These are the graduate courses that CCIB has in regular rotation. To see what is being offered in the upcoming semester, please visit the University Schedule of Classes.

Essentials Courses

Essentials of Biomathematics (56:121:520) Lecture; 3 hours; 3 credit. Topics of biomathematics required for research in computational and integrative biology. Co-requisite: 56:121:523  Syllabus From Spring 2022. 

Essentials of Biomathematics Recitation (56:121:520) Seminar; 1 hours; 1 credit. Applied problem solving recitation to accompany 56:121:521. Co-requisite: 56:121:520  Syllabus From Spring 2022. 

Essentials of Computer Science (56:121:530) Lecture; 3 hours; 3 credit. Topics of Computer Science required for research in computational and integrative biology.  Syllabus from Spring 2022   

Essentials of Integrative Biology (56:121:540) Lecture; 3 hours; 3 credits. Topics of systems biology required for research in computational and integrative biology. Syllabus From Fall 2021. 

Essentials of Biophysics (56:121:565)  Lecture; 3 hours; 3 credits.  A course in basic physics for graduate students with an emphasis in the life sciences. The course will focus on classical Newtonian dynamics, electrostatics, thermodynamics, and fluid dynamics with applications for molecular and cellular systems. Students will also conduct multiple readings from current topics in biophysics for classroom discussion, including DNA electrostatics, diffusion of lipids and proteins, molecular motors, and biodynamics. Syllabus From Fall 2020

Seminars and Workshops

Seminar in Computational and Integrative Biology (56:121:601) Lecture; 1 hour; 1 credit. Research presentations by students, faculty, and outside speakers. Open to students in the graduate program in computational and integrative biology. Syllabus From Spring 2022. 

Laboratory Practices (56:121:620) Seminar; 1 hour; 1 credit. A course in Responsible Conduct of Research that fulfills federal requirements for scientific trainees. Fourth-year PhD students and Post-doctoral fellows may audit to keep their RCR training current. Syllabus From Fall 2021. 

Manuscript and Proposal Composition (56:121:630)
Seminar; 1 hour; 1 credit. This workshop, intended for second-year PhD students, is an introduction to writing in the scientific genre, with a focus on preparation of proposals and manuscripts. Students will be guided through preparation of a short manuscript, learn expectations for publication-quality data, figures, and text, and hone their ability to write scientifically through feedback from the instructor and peers. If space is available, the course is open to second-year MS students (thesis track) with the permission of the instructor and advisor. Syllabus from Fall 2021.

Formal Electives

Molecular Biophysics (56:121:560)  Lecture; 3 hours; 3 credits.  A biophysics course for graduate students with at least two semesters of undergraduate physics, intended for students trained in either the physical or life sciences. Themes will include both novel physical insights gained from study of biological systems as well as the power of physical descriptions for advancing biological understanding. The course will explore random and diffusive phenomena in cellular processes, the effect of frictional forces on molecular motion in the low Reynolds number environment of the cell, and the role of entropy and free energy in driving reactions and assembly. Syllabus From Spring 2021

Cell Membranes (56:121:560)  Lecture; 3 hours; 3 credits.  A biophysics course for graduate students with at least two semesters of undergraduate physics, intended for students trained in either the physical or life sciences. Themes will include both novel physical insights gained from study of biological systems as well as the power of physical descriptions for advancing biological understanding. The course will explore random and diffusive phenomena in cellular processes, the effect of frictional forces on molecular motion in the low Reynolds number environment of the cell, and the role of entropy and free energy in driving reactions and assembly. Syllabus From Spring 2022

Genome Informatics (56:121:552) Lecture; 3 hours; 3 credits. This course teaches common principles, concepts and methodologies for genome-scale data analysis driven by biological questions. It explains the application of typical analytical approaches to such data and the reasoning to infer biological meaning from the results. This is a graduate course that usually gathers students with very different backgrounds. It consists of lectures, intense practical homework, active joint discussions of topics and journal club-like student presentations of recent scientific literature (individually and in teams), as well as analysis/programming projects. Many of these activities are assigned individually based on the student’s background in biology, math and programming (which are assessed in the first weeks during student presentations of their own prior research experiences). Advanced undergraduate students may be allowed to  take this course at the sole discretion of the instructor. Syllabus from Fall 2021.

Other Courses: Nearly all 3-credit graduate courses in Biology, Chemistry, Computer Science, and Mathematics also count as Formal Electives. Furthermore, most 300 and 400-level courses in Physics can be taken as a CCIB graduate cross-list.

Rotation, Research, and Independent Study

Laboratory Rotation Practicum (56:121:620) Time by Arrangement; 3 credits. Short-term involvement in a series of projects in different research laboratories over the course of a semester. Open to students in the graduate program in computational and integrative biology.

Independent Study (56:121:585) Time and Credits by Arrangement. Prerequisite: Permission of advisor. Focused literature review and composition of the Capstone Project for a non-thesis based MS. The capstone project will be designed and conducted in consultation with a sponsor from the CCIB faculty.  Open to thesis-based MS students and PhD students for the purpose of structured independent study, with the permission of the Graduate Program Director. 

Master’s Project (56:121:701) Time by Arrangement; 6 credits. Prerequisite: Permission of advisor and approval of thesis committee. Required project for master’s degree (thesis track) in computational and integrative biology. 

Dissertation Research (56:121:710) Time and Credits by Arrangement. Prerequisite: Permission of advisor. 
Research toward a doctoral degree or thesis-based MS in computational and integrative biology.