Current Course Schedule

Click on a course title to navigate to its description. Key: ** required for PhD curriculum and BCB certificate program; * required for PhD curriculum only.

Fall 2024

BCB 710: Will Valdar – Bioinformatics Colloquium

(Fall – Faculty Seminar Presentations & Computing Workshop)

Curriculum seminar course. Required for First 4 Semesters for BCB PhD Program*. Required for 4 Semesters for BCB Certificate Program. Includes research seminars from BCB faculty, student Q&A session, and a short computing workshop on unix and the computing cluster.

1 Credit Hour
August 19-December 2
Time: Mondays 4:00 PM – 5:00 PM
Location: 1131 Bioinformatics Building

BCB 715: Tim Elston – Mathematical Modeling of Gene Networks and Signaling Pathways

BCB Core Module.

This module provides an introduction to the basic mathematical techniques used to develop and analyze models of biochemical networks. Both deterministic and stochastic models are discussed.

1 Credit Hour
September 26-October 29
Time: Tuesdays and Thursdays – 2:00 PM – 3:15 PM
Location: 3112 Mary Ellen Jones (9/26, 10/8, and 10/10); 6004 Marsico Hall (All Other Dates)

BCB 715 Syllabus

BCB 720: Will Valdar – Introduction to Statistical Modeling

BCB Core Course.

This module introduces foundational statistical concepts and models that motivate a wide range of analytic methods in bioinformatics, statistical genetics, statistical genomics, and related fields. Students are expected to know single-variable calculus (differentiation and integration in 1 dimension), be familiar with matrix algebra and have some programming experience. The course will include material on partial differentiation of multiparameter functions, and use the statistical package R extensively. Familiarity with these will be an advantage but is not assumed.

3 Credit Hours
August 20-December 3
Time: Tuesdays and Thursdays – 11:00 AM -12:15 PM
Location: 2004 Marsico Hall (3116 Mary Ellen Jones on 9/24 and 9/26)

Syllabus Requirements/Preparatory Reading

BCB 722: Daniel Schrider – Topics in Population Genetics

BCB Core Module.

This module will cover methods of inferring/estimating natural selection, including the Dn/Ds ratio, the McDonald-Kreitman test, and the Poisson Random Field model. The course will feature discussions of high-profile publications that describe the application of these methods to yield insights into the forces that have shaped organismal evolution.

1 Credit Hour
August 20-September 24
Time: Tuesdays and Thursdays – 2:00 PM – 3:15 PM
Location: 6004 Marsico Hall (3112 Mary Ellen Jones on 9/24)

BCB 722_Fall 2020_Syllabus

BCB 724: Michael Love – Data Communication

BCB Core Module.

This module is designed to prepare students to be effective communicators of the results of analyses of biological and biomedical data. Students will learn methods for data assessment and exploratory data analysis (EDA), and how to visualize, write, and talk about data in contexts such as emails, reports, lab meetings, publications, and conference presentations.

1 Credit Hour
October 31-December 3
Time: Tuesdays and Thursdays – 2:00 PM – 3:15 PM
Location: 6004 Marsico Hall

BCB 724 – Data Communication

BCB 784: Michael Love – Introduction to Computational Biology

BCB Elective Course.

Introduction to molecular biology and genomics, high-throughput sequencing data and its application in computational biology, high dimensional data visualization and normalization, EM algorithm, hidden Markov models, computational biology applications using R and Bioconductor. This course makes extensive use of R and assumes basic familiarity with base R as a prerequisite. Cross-listed as BIOS 784.

3 Credit Hours
August 19-December 6
Time: Mondays and Wednesdays – 1:25 PM – 2:40 PM
Location: McGavran-Greenberg Hall 2306 (School of Public Health)

BCB 784 – Introduction to Computational Biology

BCB 870: Jason Stein – Grant Writing for Bioinformaticians and Computational Biologists

Required Course for 2nd Year BCB Students. [Students may defer this to their 3rd year only with written permission from both their advisor(s) and the BCB director.]

This course is designed to teach grant writing to graduate students in bioinformatics and computational biology. The course will start with an introduction to major funding agencies and their organization. Then, there will be lecture on grantsmanship. After that, we will hold multiple mock review panels for example grants or grants written by the students in the course. Students are expected to both write grant applications and to review those grant applications. After taking this course, students should be familiar with skills needed for grant writing and have familiarity with the process of grant review.

1 Credit Hour
August 20-October 3
Time: TTH – 12:15 PM – 1:30 PM
Location: 3112 Mary Ellen Jones

BCB 899: Katie Hoadley and Jeremy Wang – Bioinformatics and Computational Biology Student Seminars

Required Course for 2nd and 3rd Year BCB Students. Y4+ students are required to present once per year.

