Annual Meeting 2019

Abstract List




Day 1 – Tuesday, May 28

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 


Day 2 – Wednesday, May 29

Welcoming Remarks, Juli Klemm Slides

Session 1: Clinical Cancer Informatics

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


Lightning Talks 1

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


NCI Program Presentations

Tanja Davidsen, NCI CBIIT: NCI Cancer Research Data Commons Overview Slides

Tony Dickherber, NCI CSSI: Coordination with Cancer Moonshot and Other NCI Programs Slides


Session 2: Cancer Genomics

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


Lightning Talks 2

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


Day 3 – Thursday, May 30

Session 3: Cancer Genomics 2

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


Session 4: Cancer Imaging Informatics

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


Session 5: Resource Management Technologies

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


Session 6: Cancer Genomics 3

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

Created by Mervi Heiskanen Last Modified Fri May 31, 2019 2:42 pm by Mervi Heiskanen