Archive of Seminars

Spring/Summer 2014 Seminars

July 23, 2014

Janet Rader, M.D.
Chair and Professor of Obstetrics & Gynecology
Medical College of Wisconsin
Milwaukee, Wisconsin

Biologic and clinical perspective of cervical cancer

April 23, 2014

Gary P. Schroth, Ph.D.
Distinguished Scientist

Next-generation tools for gene expression profiling and fusion detection in FFPE tumor samples

2013 Seminars

December 23, 2013

Wen-Hsiung Li, Ph.D.
James D. Watson Professor, University of Chicago
Director, Biodiversity Research Center, Academia Sinica, Taiwan
Member, National Academy of Sciences, USA

Assembling a genome from next-generation sequencing reads

May 17, 2013

Kai Fai Au, Ph.D.
Postdoctoral Scholar
Department of Statistics
Stanford University
Stanford, California

Gene isoform identification of human ESC transcriptome by second/third generation sequencing

March 6, 2013

John Quackenbush, Ph.D.
Professor of Computational Biology and Bioinformatics
Department of Biostatistics
Harvard University
Director, Center for Computational Cancer Biology
Dana-Farber Cancer Institute
Boston, Massachusetts

The road to genomic medicine is paved with data

February 6, 2013

Li Ding, Ph.D.
Leader, Medical Genomics Group, The Genome Institute
Assistant Professor, Department of Medicine
Oncology Division
Washington University in St. Louis
St. Louis, Missouri

Clonal evolution in cancer treatment

January 30, 2013

Jacques R. Fresco, Ph.D.
Damon B. Pfeiffer Professor in the Life Sciences
Professor of Molecular Biology
Princeton University
Princeton, New Jersey

DNA self-catalyzed depurination, a ubiquitous mechanism for creating mutations and genomic sequence diversity

2012 Seminars

November 7, 2012

Rafael A. Irizarry, Ph.D.
Professor, Department of Biostatistics
Bloomberg School of Public Health
The Johns Hopkins University
Baltimore, Maryland

Bump hunting in the cancer epigenome

October 3, 2012

Sohrab Shah, Ph.D.
Assistant Professor
Pathology and Laboratory Medicine
University of British Columbia
BC Cancer Agency
Vancouver, BC, Canada

Measuring and modeling evolutionary dynamics in breast and ovarian cancer

September 5, 2012

Josh Stuart, Ph.D.
Associate Professor
Department of Biomolecular Engineering
University of California, Santa Cruz

Pathway-based analysis of mutation impact

July 25, 2012

Michael Ryan, Ph.D.
President, Insilico Co.
Fairfax, VA

SpliceSeq for the analysis of alternative splicing in TCGA data

July 11, 2012

Jan F. Prins, Ph.D.
Department of Computer Science
University of North Carolina
Chapel Hill, North Carolina

Revealing the transcriptome using expression-weighted splice-graphs

May 23, 2012

Michael Brudno, Ph.D.
Scientific Director
Centre for Computational Medicine
Hospital for Sick Children
Toronto, Ontario, Canada

The path to the medical genome: From sequencers to clinicians through computer science

March 14, 2012

Barry S. Taylor, Ph.D.
David H. Koch Fellow
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
New York, NY

Mechanism-based oncology through cancer genome discovery

March 7, 2012

Richard Gibbs, Ph.D.
Director, Human Genome Sequencing Center
Baylor College of Medicine
Houston, Texas

Genetics and the cancer genomics scorecard

March 1, 2012

Cheng Li, Ph.D.
Associate Professor
Department of Bioinformatics and Computational Biology
Dana-Farber Cancer Institute
Harvard School of Public Health
Boston, Massachusetts

Progress and challenges in analyzing cancer genomic data to identify drug targets and develop personalized medicine

February 28, 2012

Yu Fan
Doctoral Candidate
Department of Ecology and Evolutionary Biology
University of Connecticut
Storrs, Connecticut

