SIBS Pittsburgh 2013, Week 1 Preliminary Schedule 6/3/13 Version

SIBS Pittsburgh 2013, Week 1 Preliminary Schedule 6/3/13 version

Goals for Week 1: Become familiar with the philosophical and ethical issues involved in research with human subjects; create and evaluate appropriate study designs used to collect data to address specific questions; and perform exploratory data analysis appropriate for given study designs and hypotheses. This includes identifying hypotheses, understanding strengths and weaknesses of clinical trials, cohort studies, case-control studies and cross- sectional studies. It also includes obtaining point estimates, interval estimates, and hypothesis testing involving means and proportions, and comparing them across study groups. Student also will understand the basic structure of a scientific paper and the CONSORT guidelines for reporting clinical trials. Note: we have A425 from 9-4 on Mondays, and 9-5 on T, Th, F. We have A216 from 9-5 on Wednesdays, and Posvar 1201 from 1:30-4 on M, T, Th.

Week 1 10-12 am 1:30-3:30 pm Notes June 17-21 Monday Crabtree A425 Posvar 1201 Welcome dinner at Fuel and June 17 Introduction **start at 9:30 today** [Bertolet] Lab 0: Human Subject Protection Fuddle at 7:30 pm on 6/15 2013 [Morton] Welcome Talk 10-10:30 Certification Bach, Beethoven and Brunch [Stone] Overview of SIBS 10:30-noon on Sunday; Mellon [Wilson, Bertolet, Brooks] Review of Course Syllabi Turn in Receipt of Policies form to Student [Brooks] Intro to Study Design Affairs Park (Shadyside); last day of Pgh Arts Festival (downtown) Tuesday Crabtree A425 Posvar 1201 June 18 [Brooks] Experimental and Observational Study [Bertolet] Lab 1: Getting Started with BARI 2013 Designs and Stata; Download Stata Readings: JF Chapters 1, 5 (Except 5.3 and 5.6), 6.1 Wednesda Crabtree A216 Seminar Speakers Crabtree A216 (breakout in A522 (2-3:30)) Crabtree A216 3:30-5 pm y June 19 [Tanya Kenkre] Overview of Cardiovascular [T.Cuenco] Human Subjects [Roger Day] Clinical Trial Design: 2013 Research and Introduction to WISE; T.Cuenco, Weeks It’s Either in the Cards or the [Maria M Brooks] Introduction to BARI Case Study (discussion) Computer Did It Thursday Crabtree A425 Posvar 1201 June 20 [Wilson] Review through Case Studies: [Bertolet] Lab 2: Review of Statistical 2013 Sampling distributions, 2-sample t-test, Concepts paired t-test, chi-squared test, McNemar’s test Readings: JF Ch 11, VGSM: Skim Ch 2-3.1, DUE: Lab 0 from 6/17 and Lab 1 from 6/18 Friday Crabtree A425 Crabtree A216 (1:30-3) Carmen [Undercroft]??Carlow June 21 [Wilson] Simple Linear Regression: [Brooks, Bertolet] Journal Club [Stone] Sat: Bus/walking tour of 2013 Straight line models and their parameters; Reading abstracts and manuscripts; the city; Primanti Bros. in the Strip structural and random components; inference BARI and CONSORT statement District about regression parameters; ANOVA table; R2 Readings: See Courseweb

SIBS Pittsburgh 2013, Week 2

Goals for Week 2: Estimate and interpret a best fitting line. Perform exploratory analysis to evaluate key assumptions and utilize appropriate methods when assumptions are violated. Know how to use and interpret categorical predictors, both as main effects and in interactions. Test hypotheses, obtain confidence intervals, and evaluate the fit of an estimated line. Utilize model building techniques to identify appropriate models. Interpret predictors of interest in the presence of potential moderators.

