2009 - 2010 Course Schedule

Autumn 09 --- Winter 10 --- Spring 10 --- Summer 10

For times and locations, please check the UW Time Schedule

Autumn 2009

Genome 371: Introductory Genetics
Instructors: M.K. Raghuraman, Anne Paul
TAs: Renee George, Andy Itsara, Sarah Ng, Cailyn Spurrell

Course Description:
Three aspects of genetics are covered: 1) Mechanisms of gene transmission, including chromosome mapping and genetic pathways; 2) Mutational analysis of biological processes with an emphasis on mutations that affect chromosome transmission; 3) An introduction to genomics--the cloning and sequence analysis of whole genomes. The emphasis is on both formal genetic mechanisms and molecular techniques. For biological sciences majors. Prerequisite: minimum 1.5 in either BIOL 200 or BIOL 201; may not be repeated. Offered: AWSpS.

Genome 372: Genomics & Proteomics
Instructors: John Stamatoyannopoulos, Jim Bruce
TA: Kyle Siebenthall

Course Description:
Covers emerging fields of genomics and proteomics. Discusses key technologies and their applications to the study of human and model organism genomes. Prerequisite: GENOME 371.

Genome 453: Genetics of the Evolutionary Process
Instructor: Joe Felsenstein

Course Description:
Contributions of genetics to the understanding of evolution. Processes of mutation, selection, and random genetic events as they affect the genetic architecture of natural populations and the process of speciation. Emphasis on experimental data and observation, rather than mathematical theory. Prerequisite: either GENOME 371 or GENOME 372.

Genome 550: Methods and Logic in Genetics
Instructors: Bob Waterston, Jay Shendure

Course Description:
Critical reading and detailed discussion of genetics-related scientific research papers. Material emphasizes methodological and logical themes of importance in modern genetics, for example: origin of mutants, genetic epistasis, pulse labelling, and in vivo gene function. Prerequisite: first year Genome Sciences graduate students only.

Genome 551: Gene Regulation
Instructor: John Stamatoyannopoulos
course meets first 5 weeks of quarter only

Course Description:
Course covers fundamentals of gene regulation in eukaryotes including principles of cis and trans regulation of gene expression; DNA and RNA binding proteins; role of chromatin structure in gene expression; epigenetic regulatory mechanisms; RNA-based regulatory mechanisms; and post-transcriptional regulation. The course centers on reading and discussion of landmark primary literature in the aforementioned areas.

Genome 552: Genomics
Instructor: Debbie Nickerson
course meets second 5 weeks of quarter only

Course Description:
Introduces students to the nature of genomes, the structure of chromosomes, the organization of sequences, and the diversity of these features in different species. Discusses current and newly emerging technologies for mapping and sequencing genomes, determining linkage of simple and complex disorders, and identifying variations in DNA. Formerly called MBT 510.

Genome 576: Genetic and Genomic Analysis of Bacteria
Instructor: Colin Manoil
course meets second 5 weeks of quarter only

Course Description:
In-depth coverage of genetic and genomic strategies used to analyze complex biological processes in bacteria. Focuses on general approaches, with examples drawn from studies of pathogenic organisms where possible. A combination of lectures and seminar-style discussions of primary literature.

Winter 2010

Genome 371: Introductory Genetics
Instructors: Stan Fields, Josh Akey, Anne Paul
TAs: Ray Malfavon-Borja, Alex Nord, Cait Rippey

Course Description:
Three aspects of genetics are covered: 1) Mechanisms of gene transmission, including chromosome mapping and genetic pathways; 2) Mutational analysis of biological processes with an emphasis on mutations that affect chromosome transmission; 3) An introduction to genomics--the cloning and sequence analysis of whole genomes. The emphasis is on both formal genetic mechanisms and molecular techniques. For biological sciences majors. Prerequisite: minimum 1.5 in either BIOL 200 or BIOL 201; may not be repeated. Offered: AWSpS.

Genome 411: Gene Action
Instructor: Beth Traxler
TA: Sara Di Rienzi

Course Description:
Molecular genetics: description of fundamental genetics processes such as mutation, repair, genetic exchange, recombination, and gene expression. Use of genetic strategies to analyze complex biological processes. Focus is on prokaryotic organisms. Prerequisite: BIOL 201; either CHEM 223, CHEM 237, or CHEM 335. Offered: jointly with MICROM 411

Genome 465 / 565: Advanced Human Genetics
Instructors: Mary-Claire King, Evan Eichler
TA: Kevin Roach

Course Description:
Explores genetic analysis of naturally occurring variation in humans; origins and consequences of mutation, as mediated by selection, migration, population structure and drift; approaches to finding human disease genes and characterizing them at the molecular level; relevance of to other species to analysis of human genes. Prerequisite: GENOME 371; either GENOME 372 or BIOC 440.

Genome 540: Intro to Computational Molecular Biology
Instructor: Phil Green
TA: Alan Rubin

Course Description:
Algorithmic and probabilistic methods for analysis of DNA and protein analysis. Students must be able to write computer programs for data analysis. Prior coursework in biology and probability highly desirable. Prerequisite: permission of instructor.

Genome 547: Scientific Writing
Instructor: Leo Pallanck
5 week course - first half of quarter

Course Description:
For graduate students principally in their second and third year. Focuses on the preparation of research manuscripts for publication. Also considers other scientific writing such as thesis proposals and fellowship and grant applications. Second & Third year Genome Sciences students have priority.

Genome 553: Genetic Analysis
Instructor: Christine Queitsch
5 week course - first half of quarter

Course Description:
Discusses methods for selectively removing, adding, or altering specific proteins, to identify and order genes in a pathway, define protein function, determine tissue and temporal requirements for gene function, and distinguish among competing hypotheses to explain biological phenomena. Formerly called GENET 551. Prerequisite: GENOME 371, GENOME 551 or equivalent.

