Graduate programs that offer courses in Genomics
MCB: Molecular and Cell Biology
HBM: Molecular Genetics and Microbiology
BGE: Genetics
MAR: Marine Sciences
BME: Biomedical Engineering
BEE: Ecology and Evolution
CSE: Computer Sciences
PHY: Physics
CHE: Chemistry
Graduate Courses
MCB 503: Molecular Genetics
Introduces the classical work and current developments in lower and higher genetic systems. Covers gene structure and regulation in prokaryotic and eukaryotic organisms, mutational analysis and mapping, transposable elements, and biological DNA transfer mechanisms. Bacteriophage as well as lower and higher eukaryotic systems are used to illustrate aspects of molecular genetic structure and function. This course is offered as both MCB 503 and HBM 503. Prerequisite: matriculation in graduate program or permission of instructor
Fall, 3 credits, Letter graded (A, A-, B+, etc.)
MCB 555: Big Data in Biology
An introduction to big data in biology, with an emphasis on the concepts, research questions, methods, and data analysis. Particular emphasis is placed on sequencing methods and analysis, genomics, transcriptomics, proteomics, cellular networks, high-throughput phenotyping, and systems genetics.
2 credits, Letter graded (A, A-, B+, etc.)
May be repeated 1 times FOR credit.
BGE 510: Graduate Genetics
This course investigates fundamental aspects of the transmission and expression of genetic information in prokaryotic and eukaryotic systems. The course is organized in a way that allows the students to appreciate the breadth of genetics research, while also gaining an in-depth understanding of selected important topics. Students explore the use of both classical and molecular genetic approaches to understand biological processes in genetics model systems including yeast, flies, worms, mouse, and man.
Spring, 3 credits, Letter graded (A, A-, B+, etc.)
BGE 534: Introduction to Systems Biology
This course is geared towards teaching essential concepts and computational skills in Systems Biology. The course is centered upon two key programming languages: Matlab for modeling applications and the R language for statistical analysis and sequence manipulation.
Spring, 3 credits, Letter graded (A, A-, B+, etc.)
BME 534: Functional Genomics
Course provides foundation in concepts of functional genomics and proteomics. Topics include organization and complexity of the mammalian genome and mechanisms of expression of genes, gene expression analysis technologies with a strong focus on construction and utilization of DNA microarrays, and tools for determining gene function by perturbation of gene expression.
Spring, 3 credits, Letter graded (A, A-, B+, etc.)
May be repeated 2 times FOR credit.
BEE 567: Molecular Diversity Laboratory
This course will provide hands-on experience in established and recently developed methods of detecting and analyzing molecular variation (DNA, RNA, Proteins) in nature. Natural populations of Drosophila melanogaster will be the model material for this laboratory. The main theme of this course is that molecular variation is abundant in nature and is an important tool for understanding adaptive evolution and species relationships.
Prerequisite: permission of instructor
Fall, 3 credits, Letter graded (A, A-, B+, etc.)
BEE 520: Advanced Human Genetics
Topics include genotype/phenotype associations, the genetic architecture of disease/phenotypes, human population genetics, methylation, and ancient DNA. This class is meant to build on major concepts in human genetic research introduced in other courses. The course will emphasize hands-on engagement with genetic data and critical reading of scientific papers. Computer laboratory analysis/assignments will make up a major component of this class. Students will be evaluated based on computer assignments and a final group research project. EBH majors will have priority to register. This course is offered as both BIO 303 and EBH 370.
Prerequisite: C or better in BIO 302 or BIO 320 or BIO 304/EBH 380
3 credits
BEE 521: Genomics Laboratory
Provides a computer lab-based introduction to comparative genomics, molecular evolutionary analysis, and next generation sequencing (NGS) data and analysis. Activities will include familiarization with both web-based and command-line tools for analyzing genomic data and summarizing/visualizing results. Lectures and background reading will provide an introduction to basic principles of genomics to inform computer-based hands-on activities. Students will be evaluated based on computer lab assignments, as well as a final group project that applies learned concepts and approaches to a novel research question. This course is offered as both EBH 381 and BIO 305.
