Research Summary
My lab’s research merges my unique background in geochemistry and microbiology and my interest in synthetic biology and bioengineering to unravel and harness the role of lipids in organizing bioactivity. My lab has recently pioneered two fronts:

1. Minimal Microbial Models for Membrane Biology: We’ve established minimal bacterial systems, notably pathogenic mycoplasma and the Minimal Cell (JCVI-Syn3), as modifiable membrane platforms amenable to synthetic genomics. This approach allows us to dissect and manipulate cell membranes, offering unique insights into lipid-mediated cellular functions and interactions. We have developed approaches to tune and minimize mycoplasma and Syn3 lipidomes, demonstrating that two lipids are sufficient (but far from optimal) for life. Using these minimal bacterial organisms, we can reintroduce genomic and chemical complexity to elucidate the crucial components of a functional cell membrane, with the ultimate goal of designing bespoke synthetic cell membranes. Expanding from studies of individual lipids, we aim to understand and engineer the lipidome’s complexity and its impact on cellular behavior in the context of environments from mammalian hosts to oceans and soils.

2. Novel Membrane Sense and Response Mechanisms based on RNA-Lipid Interactions: A groundbreaking direction in our research is exploring how lipids can selectively interact with, and modulate RNAs. Beyond exploring lipid functions, this work paves the way for developing RNA-lipid interactions to create synthetic membrane sensors and riboregulatory mechanisms. The potential to design lipid-sensitive RNAs opens new avenues for synthetic biology applications, including novel forms of lipid regulation and membrane homeostasis.

Harvard PhD 1984. Professor at Harvard & MIT 1986, co-author of 716 papers, 164 patent publications & book “Regenesis”; developed methods used for the first genome sequence (1994) & 10M-fold cost reduction (fluor-NGS & nanopores), molecular barcoding/ multiplexing, DNA assembly from chips, genome editing/writing/recoding; co-initiated BRAIN Initiative (2011) & Genome Projects (GP-Read-1984, GP-Write-2016, PGP-2005:first open-access personal/precision medicine data & cells); machine learning for protein engineering, tissue reprogramming, organoids, gene therapy, aging reversal, xeno-transplantation, in situ 3D DNA/RNA/protein imaging.

My research focuses on the interplay between extrinsic and intrinsic signals that affect cell behavior by building cutting-edge molecular tools to measure and perturb such signals. Most molecular tools are being developed and function well in vitro. Current technologies are unable to measure signaling in its native context in vivo, mainly due to lack of signal amplification, slow kinetics, and incompatibility of reagents. I aim to develop and translate some of these tools in vivo to help solve issues of biomedical relevance.

My graduate training combined biophysical and systems-biology approaches for the mechano-chemical control of adult human stem cells.With my engineering background, my postdoctoral fellowship at Stanford University focused on developing synthetic biological tools to measure signals that induce cell fate. I developed a versatile receptor-based tool called CRISPR ChaCha, which senses the immediate microenvironment and activate novel genomic expression programs via CRISPR-Cas9. At Harvard University, I created molecular tools that control the secretion and sensing of signals as they arise in the developing zebrafish embryo.

As an Assistant Professor at UT Dallas, my research laboratory is developing cutting-edge tools to measure and characterize signaling mechanisms in vivo. We are developing innovative uses of biological molecules in vivo, including CRISPR/Cas systems, synthetic proteases, and fluorescent probes to gain deeper insights into endogenous signal release and response in early embryos and in the brain.

I received my BS degree in Mechatronic Eng. from National University of Engineering (UNI-Peru). I obtained my PhD in Mechanical Engineering from the University of California Riverside (UCR) under the supervision of Elisa Franco in 2017. I held a postdoctoral scholar with Ron Weiss at MIT (2017), Elisa Franco at UCLA (2019), Ming-Ru Wu at Harvard/DFCI (2023). In Fall 2024, I will join the Computational Biology Department at Carnegie Mellon University. I work at the intersection among Control Theory, Systems Biology and Synthetic Biology. I am specially interested in the design, analysis and applications of biomolecular feedback control systems and molecular neural networks for decision-making in living cells. To create a community that connects mathematical theories, models, and biomolecular experiments, I co-organize a Seminar on Biological Control Systems. it focuses on applications of mathematical modeling and control systems to biology. We host monthly talks featuring our members and invited guests.