R. A. Melnyk

Atomically accurate de novo design of antibodies with RFdiffusion

This paper designs antibodies de novo with atomic precision using RFdiffusion and yeast display, validated by cryo-EM and biophysical methods.

Commensal Pseudomonas fluorescens protect Arabidopsis from closely-related Pseudomonas pathogens in a colonization-dependent manner

The paper identifies commensal Pseudomonas strains that protect Arabidopsis from pathogens through colonization-dependent mechanisms, revealing a response regulator involved in competitive exclusion.

Structure-function analysis of distant diphtheria toxin homologs reveals insights into host adaptation

The paper determines high-resolution structures of DT homologs to investigate their host adaptation and toxicity mechanisms.

Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility

bioPROTACs as versatile modulators of intracellular therapeutic targets: Application to proliferating cell nuclear antigen (PCNA)

This paper introduces bioPROTACs as intracellular biologics for targeted protein degradation, demonstrating their effectiveness against PCNA with rapid degradation and functional effects.

Exploiting toxin internalization receptors to enhance delivery of proteins to lysosomes for enzyme replacement therapy

This study creates a chimera of diphtheria toxin and TPP1 to enhance lysosomal enzyme delivery, showing improved uptake and efficacy in a mouse model.

Inhibition of tumor growth by a novel engineered chimeric toxin that cleaves activated mutant and wild-type RAS

This paper develops a chimeric toxin that cleaves both mutant and wild-type RAS, reducing tumor burden in mouse models.

Convergent gain and loss of genomic islands drives lifestyle changes in plant-associated Pseudomonas

The paper identifies genomic islands linked to pathogenic and commensal lifestyles in Pseudomonas fluorescens using computational analysis of Arabidopsis-associated strains.

A genome-wide screen identifies genes in rhizosphere-associated Pseudomonas required to evade plant defenses

This paper identifies bacterial genes in Pseudomonas sp. WCS365 that enhance rhizosphere fitness and evade Arabidopsis plant defenses through biofilm formation and immune response modulation.

Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics

The paper identifies novel enzymes filling amino acid biosynthesis gaps in bacteria using genome-wide mutant fitness data, revealing previously unknown pathways for methionine, threonine, serine, and histidine synthesis.