MSMS 6211, BCOR 5585 - Genomics
Course guide for Genomics (MSMS 6211, BCOR 5585)
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- Computational Functional GenomicsThe course focuses on casting contemporary problems in systems biology and functional genomics in computational terms and providing appropriate tools and methods to solve them. Topics include genome structure and function, transcriptional regulation, and stem cell biology in particular; measurement technologies such as microarrays (expression, protein-DNA interactions, chromatin structure); statistical data analysis, predictive and causal inference, and experiment design. The emphasis is on coupling problem structures (biological questions) with appropriate computational approaches.
- Experimental Microbial GeneticsIn this class, students engage in independent research projects to probe various aspects of the physiology of the bacterium Pseudomonas aeruginosa PA14, an opportunistic pathogen isolated from the lungs of cystic fibrosis patients. Students use molecular genetics to examine survival in stationary phase, antibiotic resistance, phase variation, toxin production, and secondary metabolite production. Projects aim to discover the molecular basis for these processes using both classical and cutting-edge techniques. These include plasmid manipulation, genetic complementation, mutagenesis, PCR, DNA sequencing, enzyme assays, and gene expression studies. Instruction and practice in written and oral communication are also emphasized.
- Experimental Molecular GeneticsThis project-based laboratory course provides students with in-depth experience in experimental molecular genetics, using modern methods of molecular biology and genetics to conduct original research. The course is geared towards students (including sophomores) who have a strong interest in a future career in biomedical research. This semester will focus on chemical genetics using Caenorhabditis elegans as a model system. Students will gain experience in research rationale and methods, as well as training in the planning, execution, and communication of experimental biology.
- GeneticsThis course discusses the principles of genetics with application to the study of biological function at the level of molecules, cells, and multicellular organisms, including humans. The topics include: structure and function of genes, chromosomes and genomes, biological variation resulting from recombination, mutation, and selection, population genetics, use of genetic methods to analyze protein function, gene regulation and inherited disease.
- Molecular Biology and Genetics in Modern MedicineThis course provides a foundation for understanding the relationship between molecular biology, developmental biology, genetics, genomics, bioinformatics, and medicine. It develops explicit connections between basic research, medical understanding, and the perspective of patients. Principles of human genetics are reviewed. We translate clinical understanding into analysis at the level of the gene, chromosome and molecule; we cover the concepts and techniques of molecular biology and genomics, and the strategies and methods of genetic analysis, including an introduction to bioinformatics. Material in the course extends beyond basic principles to current research activity in human genetics.
- DNA's Sister Does All the Work: The Central Roles of RNA in Gene ExpressionThis course will explore the current frontiers of the world of RNA biology with primary research papers to trace how the original odd detail sometimes leads to major discoveries. As we discuss the different transcripts and processing events that enable this exciting diversity of RNA functions, we invite you to read landmark papers with us, think critically, and ask new questions, as we marvel at the wonders of RNA.
- Bioinformatic Methods 1Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful information pertaining to the system being studied. This course focuses on employing existing bioinformatic resources – mainly web-based programs and databases – to access the wealth of data to answer questions relevant to the average biologist, and is highly hands-on.
- Bioinformatic Methods 2Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful information pertaining to the system being studied. This course focuses on employing existing bioinformatic resources – mainly web-based programs and databases – to access the wealth of data to answer questions relevant to the average biologist, and is highly hands-on.
- Biology Meets Programming: Bioinformatics for BeginnersThis course will cover algorithms for solving various biological problems along with a handful of programming challenges helping you implement these algorithms in Python.
- Classical Papers in Molecular GeneticsYou have all heard about the DNA double helix and genes. Many of you know that mutations occur randomly, that the DNA sequence is read by successive groups of three bases (the codons), that many genes encode enzymes, and that gene expression can be regulated. These concepts were proposed on the basis of astute genetic experiments, as well as often on biochemical results. The original articles were these concepts appeared are however not frequently part of the normal curriculum of biologists, biochemists and medical students. This course proposes to read study and discuss a small selection of these classical papers, and to put these landmarks in their historical context. Most of the authors displayed interesting personal histories and many of their contributions go beyond not only the papers we will read but probably all their scientific papers. Our understanding of the scientific process, of the philosophy underlying the process of scientific discovery, and on the integration of new concepts is not only important for the history of science but also for the mental development of creative science.
- Genetics and Society: A Course for EducatorsHow have advances in genetics affected society? What do we need to know to make ethical decisions about genetic technologies? This course includes the study of cloning, genetic enhancement, and ownership of genetic information. Course participants will acquire the tools to explore the ethics of modern genetics and learn how to integrate these issues into their classrooms.
- Genomics: Decoding the Universal Language of LifeWhat is a genome? A genome contains all of the information that a cell needs to develop, function, and reproduce itself, and all the information needed for those cells to come together to form a person, plant, or animal. Genomes contain an organism’s complete set of genes, and also the even tinier genetic structures that help regulate when and how those genes are used. The ability to regrow a torn ligament, the clues that might predict the onset of mental illness, the nutritional potential of crops, and even the history of life itself, are all encoded in genomes. By taking this course, you will discover how scientists are deciphering the language of genomes to learn how to develop sustainable food and fuel supplies, improve disease treatment and prevention, and protect our environment.
- Introduction to Genetics and EvolutionIntroduction to Genetics and Evolution is a college-level class being offered simultaneously to new students at Duke University. The course gives interested people a very basic overview of some principles behind these very fundamental areas of biology. We often hear about new "genome sequences," commercial kits that can tell you about your ancestry (including pre-human) from your DNA or disease predispositions, debates about the truth of evolution, why animals behave the way they do, and how people found "genetic evidence for natural selection." This course provides the basic biology you need to understand all of these issues better, tries to clarify some misconceptions, and tries to prepare students for future, more advanced coursework in Biology (and especially evolutionary genetics). No prior coursework is assumed.