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...

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 ...

biorxiv.org

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.

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.

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. https://bit.ly/4yAL4wO

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.

bit.ly

César de la Fuente is on a mission to combat antimicrobial resistance by looking at nature’s own solutions.

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.

trib.al

César de la Fuente desenvolve unha IA capaz de predicir como cambian os péptidos segundo o seu contorno

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 […]

codigocero.com

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

It was a pleasure to join VinFuture Prize’s Unveil the Future podcast for a conversation about how AI could reshape medicine.

[Season 4] Ep 5: Prof. César de la Fuente on AI-Driven Biomedicine & Antimicrobial Discovery

YouTube video by VinFuture Prize

youtube.com

Designing antimicrobials with programmable mechanism and safety https://www.biorxiv.org/content/10.64898/2026.09.01.747572v1

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.

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?

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...

journals.plos.org

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.

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...

biorxiv.org

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...

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

revcyl.com

ApexFold: condition predictions of peptide secondary structure on the chemical environment @delafuentelab.bsky.social www.biorxiv.org/content/10.6...

Peptide structural plasticity is predictable from sequence and environment https://www.biorxiv.org/content/10.64898/2026.08.09.743796v1

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.

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.

www.nature.com/articles/s41...

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...

nature.com

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.

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...

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…

sciencedirect.com

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.

César de la Fuente@delafuentelab.bsky.social · 2mo ago

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...

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...

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...

biorxiv.org

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

AI and Antibiotic Discovery - Editors in Conversation

YouTube video by ASM - Microbes Make Our World

youtube.com

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...

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.”

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...

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/...

Microbial Biotechnology

We aim to bring together high quality and novel research spanning applied microbial physiology, metabolic engineering, bioenergy, environmental biotechnology, ...

nature.com

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

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. http://dlvr.it/TTJ8HF

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.