DIRECTOR – DE LA FUENTE LAB

CURRENT POSITION

University of Pennsylvania, Presidential Associate Professor

César de la Fuente is a Presidential Associate Professor at the University of Pennsylvania and Director of the Machine Biology Group. He is one of the youngest tenured professors in the history of Penn Medicine. He completed postdoctoral research at the Massachusetts Institute of Technology (MIT) and earned his PhD from the University of British Columbia (UBC).

De la Fuente’s research aims to use the power of machines to accelerate discovery in biology and medicine. He pioneered the development of the first computer-designed antibiotic shown to be effective in animal models, helping establish AI-driven antibiotic discovery as an emerging field. His laboratory develops computational methods to mine the world’s biological information, enabling the identification of more than one million antimicrobial compounds and revealing the human body as a rich, systematic source of antibiotics. This work began with the first comprehensive exploration of the human proteome for antibiotics, which uncovered a previously unrecognized branch of host immunity.

His group also launched the field of molecular de-extinction by becoming the first to identify therapeutic molecules in extinct organisms. This approach has already yielded preclinical antibiotic candidates, including neanderthalin, mammuthusin, and elephasin. Beyond eukaryotes, his laboratory has expanded antibiotic discovery across other branches of the tree of life. By computationally analyzing microbial dark matter, the team identified nearly one million additional antibiotic molecules and made them openly available to accelerate their synthesis, characterization, and development worldwide. This effort used machine learning to analyze 63,410 metagenomes and 87,920 microbial genomes. In parallel, by computationally exploring thousands of human microbiomes, de la Fuente and collaborators discovered numerous antimicrobial agents, including prevotellin-2 from the gut microbe Prevotella copri.

Collectively, these initiatives have compressed the time required to identify preclinical candidates from years to hours, with estimated speedups of several million-fold—transforming what once demanded decades of collective effort into processes completed in hours. To support this work, his laboratory has developed the APEX AI stack—APEX, ApexGO, ApexDuo, and ApexOracle—for sequence-to-function prediction, computational optimization, multimodal therapeutic design, and rapid-response discovery. Additional advances from his group include reprogramming venoms into antimicrobials; developing autonomous nanorobots to treat infections; creating resistance-proof antimicrobial materials; and inventing rapid, low-cost diagnostic devices for COVID-19 and other infections. He is an NIH MIRA investigator, and his research has received recognition and funding from numerous organizations.

De la Fuente has received numerous national and international honors. He is an elected Fellow of the American Institute for Medical and Biological Engineering (AIMBE), and was among the youngest ever inducted. MIT Technology Review recognized him as one of the world’s top innovators for “digitizing evolution to make better antibiotics.” His honors include the inaugural Langer Prize, ACS Kavli Emerging Leader in Chemistry recognition, ASM Distinguished Lecturer, Waksman Foundation Lecturer, the Miklós Bodanszky Award, AIChE’s 35 Under 35 Award, the Society of Hispanic Professional Engineers Young Investigator Award, the ACS Infectious Diseases Young Investigator Award, the Thermo Fisher Award, and the EMBS Academic Early Career Achievement Award for pioneering the development of antibiotics designed using principles from computation, engineering, and biology. He has received the Princess of Girona Prize, the ASM Awards for Early Career Applied and Biotechnological Research and for Early Career Basic Research, the Rao Makineni Lectureship Award from the American Peptide Society, and the Fleming Prize. He was also selected as a National Academy of Medicine Emerging Leader in Health and Medicine. He was named a Sloan Fellow and selected by the World Economic Forum for its Young Global Leaders Class of 2025. In 2026, de la Fuente was elected to Academia Europaea and named a Fellow of the Royal Society of Biology.

He serves on the editorial boards of numerous scholarly journals and is an Associate Editor of Drug Resistance Updates, Nature Communications Biology, Bioactive Materials, Bioengineering & Translational Medicine, and Digital Discovery. He has been named a Clarivate Highly Cited Researcher multiple times, placing him among the world’s top 1% most-cited researchers, and received an Honorary Doctorate from the University of Leon at age 39. De la Fuente has delivered approximately 400 invited lectures, including keynote and named lectures, and has spoken at TEDx. He has co-authored an influential book on machine learning for drug discovery, secured multiple patents, and published more than 200 peer-reviewed papers in journals including Cell, Science, Cell Host & Microbe, Nature Biomedical Engineering, Nature Microbiology, Nature Communications, and PNAS.