== ''' ITCR 2016 Annual Meeting Presentations:''' == Notes taken during the meeting are available here Posters are available 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 [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomic%20I-1&asset=2016-13-06-Bioconductor-Morgan.pdf Martin Morgan] Cancer Genomics: Integrative and Scalable Solutions in R / Bioconductor [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomic%20I-1&asset=02_Zhu.pdf Jingchun Zhu] Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Xena [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomic%20I-1&asset=03_Mesirov%20Jill.pdf Jill Mesirov] Gene Pattern Notebooks for Cancer Research [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomic%20I-1&asset=4.%20Ideker-NDEx-ITCR%20PI%20Meeting%202016%20v3.pdf 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 [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20I&asset=02_Kalpathy-Cramer%20Jayashree.pdf Jayashree Kalpathy-Cramer] Informatics Tools for Optimized Imaging Biomarkers for Cancer Research & Discovery [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20I&asset=03_Fedorov%20.pdfAndriy Fedorov] Quantitative Image Informatics for Cancer Research (QIICR) [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20I&asset=04_Christos%20Davatzikos%20.pdf Christos Davatzikos] [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20I&asset=01_Cooper%20Lee.pdf 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__''' [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Lightning%20Talks&asset=01_Xinshu%20Xiao.pdf Xiao Xinshu] Informatic Tools for Single-Nucleotide Analysis of Cancer RNA-Seq [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Lightning%20Talks&asset=02_%20Chennubhotla%20ChakraI.pdf Chakra Chennubhotla Srinivas] Informatics Tools for Tumor Heterogeneity in Multiplexed Fluorescence Images [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Lightning%20Talks&asset=03_Meehan%20Terry.pdf Terry Meehan] The PDX Integrator- Re-purposing KOMP2 informatics to Widely Disseminate Data from Patient Derived Xenografts [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Lightning%20Talks&asset=04_Marcus%20Daniel.pdf Daniel Marcus] Integrative Imaging Informatics for Cancer Research [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Lightning%20Talks&asset=05_Xu%20Hua2016.pdf Hua Xu] Advancing Cancer Pharmacoepidemiology Research Through EHRs and Informatics [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Lightning%20Talks&asset=06_Griffin%20Tim_slide.pdf Timothy Griffin] A Galaxy‐Based Multi‐Omic Informatics Hub for Cancer Researchers '''__Genomics Session II__''' Chair: Jill Mesirov [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20II&asset=01_Haas%20Brian.pdf Brian Haas] Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20II&asset=2.%20Krasnitz%20slides%20061316.pdf Alexander Krasnitz] Computational Framework for Single - Cell Genomics of Tumors [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20II&asset=03_Liu%20Shirley.pdf 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__''' Chair: Aviv Regev [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Clinical&asset=01_Jiang%20Guoqian.pdf 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 [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Clinical&asset=03_Bernstam%20Elmber.pdf Elmer Bernstam and Funda Meric - 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 '''__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: Me V: Software for Next Generation Genomic Data Analysis Jingshan Huang: Omni Search - A Semantic Search Tool for Discovering microRNAs Critical Roles in Human Cancer '''__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 "ITCR Technical Working Group Lunch Meeting" '''__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 '''__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 '''__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 '''Discussion of Collaboration and Integration Opportunities:''' Led by Joel Saltz and Jill Mesirov '''Closing Remarks:''' Juli Klemm and Aviv Regev