Clemson Genomics and Bioinformatics Courses

ENT 4200/6200The courses listed below reflect some but not all courses offered at Clemson University related to genomics and bioinformatics. If you are a student and would like to learn more about the courses described below, please contact the course instructor listed under their respective course. If you are an instructor and would like to have your course listed below, please contact us.

BCHM (GEN) 4400- Bioinformatics

Description: Major topics to be discussed in the course include: sequence analysis & algorithms, gene annotation, protein sequence analysis, proteomics, gene expression analysis, comparative genomics, genetic networks and pathways analysis, and systems biology.

Offered Fall semesters

Required prerequisite course(s): BCHM 3010 or BCHM 3050 or GEN 3000 or GEN 3020

Suggested prerequisite knowledge: Basic knowledge of molecular biology and statistics

Student population served: Undergraduate and graduate students, required course for majors

Course instructor: Alex Feltus, ffeltus@clemson.edu

College of Science, Department of Genetics and Biochemistry

GEN 4900- Biomedical Informatics

Description: This is an applied genomics “lab” course.  The student learns how to use high performance computing systems (e.g. Clemson’s Palmetto supercomputer) to run huge genomics datasets (e.g. The Cancer Genome Atlas) through computational genomics workflows.  Core skill development includes command line usage, bash scripting, and Python programming.

Offered Spring semesters, odd number years

Required prerequisite course(s): N/A

Suggested prerequisite knowledge: N/A

Student population served: Undergraduate students, Available to non-majors

Course instructor: Alex Feltus, ffeltus@clemson.edu

College of Science, Department of Genetics and Biochemistry

MICR 8130- Practical Bioinformatics for Microbiologists

Description: The goals of the course are to:

1) Introduce students to phylogenetic and genomic characterization of microbes.

2) Introduce students to methods used to analyze high-throughput sequence data from microbes.

3) Perform phylogenetic, comparative genome and RNAseq analyses on microbial communities using currently accepted technologies and available bioinformatics tools.

Offered Fall semesters, even number years

Required prerequisite course(s): N/A

Suggested prerequisite knowledge: Knowledge of microbiology, some genomics

Student population served: Graduate students, available to non-majors

Course instructor: Barbara Campbell, bcampb7@clemson.edu

College of Science, Department of Biological Sciences

MICR (BIOL) 4940/4941- Microbial Ecology and Bioinformatics

Description: This Creative Inquiry course immerses students in analyzing metagenome and metatranscriptome data from aquatic samples.  They will investigate links between microbial composition, function and changes in the environment.

Offered Fall and Spring semesters

Required prerequisite course(s): Junior level standing

Suggested prerequisite knowledge: Microbiology

Student population served: Undergraduate students, Available to non-majors and Creative Inquiry

Course instructor: Barbara Campbell, bcampb7@clemson.edu

College of Science, Department of Biological Sciences

BIOL 4930- Senior Seminar- Genomics

Description: Nearly all fields of biology have been impacted by the genomic revolution.  As costs of sequencing DNA have decreased, being able to understand the genetic blueprint used to build an organism has influenced medicine, changed how we understand evolution and diversity, and even entered our daily lives through ancestry and genetic testing.  During this course, we will examine various applications of genomics through discussion of scientific and non-scientific literature.

Offered Fall and/or Spring semesters

Requires prerequisite course(s): Senior level standing

Suggested prerequisite knowledge: Molecular biology and critical thinking skills for reading primary literature. No expectations of knowledge of genomics techniques.

Student population served: Undergraduate students, required course for majors

Course instructor: Kara Powder, kpowder@clemson.edu

College of Science, Department of Biological Sciences

BIOE 4400/6400- Biopharmaceutical Engineering

Description: Students learn how to apply quantitative descriptions of cell growth in bioreactors to predict outcomes. Students learn about the different modes of operating industrial bioreactors to optimize growth and productivity. These goals require the students to use fundamental knowledge of cell metabolism and recombinant technology to achieve desired outcomes.

Offered Fall semesters

Required prerequisite course(s): BCHM 3050; other biochemistry accepted

Suggested prerequisite knowledge: Math thru differential equations

Student population served: Undergraduate and graduate students, Required course for majors, available to non-majors

Course instructor: Sarah Harcum, harcum@clemson.edu

College of Engineering, Computing and Applied Sciences, Department of Bioengineering

PHYS 8190- Computational Biophysics

Description: The course introduces basic concepts about molecular biophysics and the objects being considered: proteins, DNA and RNAs. The role of amino acid and nucleic acid sequences, three dimensional structure and macromolecular interactions are outlined and appropriate computational tools are demonstrated. The course ends with linkage between human diseases, their genetic origin and connection with DNA variants.

Offered Spring semesters

Required prerequisite course(s): N/A

Suggested prerequisite knowledge: Basic protein science, molecular biophysics and genetics.

Student population served: Graduate students, elective graduate course

Course instructor: Emil Alexov, ealexov@clemson.edu

College of Science, Department of Physics and Astronomy

PHYS 8750- Methods and Resources for Modeling Effects of Human DNA Variations

Description: Teaches basic molecular mechanisms associated with disease risk, outlines tools that can be used to investigate the effects of non-synonymous variants and how the disease-causing effects may be targeted via structure-based drug design.

Offered Fall and Spring semesters

Required prerequisite course(s): N/A

Suggested prerequisite knowledge: Basic protein science, molecular biophysics and genetics.

