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César de la Fuente

@delafuentelab.bsky.social
743 followers 21 following 426 posts

Presidential Associate Professor @upenn.edu - using AI to reimagine antibiotic discovery and peptide design. Previously @MIT, @UBC 🔗 delafuentelab.seas.upenn.edu

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César de la Fuente @delafuentelab.bsky.social · 01/10/2026
A promising molecule can be hidden by noisy experimental data. Our new paper in @cp-cellrepphyssci.bsky.social introduces DEL-Ranking, an AI framework that combines ranking-aware denoising with chemically informed correction to improve compound prioritization in DNA-encoded library (DEL) screens.
cell.com
DEL-Ranking framework for ranking-aware denoising of DNA-encoded library screens for improved affinity prediction
Cao et al. develop DEL-Ranking, a ranking-aware denoising framework that improves affinity prediction from noisy DNA-encoded library screens. The approach enables more accurate prioritization of molec...
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Cell Press Events @cellpressevents.bsky.social · 23/06/2026
AI-assisted biomaterials advancement webinar w/ Joseph Wu @stanfordmedicine.bsky.social @greenstonebio.bsky.social, Cesar de la Fuente @upenn.edu & Kam Leong @columbiauniversity.bsky.social. dlvr.it/TT9f3J
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César de la Fuente @delafuentelab.bsky.social · 15/09/2026
What if peptide design could become programmable? Excited to share our new OmegAMP preprint, where we explore a step toward moving generative AI from simply producing candidate molecules to designing peptides with controllable properties and functions. www.biorxiv.org/content/10.6...
biorxiv.org
Designing antimicrobials with programmable mechanism and safety
Antimicrobial peptides (AMPs) are a promising solution to antimicrobial resistance, yet generative models for their design cannot control the physicochemical properties and motifs that shape activity ...
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César de la Fuente @delafuentelab.bsky.social · 10/09/2026
Excited to join @basecamp-research.bsky.social as a Scientific Advisor. We’ve only begun to read the code of life — and I’m looking forward to exploring what becomes possible when AI helps us learn from biology at scale.
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César de la Fuente @delafuentelab.bsky.social · 08/09/2026
Can AI reinvent how we design biomaterials? Our new piece in Nature Reviews Bioengineering @natureportfolio.nature.com examines how machine learning and deep learning begin to shift biomaterials discovery from empirical trial-and-error to predictive, generative, and increasingly autonomous design.
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University of Pennsylvania @upenn.edu · 22/07/2026
Penn researchers used a deep AI search to uncover new antibiotic candidates for drug-resistant bacteria in prions, mis-folded proteins linked to rare and fatal brain diseases. bit.ly/4yAL4wO
bit.ly
AI uncovers potential antibiotics hidden in proteins linked to fatal brain disease | Penn Today
A Penn Medicine analysis led by César de la Fuente identifies hidden peptides that may kill drug-resistant bacteria.
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MIT Technology Review @technologyreview.com · 30/07/2026
César de la Fuente is on a mission to combat antimicrobial resistance by looking at nature’s own solutions.
trib.al
The scientist using AI to hunt for antibiotics just about everywhere
César de la Fuente is on a mission to combat antimicrobial resistance by looking at nature’s own solutions.
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Código Cero @codigocero.com · 12/08/2026
César de la Fuente desenvolve unha IA capaz de predicir como cambian os péptidos segundo o seu contorno
codigocero.com
César de la Fuente desenvolve unha IA capaz de predicir como cambian os péptidos segundo o seu contorno
O investigador, catedrático da Universidade de Pensilvania e director do Machine Biology Group, lidera o desenvolvemento de ApexFold, un novo modelo de intelixencia artificial que aprende como a estrutura dos péptidos se modifica en función das condicións químicas nas que se atopan. A estrutura das moléculas biolóxicas non é necesariamente fixa. Algúns péptidos poden permanecer […]
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FEMS @femsmicro.org · 20/08/2026
Meet our next #FEMSMICRO 2027 Keynote Speaker: Prof. César de la Fuente. He is internationally recognized for pioneering computational approaches to antibiotic discovery, including methods that identify candidates in hours rather than years. 🔗 Learn more: buff.ly/FocnUnZ
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César de la Fuente @delafuentelab.bsky.social · 03/09/2026
It was a pleasure to join VinFuture Prize’s Unveil the Future podcast for a conversation about how AI could reshape medicine.
