Houston scientists develop breakthrough AI-driven process to design, decode genetic circuits

biotech breakthrough

Rice University scientists Kshitij Rai, Caleb Bashor and Ronan O’Connell have developed CLASSIC, a new AI-driven process that can generate and test millions of DNA designs at the same. Photo by Jeff Fitlow. Courtesy Rice University.

Researchers at Rice University have developed an innovative process that uses artificial intelligence to better understand complex genetic circuits.

A study, published in the journal Nature, shows how the new technique, known as “Combining Long- and Short-range Sequencing to Investigate Genetic Complexity,” or CLASSIC, can generate and test millions of DNA designs at the same time, which, according to Rice.

The work was led by Rice’s Caleb Bashor, deputy director for the Rice Synthetic Biology Institute and member of the Ken Kennedy Institute. Bashor has been working with Kshitij Rai and Ronan O’Connell, co-first authors on the study, on the CLASSIC for over four years, according to a news release.

“Our work is the first demonstration that you can use AI for designing these circuits,” Bashor said in the release.

Genetic circuits program cells to perform specific functions. Finding the circuit that matches a desired function or performance "can be like looking for a needle in a haystack," Bashor explained. This work looked to find a solution to this long-standing challenge in synthetic biology.

First, the team developed a library of proof-of-concept genetic circuits. It then pooled the circuits and inserted them into human cells. Next, they used long-read and short-read DNA sequencing to create "a master map" that linked each circuit to how it performed.

The data was then used to train AI and machine learning models to analyze circuits and make accurate predictions for how untested circuits might perform.

“We end up with measurements for a lot of the possible designs but not all of them, and that is where building the (machine learning) model comes in,” O’Connell explained in the release. “We use the data to train a model that can understand this landscape and predict things we were not able to generate data on.”

Ultimately, the researchers believe the circuit characterization and AI-driven understanding can speed up synthetic biology, lead to faster development of biotechnology and potentially support more cell-based therapy breakthroughs by shedding new light on how gene circuits behave, according to Rice.

“We think AI/ML-driven design is the future of synthetic biology,” Bashor added in the release. “As we collect more data using CLASSIC, we can train more complex models to make predictions for how to design even more sophisticated and useful cellular biotechnology.”

The team at Rice also worked with Pankaj Mehta’s group in the department of physics at Boston University and Todd Treangen’s group in Rice’s computer science department. Research was supported by the National Institutes of Health, Office of Naval Research, the Robert J. Kleberg Jr. and Helen C. Kleberg Foundation, the American Heart Association, National Library of Medicine, the National Science Foundation, Rice’s Ken Kennedy Institute and the Rice Institute of Synthetic Biology.

James Collins, a biomedical engineer at MIT who helped establish synthetic biology as a field, added that CLASSIC is a new, defining milestone.

“Twenty-five years ago, those early circuits showed that we could program living cells, but they were built one at a time, each requiring months of tuning,” said Collins, who was one of the inventors of the toggle switch. “Bashor and colleagues have now delivered a transformative leap: CLASSIC brings high-throughput engineering to gene circuit design, allowing exploration of combinatorial spaces that were previously out of reach. Their platform doesn’t just accelerate the design-build-test-learn cycle; it redefines its scale, marking a new era of data-driven synthetic biology.”

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Xiaoyu Yang, a graduate student at Rice, is the lead author on a study published in the journal Science on smart cell design. Photo by Jeff Fitlow/ Courtesy Rice University

Rice research breakthrough paves the way for advanced disease therapies

study up

Bioengineers at Rice University have developed a “new construction kit” for building custom sense-and-respond circuits in human cells, representing a major breakthrough in the field of synthetic biology, which could "revolutionize" autoimmune disease and cancer therapeutics.

In a study published in the journal Science, the team focused on phosphorylation, a cellular process in the body in which a phosphate group is added to a protein, signaling a response. In multicellular organisms, phosphorylation-based signaling can involve a multistage, or a cascading-like effect. Rice’s team set out to show that each cycle in a cascade can be treated as an elementary unit, meaning that they can be reassembled in new configurations to form entirely novel pathways linking cellular inputs and outputs.

