Mian Umair Ahsan

PALM, a protein language model, predicts domain, functional site, and variant effects with high accuracy using curated sequence data and outperforms existing models in multiple benchmarks.

The paper identifies novel oncogenic gene fusions in fusion-negative gliomas using long-read sequencing and functional validation in Drosophila.

The paper identifies noncoding de novo mutations in SCN2A associated with autism spectrum disorders using two statistical methods on large-scale sequencing data.

This study compares two RNA modification detection models, Dorado and m6Anet, using RNA004 sequencing data, finding Dorado has higher recall but both have high false discovery rates for m6A and pseudouridine.

LongReadSum provides fast, comprehensive quality control and signal summarization for long-read sequencing data across multiple platforms and formats.

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

NanoCaller improves SNP and indel detection in difficult genomic regions using long-read sequencing and haplotype-aware deep learning.