Posts Tagged ‘igvf’

AI tool that predicts gene activity could open path for disease treatments – The Washington Post

January 18, 2025

https://www.washingtonpost.com/science/2025/01/09/ai-predicts-gene-activity/

Johnson, M. (2025, January 8). Scientists trained AI to predict gene activity, a potentially powerful tool. Washington Post.
https://www.washingtonpost.com/science/2025/01/09/ai-predicts-gene-activity/

QT:{{”
Mark Gerstein, a professor of biomedical informatics at Yale School of Medicine, who was not involved in the new study, said that for 15 to 20 years experts have been systematically trying to make predictions about gene regulation, building on a trove of carefully made datasets. The data examined all genes in specific types of human cells ― for example, retinal cells or neurons ― measuring, among other things, gene expression and the binding of key proteins called transcription factors.
“This is a field poised to have this type of advancement by AI,” Gerstein said. “}}

ADASTRA – Allelic Dosage corrected Allele-Specific human Transcription factor binding sites

September 14, 2023

https://adastra.autosome.org/bill-cipher

IGVF Marker Paper

September 27, 2022

Marker paper examples, in no particular order. They have different ages, strengths/weaknesses, and describe different kinds of projects.

Human Biomolecular Atlas Program (HuBMAP)
https://pubmed.ncbi.nlm.nih.gov/31597973/

Human Cell Atlas (HCA)
https://pubmed.ncbi.nlm.nih.gov/33879355/

Human Pangenome Reference Consortium (HPRC)
https://pubmed.ncbi.nlm.nih.gov/35444317/

The NIH Extracellular RNA Communication Consortium (exRNA):
https://pubmed.ncbi.nlm.nih.gov/26320938/

Molecular Transducers of Physical Activity Consortium (Motrpac): https://pubmed.ncbi.nlm.nih.gov/32589957/

The NIH Somatic Cell Genome Editing program (SCGE)
https://pubmed.ncbi.nlm.nih.gov/33828315/

The Genotype-Tissue Expression (GTEx) project
https://pubmed.ncbi.nlm.nih.gov/23715323/

The ENCODE (ENCyclopedia Of DNA Elements) Project
https://pubmed.ncbi.nlm.nih.gov/15499007/

The NIH Roadmap Epigenomics Mapping Consortium
https://pubmed.ncbi.nlm.nih.gov/20944595/

The NIH Roadmap Epigenomics Program data resource
https://pubmed.ncbi.nlm.nih.gov/22690667/

The NIH Common Fund/Roadmap Epigenomics Program: Successes of a comprehensive consortium
https://pubmed.ncbi.nlm.nih.gov/31501771/

The 4D nucleome project (4DN)
https://pubmed.ncbi.nlm.nih.gov/28905911/

ENCODE Pilot Participants

September 24, 2022

found this:

https://authors.library.caltech.edu/74915/2/Feingold.SOM.DC1.pdf

It’s from this paper:

Feingold, E. A. and Pachter, L. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-640. ISSN 0036-8075. doi:10.1126/science.1105136.
https://resolver.caltech.edu/CaltechAUTHORS:20170308-133717579

Common Fund Data Ecosystem | NIH Common Fund

March 22, 2022

https://commonfund.nih.gov/dataecosystem

many logos

Stanford press release on IGVF

November 24, 2021

mentioned in the 2nd to the last paragraph.
https://med.stanford.edu/news/all-news/2021/11/researchers-grants-genome-variations.html

igvf awardees

September 9, 2021

https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees