Computational Mathematics for Quantitative Biomedicine (GS-SB- 401)
This course introduces essential computational, statistical and mathematical concepts to students who are interested in computational biology. It is intended that each of the concepts will be taught in the context of the real biological problems ranging from genomics bioinformatics, structural biophysics, computational neuroscience, systems biology, protein design, drug discovery, and medical bioinformatics
Credits: 8 
Term: 1-2 
Counts for 30 hr. requirement: Y 
Director: Dr. Zhandong Liu


Computational Molecular Biophysics and Structural Biology (GS-SB-402)
This course is designed for students n computationally-oriented theoretical, biophysical, biomedical and bioengineering majors to introduce the principles and methods used for computer simulations and modeling of macromolecules of biological interest.  Fundamental concepts in statistical mechanics, thermodynamics, and dynamics will be emphasized.  Protein conformation/dynamics, empirical energy functions and molecular dynamics calculations, as well as other approaches will be described.  Specific biological problems are discussed to illustrate the methodology.  Classic examples such as the cooperative mechanisms of hemoglobin and more frontier topics such as the motional properties of molecular motors and ion channels as well as results derived from the current literature are covered.  Other potential topics are protein folding/predictions, the nature of reaction rate enhancement in enzyme catalysis, physical chemistry properties of biologically relevant nano-materials, simulations of free energy changes in mutations, electrostatic properties of protein, molecular recognition, and the properties of binding sites.  Particular emphasis is also given to the applications of molecular graphics.  During the final reading period, each student carrier out an original research project that makes use of the techniques and grading is based on the written and oral presentations of the results from the final projects.
Credits: 6
Term: 1
Counts for 30 hr. requirement: Y
Director: Dr. Jianpeng Ma


Advanced X-ray Crystallography (GS-SB- 403)

X-ray crystallography is a powerful technique to determine atomic resolution structures from small, inorganic molecules to large, multi-subunit macromolecular assemblies. This course covers both theory and practical applications starting with crystallization, crystal systems, and data processing to finding a structure solution, model building, and structure refinement/validation. The course will prepare students with diverse scientific backgrounds to expand their research to protein crystallography as an analytical tool to probe the structure-function relationship of proteins and enzymes at the atomic level.
Credits: 3 
Term: 4 (not offered in AY17)
Counts for 30 hr. requirement: Y 
Director: Dr. Francis T.F. Tsai


Computer-Aided Discovery Methods (GS-SB- 405)

The objective of this course is to introduce students to the concepts, methods and tools relevant for computer-aided discovery using data collected using high-throughput technologies. The course will focus on the methods of integration of data, tools, and discovery processes and the methods of computational pattern discovery, hypothesis generation and testing. The students will master advanced applications of computing that enable new methods of discovery in a field of focus, which will initially be cancer biology. The course will not focus exclusively on technical, algorithmic or mathematical aspects nor will it focus on biology alone. Instead, the focus will be on genuine integration of the two fields.
Credits: 3 
Term: 4 
Counts for 30 hr. requirement: Y 
Director: Dr. Aleksandar Milosavljevic


Practical Introduction to Programming for Scientists (GS-SB- 406)
In this course students will learn Python, one of the most widely used scripting languages in scientific computing. The course is primarily aimed at students with little or no programming background, but those with some programming experience in other languages wishing to learn Python are also welcome. The course covers basic programming concepts and data structures, and students will learn to write simple programs to improve their data processing productivity. We will also cover a number of open source scientific libraries available in Python (Biopython, SciPy, Matplotlib, etc.). Some basic familiarity with using a computer will be expected, and each student must have a laptop computer for use in class by the beginning of the term.
Credits: 3 
Term: 3 
Counts for 30 hr. requirement: Y 
Director: Dr. Steven J. Ludtke


Current Topics in Computational Biomedicine (GS-SB- 407)
This course introduces graduate students to the diversity of biological and clinical research problems that benefit from computational approaches. On alternating weeks the students will be exposed to speakers, or they will present a journal club. The speakers are drawn from across BCM, the TMC, Rice University and the greater Houston area and occasionally will include outside seminar speakers. During this one hour, a format of two short talks from two different speakers will discuss some of the most salient current problems studied in their laboratories, often with a significant emphasis on computational aspects. Style and content vary but, generally, the level is introductory and accessible to all members of the audience. Topics range from genomics to clinical text-mining and from bioengineering to public health, representing the rich diversity of computational biology research in the Gulf Coast area. The following week, the students will present two papers at journal club. One paper will be drawn from the immediate literature of the past 3 months, and the second paper will be drawn from any past time period, focusing on highly cited past influential papers across the field of computational biology. The papers will be selected by the participating Faculty, drawn from the SCBMB program, with input from the students if they so desire.
Credits: 1 
Term: 1, 2, 3, 4 
Counts for 30 hr. requirement: N 
Director: Dr. Oliver Lichtarge and Dr. Richard Sucgang


