Informatics Technology for Cancer Research (ITCR) initiative [itcr]

ITCR 2018 Annual Meeting, May 23-24, Bethesda, MD

Agenda

Abstract Book

Presentations

Day 1 – Wednesday, May 23

NCI Welcome and Overview - Tony Kerlavage and Juli Klemm, CBIIT Slides

Imaging Session 1

Tools to Analyze Morphology and Spatially Mapped Molecular Data

Joel Saltz, Stony Brook University Slides

Quantitative Image Informatics for Cancer Research

Andrey Fedorov, Brigham and Women’s Hospital and Harvard Medical School Slides

Cancer Imaging Phenomics Software Suite: Application to Brain and Breast Cancer

Christos Davatzikos, University of Pennsylvania Slides

Quantitative Radiomics System Decoding the Tumor Phenotype

John Quackenbush, Dana-Farber Cancer Institute Slides

Integrative Imaging Informatics for Cancer Research

Daniel Marcus and Richard Wahl, Washington University in St. Louis Slides

Pathology Image Informatics for Visualization, Analysis and Management

Metin Gurcan, Wake Forest School of Medicine Slides

Lightning Talks: New ITCR Grantees

Somatic Variant Calling and Phasing using Colored de Bruijn Graphs in Heterogeneous Tumors

Giuseppe Narzisi, New York Genome Center Slides

Bioinformatics Technology to Characterize Tumor Infiltrating Immune Repertoires

Xihao Sherlock Hu, Dana Farber Cancer Institute Slides

Tools for Annotating Mutations in the 3D Cancer Genome

Kai Tan, Children's Hospital of Philadelphia Slides

Informatics Tools for Quantitative Digital Pathology Profiling and Integrated Prognosis Modeling

Lee Cooper, Emory University Slides

The TOPAS Tool for Particle Simulation, a Monte Carlo Simulation Tool for Physics, Biology and Clinical Research

Bruce Faddegon, University of California, San Francisco Slides

Detection of Somatic, Subclonal, and Mosaic CNVs from Sequencing

Alexej Abyzov, Mayo Clinic Rochester Slides

Supporting and Evolving Gene Set Enrichment Analysis and the Molecular Signatures Database for Cancer Research

Michael Reich, University of California, San Diego Slides

Database and Tools for Functional Inference and Mechanistic Insight for Cancer Research

Jie Liang, University of Illinois at Chicago Slides

Omics Session 1

Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer

Brian Haas, Broad Institute Slides

Development of Informatics Resources for Interpretation of Clinically Actionable Variants in Cancer

Obi Griffith, Washington University in St. Louis Slides

Informatics Tools for Single Nucleotide Analysis of Cancer RNA-Seq

Xinshu Grace Xiao, University of California, Los Angeles Slides

Building Protected Data Sharing Networks to Advance Cancer Risk Assessment and Treatment

Ian Foster, University of Chicago Slides

Breakout Session 1

A Network-Based Approach for Personalized Treatment of Multiple Myeloma

Alessandro Lagana, Icahn School of Medicine at Mount Sinai Slides

Integrative Genomic Framework for Dissecting Regulatory Mechanisms Underlying Hepatocellular Carcinoma

Nathalie Pochet, Brigham and Women’s Hospital Slides

Algorithms for Literature-Guided Multi-Platform Identification of Cancer Subtypes

Dongjun Chung and Linda Kelemen, Medical University of South Carolina Slides

Accelerating Cancer Genomics with Cloud-Scale Bioconductor

Vincent Carey, Brigham and Women’s Hospital Slides

Integration of Comprehensive Cancer Mutation and Expression-Associated Data for Biomarker Evaluation and Discovery

Daniel Crichton, Jet Propulsion Laboratory and Raja Mazumder, George Washington University Slides

Breakout Session 2

Developing Enabling PET-CT Image Analysis Tools for Predicting Response in Radiation Cancer Therapy

Xiaodong Wu, University of Iowa Slides

Structure-Based Selection of Tumor Antigens for T-Cell Based Immunotherapy

Dinler Antunes, Rice University Slides

CGDnet: Cancer Gene Drug Network: Using patient-specific drug-gene networks for recommending targeted cancer therapies

