Pablo Machado

This study compares the proteome of Calu-3 cells in 2D monolayers and 3D Matrigel spheroids, finding that 3D architecture drives major proteomic changes, while Matrigel's biochemical cues induce smaller but significant shifts.

The paper identifies hundreds of novel microproteins in Mycobacterium tuberculosis using proteogenomics, revealing their potential roles in bacterial growth, virulence, and antibiotic response.

This paper introduces RP3, a pipeline combining proteogenomics and ribosome profiling to identify microprotein-encoding smORFs missed by Ribo-Seq alone, improving detection and confidence.