Department Retreat
The Department Retreat began in 2008 and are held once a year. Topics vary from year to year, depending on new research and hot topics. It features speakers from both inside and outside the department. The retreat also features a lunch poster session.
2020 Retreat
Friday, January 17th from 12:30-4:30pm
Joseph B. Martin Conference Center, Rotunda, 3rd floor
Lunch is provided.
Confirmed speakers: William Kaelin, Eliezer Van Allen
Then join us at Game On Fenway for food, drinks, and games from 5:00-7:00PM.
Previous Retreats
Department Retreat
Location: Paresky Conference Center, Simmons University
Date: January 17, 2018
Time: 12:30-4:00pm
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12:30-12:45pm |
Lunch |
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12:45-12:50pm |
Welcome -- Rafael Irizarry, Chair |
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12:50-1:10pm |
CLL Genomics and Tumor Immunogenomics Catherine Wu, Professor of Medicine, Harvard Medical School and |
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1:10-1:15pm |
Q&A |
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1:15-1:35pm |
Immune Checkpoint Blockade for the Treatment of Cancer Stephen Hodi, Professor, Medicine, Harvard Medical School |
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1:35-1:40pm |
Q&A |
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1:40-2:00pm |
Partnering with patients to accelerate cancer precision medicine Nikhil Wagle, Assistant Professor, Medicine, Harvard Medical School and Dana-Farber Cancer Institute |
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2:00-2:05pm |
Q&A |
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2:05-2:25pm |
Bringing Genomics to the Pediatric Oncology Clinic at Dana-Farber / Boston Children’s and Beyond: Lessons for the Future Katherine Janeway, Assistant Professor, Pediatrics, Harvard Medical School |
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2:25-2:30pm |
Q&A |
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2:30-2:45pm |
Break |
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Lightning Talks |
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2:45-2:50pm |
X. Shirley Liu, “Technology- and Data-Driven Translational Cancer Research” |
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2:50-2:55pm |
Franziska Michor, “Updates on Current Research” |
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2:55-3:00pm |
Fangxin Hong, “New Approaches for Toxicity Assessment and Reporting in Oncology Clinical Trials” |
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3:00-3:05pm |
Giovanni Parmigiani, “Update on the Parmigiani Lab” |
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3:05-3:10pm |
Q&A |
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3:10-3:15pm |
Rachel Keller, “GI TARGET - Facilitating Oncologist Use of Patient Genomic Data” |
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3:15-3:20pm |
James Lindsay, “Informatics for ImmunoProfile” |
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3:20-3:25pm |
Haesook Kim, “TcR II” |
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3:25-3:30pm |
Aedin Culhane, “Subtype discovery using matrix factorization” |
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3:40-3:45pm |
Q&A |
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3:45-3:55pm |
Lorenzo Trippa, “Updates on Current Research” |
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3:55-4:00pm |
Chris Sander, “Interpretable Machine Learning for Perturbation Biology” |
Department of Biostatistics and Computational Biology Retreat
January 18, 2018
Simmons College, Paresky Conference Center
9:00-9:10 AM Introduction
Giovanni Parmigiani, Chair, Department of Biostatistics and Computational Biology
Rafael Irizarry, Incoming Chair, Department of Biostatistics and Computational Biology
9:10-10:15 AM Session 1: Junior Faculty Talks
Cheng-Zhong Zhang, In search of lost time: reconstructing the evolutionary history of cancer genomes
Sahand Hormoz, Inferring dynamics of cell state transitions using synthetic biology and single-cell profiling
10:15-10:30 AM Break
10:30-11:30 AM Session 1: Junior Faculty Talks, continued
Meromit Singer, T cell regulation in cancer and autoimmunity
Alexander Gusev, Integration of genome-wide association studies, epigenomics, and clinical phenotypes to understand cancer risk mechanisms
11:30-12:00 PM Session 2: Poster Presentation Overview
Poster presenters will give a brief overview of their poster.
