Informatics for Routine Personalized Cancer Therapy Demo (ITCR meeting UCSD 5.2015)

01 Jun 2015 | Presentations | Contributor(s): Elmer Bernstam, funda meric-bernsatm

Attached please find screenshots of the resources that we demonstrated at the ITCR meeting in San Diego. This resource is intended to help clinicians understand and leverage molecular profiling to choose treatments for their patients. We are also working on automating literature and clinical...

Innovative Nanoinformatics models and tools: towards a Solid, verified and Integrated Approach to Predictive (eco)Toxicology (NanoSolveIT)

04 Feb 2019 | Presentations | Contributor(s): Antreas Afantitis

Nano WG January 17, 2019NanoSolveIT (a new H2020 nanoinformatics project) aspires to introduce a ground-breaking in silico Integrated Approach to Testing and Assessment (IATA) for the environmental health and safety of Nanomaterials (NM), implemented through a decision support system packaged...

Instructional YouTube AltAnalyze Videos

13 Oct 2016 | Presentations | Contributor(s): Nathan Salomonis

Using AltAnalyze to process bulk and single-cell RNA-Seq files with the Kallisto algorithm:https://www.youtube.com/watch?v=Jylu-V7FmpY Using AltAnalyze to process pre-computed bulk and single-cell gene expression...

Instructional YouTube AltAnalyze Videos

13 Oct 2016 | Presentations | Contributor(s): Nathan Salomonis

Interactive tutorial for processing raw bulk and single-cell RNA-Seq (FASTQ) data in AltAnalyze:https://www.youtube.com/watch?v=Jylu-V7FmpY Interactive tutorials for analyzing pre-processed bulk and single-cell RNA-Seq data in...

Integrated analysis of breast cancer cell lines reveals unique signaling pathways

16 Sep 2014 | Publications | Contributor(s): Laura M Heiser, Nicholas J Wang, Carolyn L Talcott, Keith R Laderoute, Merrill Knapp, Yinghui Guan, Zhi Hu, Safiyyah Ziyad, Barbara L Weber, Sylvie Laquerre, Jeffrey R Jackson, Richard F Wooster, Wen Lin Kuo, Joe W Gray, Paul T Spellman

AbstractBackgroundCancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EgfR-MAPK pathway is common in breast cancer, though the manner in which...

Integrative Cancer Biology Program Datasets

26 Apr 2016 | Series | Contributor(s): Jonathan Bistline, Michael Reich

The NCI-ICBP promotes an integrative/systems approach to the study of cancer biology. The Program encourages scientists to study cancer as a complex biological system. Information gained from these studies are used to build reliable and testable predictive computation models of cancer processes...

Introduction to OpenRiskNet and NanoCommons projects

13 Mar 2018 | Presentations | Contributor(s): Thomas Exner

Nano WG Presentation March 8, 2018OpenRiskNet is a 3 year project (Dec 2016 - Nov 2019) with the main objective to develop an opene-Infrastructure providing resources and services to a variety of communities requiring risk assessment,including chemicals, cosmetic ingredients,...

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...

ISA-TAB-Nano 1.3 release review

09 Mar 2020 | Presentations | Contributor(s): Mervi Heiskanen, Mervi Anneli Heiskanen

Nano WG January 30th, 2020Review of the new 1.3 release with the Nano WG

ISA-TAB-Nano Update for the Nano WG

09 Feb 2017 | Presentations | Contributor(s): Mervi Heiskanen

Nano WG meeting on February 2nd, 2017 ISA-TAB-Nano Next Steps by the Duke team

ISA-TAB-Nano-Expanded: Community-Sourced Updated Templates

22 Sep 2017 | Presentations | Contributor(s): Nancy Birkner

Nano WG Presentation September 21, 2017 by Nancy Birkner, Duke University. ISA-TAB-Nano extension project with added support for environmental, health and safety assessment of nanomaterials. Center for the Environmental Implications of Nanotechnology (CEINT) took on the leadership of...

ITCR Group, an NCIP Hub Community: A 'collaboratory' for your research

23 Jun 2014 | Presentations | Contributor(s): Ishwar Chandramouliswaran

ITCR PI meeting presentation

ITCR PI Meeting June 2014 Presentations

23 Jun 2014 | Series

Informatics Technology for Cancer Research (ITCR) Initiative held its Annual PI Meeting on June 12-13, 2014 in Rockville, MD. This series contains the presentations given at the meeting.

Jaqpot - An open-source web platform for creating, using, testing and sharing predictive models in nano-informatics

20 Jun 2019 | Presentations | Contributor(s): Haralambos Sarimveis

Nano WG June 20, 2019Computational models that predict physicochemical properties, biokinetics or adverse biological effects of Engineered Nanomaterials (ENMs) are becoming increasingly important to support risk assessment and safety-by-design. This is primarily due to cost-saving and...