Amir Banaei‐Esfahani

Stringent proteogenomic discovery of novel small proteins in Mycobacterium tuberculosis clinical reference strains

The paper uses long-read assemblies and proteogenomic analysis to discover novel small proteins in Mycobacterium tuberculosis strains.

Rv1985c-Driven Transcriptional Network Rewiring Underlies Lineage-Specific Phenotypes in Mycobacterium tuberculosis

This study identifies lineage-specific transcriptional network rewiring in Mtb by analyzing proteomic and transcriptomic data from L1 and L2 strains, revealing key regulators like Rv1985c that drive phenotypic differences.

Epistasis between drug resistance-conferring mutations in Mycobacterium tuberculosis

The paper shows that epistatic interactions between RpoB and GyrA mutations in Mycobacterium tuberculosis can lead to high-fitness double-resistant strains, which are prevalent in clinical isolates.

Complex-centric proteome profiling by SEC-SWATH-MS

The paper introduces a method to quantify protein complexes using SEC-SWATH-MS and identifies 462 complexes from HEK293 cells.

Resource misallocation as a mediator of fitness costs in antibiotic resistance.

The paper investigates the fitness cost of rifampicin resistance in Mycobacterium tuberculosis using transcriptomic and proteomic profiling, finding that aberrant gene expression causes the cost and that this burden can be suppressed.