Matvei Khoroshkin

Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis

The paper identifies ZZEF1 as a tRNA-specific transcription factor that suppresses breast cancer metastasis by regulating tRNA-LysUUU expression and affecting codon-specific translation.

A generative framework for enhanced cell-type specificity in rationally designed mRNAs

This paper introduces PARADE, a generative AI framework for designing mRNA UTRs with cell-type specificity, showing improved therapeutic efficacy in preclinical models.

A Suite of Foundation Models Captures the Contextual Interplay Between Codons

The paper introduces cdsFM, a suite of codon-resolution large language models that predict the functional consequences of synonymous codon choices and identify pathogenic variants.

Systematic Identification of Post-Transcriptional Regulatory Modules

The paper systematically identifies post-transcriptional regulatory modules by integrating multimodal data on RBP interactions and functions.

Addressing biases in gene-set enrichment analysis: a case study of Alzheimer's Disease

The paper introduces pyPAGE, an improved gene-set enrichment analysis tool, and applies it to uncover AD-associated regulons and their relationship to disease pathology.

A systematic search for RNA structural switches across the human transcriptome

The paper identifies 245 putative RNA structural switches in the human transcriptome using a computational and experimental approach, validates one with DMS-MaPseq and cryo-EM, and shows its regulation by trans factors and nonsense-mediated decay.

hPSC-Derived Enteric Ganglioids Model Human ENS Development and Function

This study develops hPSC-derived enteric ganglioids to model human ENS development and function, identifying drug candidates and PDGFR inhibition as key factors in NO neuron specification.

Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting

The paper uses deep mutational scanning to explore how chemical perturbations affect ubiquitin's mutational tolerance, revealing sensitization of most positions except two.