Posts Tagged ‘bioinformatics’


Monday, August 4th, 2014

Useful listing of data sources, viz:


Protein Annotations

Site-specific protein annotations from UniProt.
Druggable target data from DrugBank.
Functional impact predictions from PolyPhen-2.

Cancer Annotations

Observed cancer mutation frequency annotations from COSMIC.
Cancer gene and mutation annotations from the Cancer Gene Census. Significant amplification/deletion region annotations from Tumorscape and theTCGA Copy Number Portal.
Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia. Significantly mutated gene annotations aggregated from published MutSiganalyses. Cancer gene annotations from the Familial Cancer Database.
Human DNA Repair Gene annotations from Wood et al.


Uses bamboo testing software

Pacbio MCF-7 transscriptome dataset

Wednesday, July 30th, 2014



PAWG-WGL Links for PCAWG upload status

Friday, July 4th, 2014 has fantastic #viz of the progress & int’l effort in the Pan-#Cancer Analysis of Whole #Genomes (#PCAWG) project

DREAM mutation calling challenge

Saturday, June 7th, 2014

Deadlines: 7/19,8/2,8/16!Synapse:syn312572

Broad Institute’s Firehose Dashboard

Monday, March 17th, 2014

Contains information on analysis pipelines and datasets produced from Broad’s Firehose. Access to the protected pages requires an NCI login.


Saturday, January 4th, 2014

BioLayout Express3D has been specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not
exclusively, from biological data.

HuRef sperm sequencing

Saturday, January 4th, 2014

huref on Solid

Saturday, January 4th, 2014

To demonstrate the promise of personalized genome analysis, the genome of HuRef was sequenced using the Life SOLiDâ„¢ platform. Nimbus Informatics performed the analytical work for this project and has made the resulting data available here, running entirely on the Amazon Cloud.

BETASEQ: A Powerful Novel Method to Control Type-I Error Inflation in Partially Sequenced Data for Rare Variant Association Testing

Monday, December 23rd, 2013

Genomics Researchers Imagine their Ideal Computer

Monday, December 9th, 2013

Paul Basken
The Chronicle of Higher Education