youtube.com
[Season 4] Ep 5: Prof. César de la Fuente on AI-Driven Biomedicine & Antimicrobial Discovery
YouTube video by VinFuture Prize
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bioRxivpreprint @biorxivpreprint.bsky.social · 02/09/2026
Designing antimicrobials with programmable mechanism and safety www.biorxiv.org/content/10.64898/20…
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César de la Fuente @delafuentelab.bsky.social · 28/08/2026
AI is changing not only how we search for antibiotics, but increasingly how we design them. Our latest piece is out in @cp-cellbiomat.bsky.social @cellpress.bsky.social.
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César de la Fuente @delafuentelab.bsky.social · 25/08/2026
What if the proteome encodes more biology than we can see from proteins alone? What if protein degradation is not simply cellular disposal, but also a source of biological function?
journals.plos.org
Encrypted immunity mediated by peptides
Encrypted peptides are short bioactive fragments hidden within larger proteins that remain largely undercharacterized, obscuring their roles in immunity. This Essay explores how proteolytically releas...
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César de la Fuente @delafuentelab.bsky.social · 21/08/2026
Mitochondria are descendants of bacteria. Could their own genomes still encode molecules with antimicrobial activity? We used AI to explore over 2,000 ancient human mitochondrial genomes and identify previously hidden peptide sequences with antibacterial potential.
biorxiv.org
Ancient human mitochondrial genomes encode antimicrobial peptides
Mitochondria are bacteria-derived organelles that coordinate major innate immune pathways, but whether mitochondrial genomes themselves encode direct antimicrobial functions is underexplored. Here, we...
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César de la Fuente @delafuentelab.bsky.social · 19/08/2026
Gracias, Revista de Castilla y León, por hablar de ApexGO y de su potencial para acelerar la optimización de candidatos antibióticos. Seguimos trabajando para usar las máquinas no como atajos, sino como herramientas en beneficio de la salud humana. www.revcyl.com/web/index.ph...
revcyl.com
César de la Fuente, doctor honoris causa de la ULE, revela un nuevo sistema de IA que acelera la búsqueda de antibióticos - La Revista Digital de la Comunidad Castellano-Leonesa
Un equipo de investigadores de la Universidad de Pensilvania (EEUU), dirigido por el egresado de la Universidad de León (ULE) César de la Fuente, destacado
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 12/08/2026
ApexFold: condition predictions of peptide secondary structure on the chemical environment @delafuentelab.bsky.social www.biorxiv.org/content/10.6...
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bioRxivpreprint @biorxivpreprint.bsky.social · 11/08/2026
Peptide structural plasticity is predictable from sequence and environment www.biorxiv.org/content/10.64898/20…
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AI x Bio Discovery @aixbiobot.bsky.social · 11/08/2026
Peptide structural plasticity is predictable from sequence and environment [new] predicts secondary structure shifts (helical, beta, disordered) across environments from sequence and medium properties for experimental design.
Peptide structural plasticity is predictable from sequence and environmentFigure 1Figure 2Figure 3
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César de la Fuente @delafuentelab.bsky.social · 12/08/2026
One reason biology is so difficult to predict is that molecules do not act in isolation. Their structures—and sometimes their functions—can change with the environments in which they operate. Understanding life therefore requires models that account not only for sequence, but also for context.
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Adrian Woolfson @adrianwoolfson.bsky.social · 03/08/2026
www.nature.com/articles/s41...
nature.com
Computational design of antimicrobial peptide nanopores - Nature Chemical Biology
A computational de novo design framework enables the design of α-helical peptides that assemble into transmembrane barrel-stave pores (TBPs). Here, TBPs are designed for antimicrobial activity, with b...
