Amin Safaeesirat

Motif-based model of transcription predicts effects of sequence variants in AR enhancers and reveals distinct functions for AR-associated transcription factors

The paper develops a motif-based model to predict sequence variant effects in AR enhancers and identifies functional classes of transcription factors, validated against mutagenesis data and GWAS risk alleles.

Inference of enhancer-specific transcription factor interactions from gene expression data using a biophysical model

The paper infers enhancer-specific transcription factor interactions from gene expression data using a biophysical model and validates it with simulated and experimental data.

Direct Counting of mRNA Copies Inside Individual Lipid Nanoparticles Using In Situ Lysis and Labeling

This paper introduces a single-particle microscopy method to directly count mRNA copies in lipid nanoparticles, showing differences in mRNA copy number, size, and empty fraction between two formulations.

Inference of Transcriptional Regulation From STARR-seq Data

The paper introduces a method to infer functional regulatory sites in enhancer sequences using STARR-seq data, showing it can identify local regulatory sites missed by global approaches.