Lecture 1: Detecting, Quantifying, and Classifying DNA http://www.ncbi.nlm.nih.gov/About/primer/genetics.html DNA: http://www.dnaftb.org/dnaftb/ http://biocrs.biomed.brown.edu/Books/Chapters/Ch%208/DH-Paper.html en.wikipedia.org/wiki/List_of_biomolecules Deoxyribonucleic Acid Single-stranded and Double Stranded RNA - single stranded Diploid and Haploid http://www.brooklyn.cuny.edu/bc/ahp/LAD/C9/C9_m_preparation.html 5' and 3' directions and ends Purines, Pyrimidines http://staff.um.edu.mt/acus1/3Molgen.htm This is great for all of it!! http://staff.um.edu.mt/acus1/4genfunction.htm (transcription, genetic code) complementarity, stability DNA extraction http://www.riedlab.nci.nih.gov/publications/2438.2413_DNA_Prep_Blood.pdf http://gslc.genetics.utah.edu/units/activities/extraction/ Primary: nucleotide sequence Secondary: Helical/Double helical Tertiary structure: Loops,, hairpins,etc. Protein quaternary - conformational Chromosomes Natural DNA replication (Cell biology, priming? Polymerase? Intron, Exon, Splicing Sites, Promoter regions Recombination crossover locations Transcription RNA http://cnx.rice.edu/content/m11416/latest/ Homozygous, Heterozygous, Hemizygous Genetics Glossary: http://ghr.nlm.nih.gov/ghr/glossary/hemizygous http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-H/hemizygous.html Homoduplex, Heteroduplex http://info.med.yale.edu/genetics/kkidd/contents.html Genes and Gene expression, Microarrays, Proteins Good introduction: http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html General bioinformatics: http://www.ncbi.nlm.nih.gov/About/primer/ http://industry.ebi.ac.uk/~alan/MicroArray/ http://www.microarrays.org/ http://rana.lbl.gov/EisenSoftware.htm http://latin.arizona.edu/galbraith/links.html dsDNA dyes, SYBR, cyanine Probes, proximity probe pairs, single probes, unlabelled probes PCR http://www.geneticorigins.org/geneticorigins/pv92/aluframeset.htm http://www.dnalc.org/shockwave/pcranwhole.html http://allserv.rug.ac.be/~avierstr/principles/pcrani.html http://www.bioteach.ubc.ca/TeachingResources/MolecularBiology/DNAReplication.html http://www.people.virginia.edu/~rjh9u/pcranim.html http://www.bio.davidson.edu/courses/Immunology/Flash/RT_PCR.html http://www.csuchico.edu/~jbell/Biol207/animations/pcr.html http://www.abpischools.org.uk/resources/poster-series/pcr/pcranim.asp http://ls126.molsci.org/PCR_top.html http://www.rvc.ac.uk/Extranet/DNA_1/7_PCR.htm http://www.vanderbilt.edu/AnS/Chemistry/Rizzo/chem224/PCR.html http://science.nhmccd.edu/biol/bio1int.htm http://www.ornl.gov/sci/techresources/Human_Genome/publicat/twistedladder/pcrdemo.h tml http://www.ens-lyon.fr/RELIE/PCR/principe/anim/presentation.htm http://www.uq.edu.au/vdu/PCRlinks.htm The PCR Jumpstation http://www.highveld.com/pages/pcr.html http://www.horizonpress.com/pcr/ Denaturation, Dissociation, Unwinding, Melting Annealing, Coiling, Pairing http://bip.weizmann.ac.il/mb/bioguide/pcr/contents.html Nested PCR http://www.bio.davidson.edu/courses/genomics/method/NestedPCR.html Hot start http://bip.weizmann.ac.il/mb/bioguide/pcr/PCRHot-start.html Touchdown PCR http://bip.weizmann.ac.il/mb/bioguide/pcr/PCRTouchdown.html Assymetric PCR Isothermal PCR (ARUP!) Fast start Polymerase Editing en.wikipedia.org/wiki/DNA_polymerase http://oregonstate.edu/instruction/bb492/lectures/DNAI.html Restriction enzymes http://www.people.virginia.edu/~rjh9u/restrenz.html http://internalmed.wustl.edu/divisions/enzymes/INDEX.HTM Other ingredients in PCR tube qPCR Background, Dilution series, Logistic, Exponential GENERAL http://www.kcl.ac.uk/depsta/biomedical/Teaching/wsinfopartic.htm Molecular Biology Links http://www.horizonpress.com/gateway/ http://oregonstate.edu/instruction/bb492/index.html ("Schedule") http://oregonstate.edu/instruction/bb492/lectures/DNAI.html http://oregonstate.edu/instruction/bb492/lectures/StructureI.html http://oregonstate.edu/instruction/bb492/lectures/StructureII.html Strange equation of reassociation dynamics:? http://oregonstate.edu/instruction/bb492/figletters/FigD1.html ---------------------------------------------------------------------------------- Mathematical Aspects: Prediction of Annealing and Denaturation for: Primer Design, Genotyping, Genotypic Identity, Microarray quantification Given NN Parameters, Derivation of NN Parameters (Santa Lucia, Me, Sugimoto, Baseline) Clustering and Classification of Microarray genes and patients Melting Curves Sequences Analysis of data always depends upon metric and preprocessing: Supervised and Unsupervised Learning, Classification vs. Clustering Melting Curve Signal/Noise-Background Separation Microarray: genewise or patientwise mean/median, logarithmic, random? filtering Oligo sequences: Multiple alignment -------------------------------------------------------------------------------------- Applications: Molecular medicine Tumor type, pathogen type specific treatment Drug reactions: patient specific treatment Transplant compatibility Algorithms and Models Overview Hierarchical Clustering, Feature and Measurement Selection, Number of Clusters Multiple Alignment, Hidden Markov Nearest Neighbor Approximation of Thermodynamic Parameters Background model and removal van't Hoff Equation Meltmap Optimal mixing for Tripartite Genotyping Primer and Probe Design Misprime prevention: Genome-wide indexing and search Sequencing Base specificity SNP and Genome database search Dye/Probe Design DNA secondary structure and DGCE, TGCE TGCE quantification Labview and other programming Visualization: 3d Transvection algorithm