Experimental Immunology (IMMU 40200). This course centers on the Immunology Journal Club and the Immunology Seminar Series and has two purposes. The first is to provide background knowledge for the seminar given each week by an outside speaker or a member of the Committee on Immunology. The second is to allow the students an opportunity to develop skills in analyzing the literature with students at the same stage of training. First and second year students are required to participate in this course., Zemmour. Autumn, Winter, Spring. (**Required for all 1st & 2nd year COI students**)
Immunogenomics I: Evolutionary and Genomic Approaches to Immunology (IMMU 48000). This course will train students to tackle immunological questions using quantitative and systems-level approaches, and think about the immune system from an evolutionary perspective. The topics covered will include: (i) introduction of innate and adaptive immunity, (ii) evolution of the different arms of the immune system, (iii) Population variation in immune responses, (iv) genomic technologies and applications, (v) study design in genomic studies, and paper-based discussion of key immunological concepts and how we can study them using systems immunology approaches. Barreiro, Roy Chowdhury. Autumn. (**Required for students on the COI-CSI track**)
Host-Pathogen Interactions (IMMU 31200). This course explores the basic principals of host defense against pathogens and pathogens' strategies to overcome host immune mechanisms. We address evolutionary aspects of innate and adaptive immune responses, while also studying specific examples of viral and bacterial interactions with their hosts. The reviews of relevant immunological mechanisms necessary for appreciation of host/pathogen interactions are incorporated in the studies of specific cases. Chervonsky. Autumn.
Protein Fundamentals (BCMB 30400). The course covers the physical‑chemical phenomena that define protein structure and function. Topics include: the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function and molecular machines; proteomics and systems biology. Workshop on X-ray Crystallography: The workshop is an addendum to Protein Fundamentals and is required for all BCMB students. This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation. (e.g. BCMB 30100, which may be taken concurrently). Koide, Keenan, Autumn.
Structure and FunMOction of Membrane Proteins (BCMB 32300). This course will be an in depth assessment of the structure and function of biological membranes. In addition to lectures, directed discussions of papers from the literature will be used. The main topics of the courses are: (1) Energetic and thermodynamic principles associated with membrane formation, stability and solute transport (2) membrane protein structure, (3) lipid-protein interactions, (4) bioenergetics and transmembrane transportmechanisms, and (5) specific examples of membrane protein systems and their function (channels, transporters, pumps, receptors). Emphasis will be placed on biophysical approaches in these areas. The primary literature will be the main source of reading. Perozo. Autumn.
Genetic Analysis of Model Organisms (HGEN 31400). Fundamental principles of genetics discussed in the context of current approaches to mapping and functional characterization of genes. The relative strengths and weaknesses of leading model organisms are emphasized via problem-solving and critical reading of original literature. Bishop, Moskowitz, Ferguson, Malamy. Autumn.
Human Genetics 1: Human Genetics (HGEN 47000). This course covers classical and modern approaches to studying cytogenic, Mendelian, and complex diseases. Topics include chromosome biology, single gene and complex disease, non-Mendelian inheritance, cancer genetics, human population genetics, and genomics. The format includes lectures and student presentations. Ober, Waggoner, Nobrega. Autumn.
Cell Biology 1 (MGCB 31600). Eukaryotic protein traffic and related topics, including molecular motors and cytoskeletal dynamics, organelle architecture and biogenesis, protein translocation and sorting, compartmentalization in the secretory pathway, endocytosis and exocytosis, and mechanisms and regulation of membrane fusion. Turkewitz, Glick. Autumn.
Statistics Methods and Applications (STAT 22000). Statistics 22000 provides an introduction to how statisticians think about describing data, data collection and research design, probability and randomness, and inference from a sample to a population. This course would only be appropriate for students with too little background to take STAT 24300. Autumn, Winter, and Spring.
Advanced Immunology (IMMU 31500). This course explores the basic principles of the immune system, including tolerance, the development and differentiation of lymphocyte subsets, the regulation of major classes of immune responses, memory, cell homing and migration, cell-cell interactions, antigen presentation and recognition. Savage. Winter. (**Required for all 1st year COI students **)
Experimental Immunology (IMMU 40200). This course centers on the Immunology Journal Club and the Immunology Seminar Series and has two purposes. The first is to provide background knowledge for the seminar given each week by an outside speaker or a member of the Committee on Immunology. The second is to allow the students an opportunity to develop skills in analyzing the literature with students at the same stage of training. First and second year students are required to participate in this course., Zemmour. Autumn, Winter, Spring. (**Required for all 1st & 2nd year COI students**)
Immunopathology (IMMU 30010). This course will expand on general immunological concepts that have implications for our understanding of immune-related disorders such autoimmune diseases, inflammatory bowel diseases, infection immunity, immunodeficiencies and transplant rejection. Students will read and discuss primary immunological papers and become familiarized with typical experiment designs in immunology. At the end of course, students will have learned how to design experiments in order to address specific hypotheses related to immune-mediated disorders. Esterhazy, Roy Chowdhury. Winter.
