[https://nciphub.org/collections/post/1306/download/ITCR_2017_Attendee_List_052617.pdf '''Meeting Attendees''']

[https://nciphub.org/collections/post/1307/download/ITCR2017Posters.pdf '''Poster Session''']


= '''Agenda and Presentations''' =

= ''' Day One''' =


'''Welcome:''' Josh Stuart

'''Resources Session I''' Chair Obi Griffith 

[https://nciphub.org/collections/post/1304/download/01_Griffith_CIViC_ITCR_Meeting2017.pdf Obi Griffith]: Development of Informatics Resources for Interpretation of Clinically Actionable Variants in Cancer

[https://nciphub.org/collections/post/1304/download/02_Meehan_PDX_finder_ITCR_Meehan.pdf Terry Meehan]:  The PDX Integrator - Re-Purposing KOMP2 Informatics to Widely Disseminate Data from Patient Derived Xenografts and Electronic Access to Mouse Tumor Data

[https://nciphub.org/collections/post/1304/download/03_Broom-Weinstein-ITCR-PI-2017-presentation.pdf John Weinstein and Bradley Broom]: Next-Generation Clustered Heat Maps for Fluent, Interactive Exploration of Omic Data

[https://nciphub.org/collections/post/1304/download/04_Waldron_MultiAssayExperiment.pdf Levi Waldron]: Cancer Genomics: Integrative and Scalable Solutions in R / Bioconductor

[https://nciphub.org/collections/post/1304/download/05_Karchin_cravat-u24-presentation.pdf Rachel Karchin]: Informatics Tools for High-Throughput Analysis of Cancer Mutations

[https://nciphub.org/collections/post/1304/download/06_Becich_ICTR_Meeting_May_31_2017_Becich_PPT_TIES_TCRN_MBv1_20170530.pdf Michael J Becich]: Advanced Development of TIES-Enhancing Access to Tissue for Cancer Research


'''Imaging Session I''' Chair Joel Saltz

[https://nciphub.org/collections/post/1304/download/07_Wu_UIowa-XWu.pdf Xiaodong Wu] Developing Enabling PET-CT Image Analysis Tools for Predicting Response in Radiation Cancer Therapy

[https://nciphub.org/collections/post/1304/download/08_ODonnell_2017_ITCR_U01_ODonnell.pdf Lauren Jean O'Donnell] Open Source Diffusion MRI Technology for Brain Cancer Research

[https://nciphub.org/collections/post/1304/download/09_Davatzikos_ITCR_2017_mov.pdf Christos Davatzikos] Cancer Imaging Phenomics Software Suite: Application to Brain and Breast Cancer

[https://nciphub.org/collections/post/1304/download/10_Quackenbush_20170531.ITCR.RadiomicsIO.JohnQ.pdf John Quackenbush] Quantitative Radiomics System Decoding the Tumor Phenotype


Lunch /  TOW Working Group Get Together


'''New Groups Lightning Talks'''

[https://nciphub.org/collections/post/1304/download/11_Carey_May31CareyOneSl.pdf Vincent Carey]: Accelerating Cancer Genomics with Cloud Scale Bioconductor

[https://nciphub.org/collections/post/1304/download/12_Pochet_NIH_NCI_ITCR_SantaCruz2017_FlashTalk_final.pdf Nathalie Pochet]: Integrative genomic framework for dissecting regulatory mechanisms underlying hepatocellular carcinoma

[https://nciphub.org/collections/post/1304/download/13_Mazumder_U01Slide_Mazumder.pdf Raja Mazumder]: Integration of comprehensive cancer mutation and expression-associated data for biomarker evaluation and discovery


'''Clinical Session I''' Chair Guergana Savova

[https://nciphub.org/collections/post/1304/download/14_Xu_2017_ITCR_Hua_Xu_slides.pdf Hua Xu and Ping Yang]: Advancing Cancer Pharmacoepidemiology Research Through EHRs and Informatics

[https://nciphub.org/collections/post/1304/download/15_Jiang_nci-itcr-2017-caCDE-QA-presentation-GJiang-0530.pdf Guoqian Jiang]: caCDE-QA: A Quality Assurance Platform for Cancer Study Common Data Elements

[https://nciphub.org/collections/post/1304/download/16_Yu_ITCR_Hong.Yu.2017.pdf Hong Yu]: EMR Adverse Drug Event Detection for Pharmacovigilance

[https://nciphub.org/collections/post/1304/download/17_Savova_2017_June_PI_meeting.pdf Guergana Savova]: Cancer Deep Phenotyping Extraction from Electronic Medical Records [https://drive.google.com/a/ucsc.edu/file/d/0B4WyAZDcgSOzY1dDQnJYVGg1N1U/view?usp=sharing Video]


'''Advanced Omics Session I''' Chair Brian Haas

[https://nciphub.org/collections/post/1304/download/18_Marth_2017-05-31_ITCR_Marth_v05.pdf Gabor Marth], Aaron Quinlan: Monitoring Tumor Heterogeneity Over Time and Space