12:00-1:15 PM Lunch/ Poster Session
1:15-2:45 PM Session 3: Lightning Talks
David Shih, Cancer driver discovery: case-control comparison of copy-number aberrations
Shengqing Stan Gu, Dissecting the mechanisms of resistance to immune checkpoint blockade
Hajime Uno, Improving analytic practices for comparative clinical trials with time-to-event outcomes
Chris Sander, Systems biology combination therapy in ovarian cancer
Anita Giobbie-Hurder, Partially weighted analyses
Xihao (Sherlock) Hu and Haesook Kim, TcR analysis
Nathanael Fillmore, Transforming VA data into a national resource for advanced healthcare analytics Catherine Del Vecchio Fitz, Finding the right patient at the right time: computational clinical trial matching and rule-based trial readiness assessment
Jamie Dean, Optimizing glioblastoma treatment schedules using mathematical modeling
Cathy Wang, Meta-analysis of Lynch syndrome genes: Likelihood approach for combining aggregated and heterogeneous cancer risk
Peng Jiang, Signatures of T-cell dysfunction and exclusion predict cancer immunotherapy response
Aedin Culhane, Gene signatures, cell types and tissues
Lorenzo Trippa, Adaptive trial designs
Mehmet Samur, Integrative genomics in multiple myeloma
2:45-3:00 PM Break
3:00-4:30 PM Session 4: Data Science Initiative
Francesca Dominici, Harvard Data Science Initiative
Heather Mattie, Health Data Sciences Program at HSPH
Franziska Michor, Cancer Data Science Program, DF/HCC
Panel moderated by Rafael Irizarry
4:30-5:30 PM Reception
Department of Biostatistics and Computational Biology Retreat
January 19, 2017
Simmons College, Paresky Conference Center
9:00-9:20am Opening Remarks
Introduction to the Retreat, Giovanni Parmigiani
A Few Words on the 40th Anniversary of the Division of Biostatistics, Richard Gelber
A Few Words on the 20th Anniversary of the Department of Biostatistics and
Computational Biology, David Harrington
9:20-10:30am Session 1: Presentation of Centers and Statistical Centers
Center for Cancer Computational Biology
John Quackenbush, Overview
Yaoyu Wang, Standardizing Extracelluar sRNASeq Analysis
Center for Functional Cancer Epigenetics
Xiaole Shirley Liu, Overview
Cliff Meyer, Navigating Gene Expression Perturbations using Maps of the Chromatin Landscape
cBio Center at Dana-Farber
Chris Sander, Overview
Ethan Cerami, Knowledge Systems Group: Overview
10:30-10:50am Break
10:50-12:00pm Session 1: Presentation of Centers and Statistical Centers, continuedCenter for Cancer Evolution
Franziska Michor, Overview
Thomas McDonald, Modeling punctuated evolution in triple negative breast cancer
ECOG-ACRIN Statistical Center
Robert Gray, Overview
Victoria Wang, Correlative Projects at ECOG-ACRIN
IBCSG Statistical Center
Meredith Regan, Overview
Anita Giobbie-Hurder, Cholesterol, Cholesterol-Lowering Medication Use and Breast Cancer Outcomes in the BIG 1-98 Trial: Analysis Using
Marginal Structural Modeling
12:00-1:15pm Lunch and Poster Session
1:15-2:30pm Session 2: Genomic Profiling at DFCI: Profile and Beyond
Chaired by Ethan Cerami
Jason Johnson, with John Methot and Eva Lepisto, Informatics Projects - Data and Tools
Fei Dong, Profile: Current State and Future Plans
Coleman Lindsley, Clinical Applications of Discovery Genomics in Myeloid Malignancies
Kathryn Gray, DNA damage and repair pathway (DDRP) mutational landscape from Profile in a localized prostate cancer cohort
2:30-2:45pm Break
2:45-4:00pm Session 3: Large-Scale Analysis of Public Genomic Data
Chaired by Svitlana Tyekucheva, Discussant: Rafael Irizarry
