Typical Course of Study
Year 1:
- First semester
- C3MB (CBIO 455/IBMS 450/CBIO 453/456) 8 credit hrs
- Complete 3 lab rotations (July 1 to Dec 15)
- Choose Ph.D. mentor (end December)
- Second semester
- GENE 500/504 6 credit hrs
- Summer semester:
- Program Directors meet with students to discuss status, mentor, and next steps. Students begin assembling Ph.D. thesis committee
Year 2:
- First semester
- GENE 511 3 credit hr
- 1 elective course (Genetics or other) 3 credit hrs
- Second semester
- 1 elective course (Genetics or other) 1-3 credit hrs
- 1 elective course (Genetics or other) 1-3 credit hrs
- Total graded courses: 24 credits minimum
- Oral Defense of Thesis Proposal (to be completed by June 30)
- Advancement to Ph.D. Candidacy
Year 3 onwards:
- Full time research
List of Courses (cross-listed courses in parentheses)
GENE 451 (EPBI 451, MPHP 451)
Principles of Genetic Epidemiology 3.0
William Bush
This course introduces the foundational concepts of genomics and genetic epidemiology through four key principles: 1) Teaching students how to query relational databases using Structure Query Language (SQL); 2) Exposing students to the most current data used in genomics and bioinformatics research, providing a quantitative understanding of biological concepts; 3) Integrating newly learned concepts with prior ones to discover new relationships among biological concepts; and 4) providing historical context to how and why data were generated and stored in the way they were, and how this gave rise to modern concepts in genomics.
GENE 452 (EPBI 452)
Statistical Methods in Genetic Epidemiology 3.0
Robert Igo
Analytic methods for evaluating the role of genetic factors in human disease, and their interactions with environmental factors. Statistical methods for the estimation of genetic parameters and testing of genetic hypotheses, emphasizing maximum likelihood methods. Models to be considered will include such components as genetic loci of major effect, polygenic inheritance, and environmental, cultural and developmental effects. Topics will include familial aggregation, segregation and linkage analysis, ascertainment, linkage disequilibrium, and disease marker association studies. Recommended preparation: EPBI 431 and EPBI 451.
GENE 488 (MBIO 488, CLBY 488, PATH 488)
Yeast Genetics/Cell Biology 3.0
Alan Tartakoff
This seminar course provides an introduction to the genetics and molecular biology of the yeasts S. cerevisiae and S. pombe by a discussion of current literature focusing primarily on topics in yeast cell biology. Students are first introduced to the tools of molecular genetics and special features of yeasts that make them important model eukaryotic organisms. Some selected topics include cell polarity, cell cycle, secretory pathways, vesicular and nuclear/cytoplasmic transport, mitochondrial import and biogenesis, chromosome segregation, cytoskeleton, mating response and signal transduction.
GENE 500
Advanced Eukaryotic Genetics I 3.0
Helen Salz
Fundamental principles of modern genetics; transmission, recombination, structure and function of the genetic material in eukaryotes, dosage compensation, behavior and consequences of chromosomal abnormalities, mapping and isolation of mutations, gene complementation and genetic interactions. Recommended preparation: BIOL 362.
GENE 504
Advanced Eukaryotic Genetics II 3.0
Helen Salz
Fundamental principles of modern genetics: population and quantitative genetics, dissection of genome organization and function, transgenics, developmental genetics, genetic strategies for dissecting complex pathways in organisms ranging from Drosophila and C. elegans to mouse and human. Recommended preparation: GENE 500 or permission of instructor.
GENE 505
Genetics Journal Club 1.0
Yan Li
Genetics Journal Club is a graduate level course designed to facilitate discussion of topics in Genetics. Students choose "hot" papers in Genetics and present them to their peers. Group presentations are designed to encourage audience participation. The intent of this class is to expose students to cutting edge topics in Genetics and to instill teaching and leadership skills.
