A. K. Dube

Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network

The paper shows that mutations in protein binding domains, combined with regulatory divergence, determine the fate of gene duplicates in a protein interaction network.

Compensatory mutations potentiate constructive neutral evolution by gene duplication

The paper duplicates and evolves an homodimeric enzyme to show that compensatory mutations can lead to functional heteromers through subfunctionalization.

Most azole antifungal resistance mutations in the drug target provide cross-resistance and carry no intrinsic fitness cost

The paper evaluates 4,000 Erg11 variants to determine azole resistance and fitness costs, finding 33% resistance, 88% cross-resistance, and minimal fitness cost.

Parallel nonfunctionalization of CK1δ/ϵ kinase ohnologs following a whole-genome duplication event

The paper investigates the evolution of HRR25 ohnologs after a whole-genome duplication in yeast, finding that nonfunctionalization, not subfunctionalization, is the main trend.

Deep mutational scanning of Pneumocystis jirovecii dihydrofolate reductase reveals allosteric mechanism of resistance to an antifolate

The paper identifies 355 resistance mutations in P. jirovecii DHFR to methotrexate using deep mutational scanning, revealing an allosteric mechanism at position F199.

Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins

This study investigates how SH3 domains of paralogous yeast myosins evolved their binding preferences, finding that differences in interactions are not due to the SH3 domains themselves but to context-dependent factors.

Evolutionary trajectories are contingent on mitonuclear interactions

This study shows that mitonuclear interactions shape evolutionary divergence in yeast populations with identical nuclear genotypes under different environmental pressures.

Epistasis between promoter activity and coding mutations shapes gene evolvability

The paper shows that expression level masks the effects of coding mutations, demonstrating that expression level dictates their fitness impact.

Asymmetrical dose-responses shape the evolutionary trade-off between antifungal resistance and nutrient use

The paper measures amino acid substitutions in yeast Fcy1 to show a trade-off between 5-FC resistance and enzyme function, with similar patterns in Cryptococcus neoformans.

Rewiring the Three-Carbon Metabolism Abrogates Multiple MAPK-Induced Cellular Dysfunctions During Metabolic Disorder

The paper withdraws its manuscript due to issues with lipidomic data reproducibility and reliability.

Expression attenuation as a mechanism of robustness to gene duplication in protein complexes

The paper investigates the fitness effects of gene duplication in budding yeast, finding that most protein complex subunits have minimal fitness impact, while large complexes are protected by reduced protein abundance.

The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs

The paper investigates how structural pleiotropy and regulatory evolution influence the retention of heteromers formed by paralogs in budding yeast.

The high turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

The paper examines de novo ORF emergence in wild yeast, finding some intergenic ORFs show gene-like characteristics despite lower translation efficiency and suggesting functional innovation potential.