NCI ITCR (Hybrid) Annual Meeting 2022
September 12 – 15, 2022
Eric P. Newman Education Center (EPNEC)
Washington University School of Medicine
St. Louis, MO
Meeting Agenda Twitter #ITCR2022, #NCIITCR, @NCIDataSci
Pre-Meeting - Monday, September 12
Imaging Data Commons (IDC) Workshop
Day 1 - Tuesday, September 12
Opening Keynote: “Leveraging the Tumor Stroma to Enhance Immunotherapy” Slides
Sheila Stewart, Washington University School of Medicine
Theme 1: Deep Learning Technologies in Computational Imaging
STAN-CT: Standardization and Normalization of CT images for Lung Cancer Patients
SlidesJin Chen
The Federated Tumor Segmentation (FeTS) platform: An Intuitive Tool Facilitating Secure Multi-Institutional Collaboration
SlidesSpyridon Bakas
Distributed Learning of Deep Learning Models for Cancer Research
SlidesDaniel Rubin and Jayshree Kalpathy-Craner
Moderator: Daniel Marcus
Theme 2: Multi-Modal Data Integration
Integrative Genomic and Epigenomic Analysis of Cancer Using Long Read Sequencing
SlidesMichael Schatz
Informatics for Functional Integration of Heterogeneous Cancer Genome and Transcriptome Sequencing Data
SlidesVakul Mohanty and Yukun Tan
Enhance UCSC Xena: Extend Interactive Visualization to Ultra-Large-Scale Multi-omics Data and Intergrate with Analysis Resources
SlidesJing Chun Zhu
PROTEAN-CR: Proteomics Toolkit for Ensemble Analysis in Cancer Research
SlidesLydia Kavraki
Moderator: Juli Klemm
Theme 3: Cancer Genomics Analysis Platforms
GenePattern and GenePattern Notebook: Integrative Omic Analysis for Cancer Research
SlidesMichael Reich
Advanced Development of the Cancer Dependency Map Portal (DepMap.org)
SlidesMike Burger
The integrative Genomics Viewer (IGV) for Cancer Research
SlidesJames Robinson
Overture: A Multi-Scale Data Platform for Cancer Genomics Research
SlidesChristina Yung
Moderator: Obi Griffith
Theme 4: Co-Clinical Data Portals
Advancing Method Benchmarking and Data Sharing Through Crowd-Sourced Competitions in Cancer Research
SlidesJames Eddy
Advancing Our Understanding of Cancer and the Human Microbiome with QIIME2
SlidesGreg Caporaso
Patient Derived Cancer Model (PDCM) Finder
SlidesZina Perova
Development of an Open-Source Preclinical Imaging Informatics Platform for Cancer Research
SlidesAndrew Lassiter
Moderator: Kooresh Shoghi
ITCR Training Network (ITN) Overview Slides
Lightning Talks:
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Hyemin Um/Thomas DeSilvio
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Day 2 - Wednesday, September 14
Welcome Introduction: Jo Kenney by Dr. Richard Wahl
Slides
Theme 5: Medical Informatics
Semi-supervised Algorithms for Risk Assessment with Noisy HER Data
SlidesChuan Hong
Optimizing the Population Representatives of Older Adults in Cancer Trials
SlidesYi Guo
Extraction of Symptom Burden from Clinical Narratives of Cancer Patients using Natural Language Processing
SlidesMeliha Yetisgen
Cancer Deep Phenotype Extraction from Electronic Medical Records
SlidesHarry Hochheiser
Moderator: Harry Hochheiser
Theme 6: Computational Genomics
Cancer-specific Gene Set Testing
SlidesRobert Frost
Utilizing Bayesian Modeling to Improve Mutational Signature Inference in Large-Scale Datasets
SlidesJoshua Campbell
Advanced Development of Lancet, an Emerging Tool for Complex Variant Calling in Cancer Genomics
SlidesGiuseppe Narzisi
Software and Algorithms for Elucidting the Structure, Function, and Evolution of Extrachromosomal DNA
SlidesVineet Bafna
Moderator: Jeremy Goecks
Theme 7: Pharmacology and Liquid DNA
Data-Driven QSP Software for Personalized Colon Cancer Treatment Slides
Leili Shahriyari
An Informatics Bridge Over the Valley of Death for Cancer Phase I Trial of Drug-Combination Therapies
SlidesLang Li
cfSNV: A Software Tool for the Sensitive Detection of Somatic Mutations from Cell-Free DNA
SlidesWenyuan Li
Predicting Transcriptional Signatures and Tumor Subtypes from Circulating Tumor DNA
SlidesGavin Ha
Moderator: Lydia Kavraki
Theme 8: Single Cell and Spatial Genomics
Identifying Molecular Signatures of Tumor-Immune Interactions from Spatial Transcriptomics Using Latent Space Factorizations
SlidesAtul Deshpande
Inferring Cell State Tumor Microenvironment Maps by Integrating Single-Cell and Spatial Transcriptomics
SlidesItai Yanai
Informatics Tools to Analyze and Model Whole Slide Image Data at the Single Cell Level
SlidesGuanghua Xiao
scDECO: A Novel Statistical Framework to Identify Differential Co-Expression Gene Combinations Systematically Using Single-Cell RNA Sequencing Data
SlidesYen-Yi Ho
Moderator: Jennifer Beane
Theme 9: ImmunoOncology
Informatics Tools for Identification, Prioritization and Clinical Application of Neoantigens
SlidesMalachi Griffith
Curve-Free Phase I/II Clinical Trial Designs for Molecularly Targeted Agents and Immunotherapy
SlidesYong Zang
Computational Approaches to Unravel Immune Receptor Sequencing for Cancer Immunotherapy
SlidesLi Zhang
The Cancer Epitope Database and Analysis Resource
SlidesBjoern Peters
Moderator: Malachi Griffith
Lightning Talks #2:
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