CMM 695D - Advanced Analysis of Human Genetic Disease: from chief complaint to drug discovery
BIOC695D, GENE695D, MCB695D, NRSC695D, PSIO695D; 3 credit hours; taught spring semester. Restifo
Course description: Perhaps you’ve been thinking, “So many diseases, so little time!” This course can help! The primary goal of CMM 695D is to teach an approach to understanding any disease, by considering (i) different degrees of genetic causation; (ii) the importance of differential diagnosis, natural history, and histopathology; and (iii) evolving insights about disease classification. Together, these strategies promote the critical analysis of research on disease pathogenesis and the challenge of developing safe and effective therapeutics. Each year, we focus on four exemplar diseases, moving from a simple Mendelian genetic disorder with well-understood pathophysiology to progressively more complex and more mysterious disorders with substantial environmental contributions.
GENE 530 - Conservation Genetics
ECOL530, WFSC530; 3 credit hours; taught fall semester. Culver
Course description: Basic methods and theories of genetic/genomic analyses together with the application of these analyses to promote conservation, proper management, and long term survival of free-ranging species, including the exploration of current conservation genetic/genomic literature. Graduate level requirements include a term project and an oral presentation
MCB 572A - Cell Systems
4 credit hours; taught fall semester. Weinert & Guttenkunst
Course description: Advanced treatment of regulation of basic cellular processes in both single-celled and multicellular eukaryotic organisms. Focus on experimental research aimed at understanding cellular networks and circuitry, as well as their evolution. An introduction to modeling cell systems will be embedded within the context of the course. This is primarily a discussion-based, student-led course.
PLP 528R - Microbial Genetics
GENE528, MCB528, MIC528, SWES528, ENVS528; 3 credit hours; taught spring semester. Cooper
Course description: Prokaryotic gene structure and function; methods of gene transfer and mapping, DNA structure, replication, transcription, and translation. Hands-on computer analysis of DNA sequences and gene cloning strategies. Principles of regulation of gene expression. Graduate-level requirements include a DNA sequence of an entire operon from any one of a variety of bacteria and additionally analyze one product from the operon using several GCG protein analysis programs plus an extensive exam.
GENE526 - Population Genetics
Course description: General introductory course on empirical and theoretical population genetics. It will involve two weekly lectures, weekly problem sets, and regular readings from the primary literature. A major goal of this course is to make students familiar with basic models of population genetics and to acquaint students with empirical tests of these models. As much as any field of biology, population genetics has been divided into a theoretical and an empirical branch. However, these two bodies of knowledge are intimately related and this course will cover both in roughly equal amounts. We will discuss the primary forces and processes involved in shaping genetic variation in natural populations (mutation, drift, selection, migration, recombination, mating patterns, population size and population subdivision), methods of measuring genetic variation in nature, and experimental tests of important ideas in population genetics. The course will also cover a few more specialized topics such as transposable elements, the evolution of multigene families, and molecular clocks. Graduate-level requirements include additional exam questions, additional readings from the literature, and presentation of a 15 minute overview and synthesis of a specialized topic in population genetics.
MCB546 - Genetic and Molecular Networks
Course description: This course will explore the analysis of biological systems using genetic and molecular tools. Discussion of primary literature papers focusing on model systems.
BIOC 568 - Nucleic Acids, Metabolism, and Signaling
GENE 568, 4 credit hours, taught fall semester. Staff
Course description: Chemistry, structure, and function of nucleic acids; replication, transcription translation, gene organization, regulation of gene expression and organelle nucleic acids. Both prokaryotic and eukaryotic systems will be considered.
BIOC 565 - Proteins and Enzymes
CHEM 565, 3 credit hours, taught fall semester. Staff
Course description: Advanced consideration of enzyme structure and function.
BIOC 555 - Methods of Physical Biochemistry
GENE 555, INSC 555, MCB 555, 3 credit hours, taught fall semester. Hausrath
Course description: Fundamental concepts in physical biochemistry; techniques necessary to understand the structure and function of biomacromolecules, especially proteins. Biophysical techniques to study protein interactions. Advanced understanding of protein structure/function, methods in protein biochemistry, enzyme mechanisms, protein-mediated cell signaling. This course is designed for advanced graduate students.
BIOC 573 - Recombinant DNA Methods and Applications
MCB 573, MIC 573, PLS 573, GENE 573, 4 credit hours, taught spring semester. Staff
Course description: This course offers an intensive lab experience to teach students the practical and theoretical aspects of modern molecular biology. In the first part of the course, recombinant DNA methods and bioinformatics are used to clone and identify an unknown gene. In the second part of the course DNA microarray technology is used to determine the effect of environmental stress on the global gene expression program in yeast, and to identify genes that control the stress response. Weekly lectures compliment the lab sessions, covering the theory and principles underlying the experiments performed during the course.
CHEM 523A - Bioanalytical chemistry
3 credit hours, taught fall semester in odd-numbered years. Staff
Course description: Bioanalytical chemistry covers the principles behind the essential measurements used for the analysis of biological systems, including but not limited to separations, mass spectrometry, microarrays, immunoassays, and DNA sequencing. The current literature is examined to understand today's research questions in bioanalysis, developments in the biotech industry, and opportunities to have a creative impact on improving human health.
