# Date Topics Slides Matlab Homework (not graded) Exams 1 Aug 24 Why probability and statistics in comutational bioengineering? Lecture_1.pdf 2 Aug 26 Random experiments. Sample space, Events, Venn diagramms.  Definitions of probability: Statistical (part 1) Lecture2.pdf 3 Aug 31 Definitions of probability: Statistical (continued) Definitions of probability: Inductive.  Paradoxes of inductive definition of probability Combinatorics Lecture3.pdf coin_toss_template.m coin_toss.m 4 Sep 2 Combinatorics (continued) Probability axioms Conditional probability Independence of events Circuit diagrams Lecture4.pdf 5 Sep 7 Circuit diagrams (continued) Bayes' theorem Specificity/Sensitivity of tests Lecture5.pdf circuit_template.m circuit.m 6 Sep 9 Bayes' theorem (continued) Monty Hall problem Lecture6.pdf monty_hall_template.m monty_hall.m hw1.pdf 7 Sep 14 Discrete random varibales, PMF. CDF, CCDF,  Mean, Variance, Skewness Uniform distribution The distribution of the Ct value in COVID-19 PCR tests Lecture7.pdf 8 Sep 16 Bernoulli trials Binomial Distribution Secretary Problem Lecture8.pdf binomial_template.m binomial.m hw1_with_solutions.pdf 9 Sep 21 Binomial Distribution (continued) Poisson Distribution Genome Assembly Lecture9.pdf poisson_template.m poisson.m 10 Sep 23 Geometric distribution. Phylogenetic trees and time to the most recent common ancestor.  Mitochondrial Eve, Y-chromosome Adam and ancestry of nuclear DNA Lecture10.pdf 11 Sep 28 Mitochondrial Eveen (continued) Negative Binomial Distribution Cancer: Driver and Passanger genes/mutations Lecture11.pdf geometric_negative_binomial_template.m geometric_negative_binomial.m 12 Sep 30 Continuous random variables. Probability Density Function, CDF, CCDF, Mean, Variance, Std Uniform continuous distribution.  Constant rate (Poisson) process. Exponential distribution. Lecture12.pdf 13 Oct 5 Erland, Gamma, Gaussian distributions Lecture13.pdf exponential_gamma_template.m exponential_gamma.m 14 Oct 7 Gaussian (continued) Fitting Gaussian distribution to the data on binding energies of protein-protein interactions Lecture14.pdf PINT_binding_energy.mat hw2.pdf 15 Oct 12 Multiple random variables. Joint, Marginal, and Conditional PMFs or PDFs. Statistical independence of variables Lecture15.pdf 16 Oct 14 Covariance Correlation coefficients: Pearson, Spearman Lecture16.pdf Excercise #1: correlation_template.m correlation.m hw2_with_solutions.pdf 17 Oct 19 Midterm preparation Lecture17.pdf Oct 21 Midterm 18 Oct 26 Samples, histograms,  median, quartiles, percentiles Box-and-whisker plots Lecture18.pdf quartiles_template.m quartiles.m 19 Oct 28 Sample mean. Its mean and variance (standard error). Central limit theorem. Parameter point estimation (part one).. Lecture19.pdf central_limit_theorem_template.m central_limit_theorem.m hw3.pdf 20 Nov 2 Parameter point estimation. Method of moments and Maximum Likelihood Estimator Lecture20.pdf moment_estimators_template.m moment_estimators.m 21 Nov 4 Sample variance; Confidence intervals of population mean and variance; Student-t and chi-squared distributions Lecture21.pdf confidence_intervals_template.m confidence_intervals.m hw3_with_answers.pdf 22 Nov 9 Confidence intervals (continued). Hypothesis testing Lecture22.pdf dark_vs_milk_chocolate_analysis_template.m dark_vs_milk_chocolate_analysis.m hw4.pdf 23 Nov 11 Pearson's chi-square Goodness of Fit (GOF) test Lecture23.pdf m_and_m_analysis_template.m m_and_m_analysis.m 24 Nov 16 Linear regression: two variables Lecture24.pdf regression_multiple_template.m expression_table.mat hw4_with_answers.pdf 25 Nov 18 Multiple Linear Regression. PCA (part one) Lecture25.pdf hw5.pdf 26 Nov 30 PCA (part two) Clustering Lecture26.pdf cancer_wdbc_pca_analysis.m clustering.m 27 Dec 2 Important nodes in networks: degree, PageRank,  betweenness-centraility. Co-expression and disease-disease networks analyzed using Gephi software Lecture27.pdf gephi_network_analysis_exercise.docx gephi_install_notes.docx coexpression_network_random start.gephi disease_disease_random_start.gephi hw5_with_answers.pdf 28 Dec 7 Final exam preparation Lecture28.pdf FINAL EXAM Dec 10  7pm-10pm  305 Materials Science & Eng Bld (the same room as classes)