Student population served: Graduate students, elective graduate course

Course instructor: Emil Alexov, ealexov@clemson.edu

College of Science, Department of Physics and Astronomy

CHE 8450- Systems Biology and Pharmacology

Description: Students learn contemporary theory and practical computation (python) related to dealing with big bioinformatics data such as mRNAseq, and dealing with “small” systems biology data such as single cell time courses. They also learn how to interpret that data to learn biology through application and case study.

Offered Fall semesters, even number years

Required prerequisite course(s): Biochemistry, Calculus, Statistics

Suggested prerequisite knowledge: Biochemistry, Calculus, Statistics

Student population served: Undergraduate and graduate students, available to non-majors

Course instructor: Marc Birtwistle, mbirtwi@clemson.edu

College of Engineering, Computing and Applied Sciences, Department of Chemical and Biomolecular Engineering

BIOL 4850- Molecular Phylogenetics and the Comparative Method

Description: Phylogenetic and diversification analyses using morphology and molecular characters. Comparative methodology including independent contrasts (using both continuous and discrete variables), reconstruction of ancestral character states, molecular clock and estimation of divergence times, diversification and the effect of traits on diversification, historical biogeography, and coevolution.

Offered Fall semesters, even number years

Required prerequisite course(s): BIOL 1100, 1110 and 3350

Suggested prerequisite knowledge: BIOL 1100, 1110 and 3350

Student population served: Graduate and undergraduate students interested in phylogenetics and diversification

Course instructor: J. Antonio Baeza, jbaezam@clemson.edu

College of Science, Department of Biological Sciences

BCHM 4360- Genes to Proteins

Description: This course is a rigorous in-depth study of DNA replication, transcription, and translation.  The course involves primary literature to reinforce the material learned from lecture.

Offered Spring semesters

Required prerequisite course(s): BCHM 3050 or BCHM 3010

Suggested prerequisite knowledge: The student should have a command of basic biochemistry as we dive into detail of DNA replication, transcription and translation.

Student population served: Undergraduate and graduate students, required course for majors, available to non-majors, graduate students regardless of field

Course instructor: Michael Sehorn, msehorn@clemson.edu

College of Science, Department of Genetics and Biochemistry

BIOL 4030/6030- Introduction to Applied Genomics

Description: An Introduction to Applied Genomics introduces students to broad range of genomic and bioinformatic skills. Core components of the course include an introducing to the Linux command line environment, principles of next generation sequencing (NGS) technology, and numerous techniques associated with the downstream processing and analysis of genomic data. These techniques include genome assembly, gene prediction, annotation, databases, gene/genome clustering, recombination detection, phylogenomics, transcriptomics, and metagenomics. The course has a strong emphasis on the practical application of bioinformatics skills (in particular the use of LINUX/bash) to solve biological problems, with these activities incorporated into the majority of course work.

Offered Fall semesters

Required prerequisite course(s): Any into biology course

Suggested prerequisite knowledge: A basic understanding of the DNA molecule and genetics.

Student population served: Undergraduate and graduate students, available to non-majors

Course instructor: Vince Richards, vpricha@clemson.edu

College of Science, Department of Biological Sciences

BCHM/GEN 4400/4400H/6400- Bioinformatics

Description: Bioinformatics is an interdisciplinary field that develops and applies computational and statistical methods to solve biological problems. All students in this course will learn how to use the available software tools to solve biological problems. Although basic programming concepts will be introduced in this course, students are not required to write their own software programs.

Offered Spring semesters

Required prerequisite course(s): BCHM 3010 or BCHM 3050 or GEN 3000 or GEN 3020

Suggested prerequisite knowledge: Basic knowledge of genetics or biochemistry

Student population served: Undergraduate and graduate students, required course for majors, available to non-majors

Course instructor: Liangjiang Wang, liangjw@clemson.edu

College of Science, Department of Genetics and Biochemistry

MATH 9810- Statistical Genetics

Description: This course is designed to familiarize students with both the traditional and advanced treatment of problems surrounding the analysis of genetic data.

Offered: Contact course instructor(s) for when this course is offered

Required prerequisite course(s): Math 8050 or equivalent

Suggested prerequisite knowledge: Basic applied and theoretical statistics

Student population served: Graduate students

Course instructor: Billy Bridges, wbrdgs@clemson.edu and Christopher McMahan, mcmaha2@clemson.edu

College of Science, School of Mathematical and Statistical Sciences

CPSC 8650 - Bioinformatics Algorithms

Description: Covers algorithms such as dynamic programming for biological problems, including sequence alignment and phylogeny tree constructions; statistical and mathematical modeling of high throughput data, such as differentially expressed genes from microarray data and HMM for gene prediction; graph and network theory for biological networks.

Offered: Spring Semesters

Required prerequisite course(s): N/A

Suggested prerequisite knowledge: N/A

Student population served: Graduate students

Course instructor: Feng Luo, luofeng@clemson.edu 

College of Engineering, Computing and Applied Sciences, School of Computing

ENT 4200/6200 - Systematics and Biodiversity

Description: In this course we discuss (and practice) reconconstructing evolutionary relationships, interpreting phylogenies, uses of phylogenies in evolutionary and conservation biology, and what we now know about the tree of life.

Offered: Spring semesters, even number years

Required prerequisite course(s): BIOL 3350

Suggested prerequisite knowledge: Basic understanding of genetics and evolution

Student population served: Undergraduate and Graduate students

Course instructor: Michael Caterino, mcateri@clemson.edu

College of Agriculture, Forestry, and Life Sciences, Department of Plant and Environmental Sciences

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