Previous research on using phosphorylation-based signaling for therapeutic purposes has focused on re-engineering pathways.

“This opens up the signaling circuit design space dramatically,” Caleb Bashor, assistant professor of bioengineering and biosciences and corresponding author on the study, said in a news release. “It turns out, phosphorylation cycles are not just interconnected but interconnectable … Our design strategy enabled us to engineer synthetic phosphorylation circuits that are not only highly tunable but that can also function in parallel with cells’ own processes without impacting their viability or growth rate.”

Bashor is the deputy director for the Rice Synthetic Biology Institute, which launched last year.

The Rice lab's sense-and-respond cellular circuit design is also innovative because phosphorylation occurs rapidly. Thus, the new circuits could potentially be programmed to respond to physiological events in minutes, compared to other methods, which take hours to activate.

Rice’s team successfully tested the circuits for sensitivity and their ability to respond to external signals, such as inflammatory issues. The researchers then used the framework to engineer a cellular circuit that can detect certain factors, control autoimmune flare-ups and reduce immunotherapy-associated toxicity.

“This work brings us a whole lot closer to being able to build ‘smart cells’ that can detect signs of disease and immediately release customizable treatments in response,” Xiaoyu Yang, a graduate student in the Systems, Synthetic and Physical Biology Ph.D. program at Rice who is the lead author on the study, said in a news release.

Ajo-Franklin, a professor of biosciences, bioengineering, chemical and biomolecular engineering and a Cancer Prevention and Research Institute of Texas Scholar, added “the Bashor lab’s work vaults us forward to a new frontier — controlling mammalian cells’ immediate response to change.”

Cemvita aims to capitalize on Brazil’s regulatory framework around biodiesel blending and Sustainable Aviation Fuel.Photo courtesy of Cemvita

Pioneering Houston biotech startup expands to Brazil for next phase

On the Move

Houston biotech company Cemvita has expanded into Brazil. The company officially established a new subsidiary in the country under the same name.

According to an announcement made earlier this month, the expansion aims to capitalize on Brazil’s progressive regulatory framework, including Brazil’s Fuel of the Future Law, which was enacted in 2024. The company said the expansion also aims to coincide with the 2025 COP30, the UN’s climate change conference, which will be hosted in Brazil in November.

Cemvita utilizes synthetic biology to transform carbon emissions into valuable bio-based chemicals.

“For decades Brazil has pioneered the bioeconomy, and now the time has come to create the future of the circular bioeconomy,” Moji Karimi, CEO of Cemvita, said in a news release. “Our vision is to combine the innovation Cemvita is known for with Brazil’s expertise and resources to create an ecosystem where waste becomes opportunity and sustainability drives growth. By joining forces with Brazilian partners, Cemvita aims to build on Brazil’s storied history in the bioeconomy while laying the groundwork for a circular and sustainable future.”

The Fuel of the Future Law mandates an increase in the biodiesel content of diesel fuel, starting from 15 percent in March and increasing to 20 percent by 2030. It also requires the adoption of Sustainable Aviation Fuel (SAF) and for domestic flights to reduce greenhouse gas emissions by 1 percent starting in 2027, growing to 10 percent reduction by 2037.

Cemvita agreed to a 20-year contract that specified it would supply up to 50 million gallons of SAF annually to United Airlines in 2023.

"This is all made possible by our innovative technology, which transforms carbon waste into value,” Marcio Da Silva, VP of Innovation, said in a news release. “Unlike traditional methods, it requires neither a large land footprint nor clean freshwater, ensuring minimal environmental impact. At the same time, it produces high-value green chemicals—such as sustainable oils and biofuels—without competing with the critical resources needed for food production."

In 2024, Cemvita became capable of generating 500 barrels per day of sustainable oil from carbon waste at its first commercial plant. As a result, Cemvita quadrupled output at its Houston plant. The company had originally planned to reach this milestone in 2029.

