César de la Fuente, Ph.D.
CURRENT POSITION
University of Pennsylvania, Presidential Associate Professor
César de la Fuente is a Presidential Associate Professor at the University of Pennsylvania, where he leads the Machine Biology Group. He completed postdoctoral research at the Massachusetts Institute of Technology (MIT) and earned a PhD from the University of British Columbia (UBC). His research goal is to use the power of machines to accelerate discoveries in biology and medicine. Notably, he pioneered the development of the first computer-designed antibiotic with efficacy in animal models, demonstrating the application of AI for antibiotic discovery and helping launch this emerging field. His lab is at the forefront of developing computational methods to mine the world’s biological information, leading to the identification of over a million new antimicrobial compounds. These efforts started by exploring the human proteome as a source of antibiotics for the first time. His team was also the first to find therapeutic molecules in extinct organisms, launching the field of molecular de-extinction. Molecular de-extinction has already yielded preclinical antibiotic candidates, such as neanderthalin, mammuthusin, and elephasin. Furthermore, de la Fuente’s lab has broadened its antibiotic discovery initiatives to explore other branches of the tree of life beyond eukaryotes. By computationally analyzing microbial dark matter, his group has identified nearly one million new antibiotic molecules. These molecules have been made freely available and open access to the scientific community to encourage researchers worldwide to synthesize, characterize, and further develop them. This collaborative effort leveraged machine learning to explore the vast diversity of the microbial world by analyzing 63,410 metagenomes and 87,920 microbial genomes. Additionally, through the computational exploration of thousands of human microbiomes, de la Fuente and collaborators discovered a myriad of new antimicrobial agents, including prevotellin-2 produced by the gut microbe Prevotella copri. Collectively, these efforts have dramatically accelerated antibiotic discovery, reducing the time required to identify preclinical candidates from years to just a few hours. Additional advances from his lab include reprogramming venoms into antimicrobials, developing autonomous nanorobots to treat infections, creating novel resistance-proof antimicrobial materials, and inventing rapid, low-cost diagnostic devices for COVID-19 and other infections. Prof. de la Fuente is an NIH MIRA investigator and has received recognition and research funding from numerous organizations. De la Fuente has received over 80 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 to be inducted. He was recognized by MIT Technology Review as one of the world’s top innovators for “digitizing evolution to make better antibiotics.” He was selected as the inaugural recipient of the Langer Prize and as an ACS Kavli Emerging Leader in Chemistry, an ASM Distinguished Lecturer, Waksman Foundation Lecturer, and received the Miklós Bondanszky Award, AIChE’s 35 Under 35 Award, Society of Hispanic Professional Engineers Young Investigator Award, and the ACS Infectious Diseases Young Investigator Award. He also received the Thermo Fisher Award, as well as the EMBS Academic Early Career Achievement Award “For the pioneering development of novel antibiotics designed using principles from computation, engineering, and biology.” Recently, Prof. de la Fuente has been awarded the prestigious Princess of Girona Prize, the ASM Award for Early Career Applied and Biotechnological Research, the ASM Award for Early Career Basic Research, the Rao Makineni Lectureship Award by the American Peptide Society, the Fleming Prize, and was selected as a National Academy of Medicine Emerging Leader in Health and Medicine. De la Fuente serves on the editorial boards of numerous scholarly journals and is currently an Associate Editor of Drug Resistance Updates (IF= 24.3; the premier international drug resistance journal), Nature Communications Biology, Bioactive Materials (IF = 18.9), Bioengineering & Translational Medicine, and Digital Discovery. He has been named a Highly Cited Researcher by Clarivate multiple times. Prof. de la Fuente has given over 300 invited lectures, including numerous 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 over 160 peer-reviewed papers in top-tier journals such as Cell, Science, Cell Host Microbe, Nature Biomedical Engineering, Nature Communications, PNAS, ACS Nano, Nature Chemical Biology, and Advanced Materials.
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)
Fleming Prize, 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
