== ''' ITCR 2016 Annual Meeting Presentations''' == ''' __Posters__ are available here __Notes__ 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=NDEx-ITCR%20PI%20Meeting%202016%20v3-final.pdf Trey Ideker] NDEx - the Network Data Exchange, a Network Commons for Biologists '''__Imaging Session I__''' Chair: Rebecca Jacobson [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20I&asset=01_Cooper%20Lee.pdf David Gutman and Lee Cooper] 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] 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 [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016&asset=itcr-june2016-emv.pdf Keynote] Eli Van Allen: Clinical interpretation of the cancer genome for precision oncology '''Poster Session''' == '''Day Two''' == '''__Opportunities for IMAT - ITCR Collaboration__''' [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016&asset=IMATOverview%20Slides.pdf Tony Dickherber] David Hill '''__Genomics Session III__''' Chair:Trey Ideker [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20III&asset=01_Karchin%20Rachel.pdf Rachel Karchin] Informatics Tools for High-¬throughput Analysis of Cancer Mutations [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20III&asset=02_Webb-Robertson.pdf Bobbie-Jo Webb-Robertson] Interactive Informatics Resource for Research-Driven Cancer Proteomics [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20III&asset=03_Wang.pdf Yaoyu Wang] Me V: Software for Next Generation Genomic Data Analysis [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20III&asset=4.%20Jingshan%20Huang%20Presentation-06142016.pdf Jingshan Huang] Omni Search - A Semantic Search Tool for Discovering microRNAs Critical Roles in Human Cancer '''__Imaging Session II__''' Chair: Xiaole Shirley Liu [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20II&asset=01.%20LesionTracker_ITCR%20PI%20Boston%202016%20Harris.pdf Gordon Harris] Extensible Open-‐Source Zero-¬‐Footprint Web Viewer for Oncologic Imaging Research [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20II&asset=2.%20Saltz%20ITCR%20%202016%20final%20saltz.pdf Joel Saltz] Tools to Analyze Morphology and Spatially Mapped Molecular Data [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20II&asset=03_Huang_ITCR%202016-Huang-b.pdf Kun Huang] Informatics Links Between Histological Features and Genetics in Cancer [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20II&asset=04_Madabhushi.pdf Anant Madabhushi] Pathology Image Informatics Platform for Visualization, Analysis and Management '''ITCR Technical Working Group Lunch Meeting''' '''__Genomics Session IV__''' Chair: Brian Haas [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20IV&asset=01_Berman%20Benjamin%20Berman-ITCR-2016-finalV2.pdf Benjamin Berman] Software Tools for Regulatory Analysis of Large Cancer Methylome Datasets [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20IV&asset=02_Sartor.pdf Maureen Sartor] Integrative Epigenomic / Genomic Profiling and Biomarker Discovery in HPV+ and HPV- [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Genomics%20IV&asset=3.%20Weinstein%20ITCR-PI-2016-presentation2.pdf 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 [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016&asset=2.%20Hong%20Yu%20ITCR-ADE.2016.pdf 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 [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20III&asset=01_Aerts%20Hugo.pdf Hugo Aerts] Quantitative Radiomics System Decoding the Tumor Phenotype [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016/Imaging%20III&asset=ITCR-ODonnell-WideScreen-Public.pdf 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