HOME	MEDED 534 , Autumn 2004 Biology and Informatics
	Class Notes and Assignments Unless otherwise specified, all assignments should be completed PRIOR to the class with which they are associated. Class Project: due at the end of the day on December 10. Class Presentations: one per student during the quarter Midterm Exam: due Thursday Oct 28 by 8 AM Week 1 Class 1 Introduction Slides Week 2 Class 1 Anatomy Assignment Class 2 Knowledge Representation in Anatomy Assignment Sally Lee slides Week 3 Class 1 Tissues and Cells Slides Reading assignments:     Marieb Chapter 2 (Cells)     Marieb Chapter 4 (Tissues)   Class 2 Imaging Informatics Reading assignments:    Chapter 9,Imaging and Structural Informatics Shortliffe Edition 3:                   Draft Figures Sections 9-9.5.1, pp 1-16.   Tagare et al, Medical image databases: a content-based retrieval approach  Brinkley et al, Design of an Anatomy Information System Catherine Kehl Slides Week 4 Class 1 Physiology Reading assignments Review physiology section of Chapter 17 in Anatomy and Physiology,   The Easy Way. Dan Cook Slides Class 2 Simulation Reading and web assignments   Just get the basic ideas from these, and understand the difference:     Lu et al, A human cardiopulmonary system model...     Hunter et al, Modelling total heart function     JSim and models based on Lu   Cook et al, ...symbolic representation of...physiological functions... Nick Anderson slides Week 5 Class 1 Molecules and pathways Reading: Lodish 2, 8.1 Shala Erlich Slides Class 2 Pathway databases Assignment Sophia Jeng slides Week 6 Class 1 Proteins Reading: Lodish 3     Class 2 Protein structure and databases Reading   Apweiler 2004, Protein sequence databases   Berman 2000, The Protein Data Bank   Levitt 1976, Structural patterns   Day 2003, Fold classification   Armen 2004, Secondary structure and disease Jessica Li slides Valerie Daggett slides Week 7 Class 1 DNA and protein synthesis Reading: Lodish 4 Peter Myler slides, Fundamentals of Molecular Biology         Class 2 Sequencing and sequence databases Reading:   Lodish Chapter 9 Molecular Genetics Techniques and Genomics   Patnaik 2001 Review of online tools and databases for sequence                      analysis   Benson 2004  Genbank sequence database   GO 2004 Gene Ontology   Gennari 2004 Mapping FMA to GO Peter Myler slides, Gene Sequencing Brent Louie slides, Finding Human Disease Genes Week 8 Class 1 Gene regulation Reading: Lodish 11, 12 (concentrate on 11)     Class 2 Measurement and analysis of gene expression Reading:   Freeman2000 Expression arrays   Leung2003  Array analysis   Stoeckert2002  Array databases and standards   Pandey2000 Proteomics   Suzuki 2004 In situ hybridization Kirsten Smith slides Jim Brinkley Gene Expression links     Week 9 Class 1 Cell signalling Reading: Lodish 13,14 Wenqing Xu slides Class 2 Systems biology Reading   Krull2003    Transpath signalling databases   Lee2003     Quantitative pathway modelling   Cook2001   Qualitative pathway modelling   Hucka2004  Systems Biology markup language   Ideker2001 Systems Biology Xian Li slides Jim Brinkley Systems Biology links Week 10 Class 1 From tissues to organs Reading: Lodish 5,6 Scott Brockenbrough Slides Massari2000, Transcription factors in development NCBI Bookshelf, Differential Gene Expression Class 2 3-D structural modelling Reading  Chapter 9,Imaging and Structural Informatics Shortliffe     Edition 3: Draft Sections 9.5.2-end, pp 16-38.  Marsh2001, Ultrastructure by serial sections  Baldock2003, Visualizing gene expression on structure  Hinshaw2002, Model based 3-D segmentation  Poliakov2004, Visualizing brain function on structure Tung Le slides Jim Brinkley 3-D modeling links Week 11 Class 1 Neurons and neuroscience Reading:Lodish 4th Edition, Chapter 21 Ric Robinson slides Class 2 Neuroinformatics Reading   Fiala2001 Neuron 3-D ultrastructure determination   Hines2002 NEURON computional modeling software   Miller2001 SenseLab neuron and modelling public database   Jakobovits2002 WIRM Experiment Management System Toolkit   Nature2000 Debate over requirements for fMRI data sharing Jim Brinkley neuroinformatics links Dhileep Sivam slides
BACK TO TOP  Last Updated: 12/16/2004	Contact the instructor at: brinkley@u.washington.edu