February 3, 2023
Program Updates, ITN and OPEN (formerly TOW) updates – Juli Klemm, Carrie Wright
Overview of new U01 award – Brooke Fridley, Oscar Ospina
Overview of new U01 award – Pablo Camara
Overview of new U01 award – Malgorzata Marjanska
January 6, 2023
Program Updates, ITN and OPEN (formerly TOW) updates – Kelly Crotty, Carrie Wright
Overview of new U01 award – Sam Volchenboum
Overview of new U24 award – Avi Ma’ayan
Overview of new U24 award – Veronica Rotemberg, Kivanc Kose
December 2, 2022
New R21 Awards:
A novel algorithm to compute adherence from electronic adherence monitoring devices - Meghan McGrady
Identifying recurrent non-Hodgkin lymphoma in electronic health data - Mara Epstein & Feifan Liu
November 4, 2022
New U01 Award - muMS2: An open source R package for analyzing and integrating multi-omics datasets to improve early cancer detection and understanding of colorectal cancer - Patrick Schloss & Marcy Balunas
New U01 Award: Development of SU24 Renewal - OpenCRAVAT: Informatics tools for high-throughput analysis of cancer mutationsmall Area Interactive Risk Maps for Cancer Control Efforts - Rachel Karchin
New R21 Award: Predicting actionable cancer vulnerabilities enabled by mutant-directed protein-protein interactions - Andrey Ivanov
October 7, 2022
ITCR Annual Meeting Updates
New R21 Awards:
Computerized platform for interactive annotation and topological characterization of tumor associated vasculature for predicting response to immunotherapy in lung cancer - Prateek Prasanna & Chao Chen
Deep learning in cervical cancer radiogenomics - Jin Zhang
A deep-transfer-learning framework to transfer clinical information to single cells and spatial locations in cancer tissues - Travis Johnson & Jie Zhang
September- No meeting
August 5, 2022
ITCR Annual Meeting Updates
Collaboration update:
HistoQC and its integration into the DSA and adaptation for IHC images - Andrew Janowczyk, Lee Cooper, David Gutmam
New U01 Award: Development of Small Area Interactive Risk Maps for Cancer Control Efforts - Jake Oleson
July- No meeting
June 3, 2022
Collaboration update:
Development of a RedCap-to-OMOP Converter - Jeremy Warner, Mike Gurley
Development of a cancer variant interrogation tool within Galaxy - Gabor Marth, Jeremy Goecks
May 6, 2022
Collaboration update:
Integration of the Single Cell Toolkit and WebMev - John Quackebush, Josh Campbell, Derrick DeConti
Support for the Lymphoma/Leukemia Profiling Project- Lee Cooper
Collaboration with the ClinGen Linked Data Hub- Melissa Cline
April 1, 2022
Collaboration update:
U24: TCIA Sustainment and Scalability - Platforms for Quantitative Imaging Informatics in Precision Medicine
U01: Distributed Learning of Deep Learning Models for Cancer Research
March 4, 2022
The NCI Patient Derived Models of Cancer (PDMC) Program: Data integration and analysis needs and collaboration opportunities - Bryan Welm
New U01 Overview: Informatics Tools to Analyze and Model Whole Slide Image Data at the Single Cell Level - Guanghua “Andy” Xiao
Collaboration update: Enhancing The Cancer Proteome Atlas with PRECISE pathway scores - Han Liang, Min Jin Ha
February 4, 2022
New R21 Overview: scDECO: A novel statistical framework to identify differential co-expression gene combinations systematically using single-cell RNA sequencing data - Yen-Yi Ho
New U24 Sustainment Overview: The Integrative Genomics Viewer (IGV) for Cancer Research - James Robinson
Collaboration update: Advanced Development and Dissemination of EMERSE for Cancer Phenotyping from Medical Records” with“Scalable Clinical Decision Support for Individualized Cancer Risk Management - David Hanauer and Guilherme Del Fiol