Jialiang Huang, Dissection of super-enhancer hierarchy based on chromatin interactions data
Joseph Paulson, Preprocessing and Tissue-Aware Normalization of the GTEx Expression Data
Aedin Culhane, Issues discovered during TCGA PanCancer study of over 10,000 tumors from 33 different cancers
4:00-5:00pm Reception
Department of Biostatistics and Computational Biology Retreat
June 16, 2015
Simmons College, Paresky Conference Center
10:00-10:15 AM Introduction
Giovanni Parmigiani
10:15-12:00 PM Session 1: Tumor Heterogeneity
Kornelia Polyak Intratumor heterogeneity: clinical and functional relevance
Mark Pomerantz Prostate cancer clonal diversity as biomarker for clinical outcome
Franziska Michor Evolutionary dynamics of tumor heterogeneity
Scott Carter Computational dissection of intra-tumor genetic heterogeneity and applications to the study of cancer treatment, evolution, and metastasis
12:00-1:30 PM Lunch/ Poster Session
1:30-3:00 PM Session 2: Immuno-oncology
Stephen Hodi Recent Developments in Cancer Immunotherapy
Anita Giobbie-Hurder Clinical Trial Considerations for Immunotherapies
Donna Neuberg Neoantigen Vaccines: Computational Biology Meets Clinical Biostatistics
3:00-3:15 PM Break
3:15-5:00 PM Session 3: Software in BCB
Panel: Rafael Irizarry, Ethan Cerami, Nikos George, Xiaole (Shirley) Liu
5:00-6:00 PM Reception
Department of Biostatistics and Computational Biology Retreat
June 26, 2014
Simmons College, Paresky Conference Center
9:00 AM — 9:20 AM Welcome and Introduction to Retreat
Giovanni Parmigiani
9:20 AM — 10:45 AM Session 1 Current challenges in Phase I clinical trials ---how can statisticians make a difference?
9:20-9:35 Jeff Clark
9:35-9:50 Suzanne Dahlberg
9:50-10:05 George Demetri
10:05-10:45 Panel Discussion
10:45 AM — 11:00 AM Coffee Break
11:00 AM — 12:30 PM Session 2 – Single Cell Biology -- Challenges and Opportunities for Computational Scientists
11:00-11:15 Stuart Orkin
11:15-11:30 Guo-Cheng Yuan
11:30-11:45 David Pellman
11:45-11:55 Open Discussion
11:55-12:10 Hua-Jun Wu
12:10-12:25 Megha Padi
12:25-12:30 Open Discussion
12:30 PM — 2:00 PM Lunch & Poster Session
2:00 PM — 3:30 PM Session 3 – Big Data
2:00-2:30 Vision and Grant Activity: John Quackenbush
2:30-2:45 Preprocessing: Rafael Irizarry
2:45-3:00 Integration: Hugo Aerts
3:00-3:15 Reproducibility: Giovanni Parmigiani
3:15-3:30 Network Science: JP Onnela
3:30-4:00 Open Discussion
4:00 PM — 5:00 PM Reception
Department of Biostatistics and Computational Biology Retreat
June 14, 2013
Simmons College, Paresky Conference Center
9:00 AM — 9:30 AM Breakfast, Welcome and Introduction to Retreat
Giovanni Parmigiani
9:30 AM — 10:45 AM Session 1 – Integral Biomarkers Trials
9:30-9:50 Overview: Robert Gray
9:50-10:00 Open discussion
10:00-10:05 Richard Gelber
10:05-10:10 Meredith Regan
10:10-10:15 Bill Barry
10:15-10:45 Open discussion
10:45 AM — 11:00 AM Coffee Break
11:00 AM — 12:30 PM Session 2 – Epigenomics
11:00-11:20 Overview: Myles Brown
11:25-11:45 Overview: Rafael Irizarry
11:45-12:00 Open Discussion
12:00-12:05 Luca Pinello
12:05-12:10 Franziska Michor
12:10-12:30 Open Discussion
12:30-2:00 Lunch
2:00 PM — 3:30 PM Session 3 – Profile Project at Dana-Farber
2:00-2:20 Overview of Profile Project: Barrett Rollins
2:20-2:40 Panel with Barrett Rollins, Bruce Johnson, Bill Barry, and Rich Gelber
2:40-3:10 Open Discussion
3:10-3:15 John Quackenbush
3:15-3:20 Giovanni Parmigiani
3:20-3:30 Open Discussion
3:30 PM — 5:00 PM Reception and Poster Session
Beer/wine and hors d'oeuvres will be served.