BE 587 - Metagenomics: From Genes to Ecosystems
3 credits; taught fall semester. Hurwitz and Youensclark. Syllabus
Course description: This course focuses on the science of metagenomics towards understanding (1) questions that metagenomics can address, (2) possible approaches for metagenomic sequencing and analysis, and (3) how genes, pathways, and environmental context are translated into ecosystem-level knowledge. This course alternates between traditional lectures and hands-on experience with programming, bioinformatics tools, and metagenomic analysis. The course concludes with several weeks of seminar-format discussions on current research in metagenomic data analysis and a final project of your choice analyzing real-world experimental data.
GENE 677 - Principles of Genetic Association Studies
EPID 677; 3 credits; taught spring semester. Klimentidis. Syllabus
Course description: Topics: selection of appropriate study design for association studies; understanding basic molecular genetics with particular focus on the genetic code; selection of candidate genes; genotype analysis; temporal sequence in genetic association studies; importance of longitudinal data in genetic association studies; genotype versus haplotype analysis; selection of haplotype tagging SNPs; use of genetic software.
GENE 526 - Population Genetics
ECOL 526; 3 units; offered spring semester. TBN
Course description: General introductory course on empirical and theoretical population genetics. It will involve two weekly lectures, weekly problem sets, and regular readings from the primary literature. A major goal of this course is to make students familiar with basic models of population genetics and to acquaint students with empirical tests of these models. We will discuss the primary forces and processes involved in shaping genetic variation in natural populations (mutation, drift, selection, migration, recombination, mating patterns, population size and population subdivision), methods of measuring genetic variation in nature, and experimental tests of important ideas in population genetics. The course will also cover a few more specialized topics such as transposable elements, the evolution of multigene families, and molecular clocks.
MCB 516A - Statistical Bioinformatics and Genomic Analysis
3 units; offered spring semester, even years only. Yao. Syllabus
The course introduces computational and bioinformatics methods for the analysis of high-throughput experimental data in functional genomics, using the analysis of next-generation RNA-sequencing as a leading example. The course discusses related biological concepts and techniques, statistical methods and models, and provides hands-on experience with data analysis using R-based open-source software Bioconductor. The course prepares the students to perform independent analyses of genomic data in an interdisciplinary environment such as a research lab or pharmaceutical company.
MCB 585 - Multidisciplinary Approaches to Solving Biological Problems
MCB 585; 4 units; offered fall semester. Paek, Sutphin, Padi. Syllabus
Course description: An advanced graduate course focused on multidisciplinary approaches to biological questions, using the central dogma as an experimental framework. Students will explore the integration of classic and modern approaches to biological problem solving through a critical and integrated analysis of existing research and through active learning exercises based on hypothesis-building and testing at the edges of current knowledge.
PLS 539 - Methods in Cell Biology and Genomics
GENE 539, MCB 539, PCOL 539, PSIO 539; 3 units; offered fall semester even years only. Galbraith
Course description: In-depth, practical and theoretical analysis of novel, experimental methods that advance our understanding of modern biology.
MCB 580 - Introduction to Systems Biology
BE 580; 3 credits; taught fall semester. Capaldi. Syllabus
Course description: The proteins in a cell are organized into networks and circuits that act to process information and control cell activity. In this course we will explore the structure and function of these circuits through discussion of the relevant literature and by building and testing mathematical models of simple/toy circuits. Emphasis will be placed on key concepts such as hysteresis, ultrasensitivity, adaptation, robustness and noise propagation. Graduate-level requirements include more complex independent projects and a formal presentation to the class.
MCB 547 - Big Data in Molecular Biology and Biomedicine
3 credits; taught fall semester. Gutenkunst, Padi. Syllabus
Course description: Recent technological advances enable the collection of massive biological data sets, both in the research lab and in the medical clinic. These Big Data offer opportunities for discovering new biology, but they also demand new analysis approaches. This course will introduce students with a strong molecular biology background to the use of Big Data statistics. Students will learn how to visualize complex data, identify biologically relevant clusters, model relationships between variables, and classify entities. They will apply these techniques to a diverse range of biological Big Data, including electronic medical records, gene expression measurements, and human population genetic sequences. Students will learn through homework, in-class exercises, and a substantive final project.
GENE 671 - Morality and Ethics in Science
1 credit; taught spring semester.
Course description: The question this 1-credit course is designed to address is what code of professional behavior does the modern scientist set for him/herself, what are the philosophical origins of this code, and how does a scientist set about applying this code to his/her professional conduct?
MCB 695E - Science, Society, and Ethics
1 credit; taught spring semester.
Course description: Practical colloquium focusing on ethical issues raised in the research laboratory setting.
PHCL 595B - Scientific Writing, Presentation and Bioethics
2 credits; taught spring semester.
Course description: This course is intended for students enrolled in a PhD program or who have completed a Ph.D. or MD and will need to extensively use writing and presentation skills in their career. The class emphasizes writing; manuscripts, manuscript and grant reviews, scientific presentations, and applications for awards, future employment etc. Significant class participation is mandatory. This course satisfies the bioethics requirement of NIH funded grants. Signature of Course Director is required for individuals who do not meet the pre-requisite requirement.
SLHS 649 - Survival Skills and Ethics
3 credits; taught spring semester.
Course description: This course is designed for graduate students and postdoctoral fellows. It provides information and experiences that will aid in successful "survival" during the graduate-student years and those following graduation. Topics include effective speaking and writing, grantspersonship, mentoring, teaching, career options, among others. Discussion of ethical issues and resources is integrated across topics.