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This story originally appeared on our sister site, EnergyCapitalHTX.

Thanks to technology advancements, Cemvita is now capable of generating 500 barrels per day of sustainable oil from carbon waste at its first commercial plant. Photo via cemvita.com

Houston company's sustainable oil product reaches milestone production capacity 5 years early

overachieving

Houston-based biotech company Cemvita has achieved a key production goal five years ahead of schedule.

Thanks to technology advancements, Cemvita is now capable of generating 500 barrels per day of sustainable oil from carbon waste at its first commercial plant. As a result, Cemvita has quadrupled output at the Houston plant. The company had planned to reach this milestone in 2029.

Cemvita, founded in 2017, says this achievement paves the way for increased production capacity, improved operational efficiency, and an elevated advantage in the sustainable oil market.

“What’s so amazing about synthetic biology is that humans are just scratching the surface of what’s possible,” says Moji Karimi, co-founder and CEO of Cemvita. “Our focus on the first principles has allowed us to design and create new biotech more cheaply and faster than ever before.”

The production achievement follows Cemvita’s recent breakthrough in development of a solvent-free extraction bioprocess.

In 2023, United Airlines agreed to buy up to one billion gallons of sustainable aviation fuel from Cemvita’s first full-scale plant over the course of 20 years.

Cemvita’s investors include the UAV Sustainable Flight Fund, an investment arm of Chicago-based United; Oxy Low Carbon Ventures, an investment arm of Houston-based energy company Occidental Petroleum; and Japanese equipment and machinery manufacturer Mitsubishi Heavy Industries.

The new collaborative hub will foster research into cell therapies, artificial intelligence, nanotechnologies, and more. Photo via tmc.edu

Houston health care leaders announce new hub for cancer-fighting bioengineering

team work

Two Houston organizations recently announced a new hub that will focus on developing cell therapies, nanotechnologies, cancer vaccines, artificial intelligence, and molecular imaging.

Rice University and The University of Texas MD Anderson Cancer Center have teamed up to “drive industry growth and advance life-saving technologies” through the newly established Cancer Bioengineering Collaborative, according to a news release announcing the initiative.

The collaboration between the two institutions includes fundamental and translational cancer research, developing new technologies for cancer detection and therapy, and securing external funding in support of further research and training.

Leading the hub will be Rice researcher and Cancer Prevention and Research Institute of Texas (CPRIT) scholar Gang Bao and MD Anderson’s Dr. Jeffrey Molldrem.

“There is tremendous potential in bringing together experts in engineering and cancer as part of this focused, collaborative framework that is truly unique, not only owing to the complementary nature of the respective strengths but also because this is the first formal joint research initiative of its kind between the two institutions,” says Bao, department chair and Foyt Family Professor of Bioengineering, professor of chemistry, materials science and nanoengineering and mechanical engineering, in the release.

The joint effort will also host monthly seminars focused on cancer bioengineering, annual retreats to highlight research and international leaders in cancer and bioengineering, and also a seed grant program to fund research projects in the early stages of development.

“From fundamental discoveries in cancer science, tumor immunology and patient care to innovative engineering advances in drug delivery systems, nanostructures and synthetic biology, there is great potential for enabling cross-disciplinary collaboration to develop new technologies and approaches for detecting, monitoring and treating cancer,” Molldrem, chair of Hematopoietic Biology & Malignancy at MD Anderson, says in the release. “Our goal is to bridge the gap between bioengineering and cancer research to create transformative solutions that significantly improve patient outcomes.”

Dr. Jeff Molldrem (left) and Gang Bao will lead the new collaborative hub. Photo via MD Anderson

The new Rice Synthetic Biology Institute is part of an $82 million investment the university put toward synthetic biology, neuroengineering, and physical biology in 2018. Photo via Rice.edu

Houston university launches new institute for synthetic biology

new to Hou

Rice University announced this month that it has officially launched the new Rice Synthetic Biology Institute.

