Computational Biology Lecture Notes 2005

Sequence Analysis Unit

LectureSubjectAssigned Reading for That Class
LecturesPart01.pptIntroduction
LecturesPart02.pptWeb Resources for Computational Molecular Biology (Entrez)Mount, Ch. 1
Mount, Ch. 2
LecturesPart03.pptSequence Comparison with Dot MatricesMount, Ch. 3
LecturesPart04.pptSequence Comparison with Dynamic Programming Needleman & Wunsch paper (read up to section 5)
Durbin, pp. 12-32 & pp. 42-44
LecturesPart05.pptStatistics of Pattern AppearanceMount, Ch. 4
LecturesPart06.pptSequence Database SearchingMount, Ch. 6 through p. 259
Altschul et al. paper
LecturesPart07.pptRepresenting and Finding Sequence FeaturesMount, pp. 210-214
Durbin, pp. 100-102
LecturesPart08.pptProtein Coding RegionsMount, Ch. 9 through p. 372
LecturesPart09.pptBasics of GenefindingMount, rest of Ch. 9
(03-510/710) Rogic et al. paper
LecturesPart10.pptPredicting from Protein SequenceMount, Ch. 10
LecturesPart11.pptRetrieving and Displaying Macromolecular Structures
LecturesPart12.pptExpression array Cluster AnalysisMount, Ch. 13
 
03-510/710 lecturesSubjectAssigned Reading for That ClassFiles
LecturesPartA.pptSequence Retrieval and Classificationgetpage.pl
getpage.java
LecturesPartB.pptMultiple Sequence AlignmentMount, Ch. 5 through p. 186
LecturesPartC.pptEstimating sequence probabilities with Markov Models and Hidden Markov ModelsDurbin, pp. 46-61
LecturesPartD.pptBaum-Welch Algorithm and HMMERMount, pp. 185-191
Durbin, pp. 61-68
Durbin, pp. 72-75
LecturesPartE.pptFamily Pairwise Search and CobblingGrundy & Bailey (1999) Bioinformatics (PDF reprint)
LecturesPartF.pptProtein Structure PredictionRost (2001) J Struct Biol (PDF reprint)
Bonneau & Baker (2001) Annu. Rev. Biophys. Biomol. Struct. 30:173 (PDF reprint)

Biological Modeling Unit

LectureSubjectAssigned Reading for That ClassWorksheets
LecturesPart13.pptSimple Ionization Models using Spreadsheets
LecturesPart14.pptCircular References and Recursion Relations
LecturesPart15.pptBiochemical Kinetics I Spreadsheet done in class with part 15
LecturesPart16.pptBiochemical Kinetics II(optional) Yeargers
Sections 7.10 through 7.12		 Part16a.mw (Analytical solution of single ordinary differential equation)

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

Part16c.mw (Add Product feedback)

LecturesPart17.pptCompartmental AnalysisYeargers
Sections 7.10 through 7.12 (handout)
(pp. 220-233)		Part17a.mw (Lead metabolism, see Yeargers, section 7.10)

Part17b.mw (Pharmacokinetics, see Yeargers, section 7.11)

LecturesPart18.pptNeuronal ModelingYeargers Ch. 8 (handout)Part18.mw (Hodgkin-Huxley)
LecturesPart19.pptCell Cylcle 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)
 
03-510 lecturesSubjectAssigned Reading for That ClassWorksheets
LecturesPartG.pptIndexing Multimedia Databases (Guest Lecture: Christos Faloutsos)
LecturesPartH.pptVirtual Cell

Biological Imaging Unit

LectureSubjectImages
LecturesPart20.pptBiological Imaging ILecturesPart20Movie1.mov (2D time series: 2.1 MB)

LecturesPart20Movie2.avi (3D focus series: 11 MB)

LecturesPart21.pptBiological Imaging IILAMP2Example.tif
Abdomen.tif
Image Filtering Operations spreadsheet
LecturesPart22.pptBiological Imaging III exampleclassif.m
EndoAndLysoImages.tgz
showthresh.m
simplefeat.m
realdata.m
 
03-510 lecturesSubjectAssociated files
LecturesPartI.pptRepresenting Distributions using Fourier Transformsfftillustrator.m (MATLAB script illustrating FFTs)
LecturesPartJ.pptSpatial Models