Boian S. Alexandrov

This study shows that efflux pump specificity is influenced by proton gradient and membrane potential, offering new strategies to combat bacterial resistance.

The paper investigates DNA breathing's role in TF-DNA interactions using in vitro and in vivo data, finding correlations between breathing features near motifs and binding affinity across multiple TFs.

The paper develops a deep surrogate model to generate DNA breathing features efficiently, improving transcription factor binding predictions.

The paper introduces JAX-EPBD, a high-throughput framework for simulating DNA breathing dynamics, showing 30x speedup and improved predictions of transcription factor binding using SELEX datasets.

The paper improves TF binding site prediction by integrating DNA biophysical properties with sequence data using a multi-modal deep learning model, achieving better performance in both in vivo and in vitro datasets.

The paper introduces pyDNA-EPBD, a software tool for simulating DNA breathing dynamics using the EPBD model, and demonstrates its ability to calculate DNA bubble probabilities and mutation effects.

SigProfilerExtractor is a tool for de novo mutational signature extraction that outperforms existing methods and identifies four novel signatures, including one linked to tobacco smoking.

This study examines intratumor heterogeneity and clonal evolution in papillary renal cell carcinomas using whole-genome sequencing and DNA methylation data, revealing distinct patterns of genomic and epigenomic evolution across subtypes.

This paper introduces NMFk, an unsupervised machine learning method, to analyze lipid phase separation in MD simulations, identifying roles of lipids, nano-domains, timescales, and physical features.

The paper develops a dynamical model of drug accumulation in bacteria, providing estimates of import/export rates and experimentally testable predictions about drug accumulation dynamics.