Clemson Genomics and Bioinformatics Courses
The 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.
GEN-8060 Molecular Diagnostics and Pathogen Genomics
students. The students will have an opportunity to explore translational research using state of the art genetic and molecular tools in a clinical laboratory setting. Through project-based learning and team formation, the students are expected to hone their skills on literature review, experimental design, research documentation, analytical thinking, presentation of results, and research leadership. The students are required to abide by all laboratory safety requirements, the Health Insurance Portability and Accountability Act of 1996 (HIPAA) law and Good Clinical Laboratory Practices (GCLP). Students enrolled in this course will be placed in projects on 1) developing methods for clinical diagnostics, or 2) performing translational research related to disease therapy. Students will have an opportunity to develop IBC/IRB protocol, design and validate molecular and biochemical assay, explore translational research on disease treatment, design point of care device / apparatus, perform genomics epidemiological surveillance of infectious disease, mentor and lead an interdisciplinary undergraduate team, draft SOP and provide digitalized high throughput solutions.
Offered Spring and Summer semesters
Required prerequisite course(s): Molecular Biology, Genetics, or equivalent
Suggested prerequisite knowledge: Knowledge of physical, chemical, and biological properties of molecules
Student population served: Graduate Students, required for majors, available to non-majors
Course instructor: Congyue Peng, congyup@clemson.edu
College of Engineering, Computing, and Applied Sciences, Department of Bioengineering
BIOE 4400/6400- Biopharmaceutical Engineering
Description: This course examines the design principles necessary to use bacteria, fungi, and mammalian cells in bioengineering applications, including molecular techniques, fermentation, process scale-up, and FDA regulations. The production of biopharmaceuticals derived from recombinant systems, including uses in medical systems, is emphasized.
Offered Fall semesters
Required prerequisite course(s): BCHM 3050 (Biochemistry). For non-majors, Math thru differential equations highly recommended.
Suggested prerequisite knowledge: Biochemistry – metabolism, structure/function of proteins, recombinant organisms
Student population served: Undergraduate and graduate students, available to non-majors
Course instructor: Sarah Harcum, harcum@clemson.edu
College of Engineering, Computing and Applied Sciences, Department of Bioengineering
PES 8060 - Variant Calling
Description: A command line-based course designed to teach you the bioinformatics
skills necessary for research projects in modern genetics, genomics, and plant breeding. We
will work through modules to call variants from sequencing data (genotyping-by-sequencing
and whole-genome resequencing), assess genetic diversity and relatedness, and link
genotype to phenotype through genetic mapping.
Offered Summer semesters
Required prerequisite course(s): GEN3000 required; GEN4400 preferred
Suggested prerequisite knowledge: Basic understanding of genetics.
Student population served: Graduate students
Course instructor: Sandra Branham, sebranh@clemson.edu
College of Agriculture, Forestry, and Life Sciences, Department of Plant and Environmental Sciences
BIOL 8710 - Special Topics (Modern Macroevolutionary Methods)
Description: This course covers best practices when implementing modern
macroevolutionary analyses using phylogenetic comparative analyses. It will consist of a
combination of mini lectures, reading, discussion and practical implementations in the statistical software ‘R’. The first section will identify the common ground between methods for
investigating continuous and discrete trait evolution as well as speciation and extinction.
Focusing on understanding the evolutionary models that are the foundations of nearly all
phylogenetic comparative methods. The second section will cover recent methodological issues identified with phylogenetic comparative methods within the literature and their potential solutions, emphasizing the usefulness of simulation-based approaches.
Offered Fall Semesters
Required prerequsite courses: None
Suggested prerequsite knowledge: Knowledge of the R statistical framework, a basic background in evolutionary biology and statistics
Student population served: Graduate Students
Course Instructor: Samantha Price, sprice6@clemson.edu
College of Science, Department of Biological Sciences
NOTE: It is planned for this course to add this course to the course catalog as a stand-alone course soon.
MATH 9810 - Statistical Genetics
Description: This course is the first of a two part series designed to familiarize students with both the traditional and advanced treatment of problems surrounding the analysis of genetics data. In particular, topics which will be covered are as follow:
- Background on data collection, cleaning, processing, imputation tech-
niques, etc. - Traditional GWAS analyses and associated techniques.
