REQUIRED COURSES – 1^ST YEAR CURRICULUM

MGCB 31400 - General Principles of Genetic Analysis.  Coverage of the fundamental tools of genetic analysis as used to study biological phenomena. Topics include genetic exchange in prokaryotes and eukaryotes, analysis of gene function, and epigenetics.  Autumn. 

HGEN 31900 - Introduction to Research. Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students in HGEN. Autumn, Winter.

HGEN 46900 – Human Genetics II:  Human Variation and Disease. This course focuses on principles of population and evolutionary genetics and complex trait mapping as they apply to humans. It will include the discussion of genetic variation and disease mapping data. Spring.

HGEN 40300 – Non-Thesis Research. Laboratory rotations, and all research prior to passing the Qualifying Examination.  Winter, Spring, Summer.

BSDG 55000 - Scientific Ethics Seminar. Required of all First Year BSD grad students. Spring

ANY ONE OF THE FOLLOWING COURSES WILL FULFILL 1 REQUIRED COURSE:

MGCB  31500 - Genetic Mechanisms. Advanced coverage of genetic mechanisms involved in genome stability and rearrangement in lower and higher organisms.  Topics include the genetics of mutagenesis, DNA repair, homologous and site specific recombination, transposition and chromosome segregation.  Winter.

DVBI 35500 -  Developmental Genetics of Non-vertebrate Model Systems.  This course explores the use of genetics in three different model systems, C. elegans, Drosophila melanogaster and Arabodopsis thaliana, to elucidate developmental mechanisms.  The class will focus on a series of interrelated topics: for each topic, introductory material presented by the lecturer will be followed by student-led discussions of individual papers.  Winter.

ECEV 35600- Principles of Population Genetics I. Examines the basic theoretical principles of population genetics, and their application to the study of variation and evolution in natural populations. Topics include selection, mutation, random genetic drift, quantitative genetics, molecular evolution and variation, the evolution of selfish genetic systems, and human evolution. Winter.

HGEN 47100 – Human Genetics III:  Introductory Statistical Genetics.  This courses 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.  Winter.

MGCB  31300 - Molecular Biology II. Eukaryotic Gene Expression. Transcription and Posttranscriptional Regulation.  Analysis of regulatory pathways and mechanisms involved in the control of eukaryotic gene activity.  Spring. 

ELECTIVE COURSES AVAILABLE TO DEPARTMENT OF HUMAN GENETICS STUDENTS:

For detailed information on course time schedules visit: http://timeschedules.uchicago.edu/

Biochemistry and Molecular Biology

BMB 30100 - Basic Biochemistry and Molecular Biology.  The course is intended as an introduction to biochemistry and molecular biology for first year graduate students, first year medical students, and advanced undergraduates.  It has three sections.  The first is the structure and function of macromolecules (proteins, including enzymes, and nucleic acids) and supramolecular aggregates such as biological membranes.  The second section is on cellular metabolism, emphasizing enzymatic mechanisms, cellular compartmentalization, and integration of metabolic systems.  The third is the beginning of molecular biology of the gene, emphasizing DNA replication, transcription, and translation. PQ: Two quarters of organic chemistry.  Autumn

BMB 30400 – Protein Fundamentals. The course covers the physico‑chemical phenomena that define protein structure and function.  Topics include:  1) the interactions/forces that define polypeptide conformation; 2) the principles of protein folding, structure and design; and 3) the concepts of molecular motion, molecular recognition, and enzyme catalysis.  PQ:  BMB 30100, which may be taken concurrently, or equivalent.  Autumn.

BMB 30500 – Fundamentals of Structural Biology. This course emphasizes the basic principles of protein structure determination by X-ray crystallography and NMR spectroscopy. The underlying physical concepts of these methods will be introduced and the capabilities of each will be discussed and compared in context of their uses in de novo structure determination and protein engineering studies. Spring

BMB 30600 - Nucleic Acid Structure and Function.  This course focused on the biochemistry of nucleic acids. Topics include nucleic acid structure, folding, and chemistry, protein-nucleic acid interactions, non-coding RNAs, and the enzymology of key processes such as DNA repair and recombination. A special emphasis is placed on primary literature. PQ: Courses in Biochemistry, molecular biology and organic chemistry. Autumn.

