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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 2020

Spring 2021


Fall 2020

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 10-November 16
Time: Mondays 4:00 PM – 5:00 PM
Location: Via Zoom

 

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 15-October 13
Time: Tuesdays and Thursdays – 11:30 AM -12:45 PM
Location: Via Zoom

 

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 sequences using state of the art sequencing platforms. Course topics will include sequence alignment, genome assembly, and computational details of contemporary protocols for DNA and RNA sequencing.

1 Credit Hour
October 15-November 17
Time: Tuesdays and Thursdays – 11:30 AM -12:45 PM
Location: Via Zoom

 

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 11-November 17
Time: Tuesdays and Thursdays – 3:00 PM – 4:15 PM
Location: Via Zoom

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
Dates: August 11-September 10
Time: Tuesdays and Thursdays – 11:30 AM – 12:45 PM
Location: Via Zoom

BCB 722_Fall 2020_Syllabus

 

BCB 725: Yun Li and Danyu Lin – Introduction to Statistical Genetics

BCB Elective Course.

This is an introductory course for graduate students in Computational Biology, Bioinformatics, Biostatistics, Genetics, Statistics, Computer Science, Epidemiology, and other related quantitative disciplines. The course will cover statistical methods for the analysis of modern genetic and genomic data. Topics will include basic principles in population genetics, commonly adopted statistical methods in genetic studies (e.g., likelihood based inference, EM algorithm, and hidden Markov models), genetic association analysis, haplotype inference, genotype imputation, meta-analysis, rare variant association analysis, and methods for massively parallel genomic sequencing data. Students will be exposed to the latest statistical methodology and computational tools on gene mapping for complex human disease.

3 Credit Hour
August 19-December 2
Time: MW – 2:40 PM – 3:55 PM
Location: Via Zoom

BCB725_Fall 2020_Syllabus

 

BCB 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 is aimed at preparing students for conducting methodological research in high-throughput transcriptomic studies. The course includes two sections: bulk RNAseq 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 followups. 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
August 19-December 2
Time: MW – 9:20 AM – 10:35 AM
Location: Via Zoom

BCB BIOS 785_Fall 2020_Syllabus

 

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

Required Course for 2nd Year BCB Students.

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 18-September 17
Time: TTH – 1:15 PM – 2:30 PM
Location: Via Zoom

 

BCB 899: Katie Hoadley, Adam Palmer, Cavin Ward-Caviness – Bioinformatics and Computational Biology Student Seminars

Required Course for 2nd and 3rd Year BCB Students.

The objective of the class is to give students in Y3+ practice at giving talks on your research to a broad audience of other quantitative students (ie, all BCB students) and to get feedback as to how they can improve. It will also give students in Y2 practice at introducing speakers.

1 Credit Hour
August 10-November 17
Time: TBA
Location: Via Zoom

Spring 2021

BCB 645: Marty Ferris – Quantitative Genetics of Complex Traits

BCB Elective Module.

1 Credit Hour
April 1-May 4
Time: TR 12:30 PM -1:45 PM
Recitation: F 1:30-2:30 PM
Location: Remote Only; Synchronous

 

BCB 710: Jesse Raab – 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 25-May 3
Time: Mondays 2:30 PM – 3:20 PM
Location: Remote Only; Synchronous

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 19-February 23

Time: TR – 11:00 AM – 12:15 PM
Lab: W – 4:00 PM – 4:50 PM
Course Location: Remote Only; Synchronous
Lab Location: Remote Only; Synchronous

 

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
March 2-April 13
Time: TR – 2:00 PM – 3:15 PM
Location: Remote Only; Synchronous

 

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 19-February 23
Time: TR – 2:00 PM – 3:15 PM
Location: Remote Only; Synchronous

 

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
January 26 – March 4
Time: TR – 3:30 PM – 4:45 PM
Location: Remote Only; Synchronous

 

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: Remote Only; Synchronous

 

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 1-March 29
Time: M – 5:00 PM – 7:10 PM
Location: Remote Only; Synchronous

 

BCB 899: Doug Phanstiel and Benjamin Vincent – Bioinformatics and Computational Biology Student Seminars

Required Course for 2nd and 3rd Year BCB Students.

The objective of the class is to give students in Y3+ practice at giving talks on your research to a broad audience of other quantitative students (ie, all BCB students) and to get feedback as to how they can improve. It will also give students in Y2 practice at introducing speakers.

1 Credit Hour
Dates: January 21-April 29
Time: 10:00 AM – 11:00 AM
Location: Remote Only; Synchronous