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How Its Done Seminar

The How It's Done Seminar Series began in January 2014 and are held once a month. Topics range from next generation sequencing pipelines to metabolomics and include both statistical and computational biology methodologies. These sessions provide a background for each topic as well as real world application of analysis techniques by members of our department and the Harvard School of Public Health. The aim of this seminar series is to provide participants with useful examples and a framework on which to build their own projects.

Presentation slides and materials for the talks will be posted on the BCB website after each session, but are only available to department members. To request a presentation, or make a suggestion for a seminar topic, please email dnunes@jimmy.harvard.edu

Location: CLSB Building, 11th Floor, room 11081.

Coming Up

September 20
12:30-2:30 PM
Introduction to R, RStudio and the “tidyverse”
Stephanie Hicks
Research Fellow, Biostatistics
Dana-Farber Cancer Institute

2017 Seminars

Please contact David Nunes at dnunes@jimmy.harvard.edu for access to presentation slides.

January 25 

Daniel Gundersen
Implications of mobile-platform respondents for design and development of web-surveys

February 28
Steffen Ventz
Statistical Designs for Platform Trials

March 28
Natalie Venskus
Grant Management within BCB

June 7
Cyrus Mehta
Methods and Tools for Adaptive Trials

June 20 12:00-1:00pm
Jonathan Chipman
Techniques for Matched Randomization in Sequential Enrollment Trials



Previous Seminars

Please contact David Nunes at dnunes@jimmy.harvard.edu for access to presentation slides.

March 10
              SEER-Medicare Linked Database: overview plus examples of research conducted within the Division of Population Sciences, Angel Cronin

September 28      Validation of Surrogate endpoints using meta-analytic approach, Wanling Xie

October 19           Basics of Cancer Immunology, Donna Neuberg

Please contact David Nunes at dnunes@jimmy.harvard.edu for access to presentation slides.

January 22
        IPython: Big Data, Black Magic and Parallel Computing, Luca Pinello

February 12      Oncology Data Retrieval System (OncDRS), Caitlin Fontes

March 5              cBio Cancer Genomics Portal: how it works, how it's built, and where it's going next, Ethan Cerami

April 30              Bioconductor II, Michael Love

May 28               Graphs and Networks in R, Mehmet Samur

Please contact David Nunes at dnunes@jimmy.harvard.edu for access to presentation slides.

January 23
            Metabolomics, Svitlana Tyekucheva

February 13           Decision Curve Analysis, Giovanni Parmigiani

March 6                   R Bioconductor, Rafael Irizarry
                                 - Installing Bioconductor
                                 - Basic Structure of Bioconductor         

April 3                     Next Generation Sequencing Pipelines, Naim Rashid

May 1                      Gene Set Enrichment Analysis, William Barry

June 12                   Propensity Score, Cory Zigler

July 24                     RStudio, Emanuele Mazzola & Su-Chun Cheng
                                   - Example      

September 25        Statistical Designs with Expansion Cohorts, Suzanne Dahlberg

October 9                Spade Clustering, Guo-Cheng Yuan

November 13          Modeling Cancer Resistance, Phillip Altrock

December 4            Beyond Proportional Hazards, Hajime Uno

March 11        Radiomics: There is more than meets the eye in Medical Imaging, Hugo Aerts, Ph.D.
Department of Radiation Oncology, Dana-Farber Cancer Institute

January 19     Functionally annotating non-protein coding risk alleles from genome wide association studies, Matthew Freedman, Assistant Professor, Department of Medicine, Harvard Medical School, Associate Physician, Dana-Farber Cancer Institute

March 1          Comparative Effectiveness Research,  Constantine Gatsonis, Henry Ledyard Goddard University Professor of Biostatistics, Brown University

March 8          Distance in gene expression from stem cells as prognostic marker, Markus Riester, Research Fellow, Dana-Farber Cancer Institute

April 4            17 months in 45 minutes: three aspects of cancer biostatistics, Emanuele Mazzola, Research Fellow, Dana-Farber Cancer Institute

April 19          Tips to reduce potential pain and fear in data analysis and reporting (with ECOG examples), Hajime Uno, Research Scientist, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute

July 9             Discovering associations that replicate from a primary study of high dimension to a follow-up study, Ruth Heller, Senior Lecturer, Industrial Engineering and Management, Techinon, Israel

August 29      Inference from whole-genome random regression models in stratified populations, Daniel Sorensen, Department of Molecular Biology and Genetics, Aarhus University, Denmark

August 31       Evaluating risk models with prospective cohorts: analyses and designs, Yingye Zheng, Fred Hutchinson Cancer Center

January 27, Disssecting and Targeting Pathologic Protein Interactions with Stapled Peptides, Loren Walensky, Dana-Farber Cancer Institute

March 31, Using Federal and State Databases for Cancer Outcomes Research, John Ayanian, Harvard Medical School

April 14, Statistical Methods for Analyzing Length-Biased Right Censored Data, Yu Shen, MD Anderson Cancer Center

2010
January 7
        Automated High-dimensional Flow Cytometric Data Analysis; Saumyadipta Pyne, Department of Medical Oncology, Dana-Farber Cancer Institute

February 25     The use of biologic, genetic, clinical and morbidity factors to determine treatment for children with cancer; Wendy B. London, Division of Hematology/Oncology, Department of Pediatrics, DFHCC/CHB, Harvard Medical School and Children’s Oncology Group (COG) Statistics and Data Center