Offered: Fall semesters
Required prerequisite course(s): None
Suggested prerequisite knowledge: None
Student population served: Graduate students
Course instructor: Rajan Sekhon, sekhon@clemson.edu
College of Science, Department of Genetics and Biochemistry
GEN4450 - Medical Bioinformatics
Description: This computational biology course will provide students hands-on experience using data-intensive computational and statistical methods to discover and interpret molecular systems underlying human phenotypes. Students will build on prior Linux command line experience to learn how to employ modern data transfer techniques, workflow managers, container technology, and software repositories to process large biological datasets. Data-intensive bioinformatics workflows will be applied by the student to process large human wild-type and cancer datasets. Representative workflows include high-throughput RNA profiling, differential gene expression analysis, co-expression network analysis, biomarker discovery using artificial intelligence and network biology approaches, functional enrichment analysis, and integrating individual patient samples for precision medicine applications.
Offered Spring semesters
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
GEN 8900 - Digital Biology
Description: Biology covers many areas including ecology, medicine, genetics, zoology, agriculture, biophysics, bioengineering, biochemistry, and many more. A recent theme in biology is the generation of a lot of biological data that needs to be analyzed by computers. For instance, DNA can now be cheaply sequenced (think 23andMe) providing insights into human ancestry and medical risk factors. Digital Biology is a dynamic scientific discipline that utilizes computational and statistical methods for solving biological problems. A major theme in digital biology is to integrate and understand biological data generated by genome sequencing projects and other high-throughput molecular biology efforts. Digital biology tools are developed to reveal fundamental mechanisms underlying the structure and function of macromolecules, biochemical pathways, disease processes, and genome evolution. In this course, you will learn some of the basic computational skills you need to study biological systems. These skills include Jupyter Notebooks, the Command Line, and the Python programming language. Then you will apply these skills to real biological datasets including all human genes and the coronavirus genome. University research labs and the biotechnology industry desperately need people with these skills, and they are challenging but FUN to learn.
Offered Fall and Spring semesters
Required prerequisite course(s): N/A
Suggested prerequisite knowledge: N/A
Student population served: Graduate Students
Course instructor: Alex Feltus, ffeltus@clemson.edu
College of Science, Department of Genetics and Biochemistry
GEN8450 - Medical Bioinformatics
Description: Bioinformatics is a dynamic scientific discipline that utilizes computational and statistical methods for solving biological problems. A major theme in bioinformatics is to integrate and understand biological data generated by genome sequencing projects and other high-throughput molecular biology efforts. Bioinformatics tools are developed to reveal fundamental mechanisms underlying the structure and function of macromolecules, biochemical pathways, disease processes, and genome evolution. Medical Bioinformatics is performing bioinformatics to understand the human organism. It can be basic research, clinical research, or translational research. In this course we will focus on the basic and applied genomics workflows to understand normal and aberrant human phenotypes.
Before you apply these workflows, you will be taught how to a Linux-based research computing system and understand the formats and locations of open-source biomedical datasets. We will learn some basic data visualization and publishing techniques. The computational skills you will learn are dovetail with molecular biology skills. The skills you will learn are highly sought after in the marketplace and will position you to be a modern biologist.
Offered Spring semesters
Required prerequisite course(s): N/A
Suggested prerequisite knowledge: N/A
Student population served: Graduate students, Available to non-majors
Course instructor: Alex Feltus, ffeltus@clemson.edu
College of Science, Department of Genetics and Biochemistry
GEN 4400/GEN6400/BCHM4400/BIO6400 - Bioinformatics
Description: Bioinformatics is a dynamic scientific discipline that utilizes computational and statistical methods for solving biological problems. A major theme in bioinformatics is to integrate and understand biological data generated by genome sequencing projects and other high-throughput molecular biology efforts. Bioinformatics tools are developed to reveal fundamental mechanisms underlying the structure and function of macromolecules, biochemical pathways, disease processes, and genome evolution.
Offered Fall semesters
Required prerequisite course(s): BCHM 3010 or BCHM 3050 or GEN 3000 or GEN 3020, with C or better. (or consent from instructor)
Suggested prerequisite knowledge: Basic molecular genetics (optional)
Student population served: Undergraduate Students, Graduate Students, required for majors
Course instructor: Alex Feltus, ffeltus@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): GEN3000 or GEN3020 or MICR4150
Suggested prerequisite knowledge: A basic understanding of the DNA molecule and genetics. Basic computational skills (i.e. Excel).