Molecular Biology 1 (MGCB 31200). Nucleic acid structure and DNA topology; methodology; nucleic-acid protein interactions; mechanisms and regulation of transcription in eubacteria, and of replication in eubacteria and eukaryotes; mechanisms of genome and plasmid segregation in eubacteria. Rothman-Denes, Bishop. Winter
Cancer Biology 2: Molecular Mechanisms of Cancer (CABI 30900). This course provides students with an in-depth understanding of how key cellular processes are deregulated in cancer and the molecular mechanisms underpinning these defects. The course covers cell cycle checkpoint control, cell death, tumor suppressor and oncogene function, DNA repair mechanisms, epigenetics of cancer, nuclear hormone receptor activity in cancer, tumor metabolism, hypoxia responses, angiogenesis and metastasis. In addition to material covered in formal lectures, discussion sessions cover tumor stem cells, "oncogene addiction," inflammatory responses, cancer therapeutics, mouse models of human cancer and other topical subjects relevant to understanding tumor initiation and progression, as well as how current research may facilitate cancer treatment.
Cell Biology 2 (MGCB 31700). This course covers the mechanisms with which cells execute fundamental behaviors. Topics include signal transduction, cell cycle progression, cell growth, cell death, cancer biology, cytoskeletal polymers and motors, cell motility, cytoskeletal diseases, and cell polarity. Each lecture will conclude with a dissection of primary literature with input from the students. Students will write and present two short research proposals, providing excellent preparation for preliminary exams. Cell Bio I 31600 is not a prerequisite. Glotzer, Kovar. Winter
Fundamentals and Applications of the Human Microbiota (MICR 38000). Thousands of microbes colonize the human body to collectively establish the human microbiota. Research findings over the past two decades have led to a growing appreciation of the importance of the microbiota in various facets of human health. This course will explore the human microbiota through a critical review of the primary scientific literature. The first portion of the course will cover distinct ways by which the human microbiota impacts mammalian health. The second part of the course will focus on established and developing microbiota-targeting biotechnologies. Students will leave the course with a general understanding of the current state of human microbiota research and its therapeutic and diagnostic applications. Light, Mimee. Winter.
Biostatistical Methods (STAT 22700). This course is designed to provide students with tools for analyzing categorical, count, and time-to-event data frequently encountered in medicine, public health, and related biological and social sciences. This course emphasizes application of the methodology rather than statistical theory (e.g., recognition of the appropriate methods; interpretation and presentation of results). Methods covered include contingency table analysis, Kaplan-Meier survival analysis, Cox proportional- hazards survival analysis, logistic regression, and Poisson regression. Cao. Winter
Statistics Methods and Applications (STAT 22000). Statistics 22000 provides an introduction to how statisticians think about describing data, data collection and research design, probability and randomness, and inference from a sample to a population. This course would only be appropriate for students with too little background to take STAT 24300. Fall, Winter, and Spring.
Statistical Theory and Methodology I, II (STAT 24300-24500). Principles and techniques of statistics, with emphasis on the analysis of experimental data. First quarter: Discrete and continuous probability distributions, transformation of random variables; principles of inference including Bayesian inference, maximum likelihood estimation, hypothesis testing, likelihood-ratio tests, multinomial distributions and chi-square tests. Second quarter: Multivariate normal distributions and transformations, Poison processes, data analysis, t-tests, confidence intervals, analysis of variance and regression analysis. Autumn, Winter.
Human Genetics 3: Introductory Statistical Genetics. (HGEN 47100). This course focuses on genetic models for complex human disorders and quantitative traits. Topics covered also include linkage and linkage disequilibrium mapping genetic models for complex traits, and the explicit and implicit assumptions of such models. Novembre. Winter.
Introduction to Scientific Computing for Biologists. (ECEV 32000). The course will cover basic concepts in computing for an audience of biology graduate students. The students will receive basic training in the use of version control systems, databases and regular expressions. They will learn how to program in python and R and how to use R to produce publication-grade figures for their manuscripts, and how to typeset scientific manuscripts and theses using LaTeX. All the examples and exercises will be biologically motivated and will make use of real data. The approach will be hands-on, with lecturing followed by exercises in class. Allesina. Winter.
Fundamentals of Computational Biology: Models and Inference (HGEN 48600). Covers key principles in probability and statistics that are used to model and understand biological data. There will be a strong emphasis on stochastic processes and inference in complex hierarchical statistical models. Topics will vary but the typical content would include: Likelihood-based and Bayesian inference Poisson processes, Markov models, Hidden Markov models, Gaussian Processes, Brownian motion, Birth- death processes, the Coalescent, Graphical models, Markov processes on trees and graphs, Markov Chain Monte Carlo. Prereq: STAT 244 or equivalent and comfort with programming, or consent of instructor. Novembre, Stephens. Winter.