Prerequisite: C grade or higher in BIO 302 or BIO 304/EBH 380
3 credits
MAR 581: Next Generation Sequencing Applications in Functional Genomics
This course provides an integrated view of how Next Generation Sequencing approaches can be used to answer questions regarding organism’s evolution, biology and ecology. The course will provide technical and analytical details on functional genomics approaches including comparative genomics, population genomics, epigenomics, transcriptomics, metagenomics and metatranscriptomics. Examples will cover various topics including biodiversity, population structures, environmental adaptation, stress responses, phylogeny of animals, aquaculture and fisheries, interaction between species.
Fall, 3 credits, Letter graded (A, A-, B+, etc.)
BEE 554: Population Genetics and Evolution
A general introduction to mathematical population genetics and evolutionary theory. The effects of mutation, recombination, selection, and migration are studied. Modern concepts in both theoretical and experimental population genetics are covered.
Prerequisite: BEE 552 or equivalent, and a course in evolution
Spring, odd years, 0-3 credits, Letter graded (A, A-, B+, etc.)
CSE 549: Computational Biology
The main objective of this course is to provide a broad overview of the major areas of Bioinformatics and Computational Biology (B/CB). Our perspective will be a computational and algorithmic one, though we will take the time to understand the necessary Biology and motivation for the problems we discuss. We will touch upon many areas of B/CB, including phylogenetics, genome structure and Biological network analysis. However, there will be a significant concentration on genomics and related problems such as high-throughput read alignment, gene finding, genome assembly and transcriptome assembly and analysis. At the end of this course, you should have a good understanding of the types of problems people work on in B/CB, and a fairly in-depth knowledge of the computational tools and techniques used to address some foundational problems in the field.
Fall, 3 credits, Letter graded (A, A-, B+, etc.)
PHYS/CHE 558: Physical and Quantitative Biology
The central idea of this course is the free energy, the quantitative way we understand driving forces, i.e., the equilibria and rates in chemistry, physics and biology. We describe the underpinning components, the entropy and energy. We explore the microscopic interactions — including hydrogen bonding, van der Waals, electrostatics and hydrophobic forces — that explain physical and chemical mechanisms in biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities are the basis for drug discovery; coupled binding is the basis for how biological machines convert energy and transduce signals; and polymer free energies are the basis for the folding of protein and RNA molecules
Fall, 3 credits, Letter graded (A, A-, B+, etc.)
BEE 577: Ecological Genetics
A lecture course introducing the concepts, research questions, and methods involved in modern ecological genetics. The goal of the course is to provide a broad conceptual framework for students planning to engage in empirical work in conservation, management, ecology, and evolutionary biology. The course covers basic Mendelian genetics, meiosis, standard population genetics methods for describing variation within and between populations, basic quantitative genetics, methods for molecular marker genotyping, informatic and genomic concepts, and organism-specific methods and case studies. The textbook for the course is <u>A Primer of Ecological Genetics</u> by J.K. Conner and D.L. Hartl (2004; ISBN 978-0-87893-202-3).
Fall, 3 credits, Letter graded (A, A-, B+, etc.)
Undergraduate programs that offer courses in Genomics
BIO: Biology
EBH: Human Evolutionary Biology
Undergraduate Courses
BIO 302: Human Genetics
Topics include the principles of inheritance, human population genetics, molecular approaches for studying DNA, the genetic basis of mutations, genetic diversity, using DNA to study ancient human history and human evolution. Human genetic diseases are discussed and an introduction is given to human chromosome maps, the Human Genome Project, and methods for mapping disease mutations. This class is meant to introduce students to the major concepts in human genetic and genomic research. The course will emphasize presentation skills and reading comprehension of current human genetics literature. Students will be evaluated based on a combination of take-home assignments, pop quizzes and a final project based on current scientific journal papers. Limited enrollment to 75 students.
