Autumn 05 --- Winter 06 --- Spring 06 --- Summer 06

For times and locations, please check the UW Time Schedule

Autumn 2005

Genome 371: Introductory Genetics
Instructors: Celeste Berg, Bonny Brewer, Anne Paul
TAs: Nathan Clark, Bungo Akiyoshi, Jamie Guenthoer, Sarah Mahoney

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 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 490: Undergraduate Seminar
Instructor: Michael MacCoss

Course Description:
Seminar for advanced undergraduate students engaged in individual research projects or those who which to gain an understanding of proteomics research by analysis of the primary literature.

The Fall 2005's presentations will explore the primary proteomics literature.  Emphasis will be placed on the critical evaluation of the current capabilities and limitations of proteomics technologies and applications.  Assignments will focus on the interpretation and presentation of articles from the literature.

Genome 550: Methods and Logic in Genetics
Instructors: Joshua Akey, Bob Waterston

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: Bob Braun
course meets first 5 weeks of quarter only

Course Description:
Will compare principals of gene regulation in prokaryotes and eukaryotes, including: how primary DNA sequence and chromatin structure affect gene expression, genetic and biochemical methods for studying gene regulation, constitutive vs inducible gene expression, different types of DNA and RNA binding proteins, combinatorial networks of gene regulation, mechanisms of posttranscriptional regulation.

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 2006

Genome 371: Introductory Genetics
Instructor: M.K. Raghuraman, Anne Paul
TAs: Mark Enstrom, Greg Finney, Joanna Kelley, Ashwin Unnikrishnan

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: Gene Structure and Function
Instructor: Janet Kurjan
TA: Alan Huang

Course Description:
Explores the structure of genes and chromosomes, the mechanisms and control of transcription and translation, and the molecular mechanisms of mutation, recombination, transposition, and development. Intended for majors in biological sciences. Prerequisite: GENOME 371.

Genome 411: Gene Action
Instructor: Colin Manoil
TAs: David Burke, Alex Berezow, Lazar Dimitrov, Mary Stewart

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: Charla Lambert

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 490: Undergraduate Seminar
Instructors: Breck Byers, Ray Monnat

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.

Presentations from the primary literature during the Winter 2005 session will focus on articles exploring DNA Repair -- The Cellular Response to DNA Breaks in Health and Disease.

Genome 540: Intro to Computational Molecular Biology
Instructor: Phil Green
TA: Aaron Klammer

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: Stan Fields
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: Celeste Berg
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 554: Genomic Informatics
Instructor: Jim Thomas
5 week course - second half of quarter

Course Description:
Introuduces students to the major methods for generating sequence alignments, practical use of web-based tools for identifying and analyzing sequences, the relationships between 3-dimensional protein structure and sequence divergence, and the meaning and interpretation of evolutionary trees in defining protein families and super-families. Prerequisite: GENOME 559 or equivalent.

Genome 559: Introduction to Statistical and Computational Genomics
Instructors: Bill Noble, Mark Rieder
5 week course - first half of quarter

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:

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 590: Population Genetics Seminar
Instructor: Joe Felsenstein

Course Description:
Weekly presentation by participants of current literature and ongoing research in evolution, molecular evolution, evolutionary genetics of natural populations, human population genetics, and quantitative genetics applied to animal and plant breeding. Credit/no credit only. Prerequisite: GENOME 562 or permission of instructor.

Spring 2006

Genome 371: Introductory Genetics
Instructor:  Mandy Schivell
TAs: Mark Budde, Audrey McConnell

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: Genomic Informatics
Instructors: Bill Noble, Jim Thomas

Course Description:
Focuses on methods for analyzing large genetic data sets and their application tobiological problems, including sequence alignment and search methods, gene prediction, phylogenetic trees, and microarray analysis. Basic programming skills are required.

Genome 475: Debates in Genetics
Instructor: Carol Sibley

Course Description:
The course will use the original scientific literature as the basis for discussion of a range of genetic issues that impact society. Discussions will be student-led; evaluation will be based both on participation in class and on a research paper.

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, Bill Noble

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 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 554.

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 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.

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 Genome Sciences grads and others supported by departmental training grants.

Summer 2006

Genome 371 : Introductory Genetics
Instructor: Mandy Schivell
TAs: Cindy Desmarais, Jennifer Gogarten

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:

• GENOME 503: An Inquiry Approach to Teaching Genetics at the Introductory High School Level
• GENOME 504: StarNet: Research Experiences for Students and Teachers
• GENOME 505: StarNet: Teacher Research Experience
• GENOME 506: The Science Education Partnership