Computational Biology Lecture Notes

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Computational Molecular Biology Unit

LectureSubjectAssigned Reading for That Class
LecturesPart01.pptIntroductionJones/Pevzner, Ch. 1
Jones/Pevzner, Ch. 2 & 3 as needed
LecturesPart02.ppt
Ch04_motifs_mod.ppt
Sequence MotifsJones/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.pptMultiple Sequence AlignmentJones/Pevzner, section 6.10
LecturesPart05.pptHidden Markov Models
MarkovDiNucs.m
Jones/Pevzner, Ch. 11
(optional) Durbin, pp. 61-68, 72-75
LecturesPart06.pptSequence Database SearchingJones/Pevzner, Ch. 9
Altschul et al. paper
LecturesPart07.pptSupervised Machine Learning and Searching for Sequence FamiliesGrundy and Bailey paper
LecturesPart08.pptProtein Coding Regions(none)
LecturesPart09.ppt
Ch06_GenePred_sim_selected.ppt
GenefindingJones/Pevzner, section 6.11 through 6.15
Rogic et al. paper
LecturesPart10.pptPredicting from Protein Sequence
LecturesPart11.pptRetrieving and Displaying Macromolecular Structures
LecturesPart12.pptExpression array Cluster AnalysisJones/Pevzner, Ch. 10 through section 10.3
LecturesPart13.pptPhylogenetic Tree ReconstructionJones/Pevzner, remainder of Ch. 10

Computational Cell Biology Unit

LectureSubjectAssigned Reading for That ClassWorksheets/Images
LecturesPart14.pptModels of Population Dynamics and Population Genetics using Recursion Relations
LecturesPart15.pptBiochemical Kinetics I
LecturesPart16.pptBiochemical Kinetics II Part16a.mw (Analytical solution of single ordinary differential equation)

Part16b.mw (Numerical integration of set of ordinary differential equations)

LecturesPart17.pptCompartmental AnalysisYeargers
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.pptCell Cycle ModelingFall 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.pptCell Simulation: Virtual Cell
LecturesPart20.pptStochastic Modeling / Neuronal ModelingYeargers Ch. 8 (handout)Part20.mw (Hodgkin-Huxley)
LecturesPart21.pptIntroduction to Bioimage InformaticsGlory & Murphy review article
LecturesPart22.pptBasics of Image Acquisition and Processing


LAMP2Example.tif
Abdomen.tif
3D.zip (5 slices from 3D stack)

LecturesPart23.pptSegmentation 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.pptClustering and Unmixing of Subcellular Patterns
LecturesPart25.pptImage-based Cell Models