César de la Fuente, Ph.D., FRSB
CURRENT POSITION
University of Pennsylvania, Presidential Associate Professor
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.
To request a Curriculum Vitae from Dr. de la Fuente, please contact Jenny Bai (bjianing@upenn.edu).
Recent work from the lab highlighted in the media:
STAT News
AWARDS AND HONORS (Selected out of >80 major awards)
Honorary Doctorate, University of Leon, 2026
Elected, Fellow of the Royal Society of Biology, 2026
Mendel Lecture, 2025.
Falling Walls Finalist Science Breakthroughs of the Year 2025 in Engineering & Technology, 2025.
World Economic Forum Young Global Leaders Class, 2025.
EMBS Distinguished Lecturer, 2025.
Sloan Fellow, 2025.
Fleming Prize, 2025.
Michael S. Brown New Investigator Research Award, 2024.
Sigma Xi Young Investigator Award, 2024.
ASM Award for Early Career Basic Research, 2024.
25 Visionaries Shaping the Future of Artificial Intelligence by Newsweek, 2024.
Miklos Bondanszky Award 2024
Named Laboratory at Universidad de León, 2024.
Alumni of Honor, Universidad de León, 2024.
Bei Zhang & Mark Erion Keystone Fellowship, 2024.
Selected as member of the Global Young Academy, 2024.
Journal of Nanobiotechnology Rising Star Award, 2024.
Scientific Advisory Board of Keystone Symposia, 2023.
Clarivate Highly Cited Researcher, 2023.
Keystone Symposia Fellow, 2023.
Joseph Priestley Society Lecture, 2023.
Invited Speaker at the 6th World Laureates Association (WLA) Forum, 2023.
Elected member, Royal Academy of Pharmacology (Galicia), 2023. Only 42 members elected since 2003.
National Academy of Medicine’s Emerging Leaders in Health and Medicine (ELHM) Scholar, 2023
National Prize in Biotechnology (VI Edition, Premios Nacionales de Tecnología, Spain), 2023
Fellow, American Institute for Medical and Biological Engineering (AIMBE), 2023
Rao Makineni Lectureship Award, 2023
Forbes Spain 23 Change Makers, 2023
Clarivate Highly Cited Researcher, 2022
Molecules 2022 Young Investigator Award, 2022
2022 Judith H. Greenberg Early Career Investigator Lecture, 2022
IJMS 2021 Young Investigator Award, 2022
Royal Spanish Society of Chemistry (RSEQ) Young Investigator Award, 2022
Forbes Top 50 Awarded Spaniards, 2021
Clarivate Highly Cited Researcher, 2021
Forbes top 100 most creative Spanish individuals, 2021
2022 ASM Award for Early Career Applied and Biotechnological Research, 2021
Antibiotics 2020 Young Investigator Award, 2021
IEEE EMBS Academic Early Career Achievement Award "For the pioneering development of novel antibiotics designed using principles from computation, engineering and biology.", 2021
Thermo Fisher Scientific Award, 2021
IADR Innovation in Oral Care Awards, 2021
Princess of Girona Prize for Scientific Research, 2021
Waksman Foundation Lecturer, 2021
ASM Distinguished Lecturer, 2021
Philadelphia Business Journal 40 Under 40, 2021
Biomedical Engineering Society (BMES) CMBE Rising Star Award, 2021
AlChE's 35 Under 35 Award, 2020
Selected by the US National Academies to serve on the committee to "Exam long-term health and economic effects of antimicrobial resistance in the US" , 2020
Selected as Chair of Panel in the World Laureate Forum, Computational Biology Summit, 2020
NIH MIRA Investigator, 2020
Brain & Behavior Research Foundation (BBRF) Young Investigator Award, 2020
Nemirovsky Prize, 2020
30 Rising Leaders In The Life Sciences, 2020
ACS Infectious Diseases Young Investigator Award, 2020
ACS 2020 Kavli Emerging Leader in Chemistry Lecture Award, 2020
Selected as Scialog Fellow by RCSA, the Paul G. Allen Frontiers Group and the Frederick Gardner Cottrell Foundation, 2020
Recipient of the Langer Prize, 2019
Society of Hispanic Professional Engineers Young Investigator Award, 2019
Elected Delegate. American Academy Achievement. 53rd International Achievement Summit, 2019
Named a Penn Presidential Professor, 2019
Named to the TR35 for “Top Young Innovators Under 35”, MIT Technology Review, 2019
Named a GEN Top 10 Under 40, 2019
Elected Judge, MIT Technology Review Innovators Under 35 Europe, 2019
Named a 2018 Wunderkind by STAT News, 2018
Elected for MISTI MIT Global Seed Funds Scientific Review Committee, 2018
Elected Judge, MIT Technology Review Innovators Under 35 Europe, 2018
Elected Judge, MIT Technology Review Innovators Under 35 Europe, 2017
Junior Fellow, ACS Nano, 2017
Innovator Under 35 (Spain), MIT Technology Review, 2016
30 Under 30 Latino Boston, 2016
Ruth & William A. Silen Award for Microbiology, Immunology, Genetics or Molecular Biology, Harvard Medical School, 2016
“Ramón Areces” Postdoctoral Fellowship, Ramón Areces Foundation, 2015
Robert Emmanuel & Mary Day Endowment Award, University of British Columbia, 2014
“la Caixa” Fellow, awarded by the King and Queen of Spain, 2012
Robert Emmanuel & Mary Day Endowment Award, University of British Columbia, 2012
