Posts Tagged ‘bioinformatics’

NAR Breakthrough Article: denovo-db: a compendium of human de novo variants

April 3, 2017

.@denovodb: a compendium of [initially ~33K] human de novo variants w. phenotype, freely downloadable as a TSV table

As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant.

Human Developmental Biology Resource (HDBR)

October 21, 2016

The MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) HDBR EXPRESSION – An online resource for studying prenatal human brain development

AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms

March 19, 2016, #Docker-based packaging [w/ web GUI & workflow mgt] for platform-agnostic implement[ations]

Hosny, A. et al. AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinformatics Advance Access, Mar 2, 2016.

Useful NIH Funding Data on Bioinformatics Education

September 6, 2015

BD2K funded programs so far…

NIGMS Comp Bio & Bioinfo funded predoctoral programs

THE NLM funded Biomedical Informatics training programs

Core services: Reward bioinformaticians

May 9, 2015

QT:{{"The research system does not recognize bioinformaticians for doing what the scientific community needs most. “People realize the importance, but currently there are no real solutions,” says Xiaole Liu, a bioinformatician at the Dana-Farber Cancer Institute in Boston, Massachusetts, and at Tongji University in Shanghai, China. This is why it can take more than six months to fill positions at a core, why many of biology’s brightest are leaving science for technology companies, and why conventional biologists wait nine months to get help to dissect their data.

Reward bioinformaticians [for collaboration] Despite #bigdata boom, biomedical analysis could be made more appealing

Summarizing 4 conferences last week: AACR ’15, ISEV ’15, BioIT ’15 & ICEBEM 2015

April 28, 2015

AACR 2015

ISEV/ERCC Education Day – ISEV – International Society for
Extracellular Vesicles

2015 Bio-IT World Conference & Expo–20150423-i0bioIT15/

8th International Conference on Ethics in Biology, Engineering & Medicine (ICEBEM 2015)–20150424-i0icebem15/

Tweets for all of them

Dan David Foundation to award three prizes of $1 million to six world renowned laureates

February 13, 2015

6 individuals will share…Dan David prizes worth $1M … #Bioinformatics Prize to C Chothia, D Haussler & M Waterman

Also, Jimmy Wales of Wikipedia fame will get a prize for the Present Information Revolution


February 8, 2015

Useful helpers for #teaching #bioinformatics: Biostars forum & Rosalind assignment evaluator

PacBio Blog: Data Release: ~54x Long-Read Coverage for PacBio-only De Novo Human Genome Assembly

August 31, 2014

We are pleased to make publicly available a new shotgun sequence dataset of long PacBio® reads from a human DNA sample. We previously released sequence data using Single Molecule, Real-Time (SMRT®) Sequencing of ~10x coverage of this sample, sufficient for
reference-based detection of structural variation. Today we expand on that release with additional data that increases the total sequencing coverage to ~54x. This long-read data has enabled the generation of the first de novohuman genome assembly from PacBio-only sequence reads. Download the 54x long-read coverage dataset.

The dataset was generated from sequencing a well-studied human cell line (CHM1htert), which is being utilized as part of a National Institutes of Health project to sequence and assemble an alternate reference genome (the “platinum genome”). This NIH project is being led by Rick Wilson from Washington University at St. Louis and Evan Eichler from the University of Washington in collaboration with investigators from the National Center for Biotechnology Information. “}}


August 4, 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