Computational Biology Lecture Notes

Sequence Analysis Unit

LectureSubjectAssigned Reading for That Class
LecturesPart01.pptIntroduction and Web Resources for Computational Molecular Biology (Entrez)Mount, Ch. 1
Mount, Ch. 2
LecturesPart02.pptRepresenting and Finding Sequence Features using Consensus SequencesDurbin, pp. 48-51
(optional) Clote & Backofen, pp. 38-47
LecturesPart03.pptRepresenting and Finding Sequence Features using Frequency MatricesMount, pp. 161-173
Mount, pp. 192-196
Mount, pp. 76-89
Durbin, pp. 100-102
LecturesPart04.pptProtein Coding RegionsMount, pp. 342-344
Mount, pp. 342-343
Durbin, pp. 12-17 & pp. 42-44
LecturesPart05.pptPCR Primer Design and Sequence Comparison with Dot MatricesMount, pp. 53-64
LecturesPart06.pptSequence Comparison with Dynamic ProgrammingMount, pp, 64-76
Durbin, pp. 17-32
Needleman & Wunsch paper (read up to section 5)
LecturesPart07.pptEfficient Database Searching MethodsMount, pp. 282-320
(optional) Altschul et al. paper
LecturesPart08.pptPredicting from Protein SequenceMount, pp. 382-397
Mount, pp. 440-450
LecturesPart09.pptRetrieving and Displaying Macromolecular StructuresMount, pp. 400-401
LecturesPart10.pptMultiple Sequence AlignmentMount, pp. 145-156
LecturesPart11.pptExpression array Cluster AnalysisMount, pp. 519-522
 
03-510/710 lecturesSubjectAssigned Reading for That ClassFiles
LecturesPartA.pptSequence Retrieval, Formats and Basic OperationsMount, pp. 27-35getpage.pl
getpage.java
PossibleSites.c
LecturesPartB.pptMarkov Models, Hidden Markov Models, and GenefindingMount, pp. 185-191
Durbin, pp. 46-68
Durbin, pp. 72-75
Rogic2001 (link to free full text)
Haussler (1998) Trends in Biochemical Sciences (PDF reprint)
Krogh (1998) from Guide to Human Genome Computing (PDF reprint)
LecturesPartC.pptFamily Pairwise Search and CobblingGrundy & Bailey (1999) Bioinformatics (PDF reprint)
LecturesPartD.pptProtein Structure PredictionRost (2001) J Struct Biol (PDF reprint)
Bonneau & Baker (2001) Annu. Rev. Biophys. Biomol. Struct. 30:173 (PDF reprint)
LecturesPartE.pptDescribing and classifying sequences with numbersInClass2004WithPartE.xls

Biological Modeling Unit

LectureSubjectAssigned Reading for That ClassWorksheets
LecturesPart12.pptSimple Ionization Models using SpreadsheetsFalls, Chapt.1
LecturesPart13.pptCircular References and Recursion Relations
LecturesPart14.pptBiochemical Kinetics I
LecturesPart15.pptBiochemical Kinetics IISpreadsheet done in class with part 15
Second version (using circular references)
Third version (allow product feedback)
LecturesPart16.pptBiochemical Kinetics III
LecturesPart17.pptBiochemical Kinetics IVYeargers
Sections 7.10 through 7.12
(pp. 220-233)		Part17a.mw (Analytical solution of single ordinary differential equation)

Part17b.mw (Numerical integration of set of ordinary differential equations)

Part17c.mw (Add Product feedback)

LecturesPart18.pptCompartmental AnalysisYeargers
Sections 7.10 through 7.12
(pp. 220-233)		Part18a.mw (Lead metabolism, see Yeargers, section 7.10)

Part18b.mw (Pharmacokinetics, see Yeargers, section 7.11)

 
03-510 lecturesSubjectAssigned Reading for That ClassWorksheets
LecturesPartFLinear Discriminant ClassifiersInClass2004WithPartF.m
LecturesPartG.pptPopulation GeneticsMaple worksheet showing derivation of Hardy-Weinberg
LecturesPartH.pptNeuronal ModelingYeargers Chapter 8Maple worksheet done in class with part H
tar file with all Maple worksheets (to avoid file conversion errors)

Biological Imaging Unit

LectureSubjectImages
LecturesPart19.pptBiological Imaging ILecturesPart19Movie1.mov (2D time series: 2.1 MB)

LecturesPart19Movie2.avi (3D focus series: 11 MB)

LecturesPart20.pptBiological Imaging IILAMP2Example.PICT
Abdomen.tif
Image Filtering Operations spreadsheet
LecturesPart21.pptBiological Imaging III
 
03-510 lecturesSubjectAssociated files
LecturesPartI.pptRepresenting Distributions using Fourier Transformsfftillustrator.m (MATLAB script illustrating FFTs)