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César de la Fuente @delafuentelab.bsky.social · 03/08/2026
Published today in @natchembio.nature.com @natureportfolio.nature.com: a framework for the de novo design of antimicrobial α-helical peptides that assemble into transmembrane barrel-stave nanopores.
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César de la Fuente @delafuentelab.bsky.social · 29/07/2026
Antimicrobial resistance is advancing faster than our ability to discover new drugs. One important question is whether the microbiome—one of the most diverse and dynamic biological systems we know—can help us uncover new antimicrobial molecules and mechanisms. www.sciencedirect.com/science/arti...
sciencedirect.com
Discovery of novel antimicrobials within microbiomes
Antimicrobial-resistant bacterial and fungal pathogens constitute a severe threat to public health. The pace at which new antimicrobials are being rel…
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César de la Fuente @delafuentelab.bsky.social · 22/07/2026
A few additional thoughts following my post: 1. There's likely far more biological data than we often assume. The challenge's that it remains highly fragmented. Large international efforts to integrate them could greatly advance understanding of complex, dynamic biological systems.
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César de la Fuente @delafuentelab.bsky.social · 20/07/2026
Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...
biorxiv.org
AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics
Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...
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César de la Fuente @delafuentelab.bsky.social · 14/07/2026
Antibiotic discovery's becoming a key test of whether AI can move science from pattern recognition to useful biological design. Grateful to join ASM’s Editors in Conversation with Cesar Arias to discuss AI, antimicrobials, infectious disease, & the path from discovery to the clinic. bit.ly/4gCNXqu
youtube.com
AI and Antibiotic Discovery - Editors in Conversation
YouTube video by ASM - Microbes Make Our World
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 08/07/2026
Special Issue Day!! July marks our Special issue focusing on Microbial Therapies: challenges and the path ahead We have reviews, forums & perspectives on the power (and pitfalls) of microbes. www.cell.com/cell-host-mi...
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César de la Fuente @delafuentelab.bsky.social · 08/07/2026
Antibiotics changed medicine because we learned how to mine nature. Our next challenge is to mine the code of life itself. Glad to share our latest piece with Anna Crysler, now out in @cp-cellhostmicrobe.bsky.social @cellpress.bsky.social : “Mining the code of life for new antibiotics.”
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MU-Peter Shimon 🀄 @mu-peter.bsky.social · 07/07/2026
Could proteins best known for their role in fatal neurodegenerative diseases encode molecules that fight infection? Deep learning reveals antimicrobial peptides within prions🧪 Marcelo Torres, Fangping Wan & César de la Fuente @delafuentelab.bsky.social www.nature.com/articles/s41...
Deep learning discovery and validation of prionins.
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César de la Fuente @delafuentelab.bsky.social · 06/07/2026
Microbes are among the most powerful biological systems on Earth—and we are only beginning to understand how to engineer them responsibly for human and planetary health. @commsbio.nature.com’s Microbiological Technology Collection is now open for submissions. www.nature.com/collections/...
nature.com
Microbial Biotechnology
We aim to bring together high quality and novel research spanning applied microbial physiology, metabolic engineering, bioenergy, environmental biotechnology, ...
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Ewa Szczurek @ewaszczurek.bsky.social · 30/06/2026
PepCompass hit unmatched success rates in experimental validation by the team at UPenn (Hyun-Su Lee, Marcelo Der Torossian Torres, César de la Fuente). Led by Marcin Możejko & Adam Bielecki with a great wider team. arxiv.org/abs/2510.01988
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Cell Press @cellpress.bsky.social · 01/07/2026
Explore AI-guided biomaterial design, generative AI, smart scaffolds, drug delivery systems, and more with Joseph C. Wu, Cesar de la Fuente, and Kam W. Leong. July 16, 12:00 p.m. ET. dlvr.it/TTJ8HF
Cell Press webinar
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César de la Fuente @delafuentelab.bsky.social · 01/07/2026
Exciting to see @basecamp-research.bsky.social launch EDEN Apps, now live in Claude, helping researchers design antibiotics and prioritize vaccine targets in minutes. It’s been a pleasure collaborating with the team on this promising work across AI, biology, and therapeutic discovery.