Genome 555: Proteomics
Instructor: Michael MacCoss
5 week course - second half of quarter

Course Description:
The course will focus on current and emerging technologies and approaches for analyzing protein structure and function, protein:protein interactions, and whole-cell protein functions ("the proteome"). We will emphasize the application of these technologies in biology, biotechnology and medicine. Prerequisite: BIOC 440, GENOME 551 or equivalent, GENOME 553

Genome 559: Introduction to Statistical and Computational Genomics
Instructors: Jim Thomas, Larry Ruzzo

Course Description:
Rudiments of statistical and computational genomics. Emphasis on basic probability and statistics, introduction to computer programming and relevant web databases. This course is intended to introduce students with non-computer science backgrounds to the major concepts of programming and statistics. Prerequisite: substantial background in molecular and cellular biology, genetics, biochemistry, or related disciplines.

Genome 465 / 565: Advanced Human Genetics
Instructors: Mary-Claire King, Evan Eichler
TA: Kevin Roach

Course Description:
Explores genetic analysis of naturally occurring variation in humans; origins and consequences of mutation, as mediated by selection, migration, population structure and drift; approaches to finding human disease genes and characterizing them at the molecular level; relevance of to other species to analysis of human genes. Prerequisite: GENOME 371; either GENOME 372 or BIOC 440.

Genome 570: Phylogenetic Inference
Instructor: Joe Felsenstein

Course Description:
Methods for inferring phylogenies (evolutionary trees) -- biological assumptions, statistical foundations, and computational methods. A comprehensive introduction for graduate students in the biological sciences to phylogenetic methods using data from molecular sequences, continuous and discrete characters, and gene frequencies. Prerequisite: introductory courses in evolution and in statistics.

Spring 2010

Genome 351: Human Genetics - The Individual and Society
Instructors: Evan Eichler, Leo Pallanck
TA: Lauren Richard

Course Description:
Principles of Mendelian inheritance as illustrated by human traits and diseases; chromosomes and sex determination; distribution of genes in populations; natural selection and evolution; counseling and genetic engineering; ethical issues. Appropriate for non-science majors.

Genome 371: Introductory Genetics
Instructors:  Mary Kuhner, Anne Paul
TAs: Rupali Patwardhan, Dan Skelly, Jennifer Reitz

Course Description:
Three aspects of genetics are covered: 1) Mechanisms of gene transmission, including chromosome mapping and genetic pathways; 2) Mutational analysis of biological processes with an emphasis on mutations that affect chromosome transmission; 3) An introduction to genomics--the cloning and sequence analysis ofwhole genomes. The emphasis is on both formal genetic mechanisms and molecular techniques. For biological sciences majors. Prerequisite: minimum 1.5 in either BIOL 200 or BIOL 201; may not be repeated. Offered: AWSpS.

Genome 373: Genome Informatics
Instructors: Jim Thomas, Jay Shendure
TA: Ryan Emerson

Course Description:
Focuses on methods for analyzing large genetic data sets and their application to biological problems, including sequence alignment and search methods, gene prediction, phylogenetic trees, and microarray analysis.

Genome 475: Debates in Genetics
Instructor: Carol Sibley

Course Description:
Utilizes the original scientific literature as the basis for discussion of a range of genetic issues that impact society Discussions are student-led; evaluations are based both on participation in class and on a research paper. Prerequisite: BIOL 200, GENOME 371.

Genome 490: Undergraduate Seminar
Instructor: Jon Gallant

Course Description:
Seminar for advanced undergraduate students engaged in individual research projects or those who wish to gain an understanding of genetic research by analysis of the primary literature. Assignments emphasize the rationale for research projects and the presentation and interpretation of research findings.

Genome 541: Intro to Computational Molecular Biology II
Instructors: Joe Felsenstein, Phil Green

Course Description:
Computational methods for studying molecular evolution. Students must be able to write computer programs for data analysis. Prior coursework in biology and probability highly desirable Prerequisite: GENOME 540 or permission of instructor.

Genome 560: Statistics for Genome Sciences
Instructor: Joe Felsenstein
5 week course - second half of quarter

Genome 561: Molecular Population Genetics and Evolution
Instructor: Willie Swanson
5 week course - first half of quarter

Course Description:
This course will survey recent literature in order to gain an understanding of the basic principles of molecular populaton genetics and evolution as applied to analysis of genome data. Some computer analysis of genome data will be performed.

Genome 580: Ethics in Biomedical Research
Instructor: Carol Sibley

Course Description:
Explores ethical issues in research and teaching and discusses avenues of responsible conduct. Intended for third year Genome Sciences grads and others supported by departmental training grants.

Genome 599 A: Chromatin & Epigenetics
Instructor: John Stamatoyannopoulos
5 week course - second half of quarter

Genome 599 B: Journal Club Preparation
Instructors: Bonny Brewer, Celeste Berg

For first year Genome Sciences grads only.

Summer 2010

Genome 371 : Introductory Genetics
Instructors: Geoff Findlay, Anne Paul
TA: Sean Schneider

Course Description:
Three aspects of genetics are covered: 1) Mechanisms of gene transmission, including chromosome mapping and genetic pathways; 2) Mutational analysis of biological processes with an emphasis on mutations that affect chromosome transmission; 3) An introduction to genomics--the cloning and sequence analysis of whole genomes. The emphasis is on both formal genetic mechanisms and molecular techniques. For biological sciences majors. Prerequisite: minimum 1.5 in either BIOL 200 or BIOL 201; may not be repeated. Offered: AWSpS.

Summer Courses for Educators: