== ''' ITCR 2016 Annual Meeting '' == ''' __Notes__ are available [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016&asset=ITCR2016AnnualMeetingNotes.pdf here'''] '''__Posters__ are available [https://nciphub.org/groups/itcr/wiki/AgendaandPresentations/ITCRAnnualMeeting2016Posters here'''] '''__Participant List__ is available [https://nciphub.org/projects/2015itcrpimeeting/files/download?subdir=ITCR%20Meeting%202016&asset=ITCR_2016_Participants.pdf here]''' == '''Day One''' == '''Welcome:''' Juli Klemm and Aviv Regev [https://nciphub.org/collections/post/919/download/Painter-ITCR-2016.pdf Keynote] Corrie Painter: Empowering Patients to Drive Biomedical Research '''__Genomics Session I__''' Chair: Joshua Stuart [https://nciphub.org/collections/post/921/download/2016-13-06-Bioconductor-Morgan.pdf Martin Morgan] Cancer Genomics: Integrative and Scalable Solutions in R / Bioconductor [https://nciphub.org/collections/post/921/download/02_Zhu.pdf Jingchun Zhu] Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Xena [https://nciphub.org/collections/post/921/download/03_Mesirov_Jill.pdf Jill Mesirov] Gene Pattern Notebooks for Cancer Research [https://nciphub.org/collections/post/921/download/4._Ideker-NDEx-ITCR_PI_Meeting_2016_v3.pdf Trey Ideker] NDEx - the Network Data Exchange, a Network Commons for Biologists '''__Imaging Session I__''' Chair: Rebecca Jacobson [https://nciphub.org/collections/post/921/download/01_Cooper_Lee.pdf Lee Cooper, David Gutman] Advanced Development of an Open Source Platform for Web-Based Integrative Digital Image Analysis in Cancer [https://nciphub.org/collections/post/921/download/02_Kalpathy-Cramer_Jayashree.pdf Jayashree Kalpathy-Cramer] Informatics Tools for Optimized Imaging Biomarkers for Cancer Research & Discovery [https://nciphub.org/collections/post/921/download/03_Fedorov_.pdf Andriy Fedorov] Quantitative Image Informatics for Cancer Research (QIICR) [https://nciphub.org/collections/post/921/download/04_Christos_Davatzikos_.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/collections/post/921/download/01_Xinshu_Xiao.pdf Xiao Xinshu] Informatic Tools for Single-Nucleotide Analysis of Cancer RNA-Seq [https://nciphub.org/collections/post/921/download/02__Chennubhotla_ChakraI.pdf Chakra Chennubhotla Srinivas] Informatics Tools for Tumor Heterogeneity in Multiplexed Fluorescence Images [https://nciphub.org/collections/post/921/download/03_Meehan_Terry.pdf Terry Meehan] The PDX Integrator- Re-purposing KOMP2 informatics to Widely Disseminate Data from Patient Derived Xenografts [https://nciphub.org/collections/post/922/download/04_Marcus_Daniel.pdf Daniel Marcus] Integrative Imaging Informatics for Cancer Research [https://nciphub.org/collections/post/921/download/05_Xu_Hua2016.pdf Hua Xu] Advancing Cancer Pharmacoepidemiology Research Through EHRs and Informatics [https://nciphub.org/collections/post/921/download/06_Griffin_Tim_slide.pdf Timothy Griffin] A Galaxy‐Based Multi‐Omic Informatics Hub for Cancer Researchers '''__Genomics Session II__''' Chair: Jill Mesirov [https://nciphub.org/collections/post/921/download/01_Haas_Brian.pdf Brian Haas] Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer [https://nciphub.org/collections/post/921/download/2._Krasnitz_slides_061316.pdf Alexander Krasnitz] Computational Framework for Single - Cell Genomics of Tumors [https://nciphub.org/collections/post/921/download/03_Liu_Shirley.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/collections/post/922/download/01_Jiang_Guoqian.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/collections/post/921/download/03_Bernstam_Elmber.pdf Elmer Bernstam and Funda Meric-Bernstam] Informatics to enable routine personalized cancer therapy [https://nciphub.org/collections/post/919/download/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/collections/post/921/download/IMATOverview_Slides.pdf Tony Dickherber] David Hill '''__Genomics Session III__''' Chair:Trey Ideker [https://nciphub.org/collections/post/921/download/01_Karchin_Rachel.pdf Rachel Karchin] Informatics Tools for High-¬throughput Analysis of Cancer Mutations [https://nciphub.org/collections/post/921/download/02_Webb-Robertson.pdf Bobbie-Jo Webb-Robertson] Interactive Informatics Resource for Research-Driven Cancer Proteomics [https://nciphub.org/collections/post/921/download/03_Wang.pdf Yaoyu Wang] Me V: Software for Next Generation Genomic Data Analysis [https://nciphub.org/collections/post/921/download/4._Jingshan_Huang_Presentation-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/collections/post/921/download/01._LesionTracker_ITCR_PI_Boston_2016_Harris.pdf Gordon Harris] Extensible Open-‐Source Zero-¬‐Footprint Web Viewer for Oncologic Imaging Research [https://nciphub.org/collections/post/921/download/2._Saltz_ITCR__2016_final_saltz.pdf Joel Saltz] Tools to Analyze Morphology and Spatially Mapped Molecular Data [https://nciphub.org/collections/post/921/download/03_Huang_ITCR_2016-Huang-b.pdf Kun Huang] Informatics Links Between Histological Features and Genetics in Cancer [https://nciphub.org/collections/post/921/download/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/collections/post/921/download/01_Berman_Benjamin_Berman-ITCR-2016-finalV2.pdf Benjamin Berman] Software Tools for Regulatory Analysis of Large Cancer Methylome Datasets [https://nciphub.org/collections/post/921/download/02_Sartor.pdf Maureen Sartor] Integrative Epigenomic / Genomic Profiling and Biomarker Discovery in HPV+ and HPV- [https://nciphub.org/collections/post/921/download/3._Weinstein_ITCR-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 and Kyle Ellrot: ESCE: Discovering Molecular Processes [https://nciphub.org/collections/post/921/download/2._Hong_Yu_ITCR-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/collections/post/921/download/01_Aerts_Hugo.pdf Hugo Aerts] Quantitative Radiomics System Decoding the Tumor Phenotype [https://nciphub.org/collections/post/922/download/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