Week 2 10-12 1:30-3:30 Notes June 24-28 Monday Crabtree A425 Posvar 1201 June 24 [Wilson ] Regression with One Continuous Covariate [Wahed, Brooks, Feingold, Wilson] 2013 Confidence and prediction intervals; assessment of regression assumptions Project Group Meetings: Descriptions and Readings: VSGM Chapter 3.3 sign-ups; initial look at project HW Due: HW from Wilson on 6/21 materials Tuesday Crabtree A425 Posvar 1201 June 25 [Wilson ] Multiple Linear Regression [Bertolet] Lab 3: A First Look at 2013 Outliers and influence. Indicator variables as predictors. Regression Interactions between indicators and continuous predictors Reading: JF Chapters 13.1-13.3 Reading: VSGM Chapters 4.1-4.3, 4.7 HW Due: Lab 3 from 6/20 HW Due: HW from Wilson on 6/24 Wednesda Crabtree A216 Seminar Speakers Crabtree A216 y June 26 [Steve Belle/Abdus Wahed] Study of Viral Resistance to [Wahed, Brooks] Journal Club 2013 Antiviral Therapy of Chronic Hepatitis C. Virahep-C and adherence [Abdus Wahed] Hepatitis C Viral Kinetics Thursday Crabtree A425 9-11 am Posvar 1201 Crabtree A425 (4-5 pm) June 27 [Youk ] Model Building [Bertolet ] Lab 4: Multivariable [Bedda Rosario-Rivera] 2013 Reading: VSGM Chapter 10 Regression Analysis of Brain Imaging Data HW Due: HW from Wilson on 6/26 Reading: Chapter 4, 8.1, 8.2 HW Due: Lab 4 from 6/25 Friday Crabtree A425 9-11 am Meet in GSPH lobby at 1:10 Weekend: June 28 [Youk ] Model Checking Allegheny County Health Department Nationality Rooms Tour (CL)?? 2013 Reading: VSGM Chapter 4.7 [Brooks/Ron Vorhees] HW Due: HW from Youk on 6/28 Ohiopyle/Fallingwater Sunday June 30

SIBS Pittsburgh 2013, Week 3

Goals for Week 3: Apply ML estimation to categorical outcome measures (i.e., logistic regression). Perform exploratory data analysis in terms of risk ratios, risk differences and odds ratios. Extend the concepts of model building, effect modification, categorical and continuous covariates, and model evaluation to logistic regression. Identify and control for possible confounding variables. Interpret predictors of interest in the presence of potential confounders and moderators.

Week 3 10-12 1:30-3:30 Notes July 1–5 Monday Crabtree A425 Posvar 1201 July 1 [Wahed] Measures of Risk and [Wahed, Brooks, Feingold, Wilson] 2013 Association for Dichotomous Outcomes Project Group Meetings (RR, OR, Intro to Logistic Regression) Readings: VSGM Chapter 5.1-5.2 HW Due: HW from Youk on 7/1 Tuesday Crabtree A425 Posvar 1201 Three Rivers Regatta 7/2-7/4/2013 July 2 [Wahed] Logistic Regression [Bertolet] Lab 5: Yin or Yang, Life or Death, Yes or 2013 Readings: VSGM Chapter 5.4 No? Binary Outcomes and Logistic Regression HW Due: Lab 5 from 6/27 Readings: JF Chapter 13, skim Chapter 4 Wednesda Crabtree A216 Seminar Speakers A216 Crabtree 1:30-3 pm Three Rivers Regatta 7/2-7/4/2013 y July 3 [Mary Marazita] Dental Epidemiology [Sally Morton] Job Opportunities and Career 2013 Dental Genetics and the COHRA Study Development [C-RAS] [Marnie Bertolet] BARI 2D Overview and Special Topics Thursday Happy 4th of July!!! – Picnic, BBQ at Eleanor Three Rivers Regatta 7/2-7/4/2013 Feingold’s at 2 pm; fireworks Friday Crabtree A425 Crabtree A216 (1:30-3) July 5 [Wahed] Confounding and Interaction; [Brooks, Stone] Journal Club: Missing Data and BARI ??Carnegie Museums 2013 Stratification 2D Quality of Life analyses Sandcastle?? Readings: VSGM sec. 5.2 [Feingold ] Introduction to Genetics ; HWE Mid-program survey SIBS Pittsburgh 2013, Week 4 Goals for Week 4: Extend the regression techniques to survival data. Identify key aspects of survival data and perform exploratory data analysis. Estimate and Interpret hazard ratios. Extend the concepts of model building, effect modification, categorical and continuous covariates, and model assessment and interpretation of Cox regression. Week 4 10-12 1:30-3:30 Notes July 8– 12 Monday Crabtree A425 Posvar 1201 July 8 [Wilson] Introduction to Survival [Bertolet] Lab 6: Tried the Rest? Now Try the Best! 2013 Analysis Model Building Features of survival data; Kaplan-Meier Reading: JF 14.1-14.5 Readings: VGSM 6.1, 3.5 HW Due: Lab 6 from 7/2 Tuesday Crabtree A425 Posvar 1201 July 9 [Wilson] Introduction to Survival [Wahed, Brooks, Feingold, Wilson] 2013 Analysis Cont. Project Group Meetings Logrank test; examples Readings: VGSM 6.1, 6.2 HW Due: HW from 7/9 Wednesday Crabtree A216 Seminar Speakers Crabtree A216 Crabtree A216 (3:30-5 pm) July 10 [Michael Fine] Evidence-based Approach [Stone, Brooks] Journal Club: PORT and Propensity 2013 for the Initial Treatment of Pneumonia Score Adjustment Panel: Current Students [Mary Ann Sevick] Overview of Behavioral Interventions and Technology-Based Self-Monitoring Class photo: Wear/bring your SIBS t-shirt, at Pitt Panther after Seminar Thursday Crabtree A425 Posvar 1201 July 11 [Wilson] Hazard functions/Ratios; Cox [Bertolet ] Lab 7: To Be or Not To Be? Survival 2013 Regression Analysis HW Due: Lab 7 from July 9 Friday Crabtree A425 [Brooks] Field Trip to RAND Sat am??? July 12 [Feingold; Wilson; Tom Songer; Meet in Parran (Desoto St) Lobby at 1 pm; bring 2013 Yu Cheng] photo id; wear office casual clothing Sat: Baseball game and Zambelli fireworks Panel: Admission to Graduate School ~7:15