The objective of the class is to give students in Y3+ practice at giving talks on their research to a broad audience of other quantitative students (ie, all BCB students) and to get feedback as to how they can improve. It gives students in Y2 practice introducing speakers. Student talks are generally scheduled so that more senior students speak earlier in the semester. Senior students who are scheduled to defend early in the same semester are given special flexibility: they may opt out of giving a seminar talk entirely, or, in consultation with BCB leadership or the instructor, may give an alternative type of presentation aimed at benefiting the student audience (eg, a retrospective on tips gleaned from their PhD, etc.).

1 Credit Hour
August 22-November 21
Time: TH 10:00 AM – 11:00 AM
Location: 1131 Bioinformatics Building

Spring 2025

BCB 645/GNET 645: Marty Ferris – Quantitative Genetics of Complex Traits

BCB Elective Module.

1 Credit Hour
Dates: January 9-February 11
Time: TR 11:00 AM -12:15 PM
Recitation: F 1:30-2:30 PM
Location: 2004 Marsico Hall

BCB 710: Anthony Zannas – Bioinformatics Colloquium

(Spring – Journal Club)

Curriculum seminar course. Required for First 4 Semesters for BCB PhD Program*. Required for 4 Semesters for BCB Certificate Program.

1 Credit Hour
Dates: January 13 – April 28
Time: Mondays 4:00 PM – 5:00 PM
Location: 1131 Bioinformatics Building

BCB 717/BIOC 670: Konstantin Popov – Structural Bioinformatics

BCB Core Module.

This module introduces methods and techniques for protein modeling including structure determination, protein architecture, approaches to folding simulations, structure prediction, and structure based drug design.

1 Credit Hour
Dates: February 11-March 24

Time: TR – 2:00 – 3:15 PM
Lab: M – 12:00 PM – 2:00 PM
Course Location: 2004 Marsico Hall
Lab Location: TBA

BCB 717 Syllabus

BCB 723: Yun Li and Fei Zou – Topics in Statistical Genetics and Genomics

BCB Elective Module.

The module will cover concepts, techniques, statistical methods for the analysis of genetic and genomic data. Topics covered will include classical linkage analysis, population-based and family‐based association analysis, genome‐wide association studies, basic principles in population genetics, analysis of next-generation or massively parallel sequencing data, and analysis of Hi-C data. Students will be exposed to the latest statistical methodology and computational tools on gene mapping for complex human disease.

1 Credit Hour
Dates: January 9-February 11
Time: TR – 12:30 PM – 1:45 PM
Location: 3112 Mary Ellen Jones Building

BCB/GNET 730: Michelle Itano and Teresa Ropp – Fundamentals of Quantitative Image Analysis for Light Microscopy

BCB Elective Module.

The module is a practical introduction to quantitative analysis of light microscopy images. During the class students will follow tutorials that will guide them through common tasks in analysis of biological images. They will be introduced to basic concepts of image processing like image registration, filtering, object detection etc.

1 Credit Hour
Dates: January 9-February 11
Time: TR – 3:00 PM – 4:30 PM
Location: 3116 Mary Ellen Jones Building

BCB 888: Various Faculty – Responsible Conduct of Research *New Information Pending

Responsible conduct of research is a classroom-based graduate level course covering critical topics for ethical and responsible conduct of experimental research. There are both classroom lecture, workshop-type discussion components, in addition to assigned outside of class readings. Case studies and hypothetical situations involving the most likely scenarios confronting graduate students will be covered, these topics include: mentor and mentee relationships, publication authorship, collaboration, peer review, conflicts of interest, intellectual property, plagiarism, data acquisition and data processing.

This is a refresher course for students in their 4th year, following up on RCR instruction they had in BBSP First Year Groups. Students defending in the same semester as this refresher course may request an exemption.

1 Credit Hour
Dates: TBA
Time: F – 2:30 PM – 4:00 PM *TBA
Location: TBA

BCB 899: Daniel Dominguez and Qingyun Liu – Bioinformatics and Computational Biology Student Seminars

Required Course for 2nd and 3rd Year BCB Students. Y4+ students are required to present once per year.

1 Credit Hour
Dates: January 30 – April 24
Time: Thurs 10:00 AM – 11:00 AM
Location: 1131 Bioinformatics Building

Summer 2025

BCB 990 Research Practicum/Internship in Bioinformatics and Computational Biology

BCB optional course, typically for Y3+ onwards.

The Research Practicum/Internship in Bioinformatics and Computational Biology (BCB) is a planned, individualized, mentored, evaluated, experiential learning opportunity that serves as a bridge between academic training and post-training practice. The internship/practicum provides special opportunities for learning that are different from, supplementary to, and supportive of the academic components of the PhD program. The internship/practicum is open to both domestic and international students. More information at the course webpage.

1-9 Credit Hours (variable)

Dates/Location: to be determined as part of setting up the practicum.