Department of Biostatistics and Computational Biology Retreat
June 20, 2012
Key Note and Townhall at Jimmy Fund Auditorium, 1 Jimmy Fund Way
Lunch and Poster Presentation: CLSB 11th Floor, 3 Blackfan Circle
9:00 AM — 9:45 AM Keynote Speech“Genomic analysis of human cancers”
Matthew L. Meyerson, MD, PhD
Professor, Department of Pathology,
Harvard Medical School
Associate Professor of Pathology,
Medical Oncology, Dana-Farber Cancer Institute
9:45 AM — 10:20 AM Discussion and Q&A with Dr. Meyerson
10:20 AM — 10:30 AM Break
10:30 AM — 11:30 AM Town Hall Meeting: The Future of the Department Retreat
11:30 AM — 11:45 AM Travel to CLSB 11th Floor
11:45 PM — 12:45 PM Lunch and Poster Session
12:45 PM — 1:00 PM Poster Session Awards
Department of Biostatistics and Computational Biology Retreat
May 25, 2011
Talks at Jimmy Fund Auditorium, 1 Jimmy Fund Way
Poster Presentation: CLSB 11th Floor, 3 Blackfan Circle
8:30 AM — 9:00 AM Breakfast, Welcome and Introduction to Retreat
Giovanni Parmigiani and John Quackenbush
9:00 AM — 10:15 AM Session 1 - chaired by John Quackenbush
Zhuoxin Sun, A Non-inferiority Two-stage Design in Acute Myeloid Leukemia
Kevin Leder, Optimizing Radiation Response in Gliomas
Cristian Tomasetti, The Role of Symmetric and Asymmetric Division of Cancer Stem Cells in Developing Drug Resistance
Kathryn Gray, Statistical Analysis for Evaluating Prognostic Features of Single Nucleotide Polymorphisms (SNPs) in Critical Signal Pathways for Renal Cell Carcinoma (RCC)
10:15 AM — 10:30 AM Coffee Break
10:30 AM — 11:45 PM Session 2 –chaired by Giovanni Parmigiani
Hajime Uno, Graphical Procedures for Evaluating Overall and Subject-Specific Incremental Values from New Predictors with Censored Event Time Data
The Admin Team, The Admin Team: Your Partners in Science
Judith Manola Prognostic Model for Survival in Patients with Metastatic Renal Cell Carcinoma: Results from the International Kidney Cancer Working Group
Matthew Schwede, Stem cell-like gene expression in ovarian cancer is prognostic and associated with Type II
12:00 PM — 1:00 PM Lunch
1:00 PM — 2:15 PM Session 3 - chaired by Paul Catalano
Fangxin Hong, Incremental value in outcome prediction with molecular signature in Diffuse Large BCell Lymphoma
Subhajyoti De, Effects of DNA Secondary structures and epigenetic changes on genomic alterations in cancer
Karen Price, Returning Clinical Trial Results to Patient Participants: A project of the Dana Farber/Harvard Cancer Center (DF/HCC) Breast Cancer Advocacy Group
Miguel Marino, Variable Selection for Fixed and Random Effects in Multilevel Models When Missing Data is Present
2:15 PM — 2:30 PM Coffee Break
2:30 PM — 3:45 PM Session 4 - chaired by Yi Li
Yoko Franchetti, A two-stage dose-response adaptive design method for establishing Proof of Concept
Benjamin Haibe-Kains, Predictive gene interaction networks in colon cancer
Julie Najita, Use of stratified subsampling in the design of retrospective marker studies
Lorenzo Trippa, Bayesian Enrichment Strategies for Randomized Discontinuation Trials
4:00 PM — 5:00 PM Poster Session with wine and hor d'oeuvres/cheese
5:00 PM — 5:15PM Wrap-up and poster prizes
Department of Biostatistics and Computational Biology Retreat
June 4, 2010
CLSB 11th Floor, 3 Blackfan Circle
8:30 AM — 9:00 AM Breakfast, Welcome and Introduction to Retreat
