Advanced Development of TIES - A Clinical Text Search Engine
18 Feb 2014 | Contributor(s): Rebecca Crowley
Archived human tissues are an essential resource for translational research. Formalin-fixed, paraffin-embedded (FFPE) tissues from cancer patients are used in a wide range of assays, including RT-PCR, SNP profiling, multiplex biomarkers, imaging biomarkers, targeted exome, whole exome, and whole...
Brain Cancer Imaging Analytics
02 Oct 2015 | Presentations | Contributor(s): Christos Davatzikos
The transition of oncologic imaging from its “industrial era” to it is “information era” demands analytical methods that 1) extract information from this data that is clinically and biologically relevant; 2) integrate imaging, clinical, and genomic data via rigorous...
Community Health Worker Genetics Education Needs Assessment
23 Nov 2015 | Downloads | Contributor(s): Andria Reyes, Manuela Orjuela, Karen Schmitt, Andria Reyes, Grace Hillyer, Stephen Emerson
Our overarching goal is to develop and establish a cancer genetics curriculum that is pertinent, culturally sensitive and understandable by a community population who is not English dominant and of a lower literacy level than that of the general New York City population. The curriculum will teach...
CRAVAT Introduction Video - Cancer Related Analysis of Variants
03 Dec 2014 | Teaching Materials | Contributor(s): Michael C Ryan
This video provides a brief overview of the CRAVAT web service(http://www.cravat.us/). CRAVAT provides annotation and analysis of cancer mutations. CRAVAT is free, very easy to use, and can handle large volumes of mutations.[[Youtube(xovmIy11Bcs)]]Please switch to 1080 resolution and watch...
Human Disease Ontology
21 Sep 2016 | External Applications | Contributor(s): Lynn Schriml
The Disease Ontology has been developed as a standardized ontology for human disease, since 2003, with the purpose of providing the biomedical community with manual curated, consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related...
Informatics to enable Routine Personalized Cancer Therapy (IPCT)
18 Feb 2014 | Presentations | Contributor(s): Elmer V. Bernstam, Funda Meric-Bernstam
Informatics Tools for High-throughput Analysis of Cancer Mutations
15 Jan 2014 | Presentations | Contributor(s): Michael C Ryan, Rachel Karchin
Introduction to the Trinity Cancer Transcriptome Analysis Toolkit
05 Feb 2015 | Teaching Materials | Contributor(s): Brian Haas, Aviv Regev, Bill Barnett
This short video provides an overview of our ITCR-funded effort to leverage RNA-Seq and de novo transcriptome assembly to assist researchers in studying cancer transcriptomes. Visit our NCGAS Trinity/Galaxy portal to access these compute...
ITCR Monthly Teleconference September 4, 2015
07 Oct 2015 | Presentations | Contributor(s): Juli Klemm
Multiclass cancer diagnosis using tumor gene expression signatures
10 Nov 2014 | Downloads
Experiment Description: The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is difficult or impossible because of atypical clinical...
NANOANALYTICS OF EXTRACELLULAR VESICLES – Standards for isolation, characterization and reporting
26 May 2017 | Presentations | Contributor(s): Shivani Sharma
Nano WG presentation on May 25, 2017. Presentation by Dr. Shivani Sharma, Associate Director of the Nano Pico Characterization Lab, UCLA. Nanoscale characterization of exosomes and their use disease biomarkers and drug delivery agents
Next-Generation Clustered Heat Maps (NG-CHM)
07 Oct 2015 | Presentations | Contributor(s): Weinstein John, Bradley Broom
Clustered Heat Maps (CHMs) have been referred to as the ubiquitous visual icons of post-genomic biology -- the most frequent type of visualization for large molecular profiling databases. However, “traditional” CHMs are static images -- a serious limitation. Accordingly, we have now...
Open source diffusion MRI technology for brain cancer research
07 Oct 2015 | Presentations | Contributor(s): Lauren O\'Donnell
Using measurements of water diffusion, dMRI can give unique insights into the microstructure and cellular orientation of tissues. There is a growing awareness in the neurosurgery community that diffusion models must move beyond the current clinical standard of the diffusion tensor for better...
Pathology Image Informatics Platform for visualization, analysis and management
07 Oct 2015 | Presentations | Contributor(s): Metin Gurcan, Anant Madabhushi, Anne Martel
This multi-institutional proposal seeks to expand on an existing, freely available pathology image viewer (Sedeen Image Viewer) to create a pathology informatics platform (PIIP) for managing, annotating, sharing, and quantitatively analyzing digital Pathology Imaging (DPI) data. Sedeen has become...
Seven Bridges Cancer Genomics Cloud Pilot TCGA 2015 symposium workshop presentation
23 May 2015 | Presentations | Contributor(s): Deniz Kural
Basic and translational cancer research creates the need to disseminate, manage, and interpret large heterogeneous datasets. The volume and complexity of the data now routinely generated by high-throughput technologies has become too costly for individual laboratories and many research...
Summary of the 2015 Epigenetic Engineering for Cancer Workshops
22 Dec 2015 | Publications | Contributor(s): Tony Dickherber
This document provides a general summary of the 2 virtual workshops held in Fall of 2015 to explore the suitability of epigenetic engineering tools to specifically modify epigenetic loci to study and/or treat cancer.
UCSC Biomedical Evidence Graph Demonstration
03 Jun 2015 | Presentations | Contributor(s): Josh Stuart, ellrott
The BMEG demonstration includes the following elements: 1) Organization of crowd-source challenges to develop best-of-breed methods including an overview of current DREAM projects, living benchmarks; 2) Enabling cloud-ready methods for mass compute with examples of recently...
Video: Learn how TIES can help manage research resources
16 Jan 2015 | Presentations | Contributor(s): Girish Chavan, Rebecca Crowley
15 Aug 2017 | Publications | Contributor(s): Stephanie Morris
Collated tweets from workshop and networking reception.