Anupama Jha, PhD
@anupamajha.bsky.social
NHGRI K99 Awardee, Postdoc in the Noble Lab, UW. Ph.D. in CS and Comp bio, Biociphers Lab, Penn. Pronouns: she/her
Reposted by Anupama Jha, PhD
HiCFoundation is a Swiss army knife for Hi-C data. Any task that takes Hi-C as input will benefit from our pre-trained model. You can do resolution enhancement, reproducibility analysis, loop calling, prediction of epigenomic profiles, or single-cell Hi-C analysis. tinyurl.com/v3nmp6np
A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species
Nuclear DNA is organized into a compact three-dimensional (3D) structure that impacts critical cellular processes. High-throughput chromosome conformation capture (Hi-C) is the most widely used method...
tinyurl.com
December 21, 2024 at 12:10 AM
HiCFoundation is a Swiss army knife for Hi-C data. Any task that takes Hi-C as input will benefit from our pre-trained model. You can do resolution enhancement, reproducibility analysis, loop calling, prediction of epigenomic profiles, or single-cell Hi-C analysis. tinyurl.com/v3nmp6np
Reposted by Anupama Jha, PhD
How can you transfer peptide IDs between runs and still control your false discovery rate? Till now, the short answer is, you couldn't. Now you can, with PIP-ECHO.
www.biorxiv.org/content/10.1...
Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation
Quantitative analysis of proteomics data frequently employs peptide-identity-propagation (PIP) — also known as match-between-runs (MBR) — to increase the number of peptides quantified in a given LC-MS...
www.biorxiv.org
December 2, 2024 at 5:10 PM
How can you transfer peptide IDs between runs and still control your false discovery rate? Till now, the short answer is, you couldn't. Now you can, with PIP-ECHO.
www.biorxiv.org/content/10.1...