Course Pre/Co-requisites:
BIO 201, BIO 202 core classes are required. BIO 204 [Fundamentals of Scientific Inquiry] is advised, but not required.
3 credits
BIO 303/EBH370: Advanced Human Genetics
An advanced course in human genetics. Topics include genotype/phenotype associations, the genetic architecture of disease/phenotypes, human population genetics, methylation, and ancient DNA. This class is meant to build on major concepts in human genetic research introduced in other courses. The course will emphasize hands-on engagement with genetic data and critical reading of scientific papers. Computer laboratory analysis/assignments will make up a major component of this class. Students will be evaluated based on computer assignments and a final group research project. EBH majors will have priority to register. This course is offered as both BIO 303 and EBH 370.
Prerequisite: C or better in BIO 302 or BIO 320 or BIO 304/EBH 380
3 credits
BIO 304/EBH380: Genomics
An introduction to the rapidly developing field of genomics. Initial lectures provide a foundation in genomic structure across the tree of life (prokaryote and eukaryote). This is followed by examination of specific forces that cause variation in genomic content both within and between species. We then discuss how to sequence, assemble and analyze genomes. Finally we focus on the architecture and evolution of the human genome and compare it to non-human primate and ancient hominin genomes, and examine how the study of non-human primates can aid human health. This course is offered as both BIO 304 and EBH 380.
Prerequisite: C or higher in BIO 201 and BIO 202
Advisory Prerequisite: BIO 211 or EBH 230; BIO 302 or BIO 312
3 credits
BIO305/EBH381 Genomics Laboratory
Provides a computer lab-based introduction to comparative genomics, molecular evolutionary analysis, and next generation sequencing (NGS) data and analysis. Activities will include familiarization with both web-based and command-line tools for analyzing genomic data and summarizing/visualizing results. Lectures and background reading will provide an introduction to basic principles of genomics to inform computer-based hands-on activities. Students will be evaluated based on computer lab assignments, as well as a final group project that applies learned concepts and approaches to a novel research question. This course is offered as both EBH 381 and BIO 305.
Prerequisite: C grade or higher in BIO 302 or BIO 304/EBH 380
3 credits
BIO 312: Bioinformatics and Computational Biology
This course uses computational methods to analyze current problems and solutions in molecular biology research. Students are exposed to algorithms and tools available for both single gene and larger scale genome research. Emphasis is on practical application. Laboratories allow students to apply their knowledge to real life molecular biology problems.
Prerequisites: BIO 202; BIO 205 or BIO 207; MAT 125 or higher or AMS 151
Advisory Pre- or Corequisite: AMS 110, or BIO 211
3 credits
BIO 320: General Genetics
Integrates classical and molecular approaches to the transmission and expression of biological information. Topics include: Mendelian and non-Mendelian inheritance; linkage analysis; population genetics; DNA replication, mutation and recombination; gene expression and its regulation; current genetic technology; developmental and cancer genetics, quantitative and complex traits, and relevant ethical issues.
Prerequisite: C or higher in BIO 202
3 credits
Bio 321/BEE 577: Ecological Genetics
A lecture course introducing the concepts, research questions, and methods involved in modern ecological genetics. The goal of the course is to provide a broad conceptual framework for students planning to engage in empirical work in conservation, management, ecology, and evolutionary biology. The course covers basic Mendelian genetics, meiosis, standard population genetics methods for describing variation within and between populations, basic quantitative genetics, methods for molecular marker genotyping, informatic and genomic concepts, and organism-specific methods and case studies. The textbook for the course is A Primer of Ecological Genetics by J.K. Conner and D.L. Hartl (2004; ISBN 978-0-87893-202-3).
Fall, 3 credits, Letter graded (A, A-, B+, etc.)