Robert Gray and John Quackenbush
9:00 AM — 10:30 AM Session 1 - chaired by Robert Gray
Clifford Meyer, Discovering cis-regulatory regions from differential nucleosome occupancy patterns
Hyunjin Shin, Dynamic Interactions of CDX2 with Chromatin and Partner Transcription Factors in Intestinal Epithelial Cell Differentiation
Samir Amin, An Integrative Analysis of Network Motifs and Gene Expression Data To Discover Experimentally Testable TF-miRNA Regulation Relationships
Benjamin Haibe-Kains, Predictive gene interaction networks in colon cancer
Mengye Guo, Voxelwise analysis of imaging response to therapy in neuro-oncology
10:30 AM — 10:45 AM Coffee Break
10:45 AM — 12:00 AM Session 2 –chaired by John Quackenbush
Zhuoxin Sun, A Non-inferiority Two-stage Design in Acute Myeloid Leukemia
Megha Padi, Modeling phase transitions in cellular networks
Kimberly Glass, Integrating protein interaction and transcription factor binding data to enhance our understanding of gene regulation
Musie Ghebremichael, The synergistic interaction between HSV-2 and HIV-1in sub-Saharan Africa: A multilevel model with correlated outcomes
12:00 AM — 1:00 PM Lunch
1:00 PM — 2:15 PM Session 3 - chaired by Giovanni Parmigiani
Hajime Uno, On the C-statistics for Evaluating Overall Adequacy of Risk Prediction Procedures with Censored Survival Data
Stefan Bentink, Whole-genome sequencing and analysis of an Ovarian Cancer Patient
Jeremy Wu, Gene expression profiling of human breast tissue samples using SAGE-Seq
Razvan Sultana, Molecular-inversion probes resequencing of 28 drug resistance – related genes in 30 strains of Mycobacterium tuberculosis
2:15 PM — 2:30 PM Coffee Break
2:30 PM — 3:45 PM Session 4 - chaired by Paul Catalano
Fangxin Hong, Systematic mapping of tumor tissues to corresponding cell line models
Daniel Gusenleitner, Discovering universal schemes of cancer biology by linking clinical covariates and gene signatures
Lillian Werner, PSA Density, PSA Velocity and Family History of Prostate Cancer are Predictors of Progression in Patients with Low Risk Prostate Cancer on Active Surveillance Protocol Using a 20-Core Saturation Biopsy Technique
Zhen Shao, Prediction of Polycomb target genes in mouse embryonic stem cells
3:45 PM — 4:45 PM Poster Session with wine and hor d'oeuvres/cheese
4:45 PM — 5:00 PM Wrap-up and poster prizes
Department of Biostatistics and Computational Biology Retreat
June 18, 2009
CLSB 11th Floor, 3 Blackfan Circle
9:00 AM — 9:45 AM Breakfast, Welcome and Introduction to Retreat
Robert Gray and John Quackenbush
Introduction and Greeting, Giovanni Parmigiani
9:45 AM — 11:00 AM Session 1 - chaired by John Quackenbush
Yi Li, “Dantzig Selector for Censored Linear Regression Models”
Housheng (Hanson) He, "Inferring nucleosome occupancy changes and key transcriptional regulators through ChIP-seq profiling of H3K4me2"
Julie Najita, “Health status and mortality among survivors diagnosed at infancy”
Mick Correll, “The Center for Cancer Computational Biology”
11:00 AM — 11:15 AM Coffee Break
11:15 AM — 12:30 PM Session 2 –chaired by Robert Gray
Donna Neuberg, “The Progeria Project”
Aedin Culhane, “Mining the published literature to gain new perspectives on the relationship between breast and ovarian cancer”
Hajime Uno, “How to make personalized disease prediction and treatment selection with clinical- and bio-markers?”