Molecular Biophysics: Methods and Principles (GS-SB-408)
This is a course lasting one semester (two BCM terms). It presents in lecture format a survey of the major techniques of molecular biophysics, and the underlying physical principles and mathematics on which they are based.
Credits: 6
Term: 1-2
Counts for 30 hr. requirement: Y
Director: Dr. Theodore Wensel


Electron Cryomicroscopy for Molecules & Cells (GS-SB- 410)

This course discusses in-depth theoretical and practical techniques in structural biophysics with a particular emphasis on electron imaging and crystallography. The topics include cryo-specimen preparative techniques, electron microscope optics, image contrast theory, specimen radiation damage, single particle image reconstruction, tomographic reconstruction, density based modeling, 3-D visualization, biological knowledge discovery from cryo-electron imaging.
Credits: 2
Term: 4 
Counts for 30 hr. requirement: N
Director: TBA


Structural Basis of Human Disease (GS-SB- 423)
This course is designed for medical and graduate students to understand the potential use of structural information for solving disease problems and to be aware of the different structural and computational tools. Each one hour lecture will be jointly led by two instructors who will present the medical problems and the structural approaches towards solving them. Attendance is required for passing this course.
Credits: 1 
Term: 4 
Counts for 30 hr. requirement: N 
Director: Dr. B.V. Venkatar Prasad


Advanced Topics in Structural & Computational Biology (GS-SB- 430)
This course is designed for the SCBMB students to read current literature in structural and computation biology, to critically review the papers and to present the topic in front of an audience. This is run similar to a journal club. Under the supervision of the two faculty members, each student will pick a topic area, research the necessary papers and make a 50 minute lecture presentation.
Credits: 1 
Term: 1, 2, 4 
Counts for 30 hr. requirement: N 
Director: Dr. Aleksandar Milosavljevic 


Special Projects (GS-SB- 435)
Faculty mentored research for students that have not been admitted to candidacy. Students are expected to consult with the faculty on the research topic to investigate; take part in laboratory research, read relevant literature, interact with laboratory personnel, attend regular research laboratory meetings, and report the research results to the faculty mentor regularly and at the end of the term.
Credits: Variable 
Term: 1, 2, 3, 4, 5 
Counts for 30 hr. requirement: N 
Director: Dr. Aleksandar Milosavljevic 


Special Topics (GS-SB- 463)
Scholarly study directed by a faculty member. Special topics allow a faculty member to develop individualized courses for students. Special topics cannot be used to satisfy the 30 hr course requirement.
Credits: Variable 
Term: 1, 2, 3, 4, 5 
Counts for 30 hr. requirement: N 
Director: Dr. Aleksandar Milosavljevic 


Readings (GS-SB-548)
Faculty directed literature projects that survey a specialized topic of interest in computational biology and biophysics. The student will pick a topic of interest and do a literature research after consulting with the faculty; hold regular meetings to discuss with the faculty on the chosen topics, and write up a summary report at the end of the term to provide a critical review on the state of the art knowledge of the chosen topics of study.
Credits: Variable 
Term: 1, 2, 3, 4, 5 
Counts for 30 hr. requirement: N 
Director: Dr. Aleksandar Milosavljevic 


Research Rotation (GS-SB- 549)
Faculty mentored research for students who have not yet selected a faculty advisor. 
Credits: Variable 
Term: 1, 2, 3, 4, 5 
Counts for 30 hr. requirement: N 
Director: Dr. Aleksandar Milosavljevic 


Dissertation (GS-SB-550)
Thesis research directed by a faculty mentor and advisory committee.  Open only to candidates for the Ph.D. or M.S. degree
Credits: Variable 
Term: 1, 2, 3, 4, 5 
Counts for 30 hr. requirement: N 
Director: Dr. Aleksandar Milosavljevic