January 7, 2022
New R21 Overview: Inferring cell state tumor microenvironment maps by integrating single-cell and spatial transcriptomics Itai Yanai
New U01 Overview: Utilizing Bayesian modeling to improve mutational signature inference in large-scale datasets, Joshua Campbell
New U24 Overview: Software and algorithms for elucidating the structure, function, and evolution of extrachromosomal DNA, Vineet Bafna
December 3, 2021
New R21 Overview “Predicting transcriptional signatures and tumor subtypes from circulating tumor DNA”, Gavin Ha
New U01 Overview “Advanced development of Lancet, an emerging tool for complex variant calling in cancer genomics”, Giuseppe Narzisi
New U24 Overview “Overture: A multi-scale data platform for cancer genomics research”, Christina Yang
November 5, 2021
Childhood Cancer Data Initiate Administrative Supplement Opportunity
New R21 Overview: “Curve-free phase I/II clinical trial designs for molecularly targeted agents and immunotherapy”, Yong Zang
New R21 Overview “Computational approaches to unravel immune receptor sequencing for cancer immunotherapy”, Li Zhang
New U01 Overview “An informatics bridge over the valley of death for cancer Phase I trials of drug-combination therapies”, Lang Li
October 1, 2021
Updates from the ITCR Training Network - Jeff Leek
August 6, 2021
Program updates with Annual Meeting Overview
Physics in Medicine and Biology Special Issue
Collaboration update: Globus and the Cancer Registry Records for Research
June 4, 2021
IMAT Program Overview
Collaboration update: TCIA Annotator Project
May 7, 2021
Collaboration update: PANGEA and CNVnator
Collaboration update: OpenCRAVAT and Trinity
Collaboration update: XCIST Collaborations
April 2, 2021
Collaboration update: Classifying Breast Histopathology Images with Ductal Instance-Oriented Pipeline (Shapiro U01 and Arnold R21)
Collaboration update: MSigDB and NDEx
Collaboration update: TOPAS Collaborations Year 2 Year 3
March 5, 2021
New U01 Overview: Elana Fertig
New U24 Overview: Ben Raphael
February 5, 2021
New R21 Overview: Jennifer Beane-Ebel, VJ Kolachalama
U24 Renewal Overview: Guergana Savova, Harry Hochheiser, Jeremy Warner
U24 Renewal Overview: Helen Parkinson, Zinaida Perova
December 4, 2020
November 4, 2020
Program Updates - IMAT PI Annual Meeting Agenda
New R21 Overview: Rob Frost
New U01 Overview: Amanda Randles
New U24 Overview: Jesse Boehm
October 2, 2020
Program updates
New R21 Overview: Clemens Grassberger
New U01 Overview: Ken Chen
New U24 Overview: Kooresh Shoghi, Dan Marcus
September 4, 2020
New R21 Overview: Subhajyoti De
New U01 Overview: Malachi Griffith
New U24 Overview: Greg Caporaso
August 7, 2020
Program Updates: Juli Klemm Slides
New U01 Overview: Satish Viswanath and Pallavi Tiwari Slides
New U24 Overview: Justin Guinney and Paul Boutros Slides
May 1, 2020
Program Updates: Juli Klemm Slides
ITCR Collaborative Project Overview: Evan Johnson and Josh Campbell Slides
April 3, 2020
General Updates: Juli Klemm Slides
Informatics for the COVID-19 and Cancer Consortium Registry: Jeremy Warner Slides
ITCR Collaboration Overview: Anthony Castanza, Dexter Pratt Slides
March 6, 2020
Program updates and Annual Meeting Information: Juli Klemm, Jeremy Goecks Slides
New U01 Overview: Spyros Bakas Slides
IMAT-ITCR Collaboration Overview: Tim Griffin Slides
ITCR Collaborative Project Overview: Alexej Abyzov, Ian Holmes Slides
February 7, 2020
General Updates: Juli Klemm Slides
Sustainability and Industry Partnership WG Update Slides
IMAT-ITCR Collaboration Overview: Raja Mazumder and Daniel Crichton Slides
IMAT-ITCR Collaboration Overview: Paul Marjoram Slides