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) 8900 - Introduction to Quantitative Genetics
Description: This is an introductory course that covers theory and analysis of complex traits from the genetic standpoint and does not assume any prior knowledge of the subject. The topics treated will tentatively be the following:
- Phenotypic, genetic, and environmental variation.
- Phenotypic model; additive, dominance, epistatic effects; population mean.
- Average and substitution effects; breeding value and dominance deviation; complications from epistasis.
- Variance and its components: phenotypic, genetic, and environmental.
- Inbreeding and its effect on means and variances; heterosis.
- Concepts and properties of heritability; resemblance between relatives and heritability estimation for quantitative and binary traits.
- Correlations among traits: phenotypic, genetic, and environmental.
- Quantitative Trait Locus (QTL) mapping by linkage and association.
- Artificial selection and its response. Relevant articles from the literature may also be used as a teaching tool.
Offered: Spring semesters
Required prerequisite course(s): None at this time
Suggested prerequisite knowledge: Basic genetics (e.g., Mendelian inheritance) and basic statistics (e.g. ANOVA and regression)
Student population served: Graduate Students, available to non-majors
Course instructor: Fabio Morgante, fabiom@clemson.edu
College of Science, Department of Genetics and Biochemistry
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: Fall Semesters
Required prerequisite course(s): N/A
Suggested prerequisite knowledge: Programming skill. Algorithm course.
Student population served: Graduate students, available to non-majors
Course instructor: Feng Luo, luofeng@clemson.edu
College of Engineering, Computing and Applied Sciences, School of Computing
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
Required prerequisite course(s): Instructor approval needed for background assessment.
Suggested prerequisite knowledge: Biochemistry, Calculus, Statistics
Student population served: 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
GEN 4020/6020 - Molecular Genetics & Gene Regulation
Description: The goal of this course is help you gain a fundamental understanding of the
molecular basis of genetics: DNA and RNA structure, replication, transcription,
translation, and the network of regulatory interactions that contribute to the
development of an organism, as well to understand the tools and techniques molecular
geneticists use every day. Successful completion of the course will give you familiarity
with the model systems and techniques that geneticists use to answer molecular
questions and the broader implications of molecular genetics for disease research, aging
and evolution. As a byproduct of the delivery format, you will also learn to manage your
own time & learning.
Offered Spring semesters
Required prerequisite course(s): Undergraduates: C or better in GEN 3020, GEN4010, and BCHM3020. Graduate students: Permission of Intructor
Suggested prerequisite knowledge: Basic Knowledge of Molecular Biology
Student population served: Undergraduate and Graduate Students, Required for majors
Course instructor: Julia Frugoli, jfrugol@clemson.edu
College of Science, Department of Genetics and Biochemistry
ENT 4200/6200 and 4201/6201 - 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, available to non-majors
Course instructor: Michael Caterino, mcateri@clemson.edu
College of Agriculture, Forestry, and Life Sciences, Department of Plant and Environmental Sciences
MICR 8130- Practical Bioinformatics for Microbiologists
Description: The goals of the course are to:
- Introduce students to phylogenetic and genomic characterization of microbes.
- Introduce students to methods used to analyze high-throughput sequence data
from microbes. - Perform phylogenetic and comparative analyses on microbial communities using
currently accepted technologies and available bioinformatics tools. - Students will, during and outside class, independently analyze one of the
following and present their results in both written and oral form:- General comparisons of different (at least 2) microbial metagenomes or 6
genomes in terms of both phylogenetic diversity and functional potential. - Comparisons between functional potential of a metagenome (or genome)
and its gene expression (metatranscriptome/transcriptome) under at least
2 conditions (control and other, or two different environmental samples). - Assemble/annotate at least one genome from related metagenomes.
- Other data (own or otherwise agreed on between instructor and student).
- General comparisons of different (at least 2) microbial metagenomes or 6
Offered Spring semesters
Required prerequisite course(s): Microbiology coursework as an undergraduate or graduate student
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
BIOE 4470/6470 - Synthetic Biology Fundamentals
Description: Synthetic biology applies engineering principles to design and implement new
biological systems and living organisms. The course will cover approaches and tools for biological design, modeling, implementation, and debugging. Topics include gene regulatory networks, DNA assembly, modeling, biosensor development, and applications in the clinic, industry, and the environment. The class will primarily emphasize genetic modification of bacteria, although the field generally extends to applications in plants, fungi, and even humans (e.g., engineered T-cells).