Bayesian phylogenetics: Model selection and methods of detecting non-independent and heterotachous molecular evolution

February 10, 2012

Chris Sander, Ph.D.
Chair, Computational Biology Program
Sloan-Kettering Institute
Memorial Sloan-Kettering Cancer Center
New York, NY

Cancer systems biology: Perturbation experiments reveal signaling networks predictive of drug response

February 8, 2012

Andrey A. Shabalin, Ph.D.
Postdoctoral Research Associate
Department of Biostatistics
University of North Carolina at Chapel Hill
Chapel Hill, NC

Reconstruction of a low-rank matrix in the presence of Gaussian noise

January 25, 2012

Ninad Dewal, Ph.D.
Keck Postdoctoral Fellow
Human Genome Sequencing Center
Baylor College of Medicine
Houston, TX

Methodologies that integrate germline and somatic variation in tumor data

January 11, 2012

Giovanni Parmigiani, Ph.D.
Chair, Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute, Boston, MA
Professor of Biostatistics, Harvard School of Public Health
Cambridge, MA

Gene set analysis as a tool for cross-platform integration in genomics

2011 Seminars

December 8, 2011

Peter Valk, Ph.D.
Head, Molecular Diagnostics
Department of Hematology
Erasmus University Medical Center
Rotterdam, The Netherlands

Integrating molecular biomarkers in the clinical diagnostics of AML

December 7, 2011

Chung-I Wu, Ph.D.
Department of Molecular Genetics
University of Chicago
Chicago, Illinois

Neutralism vs. selectionism in the evolution of cells of hepatocellular carcinomas

November 4, 2011

Jun S. Liu, Ph.D.
Professor of Statistics
Harvard University, Cambridge, Massachusetts

Reconstructing 3-D shapes of chromosomes from Hi-C data

October 20 and 21, 2011

8th Annual Biotechnology and Bioinformatics Symposium
Rice University

October 5, 2011

Michael Berger, Ph.D.
Assistant Professor, Department of Pathology
Memorial Sloan-Kettering Cancer Center
New York, New York

Massively parallel sequencing for discovery and diagnostics in cancer

September 7, 2011

Michael S. Noble
TCGA GDAC Pipeline Manager
Broad Institute
Cambridge, Massachusetts

The Broad Institute Firehose Sequencing Data Management System: Insights from early TCGA use

July 6, 2011

Ilya Shmulevich, Ph.D.
Professor, Computational Biology
Institute for Systems Biology
Seattle, Washington

Molecular networks in cancer

June 29, 2011

Andrew W. Dowsey, Ph.D.
Independent Research Fellow
Imperial College London

A sparse signal restoration framework for simultaneous baseline estimation, deisotoping and charge state deconvolution of complex mass spectra

June 1, 2011

Jill P. Mesirov, Ph.D.
Associate Director and Chief Informatics Officer
Director, Computational Biology and Bioinformatics
Broad Institute of MIT and Harvard
Cambridge, Massachusetts

Machine learning approaches for genomic medicine

May 20, 2011

W. Sabrina Lin, Ph.D.
Department of Electrical & Computer Engineering
University of Maryland, College Park, Maryland

Coalition Formation Game: A new tool for classification

May 19, 2011

Mark Kenneth Transtrum, Ph.D.
Department of Physics
Cornell University, Ithaca, New York

Sloppy models, information geometry, and data fitting

April 6, 2011

Terry Speed, Ph.D.
Professor Ermeritus, Program in Biostatistics
University of California, Berkeley

Bioinformatics Division
Walter & Eliza Hall Institute of Medical Research
Parkville, Australia

Dealing with the GC-content bias in second-generation DNA sequence data

March 23, 2011

Thang Vu
Department of Electrical and Computer Engineering
Texas A&M University, College Station, Texas

The bootstrap in supervised learning and its applications in genomics and proteomics

March 17, 2011

Kosuke Yoshihara, M.D., Ph.D.
Graduate School of Medical and Dental Sciences
Niigata University, Niigata City, Japan