BMB 32100 - Designer Proteins and Peptides. This graduate level course will deal with the design, synthesis, and characterization of novel non-natural proteins and peptides.  Some specific topics included are the following:  Peptide models of transmembrane domains, membrane fusion and membrane binding proteins, apolipoproteins, and peptide hormones.  Side chain modified peptides and proteins, peptide backbone modified peptides, covalent lipid-peptide and nucleotide-peptide adducts, peptide block copolymers, e.g., PEG-peptides, synthetic supersecondary structures, including 4- and 6-helix bundles, synthetic bab structures, and template assisted folding of b-sheet structures.  Readings would consist of entirely of journal articles.  Spring

BMB 32200 - Molecular Biophysics: Theory and Applications.  The course will expose students to modern biophysical methods and to provide background for use of existing facilities at The University of Chicago. Topics will include the measurement of physical properties of biological molecules including structure, thermodynamics, and kinetics. The primary focus will be on practical aspects but will cover a sufficient amount of theoretical background for the proper understanding of the technique.  PQ: BMB 30500 or consent of instructor. Winter.

BMB 32300 – Protein Molecular Structure and Function. This course presents a series of advanced case studies designed to familiarize students with current protein research and to expand on the protein fundamentals taught in Biochemistry 30400. Topics include: post-translational modification of proteins; protein-protein interactions; principles of enzyme catalysis; natural inhibitors of enzyme action; integral membrane proteins and ion channels; molecular motors; allosteric phenomena; conversion of light energy in photosynthesis.  PQ:  BMB 30400 or equivalent.  Winter.

DEVELOPMENTAL BIOLOGY

DVBI 35400 - Advanced Developmental Biology. This course provides an overview of the fundamental questions of developmental biology, presenting both the classical embryological experiments that defined these questions, and the modern molecular and genetic experiments that have been employed to try to reach mechanistic answers to these questions.  The first portion of the course will focus on the mechanism of axis formation in a variety of organisms; the second part of the course will explore selected topics in the field. Fall.

 DVBI 35600  - Vertebrate Developmental Genetics. This advanced-level course combines lectures, student presentations, and discussion sections.  It covers major topics in the developmental biology of vertebrate embryos (e.g., formation of the germ line, gastrulation, segmentation, nervous system development, limb patterning, organogenesis).   The course makes extensive use of the current primary literature and emphasizes experimental approaches including embryology, genetics, and molecular genetics. Spring.

DVBI 35700 - Developmental Evolution. This course uses the developmental genetics of established invertebrate and vertebrate model systems as an entry point to explore the developmental basis of evolutionary change. Topics range from the evolution of gene regulation to the origin of novelties such as eyes and wings. We will study original research papers. The purpose of this course is to provide graduate students (and advanced undergraduates) with a developmental genetic perspective on evolutionary questions that have emerged in various disciplines including developmental biology, paleontology and phylogenetic systematics. Winter.

DVBI 35800 - Developmental Neurobiology.  Topics include neural induction, early patterning of the central nervous system, axon guidance and neuronal migration, the development of brain activity, and the mechanisms of plasticity that fine-tune brain function. Approaches will range from molecular to cellular to systems neurobiology. Focus will be on the vertebrate CNS but attention will be given to important lessons from invertebrate systems. Winter.

ECOLOGY AND EVOLUTION

ECEV 30600 - Molecular Evolutionary Genetics. Advanced topics in evolutionary genetics and molecular evolution. The main goal is to survey the frontiers and to develop research projects of the future.

ECEV 30700 - Computational Biology.  This course provides mathematical and statistical backgrounds and computational skills in computational biology.  Topics will cover theory and methods for comparative analyses of DNA and protein sequence data; statistical tests of molecular clocks; methods of phylogenetic reconstruction and statistical tests of phylogenies; gene identification in DNA sequences; protein homology detection; and structure prediction methods using protein sequences.

