H. Tomas Rube

SPRINT-MS identifies protein-protein interactions using pooled IP-MS and sparse signal recovery, achieving high throughput and efficiency comparable to individual IP-MS experiments.

SPIDR is a high-throughput method for mapping RNA-protein interactions that identifies 4EBP1's role in selectively repressing mRNA translation under mTOR inhibition.

The paper develops a sequence-to-affinity model for SH2 domains using multi-round peptide binding assays and free-energy regression to predict binding specificity and variant effects.

The paper shows Hox paralogs use different cofactors in distinct domains to activate specific gene regulatory networks in Drosophila legs.

The paper introduces ProBound, a machine learning framework that quantifies biophysical parameters of protein-ligand interactions using NGS data, and couples it with Kd-seq to determine absolute affinities.

The paper investigates how DNA sequence influences the formation of transcription factor complexes and shows that non-canonical binding sites arise from direct interactions with functionally bound sites.

This study identifies differences in DNA-binding preferences between androgen and glucocorticoid receptors using SELEX-seq and SelexGLM, revealing AR's greater sequence sensitivity and enthalpy-driven binding.

The paper investigates how sequence mismatches affect Cas9 binding affinity and endonuclease activity, finding that these effects are sometimes decoupled and depend on the PAM region.