Fall 2019

 

BCB 710: Will Valdar – Bioinformatics Colloquium

(Fall – Faculty and Senior Student Presentations)

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

1 Credit Hour
August 26-December 2
Time: Mondays 2:30-3:30 PM
Location: G074 Bondurant Hall

 

BCB 715: Tim Elston – Bioinformatics and Mathematics Modeling

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 24-October 24
Time: Tuesdays and Thursdays – 11:00 AM -12:15 PM
Location: 3106 Mary Ellen Jones

 

BCB 716:  Joel Parker and Jan Prins – Sequence Analysis

BCB Core Module.

This module is designed to introduce students to concepts and methods in the comparative analysis of nucleic acid and protein sequences, including sequence alignment, homology search, phylogenetics and genome assembly.

1 Credit Hour
October 29-December 3
Time: Tuesdays and Thursdays – 11:00 AM -12:15 PM
Location: 3106 Mary Ellen Jones

 

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 – 9:30 AM -10:45 AM
Location: 6004 Marsico Hall

Course Description & Syllabus

 

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
Dates: August 20-September 19

Time: Tuesdays and Thursdays – 11:00 AM – 12:15 PM
Location: 3106 Mary Ellen Jones

 

Spring 2020

 

BCB 710: Will Valdar – 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
January 13-April 24
Time: Mondays 2:30-3:30 PM
Location: TBA Bondurant Hall

BCB 717: Andrew Leaver-Fay – 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
January 9-February 11

Time: TR – 9:30 am – 10:45 am
Lab: W – 3:35 am – 4:25 pm

Location: TBA Marsico Hall

 

BCB 718: Jeremy Purvis – 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
February 13-March 24
Time: TR – 2:00 pm– 3:15 pm
Location: TBA Marsico Hall

 

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
January 9-February 11
Time: TR – 12:00 pm– 1:15 pm
Location: TBA Bondurant Hall

 

BCB 730: Kasia Kedziora and Jeremy Purvis – 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
March 24 – April 23
Time: TR – 3:30 pm – 4:45 pm
Location: TBA

 

BCB/BIOS 785: Yuchao Jiang – Statistical Methods for Gene Expression Analysis

BCB Elective Course.

This course is designed to provide graduate students interested in statistical genetics and genomics with an opportunity to gain or enhance knowledge in gene expression analysis by next-generation sequencing. The course includes two sections: bulk RNA-seq and single-cell RNA-seq (scRNA-seq). Each section starts with biological background, followed by statistical and computational methods, and finishes with biological interpretations and follow-ups. Topics include: data normalization, measurement of error models, dispersion shrinkage, dimensionality reduction, zero-inflated factor analysis, batch correction, clustering algorithm, deconvolution, pseudotime reconstruction, deep neural network, and autoencoder, etc.

3 Credit Hour
January 9-April 23
Time: TR – 11:00 am– 12:30 pm
Location: TBA McGavran-Greenberg Hall

 

BCB 888: Various Faculty – Responsible Conduct of Research

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.

1 Credit Hour
Dates To Be Announced
Time: F – 2:30 pm– 4:00 pm
Location: To Be Announced

 

BCB 891: Katherine HoadleyChuck Perou, & Greg Forest – Cancer Genomics and Class Discovery

BCB Elective Module.

The objectives of this module are to: Gain an understanding of the genomic data types being collected on human tumors; Learn about the basics of RNA and DNA NGS sequence analysis; Learn about pattern discovery tools including hierarchical clustering and biclustering; Understand the challenges of integrating heterogeneous data types; and learn real world examples of complex data integration for class discovery.

1 Credit Hour
February 17-March 30
Time: M – 5:00 pm– 7:00 pm
Location: To Be Announced