Offered Spring semesters
Required prerequisite course(s): MATH 2080
Suggested prerequisite knowledge: Basic understanding of biology; ordinary differential equation models (e.g., MATH 2080); scripting in Matlab or other similar packages/languages.
Student population served: Undergraduate and Graduate Students; available to non-majors
Course instructor: David Karig, dkarig@clemson.edu
College of Engineering, Computing, and Applied Sciences, Department of Bioengineering
PES 4050/6050 - Plant Breeding and Genetics
Description: Introduction to general principles, practices, and techniques used to
breed plants, select traits, and develop crop cultivars. Concepts discussed will range from quantitative and population genetics, historical through conventional plant breeding (through self- and cross-pollinations) and hybridization, then end with exploration of contemporary approaches to improve plant traits including molecular breeding and genetic engineering. The course will also explore the interrelationships between mode of reproduction in plants and breeding methods.
Offered Spring semesters
Required prerequisite course(s): GEN 3000
Suggested prerequisite knowledge: Basic statistics, working knowledge of plant biology
Student population served: Undergraduate and graduate students; required for majors, available to non-majors
Course instructor: Christopher Saski, saski@clemson.edu
College of Agriculture, Forestry, and Life Sciences, Department of Plant and Environmental Sciences
BIOL 4850 - Molecular Phylogenetics and the Comparative Method
Description: The use of molecular markers for unraveling evolutionary relationships is currently widespread and the importance of molecular phylogenies and phylogenetically corrected comparative methods in many fields of evolutionary biology is now recognized as
invaluable. Molecular phylogenies and comparative methods have advanced, among
others, the study of adaptation, biogeography, coevolution and cospeciation, and the
tempo and mode of diversification. Molecular markers and phylogenetics have also
become increasingly important in applied sciences, including human welfare, forensics,
conservation biology, resource management, and invasion ecology.
Offered Fall semesters
Required prerequisite course(s): BIOL 1100, 1110 and 3350
Suggested prerequisite knowledge: BIOL 1100, 1110 and 3350
Student population served: Undergraduate and Graduate Students
Course instructor: J. Antonio Baeza, jbaezam@clemson.edu
College of Science, Department of Biological Sciences
MICR (BIOL) 4940/4941- Microbial Ecology and Bioinformatics
Description: Students will develop individual proposals including benchmarks for progress, and receive feedback at weekly group and individual meetings, on technical, composition,
and social development.
Offered Fall and Spring semesters
Required prerequisite course(s): General Biology and Chemistry laboratory-based courses
Suggested prerequisite knowledge: General Microbiology coursework
Student population served: Undergraduate Students; Available to non-majors; Creative Inquiry for undergraduate experiential learning
Course instructor: Barbara Campbell, bcampb7@clemson.edu
College of Science, Department of Biological Sciences
BCHM (GEN) 8900 - Regulatory Genomics
Description: In this course, we will talk about concepts of gene regulation and using
computational and statistical methods, computer programs, to solve genomics problems. Specifically, we will talk about the role of transcription factors and chromatin in gene regulation, functional genomics data types, analysis pipelines, computational methods and strategies, results interpretation, and plotting figures. The goal is to understand functional genomics and some concepts of gene regulatory networks. We will learn skills to use software to analyze public data as well as your data, such as identifying cell populations, identifying cis-regulatory elements and the master transcription factors, constructing gene regulatory networks, performing a comparison between two conditions based on genomics data,and studying dynamics of gene regulation.
Offered: Spring semesters
Required prerequisite course(s): None
Suggested prerequisite knowledge: Knowledge of statistic and basic programming background is recommended but not required.
Student population served: Graduate Students, required for majors, available to non-majors
Course instructor: Zhana Duren, zduren@clemson.edu
College of Science, Department of Genetics and Biochemistry
BCHM 4360 - Molecular Biology: 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 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
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
HCG 9150- Principles of Pharmacogenomics
Offered alternating spring semesters
Required prerequisite course(s): N/A
Suggested prerequisite knowledge: A basic background in genetics
Student population served: Graduate students
Course instructor: Christopher Farrell, clf@clemson.edu
College of Behavioral, Social and Health Sciences, School of Nursing
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