Milad Miladi

CodonBERT is a large language model for mRNA design and optimization that outperforms previous methods on a flu vaccine dataset.

DEWSeq improves eCLIP data analysis by increasing the detection of RNA-binding protein binding sites and their functional elements.

The paper presents a global, community-maintained platform for analyzing SARS-CoV-2 genomic data, demonstrating its utility in variant detection and reanalysis of existing datasets.

This study uses direct RNA sequencing to identify RNA modifications in SARS-CoV-2 isolated from human lung cells, revealing conserved modification patterns across isolates.

GraphClust2 improves RNA clustering and annotation by integrating sequence and structural data, revealing conserved structures in long non-coding RNAs and targets of Roquin-1.

The paper integrates SHAPE data into RNA-RNA interaction prediction to improve accuracy using the IntaRNA tool.

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.