December 6, 2019
New R21 Overview: Tianxi Cai Slides
Globus/eRA Commons integration: Brigitte Raumann Slides
Training and Outreach WG Update: David Hanauer Slides
General program updates: Juli Klemm
November 1, 2019
General Updates
New U01 Overview: Daniel Rubin Slides
New U01 Overview: Melissa Cline Slides
New R21 Overview: Leili Shahriyari, Suvra Pal, Souvik Roy Slides
October 4, 2019
General Updates
ITCR Educational Resource UE5 Overview: Betsy Hsu Slides
New R21 Overview: Eliezer Van Allen and Felix Dietlein Slides
New U24 Overview: Yaoyu Wang and John Quackenbush Slides
September 6, 2019
General Updates: Juli Klemm
New R21 Overview: Jin Chen Slides
User-Centered Design for the PDX Finder Project: Nathalie Conte Slides
August 2, 2019
General Updates: Juli Klemm Slides
New R21 Overview: Emilie Roncali Slides
Sustainability and Industry Partnership WG Update and Next Steps: Michael Becich and Christos Davatzikos White Paper (login required)
May 3, 2019
General Updates: Juli Klemm
ITCR 2019 Annual Meeting: Gabor Marth Slides
Collaboration Opportunities to Further Advance ITCR Platforms: Tony Dickherber Slides
April 5, 2019
General Updates: Juli Klemm Slides
New R21, Bayesian learning algorithms for identifying and classifying heterogeneity of cell types in variety of solid tumors: Anjishnu Banerjee Slides
CIViC Collaboration Update: Obi Griffith Slides
March 1, 2019
General Updates: Juli Klemm
Overview of new U01 project: A Unified Machine Learning Package for Cancer Diagnosis: Linda Shapiro Slides
Collaboration Update: JBrowse and CIViC: Ian Holmes Slides
Collaboration Update: Globus and Pittsburgh cancer registry data: Ian Foster and Jonathan Silverstein Slides
February 1, 2019
General Updates: Juli Klemm
ITCR 2019 Annual Meeting Update, Gabor Marth, Slides
FDA’s High Throughput Truthing Project: Brandon Gallas Wiki Slides
ITCR-IMAT Collaboration project overview: Simina Boca, Timothy Spicer Slides
December 7, 2018
General Updates: Juli Klemm Slides
New ITCR R21: Statistical Evaluation and Selection of Normalization Methods for microRNA Sequencing Data in Cancer Biomarker Studies: Li-Xuan Qin Slides
Collaboration project overview: Integration of EMERSE and the OpenCDS platform: David Hanauer, Guilherme Del Fiol, Kensaku Kawamoto Slides
Collaboration project overview: Integration of the IGV into the cBioPortal analysis and visualization environment: JJ Gao Slides
November 2, 2018
New ITCR R21: Inferring kinase activity profiles from phosphoproteomic data: Kristen Naegle Slides
New ITCR U24: A federated Galaxy for user-friendly, large-scale cancer genomics research: Jeremy Goecks, James Taylor Slides
Collaboration project overview: Enabling data distribution and sharing networks to address cancer health disparities: Brigitte Raumann Slides
October 5, 2018
Overview of 2019 Annual Meeting Plans Hosted by University of Utah: Gabor Marth Slides
ITCR Explainer Videos and ITCR News: Mervi Heiskanen Slides
New R21 Award Overview: Predicting the Presence of Clinically Significant Prostate Cancer Using Multiparametric MRI and MR-US Fusion Biopsy: Corey Arnold Slides
New U01 Award Overview: Network Analysis for a Data-Driven Approach to Cancer Care: Jeremy L. Warner Slides
September 7, 2018
Overview of JCO Clinical Cancer Informatics: Jeremy Warner Slides
Collaborative project overview: Vincent Carey and Nathalie Pochet Slides
Collaborative project overview: Raja Mazumder and Evan Johnson Slides
August 3, 2018
New ITCR R21 Grantee Presentation: An Ontology-driven Faceted Query Engine for the Kentucky Cancer Registry Slides
New ITCR R21 Grantee Presentation: Proteomic-based integrated subject-specific networks in cancer Slides
