Screening for Small Molecules: Target Discovery Against miRNAs for Breast Cancer Treatment

18 Aug 2015 | Contributor(s): Odemaris Narvaez del Pilar

Breast cancer is one of the leading causes of cancer related deaths and morbidity among women worldwide. Identifying new targets and developing new therapies is very important in order to improve patient outcomes and minimize this health burden. MicroRNAs, a type of non-coding RNA, are potential...

Trinity: RNA-Seq De novo Assembly Application

30 Jun 2015 | External Applications | Contributor(s): Grabherr MG, Brian Haas, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Di Palma F, Birren BW, Nusbaum C, Lindblad-toh K, Friedman N, Regev A

 Quick Guide for the ImpatientTrinity assembles transcript sequences from Illumina RNA-Seq data.Download Trinity here.Build Trinity by typing make : ; in the base installation directory.Assemble RNA-Seq data like so:Trinity --seqType fq --left reads_1.fq --right reads_2.fq...

CRAVAT - Cancer-Related Analysis of Variants Toolkit

23 Jun 2015 | External Applications | Contributor(s): Rachel Karchin, Michael C Ryan

cravat is a bioinformatics pipeline : ; that performs high-throughput cancer-related analysis of variants. it : ; utilizes three applications: CHASM (Cancer-Specific Analysis of Somatic Mutations), VEST and SVN-Get. More information on these tools is available at CHASM Software.Release...

Tools for Creation of Integrated Data Repository for Cancer Research

16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang

Admin Supplement Proposal Parent Projects: DeepPhe (PIs: Savova and Jacobson) caCDE-QA (PI: Jiang)

A Semantic Web-based Quality Assurance Tool for Cancer Study Common Data Elements

16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang

A poster presentation from the caCDE-QA project (PI: Jiang)  

Notes from the ITCR Annual Meeting May 27-28, 2015

10 Jun 2015 | Downloads | Contributor(s): Ishwar Chandramouliswaran, Juli Klemm

Notes from the ITCR Annual Meeting May 27-28, 2015

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...

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...

Report to the DICOM Standards Committee - December 4, 2015

10 Dec 2014 | Downloads | Contributor(s): Joseph Kalen

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...

LBL ICBP50 integrative genomic data

13 Nov 2014 | Downloads | Contributor(s): Joe Gray, Jonathan Bistline

From Joe Gray, Lawrence Berkeley National Laboratory.  There are seventeen (17) files in this study: Affymetrix U133A gene expression data (icbp_u133a.gct) Affymetrix U133A gene expression data (ICBP_U133a.zip) Affymetrix splice junction exon-exon data (ICBP_Junction.zip) Affymetrix...

Baylor Residual breast cancer

13 Nov 2014 | Downloads | Contributor(s): Creighton C, Lewis M, Chang J, Jonathan Bistline

Residual breast cancers after conventional therapy display mesenchymal as tumor-initiating features.  There are four (4) files included in this study: Sample Annotation (combined_sample_annotation.txt) Gene expression data from CD44+/CD24- cells sorted by flow cytometry (GSE7513.gct) Human...

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...

Tools to Analyze Morphology and Spatially Mapped Molecular Data

03 Oct 2014 | Presentations | Contributor(s): Joel Saltz

Talking Science: Designing and Delivering Successful Oral Presentations

18 Sep 2014 | Downloads | Contributor(s): Shawn Mullen

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...

"DICOM 301" - Enhanced Multi-frame and Quantitation:

04 Sep 2014 | Presentations | Contributor(s): David Clunie

 In-depth presentation on the Digital Imaging and Communications in Medicine StandardA one-hour  presentation of DICOM presented by Dr. David Clunie for the members of DICOM Working Group 30, Small Animal Imaging.