| Lecture | Subject | Assigned Reading for That Class | |
| LecturesPart01.ppt | Introduction/Representing and Retrieving Sequences | Mount, Ch. 1 Mount, Ch. 2 | |
| LecturesPart02.ppt | Sequence Comparison with Dot Matrices | Mount, Ch. 3 | |
| LecturesPart03.ppt | Sequence Comparison with Dynamic Programming and Similarity Matrices |
Needleman & Wunsch paper (read up to section 5) Durbin, pp. 12-32 & pp. 42-44 | |
| LecturesPart04.ppt | Statistics of Pattern Appearance | Mount, Ch. 4 | |
| LecturesPart05.ppt | Multiple Sequence Alignment | Mount, Ch. 5 through p. 186 | |
| LecturesPart06.ppt | Sequence Database Searching | Mount, Ch. 6 through p. 259 Altschul et al. paper | |
| LecturesPart07.pdf | Intro to Machine Learning | Optional material on SVMs | |
| LecturesPart08.ppt | Representing and Finding Sequence Features | Mount, pp. 210-214 Durbin, pp. 100-102 | |
| LecturesPart09.ppt | Baum-Welch Algorithm and HMMER | Mount, pp. 185-191 Durbin, pp. 61-68 Durbin, pp. 72-75 | |
| LecturesPart10.ppt | Protein Coding Regions | Mount, Ch. 9 through p. 372 | |
| LecturesPart11.ppt | Genefinding | Mount, rest of Ch. 9 (03-510/710) Rogic et al. paper | |
| LecturesPart12.ppt | Predicting from Protein Sequence | Mount, Ch. 10 | |
| LecturesPart13.ppt | Retrieving and Displaying Macromolecular Structures | ||
| LecturesPart14.ppt | Expression array Cluster Analysis | Mount, Ch. 13 |
| Lecture | Subject | Assigned Reading for That Class | Worksheets |
| LecturesPart15.ppt | Simple Ionization Models using Spreadsheets | ||
| LecturesPart16.ppt | Circular References and Recursion Relations | ||
| LecturesPart17.ppt | Biochemical Kinetics I | ||
| LecturesPart18.ppt | Biochemical Kinetics II | (optional) Yeargers Sections 7.10 through 7.12 |
Part18a.mw (Analytical solution of single ordinary differential equation)
Part18b.mw (Numerical integration of set of ordinary differential equations) |
| LecturesPart19.ppt | Compartmental Analysis | Yeargers Sections 7.10 through 7.12 (handout) (pp. 220-233) | Part19a.mw (Lead metabolism, see Yeargers, section 7.10)
Part19b.mw (Pharmacokinetics, see Yeargers, section 7.11) |
| LecturesPart20.ppt | Neuronal Modeling | Yeargers Ch. 8 (handout) | Part20.mw (Hodgkin-Huxley) |
| LecturesPart21.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) |
| Lecture | Subject | Images |
| LecturesPart22.ppt | Biological Imaging I | LecturesPart22Movie.avi (3D focus series: 11 MB) |
| LecturesPart23.ppt | Biological Imaging II | LAMP2Example.tif
Abdomen.tif Image Filtering Operations spreadsheet |
| LecturesPart24.ppt | Automated Interpretation of Subcellular Patterns in Microscope Images I |
Gia_d.avi
Tfr_d.avi Tub_d.avi Glut1_TI_d.avi |
| LecturesPart25.ppt | Automated Interpretation of Subcellular Patterns in Microscope Images II |
exampleclassif.m
finddecisionboundary.m EndoAndLysoImages.tgz showthresh.m realdata.m simplefeat.m realWave.m showWaveDecomp.m rwt.tgz (Rice Wavelet Toolbox for Mac OS X); version for other OS available from http://dsp.rice.edu/software/rwt.shtml |
| LecturesPart26.ppt | Virtual Cell | |
| LecturesPart27.ppt | Representing Distributions using Fourier Transforms | fftillustrator.m (MATLAB script illustrating FFTs) |
| LecturesPart28.ppt | Automated Interpretation of Subcellular Patterns in Microscope Images III |