| Lecture | Subject | Assigned Reading for That Class |
| LecturesPart01.ppt | Introduction | Jones/Pevzner, Ch. 1 Jones/Pevzner, Ch. 2 & 3 as needed |
| LecturesPart02.ppt Ch04_motifs_mod.ppt | Sequence Motifs | Jones/Pevzner, Ch. 4 |
| LecturesPart03.ppt Ch06_EditDist_mod.ppt | Sequence Alignment dotplotexample.m |
Jones/Pevzner, Ch. 6 through section 6.9 (page 185)
Needleman & Wunsch paper (read up to section 5) (recommended) Durbin, pp. 17-32 |
| Ch06_Alignment.ppt LecturesPart04.ppt | Similarity Matrices/Statistics of Pattern Appearance PossibleSites.c | (none) |
| Ch06_MultAlign.ppt | Multiple Sequence Alignment | Jones/Pevzner, section 6.10 |
| LecturesPart05.ppt | Hidden Markov Models MarkovDiNucs.m | Jones/Pevzner, Ch. 11 (optional) Durbin, pp. 61-68, 72-75 |
| LecturesPart06.ppt | Sequence Database Searching | Jones/Pevzner, Ch. 9 Altschul et al. paper |
| LecturesPart07.ppt | Supervised Machine Learning and Searching for Sequence Families | Grundy and Bailey paper |
| LecturesPart08.ppt | Protein Coding Regions | (none) |
| LecturesPart09.ppt Ch06_GenePred_sim_selected.ppt | Genefinding | Jones/Pevzner, section 6.11 through 6.15 Rogic et al. paper |
| LecturesPart10.ppt | Predicting from Protein Sequence | |
| LecturesPart11.ppt | Retrieving and Displaying Macromolecular Structures | |
| LecturesPart12.ppt | Expression array Cluster Analysis | Jones/Pevzner, Ch. 10 through section 10.3 |
| LecturesPart13.ppt | Phylogenetic Tree Reconstruction | Jones/Pevzner, remainder of Ch. 10 |
| Lecture | Subject | Assigned Reading for That Class | Worksheets/Images |
| LecturesPart14.ppt | Models of Population Dynamics and Population Genetics using Recursion Relations | ||
| LecturesPart15.ppt | Biochemical Kinetics I | ||
| LecturesPart16.ppt | Biochemical Kinetics II |
Part16a.mw (Analytical solution of single ordinary differential equation)
Part16b.mw (Numerical integration of set of ordinary differential equations) | |
| LecturesPart17.ppt | Compartmental Analysis | Yeargers Sections 7.10 through 7.12 (handout) (pp. 220-233) | Part17a.mw (Lead metabolism model using Maple, see Yeargers, section 7.10)
Part17b.mw (Pharmacokinetics model using Maple, see Yeargers, section 7.11) Part17c.m (Pharmocokinetics model using Matlab) drugmetab.m (helper function for Part17c.m) |
| LecturesPart18.ppt | Cell Cycle Modeling | Fall Ch. 10 through section 10.5 (handout) | CompCellBiolFigure10-3.mw (cyclin/CDK vs. APC phase plane) CompCellBiolFigure10-4.mw (cyclin/CDK vs. "p" bifurcation) CompCellBiolFigure10-6.mw (kinetics) |
| LecturesPart19.ppt | Cell Simulation: Virtual Cell | ||
| LecturesPart20.ppt | Stochastic Modeling / Neuronal Modeling | Yeargers Ch. 8 (handout) | Part20.mw (Hodgkin-Huxley) |
| LecturesPart21.ppt | Introduction to Bioimage Informatics | Glory & Murphy review article | |
| LecturesPart22.ppt | Basics of Image Acquisition and Processing |
| |
| LecturesPart23.ppt | Segmentation and Feature Calculation for Automated Interpretation of Subcellular Patterns |
fftillustrator2.m (MATLAB script illustrating FFTs)
exampleclassif.m finddecisionboundary.m EndoAndLysoImages.tgz showthresh.m realdata.m simplefeat.m realWave2.m showWaveDecomp2.m dwtreshape.m | |
| LecturesPart24.ppt | Clustering and Unmixing of Subcellular Patterns | ||
| LecturesPart25.ppt | Image-based Cell Models |