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Cell Press @cellpress.bsky.social · 23/06/2026
AI-assisted biomaterials advancement webinar w/ Joseph Wu @stanfordmedicine.bsky.social @greenstonebio.bsky.social, Cesar de la Fuente @upenn.edu & Kam Leong @columbiauniversity.bsky.social. dlvr.it/TT9f3H
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La Voz de Galicia 🤖 @lavozdegalicia-bot.bsky.social · 19/06/2026
Cesar de la Fuente, biotecnólogo: «La beca cambió mi trayectoria» www.lavozdegalicia.es/noticia/socie…
lavozdegalicia.es
Cesar de la Fuente, biotecnólogo: «La beca cambió mi trayectoria»
El programa de becas de posgrado en el extranjero de la Fundación la Caixa impulsa el talento joven en la ciencia
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La Opinión A Coruña @laopinioncoruna.es · 20/06/2026
Nuevo avance del científico coruñés César de la Fuente: las proteínas causantes del mal de las vacas locas, posibles fuentes de antibióticos
laopinioncoruna.es
Nuevo avance del científico coruñés César de la Fuente: las proteínas causantes del mal de las vacas locas, posibles fuentes de antibióticos
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Asaf Levy @asaflevylab.bsky.social · 25/06/2026
Our new review paper is out: Discovery of novel antimicrobials within microbiomes www.sciencedirect.com/science/arti... A fun collaboration with @delafuentelab.bsky.social and the 1st paper of Erez Weisberg and Aya Friedman
sciencedirect.com
Discovery of novel antimicrobials within microbiomes
Antimicrobial-resistant bacterial and fungal pathogens constitute a severe threat to public health. The pace at which new antimicrobials are being rel…
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Nature Portfolio @natureportfolio.nature.com · 19/06/2026
🧪 @natmicrobiol.nature.com
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César de la Fuente @delafuentelab.bsky.social · 24/06/2026
En La mecánica del caracol conversé con Itziar Alkorta e Iñigo Lasa sobre cómo la investigación científica está desarrollando nuevas estrategias para hacer frente a la resistencia a los antibióticos. Gracias a @evacaballero.bsky.social y al equipo del programa por contar conmigo. bit.ly/3QVuwP4
bit.ly
Investigación para hacer frente a la crisis de la resistencia a los antibióticos - La mecánica del caracol - Podcast en iVoox
Escucha este episodio de La mecánica del caracol gratis en iVoox. Hoy analizamos el fenómeno de la proliferación de bacterias resistentes a los antibióticos con tres especialistas que investigan posib...
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Nature Microbiology @natmicrobiol.nature.com · 19/06/2026
Out Now! Deep learning reveals antimicrobial peptides within prions #MicroSky
go.nature.com
Deep learning reveals antimicrobial peptides within prions
Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02408-1Deep learning reveals that prion-related proteins contain hidden ‘prionin’ peptides with antibacterial activity, including two candidates that reduced infections in mice.
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Paulina Szymczak @szymczakpau.bsky.social · 20/06/2026
Extremely proud that our competition on AMP generative AI design will be a part of @neuripsconf.bsky.social 2026! It's going to be a blast 💥 with @ewaszczurek.bsky.social , @delafuentelab.bsky.social , at @helmholtzmunich.bsky.social, @upenn.edu 🙂 szczurek-lab.github.io/amp-challeng...
szczurek-lab.github.io
AMP Challenge
The first head-to-head benchmarking competition for generative AI in antimicrobial peptide design.
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César de la Fuente @delafuentelab.bsky.social · 19/06/2026
Our paper, “Deep learning reveals antimicrobial peptides within prions,” is now published in Nature Microbiology @natureportfolio.nature.com. We used AI to ask an unexpected question: could proteins best known for their role in fatal neurodegenerative diseases encode molecules that fight infection?