SIBS Pittsburgh 2013, Week 5 Goals for Week 5: Apply survival analysis methods learned in the previous lectures to a dataset from a cancer clinical trial, focusing in answering research questions. Apply previously-introduced statistical methods to problems in genetic epidemiology. Consider statistical issues arising from “genomic” applications that have very large-scale data .

Week 5 10-12 1:30-3:30 Notes July 15– 19 Monday Crabtree A425 Posvar 1201 July 15 [Wahed] Survival Case Study [Bertolet] Lab 8: Is it All in the 2013 Genes? Genetic Applications Reading: JF 18.4 HW Due: Lab 8 from 7/11 Tuesday Crabtree A425 Posvar 1201 July 16 [Feingold ] Methods for Genetic Association Studies [Wahed, Brooks, Feingold, Wilson] 2013 Project Group Meetings Wednesda Crabtree A216 – Seminar Speakers Crabtree A216 y July 17 [Hasan Guclu] Network Analysis 2013 [John Grefenstette] Agent-based Modeling in Public Health 1:30-3:00 Applied Statisticians Panel* Thursday Crabtree A425 Posvar 1201 July 18 [Feingold] Special Topics in Genetic Epidemiology [Bertolet] Lab 9: Walk down 2013 Memory Lane [Feingold, T.Cuenco] Journal Club: Race and Ethnicity in Genetic Studies

Friday Crabtree A425 Crabtree A425 Sat: 11 am-12:30 pm Aviary July 19 [Wilson] Non-parametrics; Randomization Tests and the TBA (behind the scenes penguin tour); zoo?? 2013 Bootstrap Parran (Desoto St). Lobby at 1 pm [Bertolet] What the P-value?!?! Reasons I’m a Bayesian and Field Trip 1:30-3:30 You Should Be Too! SIBS Pittsburgh 2013, Week 6

Goals for Week 6: Complete the independent projects. Present work to your peers and turn in extended abstracts.

Week 6 10-12 1:30-3:30 Notes July 22– 26 Monday Crabtree A425 Posvar 1201 309B Parran [DeArment] July 22 Project group meetings; Draft abstracts and presentations Work on project presentations Focus Group 1 2013 due to group leader; practice/revise presentations (VIRAHEP-C; COHRA) 1:30-3 pm

Tuesday Crabtree A425 Posvar 1201 309B Parran [DeArment] July 23 Practice/revise presentations (within teams) Practice/revise presentations Focus Group 2 2013 (within teams) (BARI 2D; WISE) 1:30-3 pm

Wednesday Crabtree A216 Crabtree A216 July 24 Student Presentations Student Presentations 2013 10-12 am VIRAHEP-C 1:30-3:30 COHRA

Thursday Crabtree A425 Crabtree A425 Gateway Clipper Dinner Cruise July 25 Student Presentations Student Presentations 7-9 pm; 2013 10-12 am BARI 2D 1:30-3:30 WISE board at 6 pm at Station Square

Friday Kennywood Day Final gathering Depart on Saturday, July 27 July 26 Move out of dorm by 1 pm 2013 6/3/2013 RAS