Win Hide, "Using gene expression bias as a tool for clinical translation"
12:30 PM — 1:30 PM Lunch
1:30 PM — 2:30 PM Session 3 - chaired by John Quackenbush
Jessica Mar, “Identifying Cell Lineage-Specific Gene Expression Modules”
Molin Wang, “Mantel-Haenszel estimating function for sparse clustered binary data”
Fangxin Hong, “Statistical design for charactering ethnic disparities in common somatic genetic mutations”
2:30 PM — 2:45 PM Coffee Break
2:45 PM — 3:30 PM Session 4 - chaired by Robert Gray
Xiangfeng (Brian) Wang, "Dissecting Arabidopsis RNAi Pathways by Gene Co-expression Network"
Ann Lazar, “Subgroup Analysis and Multiple Testing with Applications to Biomarker Data”
3:30 PM — 4:30 PM Poster Session with wine and hor d'oeuvres/cheese
4:30 PM — 5:00 PM Wrap-up and poster prizes
Department of Biostatistics and Computational Biology Retreat
June 18, 2008
CLSB 11th Floor, 3 Blackfan Circle
8:30 AM — 9:00 AM Breakfast Welcome from David Harrington
Robert Gray and John Quackenbush, Introduction to Retreat
9:00 AM — 10:15 AM Session 1 - chaired by David Harrington
Paul Catalano, “Representativeness of CanCORS Participants Relative to the Surveillance, Epidemiology and End Result (SEER) Cancer Registries”
Suzanne Dahlberg, “Bevacizumab: Wicked Awesome or Wicked Bad?”
Rebecca Gelman, “Lab Tests in Developing Countries”
Bob Gray, "An Overview of the Eastern Cooperative Oncology Group"
10:15 AM — 10:30 AM Coffee Break
10:30 AM — 11:45 AM Session 2 –chaired by John Quackenbush
Nikos George, “Current State of Computing at BCB”
David Harrington/Keith Betts, “Predicting survival and estimating prediction error with right censored data”
Haesook Kim, “Data analysis in previously treated CLL”
Cheng Li, “Analysis of cancer genomic alterations using SNP arrays”
11:45 AM — 12:45 PM Lunch
12:45 PM — 2:00 PM Session 3 - chaired by Robert Gray
Sandra Lee, “CISNET: Early Detection of Disease and Stochastic Models with Applications to Breast Cancer”
Cliff Meyer, "Understanding Epigenetics and Transcriptional Regulation through ChIP-chip and ChIP-seq"
John Quackenbush, “Cancer Computational Biology: Application to Breast and Ovarian Cancer”
Armin Schwartzman, "Statistical Signal and Image Analysis in Cancer Research"
2:00 PM — 2:15 PM Coffee Break
2:15 PM — 3:30 PM Session 4 - chaired by John Quackenbush
Meredith Regan, “The International Breast Cancer Study Group (IBCSG): Improving Treatment Options and Quality of Life of Women Affected by Breast Cancer”
Edie Weller, “Lunenberg Lymphoma Biomarker Consortium: An International Study to Establish a Clinco-Biological Prognostic Index for Diffuse Large B-Cell Lymphoma”
Joe White, “Development of a Data Warehouse and Web Portal for Multiple Myeloma”
Guo-Cheng Yuan, “Topics in Epigenomics”
3:30 PM — 5:00 PM Poster Session with wine and hor d'oeuvres/cheese
5:00 PM — 5:30 PM Wrap-up and poster prizes