Molecular Mechanisms of Immune Cell Development and Function (IMMU 32000). This class will explore the molecular and biochemical mechanisms by which lymphocytes develop and are activated in response to antigen. This will include the signal transduction pathways and transcriptional networks involved in these processes, as well as the molecular mechanisms underlying the generation of receptor diversity. Kee. Spring. (**Required for all 1st year COI students **)
Experimental Immunology (IMMU 40200). This course centers on the Immunology Journal Club and the Immunology Seminar Series and has two purposes. The first is to provide background knowledge for the seminar given each week by an outside speaker or a member of the Committee on Immunology. The second is to allow the students an opportunity to develop skills in analyzing the literature with students at the same stage of training. First and second year students are required to participate in this course., Zemmour. Autumn, Winter, Spring. (**Required for all 1st & 2nd year COI students**)
Immunogenomics II: Data Science in Systems Immunology (IMMU 48900). This course teaches fundamental concepts in genomic data science and trains students to apply them critically in immunological contexts. Students will gain an understanding of how to use basic statistics, linear algebra, and computation to explore, analyze, and interpret published RNA-sequencing data (bulk and single-cell) and immune-cell receptor sequencing data. Student performance will be assessed through in-class discussions, take-home assignments and exams, and an end-of-term final project of the student’s choice. Basic R or Python programming skills are prerequisite. Riesenfeld, Weinstein. Spring. (**Required for students on the COI-CSI track**)
Cancer Immunology (IMMU 30810). This course is a literature-based course covering classical and contemporary topics in cancer immunology and immunotherapy. At each session, two students will each lead a discussion of one primary research paper. The course is expected to span the following topics: 1. Induction of tumor-specific immunity in mice and the immunosurveillance hypothesis, 2. Tumor-associated and tumor-specific antigens, 3. Tumor heterogeneity and cancer genomics, 4. Tumor-associated antigen presenting cells, 5. Tumor-associated regulatory T cells, 6. Immunity to solid vs. hemotological malignancies, 7. T cell-expressed co-inhibitory receptors (CTLA-4 and PD-1), 8. Immunotherapy using "checkpoint blockade" antibodies, 9. Immunotherapy via adoptive T cell transfer and chimeric antigen receptor T cells, 10. Novel combination therapies for the immunotherapy of cancer. Savage, Kline. Spring (odd years).
Barrier Immunity (IMMU 35000). Nowhere is the body’s immune system so critical in saving an organism from death as at barrier sites, where we are directly exposed to the external environment. However, inflammatory responses to exclude pathogens and toxins need to be balanced with tolerance to benign agents like our microbiome or food, and a homeostatic role of the immune system in tissue repair. Failure to make the right call on defensive versus immunosuppressive reactions leads to severe pathologies such as chronic inflammation, allergies, autoimmunity and cancer. These challenges are met by a plethora of innate and adaptive immune cells, some exclusively found at barriers. Complexity is added by local challenges due to tissue location and function. The fascinating uniqueness of Barrier Immunity is the subject of this course. Using primary literature as a basis, expert faculty will help explore how the immune systems of the intestine, the lung, the skin and the vaginal tract deal with maintaining defense while not jeopardizing tissue function in men and mice. We will then study the immunological diseases at barriers, what makes a site prone to tissue-specific pathologies, and how a barrier dysfunction may lead to systemic immune diseases. A particular focus will be the critical role of the local microbiome in preventing or promoting barrier pathology. The course will also stimulate thought on the evolution of a complex immune system, the origin of diseases and disease tolerance. Esterhazy. Spring.
Genomics and Systems Biology (IMMU 47300). This lecture course explores technologies for high-throughput collection of genomic-scale data, including sequencing, genotyping, gene expression profiling, and assays of copy number variation, protein expression and protein-protein interaction. In addition, the course will cover study design and statistic analysis of large data sets, as well as how data from different sources can be used to understand regulatory networks, i.e., systems. Statistical tools that will be introduced include linear models, likelihood-based inference, supervised and unsupervised learning techniques, methods for assessing quality of data, hidden Markov models, and controlling for false discovery rates in large data sets. Readings will be drawn from the primary literature. Evaluation will be based primarily on problem sets.
Molecular Biology 2 (MGCB 31300). The content of this course covers the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions highlight the most significant recent developments, their implications and future directions. Staley, Ruthenburg. Spring.
Introduction to Virology (MICR 34600). This class on animal viruses considers the major families of the viral kingdom with an emphasis on the molecular aspects of genome expression and virus-host interactions. Our goal is to provide students with solid appreciation of basic knowledge, as well as instruction on the frontiers of virus research.
Instructor: Golovkina
Statistics Methods and Applications (STAT 22000). Statistics 22000 provides an introduction to how statisticians think about describing data, data collection and research design, probability and randomness, and inference from a sample to a population. This course would only be appropriate for students with too little background to take STAT 24300. Autumn, Winter, and Spring.