Gene expression profile for predicting survival in patients with advanced-stage serous ovarian cancer

February 25, 2011

Sang Mee Lee
Ph.D. Candidate, Division of Biostatistics
University of Minnesota, Minneapolis, Minnesota

Likelihood-based approach to gene set enrichment analysis with a finite mixture model

February 24, 2011

Siyuan Zheng, Ph.D.
Postdoctoral Research Fellow, Department of Biomedical Informatics
Vanderbilt University, Nashville, Tennessee

Exploring molecular mechanisms of diseases using a systems biology approach

February 18, 2011

Chaeryon Kang
University of North Carolina, Chapel Hill, North Carolina

Change-line classification and regression for chemical toxicity analysis

February 11, 2011

Soyoung Ryu
Department of Statistics
University of Washington, Seattle, Washington

A atatistical approach to peptide identification from clustered tandem mass spectrometry data

2010 Seminars

November 29, 2010

Yolanda Gil, Ph.D.
Principal Investigator and Project Leader, Interactive Knowledge Research Group
Information Sciences Institute
University of Southern California, Marina del Rey, CA

Bringing semantics to computational workflows: Reproducibility and assistance for complex data analysis

October 27, 2010

Ilya Kupershmidt
Cofounder and VP of Products
NextBio, Cupertino, CA

Making sense of your data and gaining clinical insights through NextBio's integrative genomics and genetics platform

October 19, 2010

Michael Ryan, Ph.D.
President and Bioinformatics Specialist
In Silico Solutions, Fairfax, VA
Founding Partner and Technical Consultant
Tiger Team Consulting, Fairfax, VA

Next-Gen Splice Tool - Motivation and concepts

July 23, 2010

Di Wu
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
Parkville, Victoria, Australia

Analysis of transcriptional signatures reveals the cell of origin for breast cancer subtypes

May 24, 2010

Anatoly Ulyanov
Principal Research Investigator and Head of Bioinformatics Group
Sanofi-Aventis, Boston, Massachusetts

Data-driven biomarker discovery

March 29, 2010

Xiaobo Zhou, Ph.D.
Associate Member, The Center for Bioengineering and Informatics
The Methodist Hospital Research Institute, Houston, Texas
Associate Professor of Radiology
Weill Cornell Medical College, New York, New York

Imaging informatics and computational systems bioinformatics for pathway analysis and optimal drug therapy

March 18, 2010

Hyungwon Choi, Ph.D.
Research Fellow, Department of Pathology
University of Michigan Medical School, Ann Arbor, Michigan

Analysis of protein-protein interactome: Evaluation of protein-protein interactions from label-free quantitative proteomics data

March 16, 2010

Wenyi Wang, Ph.D.
Postdoctoral Fellow, Stanford Genome Technology Center
Stanford University School of Medicine, Palo Alto, California

Statistical methods for DNA resequencing analysis in disease-gene studies

February 25, 2010

Peng Qiu, Ph.D.
Integrative Cancer Biology Program, Department of Radiology
Stanford University, Stanford, California

Discovering biological progression underlying microarray samples

February 22, 2010

Hao Wu, M.S.
Department of Biostatistics
Bloomberg School of Public Health
The Johns Hopkins University, Baltimore, Maryland

Genomic “bump finding” from ChIP-chip data and DNA sequence

February 16, 2010

Ju Hee Lee, M.S.
Department of Statistics
The Ohio State University, Columbus, Ohio

Minimally informative prior distributions for nonparametric Bayesian analysis

February 8, 2010

Qi Tang, M.S.
Department of Statistics
University of Wisconsin-Madison

A new Bayesian variable selection method: Bayesian lasso with pseudo variables

January 13, 2010

Roel Verhaak, Ph.D.
Postdoctoral Fellow
Broad Institute of Harvard and MIT, Cambridge, Massachusetts

Integration of genomic data from The Cancer Genome Atlas Data based on gene expression subtypes provides new insights in the pathogenesis of glioblastoma and serous ovarian cancer