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UofT-TCAIREM @uoft-tcairem.bsky.social · 17/06/2026
Penn researchers develop predictive #AI model for #antibiotic discovery @delafuentelab.bsky.social www.thedp.com/article/2026... #AIhealth #AI #HealthAI #MedTech
thedp.com
Penn researchers develop predictive AI model for antibiotic discovery
The model, called ApexGO, tells researchers whether a given peptide is “likely to have antimicrobial properties.” 
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César de la Fuente @delafuentelab.bsky.social · 16/06/2026
It was a pleasure to join Beyond Sciences Initiative Toronto’s Conference 2026 as a keynote speaker and share our work with such a fantastic community. Watch the keynote video: www.youtube.com/watch?v=2Ox_...
youtube.com
Conference 2026 Day 1 Keynote | Dr. Cesar de la Fuente
YouTube video by Beyond Sciences Initiative Toronto
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César de la Fuente @delafuentelab.bsky.social · 12/06/2026
Thank you @smjyoti.bsky.social and @nature.com for featuring our work on peptide design. AMR is one of the defining scientific and medical challenges of our time. Excited to see AI-driven peptide discovery recognized as part of the broader effort to tackle AMR. www.nature.com/articles/d41...
nature.com
AI is taking on antibiotic resistance — here’s how
A suite of artificial-intelligence tools is helping to speed up the process of discovering new antibiotics.
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César de la Fuente @delafuentelab.bsky.social · 04/06/2026
Thrilled to join Fundación Innovación Bankinter’s Future Trends Forum on Synthetic Biology in Madrid, moderated by @francesssellers.bsky.social. We’re moving from reading biology to writing it—and must shape that future responsibly across health, food, sustainability, industry & society.
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Treintayseis @treintayseis.bsky.social · 01/06/2026
El científico gallego César de la Fuente, elegido miembro de la Academia Europaea
dlvr.it
El científico gallego César de la Fuente, elegido miembro de la Academia Europaea
Se trata de una de las principales academias de ciencias de Europa, que cuenta con 88 integrantes galardonados con el Premio Nobel Te puede interesar: La UDC lidera en A Coruña un estudio para prevenir futuras pandemias desde el comportamiento humano
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César de la Fuente @delafuentelab.bsky.social · 03/06/2026
Honored to join @acad-euro.bsky.social and its distinguished community of scholars and scientists, including more than 80 Nobel Laureates. Deeply grateful to be part of a community devoted to advancing the boundaries of knowledge and discovery. www.ae-info.org/ae/Member/de...
ae-info.org
Academy of Europe: de la Fuente Cesar
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The Warren Center for Network & Data Sciences @warrencenter.bsky.social · 29/05/2026
At a Penn Alumni Weekend panel event, President J. Larry Jameson brought together researchers César de la Fuente and Warren Center affiliate Hamsa Bastani to discuss how AI is helping to accelerate breakthroughs in biology and personalize learning. penntoday.upenn.edu/...
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Quincemil @quincemil.bsky.social · 01/06/2026
El científico gallego César de la Fuente, elegido miembro de la Academia Europaea #ACoruña #Coruña #Galicia
dlvr.it
El científico gallego César de la Fuente, elegido miembro de la Academia Europaea
Se trata de una de las principales academias de ciencias de Europa, que cuenta con 88 integrantes galardonados con el Premio Nobel Te puede interesar: La UDC lidera en A Coruña un estudio para prevenir futuras pandemias desde el comportamiento humano
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César de la Fuente @delafuentelab.bsky.social · 28/05/2026
Enjoyed joining Larry Bernstein on his podcast to discuss “Using Peptides for Medical Breakthroughs.” Peptides're tiny chains of amino acids with enormous potential. With AI, we may learn to program them—unlocking new possibilities in medicine, biotech, sustainability, and beyond. bit.ly/4dKPxmT
whathappensnextin6minutes.com
Using Peptides for Medical Breakthroughs
Speakers: Cesar de la Fuente
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