[https://nciphub.org/collections/post/1304/download/19_Antunes_ITCRmeeting_2017.pdf Dinler Antunes]: Structure-Based Selection of Tumor-Antigens for T-Cell Based Immunotherapy

[https://nciphub.org/collections/post/1304/download/20_Xiao.SNV.pdf Xinshu Grace Xiao]: Informatics Tools for Single-Nucleotide Analysis of Cancer RNA-Seq

[https://nciphub.org/collections/post/1304/download/21_Haas_ITCR_Trinity_May312017_SantaCruz.pdf Aviv Regev and Brian Haas]: Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer

Ben Raphael (Keynote): Algorithms for Inferring Evolution and Migration of Tumors




= '''Day Two''' =



'''Imaging Session II''' Chair Andrey Fedorov

[https://nciphub.org/collections/post/1305/download/01_Fedorov_2017-ITCR-Fedorov.pdf Andrey Fedorov]: Quantitative Image Informatics for Cancer Research (QIICR)

[https://nciphub.org/collections/post/1305/download/02_Moore_ITCR_Moore_Flavin_2017-final.pdf Daniel Marcus and Richard Wahl:] Integrative Imaging Informatics for Cancer Research

[https://nciphub.org/collections/post/1305/download/03_Martel_annePIIP_ITCR_2017.pdf Avant Madabhushi and Anne Martel]: Pathology Image Informatics Platform for Visualization, Analysis and Management

[https://nciphub.org/collections/post/1305/download/04_Huang_ITCR_2017_Kun_Huang_OSU.pdf Kun Huang]: Informatics Links between Histological Features and Genetics in Cancer

[https://nciphub.org/collections/post/1305/download/05_Kalpathy_ictr_f2f2017.pdf Jayashree Kalpathy-Cramer]: Informatics Tools for Optimized Imaging Biomarkers for Cancer Research & Discovery

[https://nciphub.org/collections/post/1305/download/06_Saltz_ITCR_Saltz_6_1_2017.pdf Joel Saltz]: Tools to Analyze Morphology and Spatially Mapped Molecular Data


'''Resources Session II''' Chair Jing Zhu

[https://nciphub.org/collections/post/1305/download/07_Mesirov_ITCR_2017_final.pdf Jill Mesirov]: The Integrative Genomics Viewer (IGV): Visualization Supporting Cancer Research

[https://nciphub.org/collections/post/1305/download/08_Griffin_Jagtap_U24_ITCR_2017_FINAL.pdf Timothy Griffin]: A Galaxy-Based Multi-Omic Informatics Hub for Cancer Researchers

[https://nciphub.org/collections/post/1305/download/09_Ellrott_itcr-santacruz-f2f-20170601.gslides.pdf Josh Stuart and Kyle Ellrott]: BMEG: Biomedical Evidence Graph

[https://nciphub.org/collections/post/1305/download/10_Pratt_NDEx-ITCR_PI_Meeting_2017.pdf Trey Ideker and Dexter Pratt]: NDEx - the Network Data Exchange, A Network Commons for Biologists

[https://nciphub.org/collections/post/1305/download/11_Zhu_Xena_ITCR_Annual_mtg_2017.pdf Jiang Zhu]: UCSC Xena - Cloud Based Resource for Data Hosting, Visualization and Analysis


'''Advanced Omics Session II''' Chair Alexander Krasnitz

[https://nciphub.org/collections/post/1305/download/12_Liang_ITCR_project_HLiang.pdf Han Liang]: The Cancer Proteome Atlas, TCPA: An Integrated Bioinformatics Resource for Functional Cancer Proteomic Data

[https://nciphub.org/collections/post/1305/download/13_Chung_Dongjun_Chung_presentation.pdf Dongjun Chung]: Algorithms for Literature-Guided Multi-Platform Identification of Cancer Subtypes

[https://nciphub.org/collections/post/1305/download/14_Krasnitz_ITCR2017AKrasnitz.pdf Alexander Krasnitz]: Computational Framework for Single-Cell Genomics of Tumors

[https://nciphub.org/collections/post/1305/download/15_Huang_Presentation-06012017.pdf Jingshan Huang]: Omni Search: A Semantic Search Tool for Discovering Micro RNAs' Critical Roles in Human Cancer


'''Imaging Session III''' Chair Hiroyuki Yoshida

[https://nciphub.org/collections/post/1305/download/16_Chennubhotla_ITCR2017PittGE.pdf Srinivas Chakra Chennubhotla and Daryl Sarachan]: nformatics Tools for Tumor Heterogeneity in Multiplexed Fluorescence Images

[https://nciphub.org/collections/post/1305/download/17_Urban_ITCR_LesionTracker_1June2017.pdf Trinity Urban]: Next Steps for Lesion Tracker: Integration with a Clinical Trials Workflow Informatics System

David Andrew Gutman: Advanced Development of an Open-source Platform for Web-based Integrative Digital Image Analysis in Cancer

Group Discussion