New ITCR Working Group Proposal: Sustainability and Industry Partnership WG Slides
June 1, 2018
Introduction: Game Technologies for Data Analysis and User Engagement – Dave Miller, NCI Slides
Graphspace and Flud -TM Murali, Virginia Tech Slides
Science Game Lab – Nick Fortugno, Playmatics
May 4, 2018
General Announcements and ITCR 2018 Annual Meeting Slides
SEER Overview, Paul Fearn Slides
CISNET Overview, Rocky Feuer Slides
April 6, 2018
General Announcements and ITCR 2018 Annual Meeting Slides
Overview of Human Tumor Atlas Network, Shannon Hughes Slides
March 2, 2018
ITCR Program Evaluation and Annual Meeting Updates, Juli Klemm & Mervi Heiskanen Slides
Overview of CANDLE - Cancer Distributed Learning Environment, Eric Stahlberg Slides
February 2, 2018
Overview of the Physical Sciences in Oncology Network, Nastaran Zahir Slides
Overview of the Cancer Systems Biology Consortium, Shannon Hughes Slides
January 5, 2018
“Crowds Cure Cancer” Collaboration, Jayashree Kalpathy-Cramer Slides
Admin Supplement Overview: Establishing Prognostic Quantitative Imaging Features of LGGs Slides, Lee Cooper Slides
December 1, 2017
Developing the JBrowse Genome Browser to Visualize Structural Variants and Cancer Genomics Data (U24) Lincoln Stein, Ian Holmes Slides
Integrating TIES and Xena to Support Semantic Clinical Queries in Complex Genomic Situations (Admin Supplement) Michael Becich, David Haussler Slides
Integrative Analysis of Cancer Single-cell Transcriptomic and Functional Proteomic Data Han Liang (ITCR) Lidong Qin (IMAT) (IMAT-ITCR Collaboration) Slides
A Bioconductor Software Package for LISH-seq Probe Design and Data Analysis Kasper Hansen/Martin Morgan (ITCR), Ben Larman (IMAT) (IMAT-ITCR Collaboration) Slides
November 3, 2017
Building protected data sharing networks to advance cancer risk assessment and treatment (U24) Ian Foster Slides
Advanced development and dissemination of EMERSE for cancer phenotyping from medical records (U24) David Hanauer Slides
TCIA sustainment and scalability - Platforms for quantitative imaging informatics in precision medicine (U24) Fred Prior, Joel Saltz, Ashish Sharma Slides
Integrative analysis of the IvyGAP data Christos Davatzikos, Joel Saltz, Jayashree Kalpathy-Cramer, John Weinstein/Bradley Broom Slides
Facilitating curation of BRCA variants with 3D structure context Rachel Karchin Slides
October 6, 2017
General Updates Slides
A network-based approach for personalized treatment of Multiple Myeloma (R21) Slides
An interactive analysis toolkit for single cell RNA-seq in cancer research (U01) Slides
The cBioPortal for Cancer Genomics (U24) Slides
Scalable Clinical Decision Support for Individualized Cancer Risk Management (U24) Slides
July 7, 2017
Overview of collaborative set-aside project – Gabor Marth, Aaron Quinlan Slides
Overviews of ITCR-IMAT collaborative supplement projects – Tim Griffin Slides, Obi Griffith Slides
May 5, 2017
Ivy Glioblastoma Atlas Project (GAP) Data - Juli Klemm Slides
April 7, 2017
Overviews of Collaborative Set-Aside Projects - Helga Thorvaldsdóttir Slides and Han Liang Slides
March 3, 2017
TCIA Glioma Image Segmentations: Christos Davatzikos Slides
The ISB Cancer Genomics Cloud: Sheila Reynolds Slides
February 3, 2017
Creating MOOCs for Bioinformatics: Phillip Compeau Slides
January 6, 2017
Extending 3D Slicer to support pathology tissue segmentation data
December 2, 2016
November 4, 2016
October 7, 2016
September 2, 2016
August 5, 2016
May 6, 2016
April 1, 2016
March 4, 2016
February 5, 2016
December 4, 2015
November 6, 2015
Presentations
October 2, 2015
Presentations
September 4, 2015
Presentations