UW CSE (Allen School)

Faculty In Focus: Jeff Nivala

Assistant Professor Jeff Nivala of the Paul G. Allen School outlines a new technology that reads individual protein molecules end‑to‑end, preserving their native structure. The Molecular Information Systems Lab sits at the crossroads of computer science and biotechnology, aiming to make the invisible complexity of nanoscale biology observable. Current protein‑sequencing methods fragment proteins into short peptides and computationally reassemble them, discarding crucial information about full‑length conformation and post‑translational modifications. Nivala’s approach captures whole proteins directly, providing a more accurate view of how genes translate into functional molecules. “The rubber really meets the road at the level of proteins,” Nivala says, emphasizing the shift from gene‑centric to protein‑centric analysis. His interdisciplinary team—spanning molecular biology, biochemistry, microbiology, machine learning, and hardware engineering—has already demonstrated proof‑of‑concept experiments that read intact proteins in a CS‑building wet lab. If scaled, the technology could transform diagnostics by detecting disease‑related protein changes earlier, accelerate therapeutic design, and give researchers a universal tool for fundamental biology. Nivala envisions widespread adoption by biologists, clinicians, and engineers within the next decade.