Conference Welcome - Gabor Marth, University of Utah and Juli Klemm, NCI
Opening Address - Dr. Mary Beckerle, CEO, Huntsman Cancer Institute
Keynote - Dr. Elaine Mardis, Co-Executive Director, Institute for Genomic Medicine, Nationwide Children’s Hospital
Welcoming Remarks, Juli Klemm Slides
Ken Kawamoto, University of Utah: Using Standards-Based Clinical Decision Support Algorithms to Identify and Manage Patients who Meet Evidence-Based Criteria for
Genetic Evaluation of Familial Cancer Slides
David Hanauer, University of Michigan: EMERSE: The Electronic Medical Record Search Engine Slides
Jeremy Warner, Vanderbilt University: HemOnc: A New Standard Vocabulary for Chemotherapy Regimen Representation in the OMOP Common Data Model Slides
GQ Zhang, The University of Texas Health Science Center at Houston: An Ontology-driven Faceted Query Engine for the Kentucky Cancer Registry Slides
Paul Fitzgerald, GE Research: Introducing a new open-source tool: XCIST (X-ray-based Cancer Imaging Simulation Toolkit) Slides
Clifford Meyer, Dana-Farber Cancer Institute / Harvard School of Public Health: Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis Slides
Paul Marjoram, University of Southern California: Conservation and Functional-Characterization of Tumor Methylation Sites Slides
Andrew Janowczyk, Case Western Reserve University: HistoQC: A quality control pipeline for digital pathology slides Slides
Joshua Campbell, Boston University School of Medicine: Enhanced Deconvolution and Prediction of Mutational Signatures Slides
Fuyong Xing, University of Colorado Anschutz Medical Campus: Deep Pixel-to-pixel Learning for Single-stage Nucleus Recognition in Digital Pathology Images Slides
Gordon Harris, Massachusetts General Hospital: Precision Imaging Metrics: All-in-One Cloud-Hosted Quantitative Imaging Assessment and Workflow Management System for
Cancer Centers Slides
Trinity Urban, Massachusetts General Hospital: Crowds Cure Cancer: Crowd-sourcing ground-truth measurements on publicly available imaging data Slides
Yusen He, University of Iowa: What does AI see? Deep segmentation networks discover biomarkers for lung cancer survival Slides
Anjishnu Banerjee, Medical College of Wisconsin: Stochastic covariance functions for understanding the histology and improving detection in solid tumors Slides
Tanja Davidsen, NCI CBIIT: NCI Cancer Research Data Commons Overview Slides
Tony Dickherber, NCI CSSI: Coordination with Cancer Moonshot and Other NCI Programs Slides
Tim Griffin, University of Minnesota: A resource for complete proteogenomic informatics in cancer research: Built on ITCR Tools Slides
Brian Haas, Broad Institute: Latest Developments in the Trinity Cancer Transcriptome Analysis Toolkit Slides
Evan Johnson, Boston University: Interactive single cell RNA-Seq analysis with the Single Cell Toolkit (SCTK) Slides
Ravi Madduri, University of Chicago: Applying ConVarCal, A High Performance Consensus Variant Calling, For Discovery of Prevalence of Inherited Mutations in Breast Cancer
Predisposition Genes among Uganda and Cameroon Women Slides
Giuseppe Narzisi, New York Genome Center: Somatic variant analysis of linked-reads sequencing data with Lancet Slides
Li Song, Dana-Farber Cancer Institute: Bioinformatics Technology to Characterize Tumor Infiltrating Immune Repositories Slides
Simina Boca, Georgetown University Medical Center: CDGnet: Cancer Drug Gene Network Slides
Hayley Dingerdissen, The George Washington University: OncoMX: a web resource for exploring integrated cancer biomarker data in the context of
mutation, differential expression, evolutionarily conserved expression patterns, and automatically mined literature evidence Slides
Ian Holmes, University of California at Berkeley: The JBrowse Cancer Genome Browser Slides
Min Jin Ha, University of Texas MD Anderson Cancer Center: Personalized Integrated Network Modeling of the Cancer Proteome Atlas Slides
Martin Morgan, Roswell Park Comprehensive Cancer Center: Cancer Genomics: Integrative and Scalable Solutions in R / Bioconductor Slides
Kristen Naegle, University of Virginia: Inferring Kinase Activity Profiles from Phosphoproteomic Data Slides
Li-Xuan Qin, Memorial Sloan Kettering Cancer Center: Statistical Evaluation and Selection of Normalization Methods for microRNA Sequencing Data in Cancer Biomarker Studies Slides
Michael Reich, University of California, San Diego: GenePattern Notebooks for Cancer Research Slides
Ei-Wen Yang, University of California, Los Angeles: Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA Slides
Joel Saltz, Stony Brook University: Actionable Pathomics Slides
Linda Shapiro, University of Washington: A Unified Machine Learning Package for Cancer Diagnosis Slides
Dinler Antunes, Rice University: Conformational sampling of large ligands made possible by a parallelized incremental meta-docking approach Slides
Yi Qiao, University of Utah: scBayes: a computational method to study tumor subclone-specific gene expression and chromatin accessibility using single cell RNA
sequencing and single cell ATAC sequencing in combination of bulk DNA sequencing Slides
Ethan Cerami, Dana Farber Cancer Institute: The cBioPortal for Cancer Genomics Slides
Jeremy Goecks, Oregon Health and Science University: Galaxy Workflows for the Human Tumor Atlas Network Slides
Rachel Karchin, Johns Hopkins University: Informatics Tools for High-Throughput Analysis of Cancer Mutations Slides
Han Liang, The University of Texas MD Anderson Cancer Center: Systematic Identification of Cancer Therapeutic Liabilities through Adaptive Functional Proteomics Slides
Corey Arnold, University of California, Los Angeles: Classifying Prostate Cancer from Multiparametric Magnetic Resonance Imaging and Whole Slide Histology Imaging using
Machine Learning Slides
Ahmed Hosny, Harvard-DFCI: ModelHub.AI: Dissemination Platform for Deep Learning Algorithms Slides
Despina Kontos and Christos Davatzikos, University of Pennsylvania: The Cancer Imaging Phenomics Toolkit (CaPTk) Slides
Ashish Sharma, Emory University: PRISM – Platforms for Quantitative Imaging Informatics in Precision Medicine Slides
David Gutman, Emory University: The Digital Slide Archive 2.0: MultiChannel Image Support and Dockerized Algorithm Support Slides
Dexter Pratt, University of California, San Diego: NDEx in 2019: Workflows and Application Integration Slides
Joseph Perl, SLAC National Accelerator Laboratory: The TOPAS Tool for Particle Simulation, a Monte Carlo Simulation Tool for Physics, Biology and Clinical Research Slides
Nathalie Conte, EMBL-EBI: Implementing novel functionality for PDX Finder through collaborations with ITCR and other community resources Slides
Lee Cooper, Emory University: Cell Detection and Classification in Hematopathology Slides
Obi Griffith, Washington University School of Medicine: Aggregating evidence to determine the clinical significance of cancer variants in the CIViC Slides
Alexej Abyzov, Mayo Clinic: Application of CNVnator to analyze copy number alterations in cancer Slides
Vincent Carey, Harvard Medical School: Opening Apps and Notebooks for Cloud-Scale Cancer Genomics with Bioconductor Slides
Kai Tan, University of Pennsylvania: Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers Slides
Anthony Castanza, University of California, San Diego: MSigDB 7 and Beyond, a Scalable Resource for Transcriptome Interpretation Slides