About The Blueprint of Life
For much of its history, biology has taken a narrow, gene-centric view of development: one gene, one function, one outcome. However, as we take a step back, this approach revealed important insights but left us with an incomplete picture. Development is not the product of single switches. It is a dynamic network of genomes, proteins, metabolites, and regulatory layers working together across time. To truly understand how organisms grow and evolve, we need to step back and see the whole system.
The Blueprint of Life does exactly that. By combining genomics, transcriptomics, proteomics, and metabolomics, we are building a comprehensive map of development across species, populations, and molecular layers. This systems-level approach allows us to uncover the hidden rules that shape life’s complexity; we'd otherwise miss them if we only focused on single genes.
Why a multi-layered approach?
Take the butterflies of the Heliconius genus; around 40 species that serve as a natural laboratory for studying color pattern evolution. Across South America, two species, H. erato and H. melpomene, have evolved into mimetic pairs: in each region, the two look almost identical even though they are not closely related. This “copy-cat” strategy is called mimicry (Fig. 1); by sharing the same bright warning colors, both species teach predators to stay away after just one bad tasting experience.
Fig 1. Geographic races of Heliconius erato and H. melpomene exhibit parallel mimicry across South America. Comparative genomic analyses around the WntA locus reveal regulatory divergence despite convergent wing phenotypes. CRISPR knockouts of WntA produce distinct outcomes: expanded red forewing patterning in H. erato demophoon versus minimal effect in H. melpomene rosina. (Papa et. al. 2025)
For years, researchers probed this diversity using single-gene knockouts. Yet results often defied expectations. Knocking out the same gene, WntA, in two closely related races produces very different outcomes: in H. erato demophoon, a large red patch spreads across the forewing, while in H. melpomene rosina, the wings barely change.
One gene, two species, two very different stories.
This inconsistency highlights the need for a multi-species, multi-layer approach. Current reference genomes for Heliconius charithonia and Danaus plexippus are based on only a few individuals, barely scratching the surface of genomic diversity. To capture the true blueprint of life, we must analyze variation across populations, life stages, and regulatory layers.
Heliconius charithonia, a native species to Puerto Rico. Filmed by Florence Piel
Questions for a pangenome approach?
Single-gene studies cannot explain:
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How proteins are modified and interact.
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How enzymes and metabolites drive cellular processes.
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How epigenetics and alternative splicing fine-tune gene function.
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How structural variants and gene duplications fuel evolution.
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How genomic organization changes over time.
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Which molecular interactions are robust and which are flexible.
By weaving these layers together, we move beyond a “parts list” and reveal how their interactions build and diversify systems.
Pictured from left to right is Nicolas, Estefania, and Liz; three members of our lab out in the field.
Drawing patterns with new pipelines
What also sets the Blueprint of Life apart is its technology. Our team includes not only biologists but also mathematicians, chemists, computer scientists, and AI experts, working together to design new ways of handling biological data. Instead of static pipelines, we are developing standardized computational models built on mathematical principles and powered by AI. This shift will move biology from description to prediction. Our AI will not be pre-trained with assumptions, it will learn directly from biological data, detecting patterns across genes, molecules, and developmental stages. In doing so, it will transform biology into a predictive science, capable of anticipating developmental outcomes and regulatory changes. And while butterflies are our starting point, the vision is broader. By uniting AI with biology, we aim to create tools that accelerate discovery across the life sciences. Our goal is not just to use AI to analyze data, but to harness it to predict the fundamental rules of life itself.
Final Thoughts
Our aim is simple: to understand how living organisms create organized instructions that lead to unique cell identities, tissues, organs and complex body structures. How does the same genome give rise to neurons, muscle fibers, or wing scales? What triggers the networks that sets cells on their developmental paths? The Blueprint of Life will help decode these molecular signatures of identity, showing how genes, proteins, and metabolites converge to give cells their distinct roles.
Want to learn more?
Read our information doc below
Location and Collaboration
Puerto Rico, the Enchanted Island, is where the Blueprint of Life established its foundation. As home to some of the most advanced research centers in Latin America and the Caribbean, the island provides an exceptional environment for scientific discovery and collaboration. With its rich natural heritage, internationally recognized teaching facilities, and a dynamic community of Boricua and international students, Puerto Rico stands as a hub for research excellence, education, and innovation in the life sciences.
Bienvenido a La Isla del Encanto
Punta Borinquen, Puerto Rico. Picture credited to Nicolas A. Miranda Diaz
Cayey de Muesas, Puerto Rico
Unitersity of Puerto Rico at Río Piedras , Puerto Rico
The Blueprint of Life is not tied to a single university or laboratory...
Our collaborations span institutions, disciplines, and industries. The project's aim is to unite Puerto Rican researchers, educators, and non-profits across the economic sector. This wide network is essential not only for advancing our own research goals, but also for ensuring the long-term sustainability and outreach impact of our work.
Old San Juan, Puerto Rico
The Blueprint of life is not localised to one campus, but rather collaborates across the University of Puerto Rico's affiliated research centers. By working with multiple campuses, we unite diverse expertise in biology, medicine, engineering, and education.
Academic Collaborators
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Map of our academic research center collaborators across Puerto Rico
Industry & Government Partners
We partner with organizations that strengthen Puerto Rico’s scientific-entrepreneurial ecosystem, creating opportunities for Boricua students and researchers while addressing broader economic challenges.
Industry engagement, for example is central to this mission. By ensuring that innovations in genomics and biotechnology move beyond the laboratory to fuel entrepreneurship, we can inform Puerto Rican public policy, and drive economic growth.
Ultimately, our goal goes beyond economic growth, the Blueprint of Life aspires to position Puerto Rico at the forefront of the global knowledge economy, driving discovery, scientific innovation, and a more sustainable future.
La Poza de las Mujeres - one of our many gorgeous Puerto Rican beaches in Manati
E-RISE Collaboration
Finally, it is important to mention that The Blueprint of Life would not be possible without the NSF EPSCoR Research Incubators for STEM Excellence (E-RISE) RII Program. The E-RISE RII program funds and supports the development and implementation of sustainable broad networks of individuals, institutions, and organizations that will transform the science, technology, engineering and mathematics (STEM) research capacity and competitiveness in a jurisdiction within a field of research aligned with the jurisdiction's science and technology priorities.