March 17          The Challenge of Animal Studies, Donna Neuberg, Senior Lecturer, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute

April 8              Nuts and Bolts:
                               Interactive SAS (Julie Aldridge)
                               Making Figures in R(Judi Manola)
                               Sample Size for Cox Models in Stata – Shari Gelber
                               Cool Stuff with ODS Proc Freq in SAS – Paul Catalano

April 22             Computational Genomics of Gene Regulation;  Xiaole (Shirley) Liu, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute

May 12              Developing an Information Infrastructure Focused on Cancer Comparative Effectiveness Research; David A. Fenstermacher, PhD, Chair and Executive Director, Department of Biomedical Informatics, H. Lee Moffitt Cancer Center & Research Institute

June 17             Integrative model system analysis of gene expression; David Weiss, Ph.D., Bioengineer, IRIDIA-CoDE, Belgium

July 1                Gene expression profiling and clinical decision making with breast cancer patients, Hal Burstein, Associate Professor of Medicine, Harvard Medical School and the Breast Oncology Center, Dana-Farber Cancer Institute

October 21        Estimating the risk of acquiring a blood borne pathogen as a result of hemodialysis machine contamination, Nathan Taback, University of Toronto

December 16    Evolutionary Dynamics of Cancer, Franziska Michor, Dana-Farber Cancer Institute

2009

January 8           Analyses of Cumulative Incidence Function via Non-parametric Multiple Imputation, Ping Ruan

January 22         Issues with the design, monitoring and analysis of cancer treatment studies when most patients are “cured”, James Anderson

February 12        Evaluating Prediction and Risk Stratification in Right Censored Time-to-Event Data, Keith Betts

February 26        Confirming Non-Adherence in Clinical Trials, Robert Gray and Meredith Regan  

March 26              Age-Adjusted Median Differences in Nutritional Intake Between Black and White Males Presenting for Prostate Cancer Screening, Stuart Lipsitz

April 2                  Multiple Imputation in a Large-scale Complex Survey, Yulei He  

June 25                A Propensity Score Approach for the Analysis of Population-Based Genetic Association Studies, Nandra Mitra

July 16                 Make life easier with LyX and R: An efficient way for making an analysis report, Hajime Uno 

October 8             Breast cancer tumour growth estimated through Norwegian mammography screening data, including a short presentation of the Norwegian Cancer Registry, Harald Weedon-Fekjær, Ph.D.

October 22           Modeling risk in families with cancer, Giovanni Parmigiani

2008

January 17           Anti-angiogenic Potential of GIPC1 Silencing in Human Disease, Tom Chittenden, PhD.

February 28         Letrozole Compared with Tamoxifen for Elderly Patients with Endocrine Responsive Early Breast Cancer in BIG 1-98: Efficacy, Treatment, and Adverse Events, Zhuoxin Sun, PhD

                             Outcomes for Elderly, Advanced-Stage Non-Small Cell Lung Cancer Patients Treated with Bevacizumab in Combination with Carboplatin and Paclitaxel: Analysis of E4599, Suzanne Dahlberg, ScD

                             Reporting of Subgroup Analyses in Clinical Trials: A Discussion, Steve Lagakos, PhD

June 5                   An Example of SNP Analysis, Haesook Kim, Ph.D.

September 25      The Role of Hormone Receptors in Cancer, Myles Brown, M.D.

November 20        BCB Speed-Dating Journal Club
                              One hour: 4 recent publications by your BCB colleagues!
                              Gefininib for Recurrent NSCLC: All things are not created equal, Suzanne Dahlberg
                              Premenopausal endocrine-responsive early breast cancer: who receives chemotherapy?, Meredith Regan
                              Dissociation of its opposing immunologic effects is critical for the optimization of antitumor CD8+ t-cell responses induced by interleukin 21, Kristen Stevenson
                              Model-based analysis of ChIP-Seq (MACS), Yong Zhang

December 11        Research and Progress of the Department of Cancer Biology: Division of Metabolism and Chronic Diseases, Dr. Bruce Spiegelman


2007

January 18         Putting microarray data in context: Multivariate approaches for exploratory analysis of multiple biological datasets, Aedin Culhane, Ph.D.

February 22       Global View of Chromatin, Guo-Cheng Yuan, Ph.D.

April 12              Prediction of U.S. Mortality Counts Using Semiparametric Bayesian Techniques, Ram Tiwari

May 21               Where Do We Stand in Microarray Data Analysis? Lessons of the Past and Hopes for the Future, Andrei Yakovlev

June 13              Clinical Research-Strategies to Fulfill our Mission, Phillip Kantoff

September 20    Electronic Data Capture (eDC) implementation for PI Initiated Studies at the DF/HCC, Marina Nillni

October 11         Spatial analysis of cancer data incorporating residential history, Al Ozonoff, Ph.D.

October 23         PLASQ: A Generalized Linear Model-Based Procedure to Determine Allelic Dosage in Cancer Cells from SNP Array Data, David Harrington, Ph.D.

November 8       Understand Racial Disparities in Cancer Cures: Results from Large Population Science Studies, Yi Li    

December 6       Phase III Intergroup Study of Adriamycin/Taxotere vs. Adriamycin/Cytoxan in the Adjuvant Treatment of Node Positive and High-Risk Node Negative Breast Cancer: Statistical Challenge, Robert Gray

 

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