Semyon K. Kolmykov

Identification of methylation-sensitive human transcription factors using meSMiLE-seq

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.

Statistical framework for calling allelic imbalance in high-throughput sequencing data

The paper introduces MIXALIME, a statistical framework for detecting allele-specific events in sequencing data, and demonstrates its application in constructing an atlas of allele-specific chromatin accessibility.

Modification and Analysis of Context-Specific Genome-Scale Metabolic Models: Methane-Utilizing Microbial Chassis as a Case Study

The paper develops a computational workflow for reconstructing and validating context-specific genome-scale metabolic models in non-model microbes using Methylotuvimicrobium alcaliphilum 20ZR as a case study.

Landscape of allele-specific transcription factor binding in the human genome

The paper identifies allele-specific transcription factor binding events across the human genome using ChIP-Seq data, revealing regulatory variants linked to disease and molecular mechanisms.