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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 2023

Spring 2024

Fall 2023

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 21-December 4
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 28-October 31
Time: Tuesdays and Thursdays – 11:00 AM -12:15 PM
Location: 6004 Marsico Hall

 

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 22-December 5
Time: Tuesdays and Thursdays – 2:00 PM – 3:15 PM
Location: 6004 Marsico Hall

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 22-September 26
Time: Tuesdays and Thursdays – 11:00 AM -12:15 PM
Location: 6004 Marsico Hall

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
November 2-December 5
Time: Tuesdays and Thursdays – 11:00 AM -12:15 PM
Location: 6004 Marsico Hall

BCB 724 – Data Communication

 

BCB 731:  Alexander Rubinsteyn – Critical Readings in Biomedical Statistics and Machine Learning

BCB Elective Module.

BCB 731 (Critical readings in biomedical statistics and machine learning), is a new course that explores the myriad ways in which high profile biomedical research findings turn out to be wrong. The course is structured as a survey with each week focusing on a paper that exemplifies a specific misapplication of statistics or machine learning. Though a few instances of outright fraud are discussed, the primary focus is the hazy space in which good intentions meet motivated reasoning and high dimensional data.

2 Credit Hours
October 2-December 6
Time: Mondays and Wednesdays – 2:00 PM – 3:15 PM
Location: 5004 Marsico Hall

BCB 731 Fall 2023 Syllabus

 

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 22-October 5
Time: TTH – 12:15 PM – 1:30 PM
Location: 3104 Mary Ellen Jones Building

 

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 24-November 30
Time: TH 10:00 AM – 11:00 AM
Location: 1131 Bioinformatics Building

Spring 2024

BCB 645: Marty Ferris – Quantitative Genetics of Complex Traits

BCB Elective Module.

1 Credit Hour
Dates: January 11-February 8
Time: TR 12:30 PM -1:45 PM
Recitation: F 1:30-2:45 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 10 – April 29
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 15-March 27

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

 

BCB 718: Adam Palmer – Computational Modeling Laboratory

BCB Elective Module.

This module provides a hands-on, laboratory-style course on computational modeling of biological systems.
Students will develop a model of their own choosing and be responsible for all aspects of its design, construction, simulation, and analysis.

1 Credit Hour
Dates: February 6-March 19
Time: TR – 2:00 PM – 3:15 PM *TBA
Location: 3112 Mary Ellen Jones Building

 

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 11-February 15
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 11-February 15
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: Elisa Pieri and Daniel Dominguez – 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
Dates: January 11 – April 25
Time: Thurs 10:00 AM – 11:00 AM
Location: 1131 Bioinformatics Building