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
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
The Integrative Genomics Viewer (IGV): Visualization Supporting Cancer Research
Jim Robinson, University of California, San Diego Slides
GenePattern Notebooks for Cancer Research
Michael Reich, University of California, San Diego Slides
Advanced Development of TIES Enhancing Access to Tissue for Cancer Research
Michael Becich, University of Pittsburgh Slides