GENE 467 (LAWS 5341, MGMT 467, EBME 467 and EECS 467)
Commercialization and Intellectual Property Management 3.0
This interdisciplinary course covers a variety of topics, including principles of intellectual property and intellectual property management, business strategies and modeling relevant to the creation of start-up companies and exploitation of IP rights as they relate to biomedical-related inventions. The goal of this course is to address issues relating to the commercialization of biomedical-related inventions by exposing law students, MBA students, and Ph.D. candidates (in genetics and proteomics) to the challenges and opportunities encountered when attempting to develop biomedical intellectual property from the point of early discovery to the clinic and market. Specifically, this course seeks to provide students with the ability to value a given technological advance or invention holistically, focusing on issues that extend beyond scientific efficacy and include patient and practitioner value propositions, legal and intellectual property protection, business modeling, potential market impacts, market competition, and ethical, social, and healthcare practitioner acceptance. During this course, law students, MBA students, and Ph.D. candidates in genomics and proteomics will work in teams of five (two laws students, two MBA students and one Ph.D. candidate), focusing on issues of commercialization and IP management of biomedical-related inventions. The instructors will be drawn from the law school, business school, and technology-transfer office. Please visit the following website for more information: fusioninnovate.com.
GENE 511
Grant Proposal Workshop 3.0
Paul Tesar
This is an introductory graduate course in grant writing and reviewing skills. During this course each student will write a research grant on a topic of his or her choice. Proposals may form the basis for the written component of the preliminary examination in the Genetics and Genome Sciences Department. Students will also participate in editing and reviewing the proposals of their classmates.
GENE 513
Adv. Developmental Genetics 3.0
Ron Conlon
This course covers the mechanisms of development in the context of the major events of mammalian embryogenesis. The focus is on how genes act in cells to create and pattern the tissues and organs of the adult. Students can expect to acquire a deep understanding of the embryology of mammals, and how genetic manipulations have led to our current understanding of pattering mechanisms. The material will be taught by a combination of self-study exercises, discussions of the primary literature, student presentations, and facilitator guided, student-led, problem-based learning.
GENE 520
Computational Human Genomics and Epigenomics. 4.0
Tom LaFramboise
The purpose of this course is to acquaint students with current high-throughput techniques and computational pipelines to assay the human genome, epigenome, and transcriptome on a large scale. The course will be a combination of lecture, discussion, and hands-on sessions. Topics will include next-generation sequencing pipelines (DNA variant calling, RNA sequencing, ATAC-seq, single-cell sequencing, spatial transcriptomics, etc.), as well as "best practices" for programming, software development, and distribution.
GENE 524
Advanced Medical Genetics: Molecular & Cytogenetics 2.0-3.0
Becky Darrah/Michelle Merrill/Anna Mitchell
An in-depth forum for discussion of fundamental principles regarding clinical cytogenetics and molecular genetics and their relevance to medical genetics, genomics and genetic counseling. Following a historical overview, topics include a discussion of numerical and structural aberrations, sex chromosome abnormalities, issues regarding population cytogenetics, clinical relevance of such findings as marker chromosomes, mosaicism, contiguous gene deletions and uniparental disomy. The course will cover principles of molecular genetics including structure, function and regulations of genes (DNA, RNA, proteins), genetic variation, inheritance patterns and both cytogenetic and molecular laboratory techniques (fluorescence in situ hybridization, micro-array, SNP analyses, sequencing) in the clinical laboratory.
GENE 525
Advanced Medical Genetics: Clinical Genetics 2.0-3.0
Michelle Merrill
Fundamental principles regarding congenital malformations, dysmorphology and syndromes. Discussion of a number of genetic disorders from a systems approach: CNS malformations, neurodegenerative disorders, craniofacial disorders, skeletal dysplasias, connective tissue disorders, hereditary cancer syndromes, etc. Discussions also include diagnosis, etiology, genetics, prognosis and management.
GENE 526
Advanced Medical Genetics: Quantitative Genetics & Genomics 2.0-3.0
Anna Mitchell/Becky Darrah
This course provides a foundation in quantitative genetics as well as genomic approaches and technologies which have greatly expanded our understanding of not only rare genetic disorders but common ones as well. Concepts related to risk assessment and calculation and its application to medical genetics including principles and application of Hardy Weinberg equilibrium and applying Bayes' Theorem as a mechanism to refine risk assessment based on patient specific data are covered. The clinical implications of interpreting next generation sequencing results, identifying limitations of genomic technologies, and practicing annotation and interpretation of genomic testing results are also covered. In addition, resources and bioinformatics tools including national databases and clinical labs to aid in the interpretation of genomic test results including variants of uncertain significance are discussed.
GENE 527
Advanced Medical Genetics: Metabolism 2.0-3.0
Michelle Merrill
Fundamental principles of metabolic testing; amino acid disorders; organic acid disorders; carbohydrate disorders; peroxisomal disorders; mitochondrial disorders; etc. Discussion of screening principles and newborn screening as well as approaches to diagnosis, management and therapy for metabolic diseases.