ECEV 30800 - Current Topics in Evolutionary Genomics. This course will cover current topics in evolutionary genomics including comparative genomics, evolution of duplicate genes, evolution of genome structure and organization, evolution of protein-protein interaction network, and evolution of gene expression. It will also review methods for data analyses. Some background in molecular evolution is required.

ECEV 30900 - Evolution and Medicine. A seminar-reading-discussion course on medical implications of different areas in the evolutionary half of biology.

ECEV 31000 - Evolutionary Processes. Discussion, essays, and much reading on conceptual and empirical aspects of the evolutionary half of biology.  Also a laboratory in the philosophy of science.

ECEV 31200- Data Analysis in Ecology and Evolution. Covers the design and analysis of experiments, focusing on tests used commonly in evolutionary biology.  Both parametric and nonparametric tests will be considered.

ECEV 31400 - Geographical Variation. Theoretical and empirical aspects of geographical variation in population genetics.  Theoretical topics will include protected polymorphism and clines maintained by migration and selection; random genetic drift in a cline; and spatial patterns under migration, mutation, and random genetic drift. Estimation from molecular gene-frequency data of parameters that describe population structure and the relative contribution of random genetic drift and natural selection will be covered.

ECEV 31500 - Quantitative Genetics.  Theoretical topics include basic population genetics; the decomposition of the variance and the correlation between relatives with random mating, inbreeding, and assortative mating; selection; mutation-selection balance; and random genetic drift. Empirical examples from human genetics will be presented.

ECEV 32900 -  Plant Development and Molecular Genetics. Growth, differentiation and development in plants at the organismal, cellular, and molecular level. The regulatory function of environmental factors, hormones and phytochrome on gene expression and the possible evolutionary relationships will be studied.  The molecular genetic advances in Arabidopsis and maize are a central feature of the course. Spring

ECEV 33500 - Experimental Evolutionary Ecology. Students and instructors will propose simple research questions on any question of ecological or evolutionary interest. In addition to conducting a set number of class-chosen experiments, the bulk of the class work will consist of statistically analyzing and interpreting the results. It is expected that the projects have the potential to produce publishable results.

ECEV 34600 - Current Issues in Evolution. A seminar on unresolved problems in the evolutionary half of biology.

ECEV 34700 - Evolution of Development.  A seminar on developmental aspects of evolution and evolutionary aspects of development.

ECEV 35700 - Principles of Population Genetics II. Examines the basic theoretical principles of population genetics, and their application to the study of variation and evolution in natural populations. Topics include selection, mutation, random genetic drift, quantitative genetics, molecular evolution and variation, the evolution of selfish genetic systems, and human evolution. Spring.

ECEV 35800 - Classics of Evolutionary Genetics.  Major classic papers in evolutionary genetics that had great impact on the development of the field are reviewed.

ECEV 35900 - Evolution at the Genomic Level.  We focus on the newly proposed and solved problems related to evolution of genomes.  Instructors will give a series of lectures, dealing with basic concepts and techniques used in the research of topics.  Students will present and evaluate literatures.

ECEV 36200 - Empirical Evolutionary Biology. Critical analysis of recent literature on empirical research in evolutionary biology. Prerequisite: some knowledge of population genetics, evolutionary biology or consent of instructor.

ECEV 36300 – Speciation. A review of the literature on the origin of species beginning with Darwin and continuing through contemporary work. Both theoretical and empirical studies will be covered, with special emphasis on the genetics of speciation.

ECEV 37500 - Sexual Selection. A discussion and critical analysis of sexual selection. The course will consist of lectures, reading and discussion.

ECEV 42500 - Concepts in Ecology.  Using a combination of lecture and student-led discussion, this course will introduce students to the classical ecological literature as well as the latest work in each of several topics.  The goal is to provide students with a solid framework upon which to build their own research programs.

