Alexander Joel Federation

Structure-free, site-resolved contrastive learning extends small-molecule discovery beyond the reach of structure-based modeling

Ptarmigan-1 uses contrastive learning to predict small molecule-protein interactions without requiring 3D structure, outperforming traditional methods on challenging targets.

Development of PROTACs for targeted degradation of oncogenic TRK fusions

This paper develops PROTACs to degrade oncogenic TRK fusions, showing improved efficacy compared to traditional inhibitors.

Native, Spatiotemporal Profiling of the Global Human Regulome

This paper introduces a method to profile the regulome across human cell lines and perturbations, revealing transcription factor dynamics and drug responses.

A flexible workflow for building spectral libraries from narrow window data independent acquisition mass spectrometry data

This paper introduces a workflow to build spectral libraries from DIA mass spectrometry data, showing it can detect phosphorylated peptides and outperforms library-free methods in accuracy and sensitivity.

Quantitative dialing of gene expression via precision targeting of KRAB repressor

This study demonstrates precise control of gene expression levels by targeting the KRAB repressor domain in human cells.

Quantification of nuclear protein dynamics reveals chromatin remodeling during acute protein degradation

This study develops a method to quantify nuclear protein dynamics by isolating chromatin compartments and using mass spectrometry, revealing chromatin remodeling during BET protein degradation.

Identification of candidate master transcription factors within enhancer-centric transcriptional regulatory networks

The paper constructs transcriptional regulatory networks to identify master transcription factors in cell types and applies the method to chronic lymphocytic leukemia, showing efficacy of targeting these factors.