Simina Boca, Georgetown University Slides

An Integrative Analysis Toolkit for Single Cell RNA-Seq in Cancer Research

William Evan Johnson, Boston University Slides

Imaging/Clinical Session 2

Advanced Development and Dissemination of EMERSE for Cancer Phenotyping from Medical Records

David Hanauer, University of Michigan Slides

Cancer Deep Phenotyping Extraction from Electronic Medical Records

Guergana Savova, Boston Children’s Hospital and Harvard Medical School Slides

Advancing Cancer Pharmacoepidemiology Research Through EHRs and Informatics

Jeremy Warner, Vanderbilt University Slides

Scalable Clinical Decision Support for Individualized Cancer Risk Management

Guilherme Del Fiol and Kensaku Kawamoto, University of Utah Slides

Informatics Tools for Tumor Heterogeneity in Multiplexed Fluorescence Images

S. Chakra Chennubhotla and Brion Sarachan, University of Pittsburgh and GE Global Research Slides

Extensible Open-Source Zero-Footprint Web Viewer for Oncologic Imaging Research

Gordon Harris, Massachusetts General Hospital Slides

Open Source Diffusion MRI Technology for Brain Cancer Research

Lauren Jean O`Donnell, Brigham and Women’s Hospital and Harvard Medical School Slides

The PDX Integrator – Re-purposing KOMP2 Informatics to Widely Disseminate Data from Patient Derived Xenografts and Electronic Access to Mouse Tumor Data

Terry Meehan, European Molecular Biology Laboratory Slides

Day 2 – Thursday, May 24

Omics Session 2

Computational Framework for Single-Cell Genomics of Tumors

Alexander Krasnitz, Cold Spring Harbor Laboratory Slides

NDEx – The Network Data Exchange, A Network Commons for Biologists

Trey Ideker and Dexter Pratt, University of California, San Diego Slides

Next Generation Clustered Heat Maps for Fluent, Interactive Exploration of Omic Data

John Weinstein and Bradley Broom, University of Texas - MD Anderson Cancer Center Slides

UCSC Xena – Platform for Functional Genomics Visualization and Analysis

Jing Zhu, University of California, Santa Cruz Slides

The cBioPortal for Cancer Genomics

Ethan Cerami, Dana Farber Cancer Institute Slides

Informatics Links between Histological Features and Genetics in Cancer

Kun Huang, Indiana University Slides

Cancer Genomics: Integrative and Scalable Solutions in R/Bioconductor

Levi Waldron, City University of New York Slides

Plenary Talk

NCI Director, Dr. Norman E. Sharpless Slides

Lightning Talks: Investigators Developing Data Compression Methods Funded by BD2K Targeted Software Development Program

MMTF-Spark: Interactive, Scalable, and Reproducible Datamining of 3D Macromolecular Structures

Peter Rose, University of California, San Diego Slides

Task-based Compression of Pathology Images

Ali Bilgin, University of Arizona Slides

Integrated Querying of Biological Network Databases

Mehmet Koyuturk, Case Western Reserve University Slides

Multiomics Data Compression

Mikel Hernaez, University of Illinois, Urbana-Champaign Slides

Imaging Session 3

Informatics Tools for Optimized Imaging Biomarkers for Cancer Research and Discovery

Jayashree Kalpathy-Cramer, Massachusetts General Hospital Slides

Advanced Development of an Open-Source Platform for Web-Based Integrative Digital Image Analysis in Cancer

David Andrew Gutman and Lee Cooper, Emory University Slides

TCIA Sustainment and Scalability – Platforms for Quantitative Imaging Informatics in Precision Medicine

Ashish Sharma, Emory University Slides

Omics/Clinical Session 3

Monitoring Tumor Subclonal Heterogeneity Over Time and Space

Gabor Marth, University of Utah Slides

A Galaxy-Based Multi-Omic Informatics Hub for Cancer Researchers

Timothy Griffin and Pratik Jagtap, University of Minnesota Slides

Informatics Tools for High-Throughput Analysis of Cancer Mutations

Rachel Karchin, Johns Hopkins University Slides

The Cancer Proteome Atlas, TCPA: An Integrated Bioinformatics Resource for Functional Cancer Proteomic Data

Han Liang and Gordon Mills, University of Texas - MD Anderson Cancer Center Slides