ECEV 42600 - Community Ecology.  Advanced topics in multi-species systems, and an introduction to basic theoretical approaches.

ECEV 44000 - Fundamentals of Molecular Evolution.  Covers major theories that form the foundation for understanding evolutionary forces governing molecular variation and divergence and genome organization.  It explores the evolutionary assembly of genes, the origin of novel gene function, the population genetics of repetitive DNA variation, and the evolution of multi-gene families.

GENETICS

GENE 38000 - Genomic & Proteomic Approaches to Biological Questions. Lectures with emphasis on concepts and experimental approaches in Genomics and Proteomics.  Topics to include: Bioinformatic tools for DNA analysis and protein analysis, genomic tools for high-throughput genetics, arrays for DNA & RNA detection, genome organization, comparative genomics, human evolution, current technologies for profiling proteomes, high-throughput protein expression and characterization, protein interaction networks, and markers of disease and drug targets. Spring.

MOLECULAR GENETICS AND CELL BIOLOGY

MGCB 31000 - Fundamentals in Molecular Biology.  The course covers nucleic acid structure and DNAtopology, recombinant DNA technology, DNA replication, DNA damage, mutagenesis and repair, Transposons and site-specific recombination, prokaryotic and eukaryotic transcription and its regulation, RNA structure, splicing and catalytic RNAs, protein synthesis, and chromatin.  Winter.

MGCB 31200 - Molecular Biology I.  Nucleic acid structure; mechanisms of transcription and replication.  Regulation of transcription in prokaryotes, and of DNA replication in prokaryotes and eukaryotes.    Winter.

MGCB 31600 - Cell Biology. 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.  Autumn.

MGCB  31700 - Advanced Cell Biology. Chromatin structure and its role in transcription communication between nucleus and cytoplasm, translation, protein folding and assembly, molecular chaperones, elements of signal transduction, homeostasis, growth control and the cell cycle, cytoarchitecture, cell adhesion and migration. Winter.

MGCB  34300 - Principles and Practices of Electron Microscopy. This course deals with the principles involved in obtaining electron micrographs of biological specimens. Preparation techniques and analytical procedures will be offered at an individualized level. Spring.           

MGCB  34600 - Viruses of Eukaryotes.  An advanced lecture course on viruses infecting animals and humans.  Spring.

STATISTICS

STAT 22000 - Statistic Methods and Applications. 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. Fall, Winter, and Spring.

STAT 22600 – Analysis of Qualitative Data. This is an introduction to the theory and applications of statistical methods for investigating the relationships among discrete variables. The course will present methods for analyzing categorical data, standard methods for contingency tables such as odds ratios, tests of independence and various measures of association, generalized linear models for binary data and count data, logistic regression for binomial data, loglinear models for Poisson data. The statistical techniques discussed will be presented by many real examples involving both physical and social science data. PQ: Statistics 22000 or equivalent. It is expected that the students have a good understanding of basic descriptive statistics such as means, variances and expectation, of the inferential notions of estimate, confidence intervals and significance or hypothesis testing. Familiarity with one statistical package, e.g. Stata, Sas, Splus, Spss, Minitab and ability to access Web sites and to download files from the Web are required. Winter

STAT 24400-24500 - Statistical Theory and Methodology. 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.

STAT 35500 – Statistical Genetics. This is an advanced course in statistical genetics. Prerequisites are Human Genetics 47100 and Statistics 24400 and 24500. Students who do not meet the prerequisites may enroll on a P/NP basis with consent of the instructor. This is a discussion course and student presentations will be required. Topics vary and may include, but are not limited to, statistical problems in linkage mapping, association mapping, map construction, and genetic models for complex traits.  Spring.

MICROBIOLOGY

MICR 34000 Bacterial Pathogenesis. This course focuses on the genetics and molecular biology of bacterial pathogens with emphasis on host-pathogen interactions.  The course will cover topics ranging from toxin production and secretion to evasion of host-responses and antibiotic resistance.  Current techniques and discoveries will be covered in a paper-based discussion section.  Winter.