clustering, and pattern mining approaches. Data mining systems and applications are also covered, along with selected topics in current research. Offered in alternate years.
CS 57800 – Statistical Machine Learning
This introductory course will cover many concepts, models, and algorithms in machine learning. Topics include classical supervised learning (e.g., regression and classification), unsupervised learning (e.g., principle component analysis and K-means), and recent development in the machine learning field such as variational Bayes, expectation propagation, and Gaussian processes. While this course will give students the basic ideas and intuition behind modern machine learning methods, the underlying theme in the course is probabilistic inference.
CS 57900 – Bioinformatics Algorithms
Review of Genomes, DNA, RNA, proteins, proteomes. Biological Sequences: dynamic programming; pairwise global, local, and semi-global alignments of genes and proteins; constant, affine, and general gap penalties; RNA alignments; BLOSUM and PAM scoring matrices. Multiple alignment of proteins: approximation algorithms; iterative and progressive alignment methods. Database search for sequences: BLAST and variants. Phylogenetic Trees: distance-based methods, ultrametric and additive distance functions; parsimony, and maximum likelihood methods. Whole Genome Alignment: suffix trees and suffix arrays. Systems Biology: Module discovery in biological networks, spectral algorithms for graph clustering. Network alignment: quadratic programming formulations and graph matching. Genetic Variation: haplotype inference, the perfect phylogeny problem and chordal graphs. Additional topics such as next-generation sequencing, analysis of multidimensional data from flow cytometry, and gene expression data, if time permits.
CS 58000 – Algorithm Design, Analysis and Implementation
Basic techniques for designing and analyzing algorithms: dynamic programming, divide and conquer, balancing. Upper and lower bounds on time and space costs, worst case and expected cost measures. A selection of applications such as disjoint set union/find, graph algorithms, search trees, pattern matching. The polynomial complexity classes P, NP, and co-NP; intractable problems.
CS 59000 – Computing for Life Sciences
Directed study for students who wish to undertake individual reading and study on approved topics. Permission of instructor required.
CS 61500 – Numerical Methods For Partial Differential Equations I
Finite element method for elliptic partial differential equations; weak formulation; finite-dimensional approximations; error bounds; algorithmic issues; solving sparse linear systems; finite element method for parabolic partial differential equations; backward difference and Crank-Nicolson time-stepping; introduction to finite difference methods for elliptic, parabolic, and hyperbolic equations; stability, consistency, and convergence; discrete maximum principles.
MA 51400 – Numerical Analysis
Alternative methods for solving nonlinear equations; linear difference equations, applications to solution of polynomial equations; differentiation and integration formulas; numerical solution of ordinary differential equations; roundoff error bounds.
MA 61500 – Numerical Methods For Partial Differential Equations I
Finite element method for elliptic partial differential equations; weak formulation; finite-dimensional approximations; error bounds; algorithmic issues; solving sparse linear systems; finite element method for parabolic partial differential equations; backward difference and Crank-Nicolson time-stepping; introduction to finite difference methods for elliptic, parabolic, and hyperbolic equations; stability, consistency, and convergence; discrete maximum principles.
MCMP 69000 – Computer-Aided Drug Design
Special topics, projects, or laboratory exercises in selected areas of medicinal chemistry and molecular pharmacology. Permission of instructor required.
PHYS 57000 – Computational Biomolecular Physics
Specialized topics in physics selected from time to time. Permission of instructor required.
PHYS 58000 – Computational Physics
Introduction to computationally based problem solving in physics, emphasis on understanding and applying various numerical algorithms to different types of physics problems. Topics will include chaos in mechanical systems, stochastic systems including percolation and fractal structures, molecular dynamics and the properties of simple fluids, Monte Carlo methods and phase transitions, and time dependent as well as time dependent problems in quantum mechanics.
STAT 54500 – Introduction to Computational Statistics
This introductory course covers the fundamentals of computing for statistics and data analysis. It starts with a brief overview of programming using a general purpose compiled language (C) and a statistics-oriented interpreted language (R). The course proceeds to cover data structures and algorithms that are directly relevant to statistics and data analysis and concludes with a computing-oriented introduction to selected statistical methods. A significant part of the course involves programming and hands-on experimentation demonstrating the covered techniques, ration, and Markov chain Monte Carlo methods.
