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Tufts Gene Expression Data for Low Dose Radiation Experiments
13 Nov 2014 | Downloads | Contributor(s): Lynn Hlatky, Edward Rietman, Jonathan Bistline
Expression signatures from low dose radiation exposure of various types of tissues. There are eight (8) files in this study: 1-7. Gene expression of cell lines exposed to low-dose radiation (5727049056.zip to 7196780010.zip) 8. Sample Annotation (ICBP_Data_Upload_Samples.xlsx)...
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OSU ICBP45 integrative genomic data
13 Nov 2014 | Downloads | Contributor(s): Jonathan Bistline
There are forty one (41) datasets in this study: 1-40. MBDCap-seq data (100727_s_3_sorted.tdf to 100910_s_4_sorted.tdf) 41. Sample Annotation (osu_icbp45_sample_annotation.txt) These datasets have been exported from the Broad Institute's ICBP Data & Analysis Portal.
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OSU/IU ICBP50 integrative genomic data
13 Nov 2014 | Downloads | Contributor(s): Yunlong Liu, Jonathan Bistline
Multi-domain assays of genome-wide DNA methylation and histone modification patterns in MCF7 and OHT drug resistant cells. Data are produced at LBNL and the OSU, provided from Indiana University School of Medicine (Yunlong Liu). There are eighteen (18) datasets in this study:...
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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...
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LBL Expanded ICBP43 integrative genomic data
13 Nov 2014 | Downloads | Contributor(s): Joe Gray, Jonathan Bistline
There are six (6) datasets in this study: Reverse protein lysate array (JWGray_BCCL_RPPA_timecourse_Lapatinib_v1-1.txt) Reverse protein lysate array readme (JWGray_BCCL_RPPA_timecourse_Lapatinib_v1-1_readme.txt) Affymetrix SNP data (icbp43_affy_snp.zip) Segmented copy number data...
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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...
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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...
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Analysis, integration and visualization of DNA methylation sequencing data
07 Nov 2014 | Presentations | Contributor(s): Maureen Sartor
Integrative epigenomic/genomic profiling and biomarker discovery of HPV+ and HPV- squamous cancers.
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Summarization of Big Data
07 Nov 2014 | Presentations | Contributor(s): Jeffrey A. Blimes
All about assay selection...
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CIBMTR Data Elements Subset
04 Nov 2014 | Downloads | Contributor(s): Denise Warzel
Data Elements used in CIBMTR.
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JPI Editorial: Evaluating Whole Slide Imaging: A Working Group Opportunity
03 Nov 2014 | Publications | Contributor(s): Brandon D. Gallas
This document is a pre-publication version of an editorial to be published in the Journal of Pathology Informatics. It outlines the goals of the organizers envisioned for the WSI working group.
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Slides updating WSI working group: presented to Internation Color Consortium Medical Imaging Working Group
03 Nov 2014 | Publications | Contributor(s): Brandon D. Gallas
The slides introduce the WSI working group organizers, the goals of the organizers, and the working group portal.
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Overview of the National Cancer Institute (NCI) Nanotechnology Characterizaton Laboratory (NCL)
03 Nov 2014 | Presentations | Contributor(s): Jennifer Hall Grossman
Working in concert with the National Institute of Standards and Technology (NIST) and the U.S. Food and Drug Administration (FDA), the National Cancer Institute (NCI) established the Nanotechnology Characterization Laboratory to perform preclinical efficacy and toxicity testing of...
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TESTING1042
30 Oct 2014 | Teaching Materials | Contributor(s): Ethan Wang
TESTING
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CERR: A Computational Environment for Radiotherapy Research
28 Oct 2014 | External Applications | Contributor(s): Joseph Deasy
CERR (pronounced 'sir') is a software platform for developing and sharing research results in radiation therapy treatment planning.CERR is written in the widely-used Matlab language (version 7.0 or later), allowing for low-cost development of visualization and analysis tools.CERR will...
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Quantitative Imaging Network(QIN) BIDS Related Tools
27 Oct 2014 | Downloads | Contributor(s): Andrey Fedorov, Thomas Casavant
An inventory of the software tools used by the QIN sites to facilitate collaborative efforts such as sharing of analysis results and software tools.
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QIN Tools Inventory Summary
15 Oct 2014 | Teaching Materials | Contributor(s): Andrey Fedorov
QIN Tools survey has been conducted in two iterations starting from the Spring 2014 [1]. In the beginning of Summer 2014, a revised version of the survey has been released [2]. The results of the survey are available at [3], and also include the analysis of other data sources (such as “QIN...
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Biomedical Evidence Graph
03 Oct 2014 | Presentations | Contributor(s): Josh Stuart
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Tools to Analyze Morphology and Spatially Mapped Molecular Data
03 Oct 2014 | Presentations | Contributor(s): Joel Saltz
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caNanoLab Data Portal Presentation
25 Sep 2014 | Presentations | Contributor(s): Sharon Gaheen
caNanoLab is a data sharing portal designed to facilitate information sharing across the international biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support for the annotation of nanomaterials with...