== ''' ITCR 2016 Annual Meeting Presentations:''' ==
 
Notes taken during the meeting are available [https://nciphub.org/resources/993 here] 


== '''Day One''' ==


'''Welcome:'''  Juli Klemm and Aviv Regev

'''[https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016&asset=Painter-ITCR-2016.pdf Keynote] Corrie Painter: Empowering Patients to Drive Biomedical Research 


'''Genomics Session I''' Chair: Joshua Stuart

	Martin Morgan: Cancer Genomics: Integrative and Scalable Solutions in R / Bioconductor

	Jingchun Zhu: Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Xena
	
	Jill Mesirov: GenePattern Notebooks for Cancer Research

	Trey Ideker: NDEx  - the Network Data Exchange, a Network Commons for Biologists


'''Imaging Session I''' Chair: Rebecca Jacobson

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

	Jayashree Kalpathy-Cramer Informatics: Tools for Optimized Imaging Biomarkers for Cancer Research & Discovery

	Andriy Fedorov: Quantitative Image Informatics for Cancer Research (QIICR)

	Christos Davatzikos and Lee Cooper: Cancer Imaging Phenomics Software Suite: Application to Brain and Breast Cancer


 '''ITCR Training and Outreach Working Group Lunch Meeting'''
	
	
'''Lightning Talks for New Groups'''

	Xiao Xinshu: Informatic Tools for Single-Nucleotide Analysis of Cancer RNA-Seq

        Chakra Chennubhotla: Srinivas Informatics Tools for Tumor Heterogeneity in Multiplexed Fluorescence Images

	Terry Meehan: The PDX Integrator- Re-purposing KOMP2 informatics to Widely Disseminate Data from Patient Derived Xenografts

	Daniel Marcus: Integrative Imaging Informatics for Cancer Research

	Hua Xu: Advancing Cancer Pharmacoepidemiology Research Through EHRs and Informatics

	Timothy Griffin: A Galaxy‐Based Multi‐Omic Informatics Hub for Cancer Researchers


'''Genomics Session II''' Chair: Jill Mesirov

	Brian Haas	Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer

	Alexander Krasnitz: Computational Framework for Single-¬Cell Genomics of Tumors

	Xiaole Shirley Liu: Developing Informatics Technologies to Model Cancer Gene Regulation


'''Technical Working Group Demonstration Projects''' Led by Jayashree Kalpathy-Cramer and Tahsin Kurc


'''Clinical Session I''' Chair: Aviv Regev 

	Guoqian Jiang: caCDE-QA: A Quality Assurance Platform for Cancer Study Common Data Elements
	
	Rebecca Jacobson: Advanced Development of TIES-¬‐Enhancing Access to Tissue for Cancer Research

	Elmer Bernstam: Informatics to enable routine personalized cancer therapy


'''Keynote:''' Eli Van Allen: Clinical interpretation of the cancer genome for precision oncology


'''Poster Session'''



== '''Day Two''' ==


'''Opportunities for IMAT-ITCR Collaboration''' Tony Dickherber and David Hill
	

9:00	Genomics Session III
	Chair: Trey Ideker

	Rachel Karchin and Mike Ryan
	Informatics Tools for High-¬throughput Analysis of Cancer Mutations
	
	Bobbie-¬‐Jo Webb-¬‐Robertson 
Interactive Informatics Resource for Research-¬‐ Driven Cancer Proteomics

	Yaoyu Wang 	MeV: Software for Next Generation Genomic Data
		Analysis

	Jingshan Huang 	OmniSearch: A Semantic Search Tool for Discovering
		microRNAs Critical Roles in Human Cancer
10:20	Break


10:40 	Imaging Session II
	Chair: Xiaole Shirley Liu

	Gordon Harris 	Extensible Open-‐Source Zero-¬‐Footprint Web Viewer for Oncologic Imaging Research

	Joel Saltz 	Tools to Analyze Morphology and Spatially Mapped Molecular Data

	Kun Huang  	Informatics Links Between Histological Features and Genetics in Cancer

	Anant Madabhushi 	Pathology Image Informatics Platform for Visualization, Analysis and Management

12:00	Lunch
	ITCR Technical Working Group Lunch Meeting, Room xxx

1:30	Genomics Session IV
	Chair: Brian Haas
	
	Benjamin Berman 	Software Tools for Regulatory Analysis of Large Cancer Methylome Datasets

	Maureen Sartor 	Integrative Epigenomic / Genomic Profiling and
		Biomarker Discovery in HPV+ and HPV-

	John Weinstein and Bradley Broom
Next-¬‐Generation Clustered Heat Maps for Fluent, Interactive Exploration of Omic Data

2:30	Big Data and EMR Session
	Chair: Rachel Karchin

	Joshua Stuart 	ESCE: Discovering Molecular Processes

	Hong Yu  		EMR Adverse Drug Event Detection for Pharmacovigilance

	Guergana Savova 	Cancer Deep Phenotype Extraction from Electronic
		Medical Records

3:25	Break

3:40	Imaging Session III
	Chair: Robert Majovski
	
	Hugo Aerts  	Quantitative Radiomics System Decoding the Tumor Phenotype

	Lauren O'Donnell 	Open Source Diffusion MRI Technology for Brain Cancer Research

4:20	Discussion of Collaboration and Integration Opportunities
	Led by Joel Saltz, Metin Gurcan and Jill Mesirov

4:40 	Closing Remarks
	Juli Klemm and Aviv Regev