César de la Fuente is a Presidential Associate Professor at the University of Pennsylvania, where he is 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 a 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 with efficacy in animal models, helping establish AI-driven antibiotic discovery as an emerging field. His lab develops computational methods to mine the world’s biological information, enabling the identification of more than one million antimicrobial compounds and reframing the human body itself as a rich, systematic source of antibiotics. This work began with the first comprehensive exploration of the human proteome for antibiotics, which revealed 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, an approach that has already yielded preclinical antibiotic candidates including neanderthalin, mammuthusin, and elephasin. Beyond eukaryotes, his lab 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 released them open access to accelerate worldwide synthesis, characterization, and development. This effort leveraged machine learning to analyze 63,410 metagenomes and 87,920 microbial genomes. In parallel, through computational exploration of 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 on the order of several million-fold—saving years of human research and transforming what once demanded decades of collective effort into workflows that can be executed within hours. To support this work, his lab 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 lab 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 has received recognition and research funding from numerous organizations.
De la Fuente has received numerous national and international awards. He is an elected Fellow of the American Institute for Medical and Biological Engineering (AIMBE), becoming one of the youngest ever inducted, and was recognized by MIT Technology Review as one of the world’s top innovators for “digitizing evolution to make better antibiotics.” His honors also 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. More recently, 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, and was selected as a National Academy of Medicine Emerging Leader in Health and Medicine. He has been named a Sloan Fellow and selected by the World Economic Forum to the Young Global Leaders Class of 2025. In 2026, de la Fuente was elected as a Fellow of the Royal Society of Biology.
He serves on the editorial boards of numerous scholarly journals and is currently 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 (top 1% most cited in the world) multiple times and received an Honorary Doctorate from the University of Leon at age 39. Prof. de la Fuente has delivered around 400 invited lectures, including many keynote and named lectures, and has also spoken at TEDx. He has co-authored an influential book on machine learning for drug discovery, secured multiple patents, and published around 200 peer-reviewed papers in journals including Cell, Science, Cell Host & Microbe, Nature Biomedical Engineering, Nature Microbiology, Nature Communications, and PNAS.
** The picture of César de La Fuente, in an image taken on the granting of the Princess of Girona award in 2021.
MARTÍ E. BERENGUER (©MART E. BERENGUER)