The institute aims to strengthen the synthetic biology community across disciplines at the university, according to an announcement from Rice. It is part of an $82 million investment the university put toward synthetic biology, neuroengineering, and physical biology in 2018.

RSBI will be led by Caroline Ajo-Franklin, professor of biosciences, bioengineering, and chemical and biomolecular engineering, with support from a faculty steering committee.

Caroline Ajo-Franklin, professor of biosciences, bioengineering, and chemical and biomolecular engineering, will lead the new institute. Photo via Rice.edu

“At Rice, we have such deep expertise in synthetic biology,” Ajo-Franklin said in the announcement. “Connecting that deep expertise through this institute will lead to better science and more innovation.”

Synthetic biology is a discipline in which "researchers design living systems with new properties to address societal needs," according to Rice, with applications in medicine, manufacturing and environmental sustainability.

The university says that there are currently 18 faculty and more than 100 students and postdoctoral scholars at Rice working in this field within the schools of engineering and natural sciences.

The institute will initially focus on four research themes:

  1. Controlling the biological synthesis and patterning of proteins and cells into living materials that self-replicate and self-repair across a range of length scales
  2. Understanding cells as natural sensors and repurposing them into living therapeutics to detect and treat diseases, maintain health and prevent infections
  3. Developing living electronics to convert biochemical information into information-dense electronic signals in real-time at the cell-material interface
  4. Supporting cross-cutting scholarship aimed at accelerating the Design-Build-Test-Learn cycle and understanding the ethical, legal and social implications of translating these technologies into the public domain.

“Rice University is an amazing place to learn, teach, research and innovate,” Ramamoorthy Ramesh, executive vice president for research, added. “The Rice Synthetic Biology Institute will ensure that our researchers are recognized on the international stage for the life-changing work they are doing in Houston and around the world.”

Last year, Rice also launched the new Center for Human Performance with Houston Methodist inside Rice’s Tudor Fieldhouse. The interdisciplinary space aims to advance the study of exercise physiology, injury prevention, and rehabilitation while serving Rice student-athletes.

The university also unveiled another massive, collaborative space this academic year: The 250,000-square-foot Ralph S. O’Connor Building for Engineering and Science. Click here to read more about the state-of-the-art building.

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Houston medtech startup clears FDA approval for new surgical tool

precision surgery

Houston-based Prana Surgical will soon bring a new electrosurgical tool to operating rooms around the country. The Prana System officially cleared U.S. Food and Drug Administration (FDA) approval earlier this month.

"Receiving FDA clearance for the Prana System represents a defining milestone for our company," Joanna Nathan, CEO and co-founder of Prana Surgical, said in a news release. "Surgeons today are increasingly focused on achieving precise outcomes while minimizing disruption to healthy tissue. The Prana System was designed to support that shift by integrating targeting and excision into a single, streamlined tool."

Prana Surgical began as Prana Thoracic in 2022. Back then, the company primarily focused on developing screening tools for lung cancer diagnosis. It raised $6 million in series A funding rounds in 2023 and 2024 before transitioning to broader surgical needs in 2025.

The Prana System is a minimally invasive, image-guided, single-use tissue extraction tool designed to retrieve samples without damaging healthy tissue. The tool is still designed with the respiratory system in mind, helping Prana in the fight against lung cancer and other thoracic diseases.

Reducing the impact of tissue extraction via electrosurgery and enhanced image scanning can significantly reduce complications. The Prana System combines localization and tissue-cutting capabilities in one, which keeps surgeons from having to swap out components during a procedure, making for a smoother process. It can core, cut and feel blood vessels on the way toward the intended target, giving surgeons greater control over tissue preservation.

"Electrosurgery is foundational to modern surgery, but there is still opportunity to improve how energy-based tools are applied in minimally invasive settings," Nathan added. "Our goal is to introduce a new class of image-guided surgical tools that enable more precise intervention across a range of procedures."

The company projects sales of $7.5 billion from the Prana System in the United States, estimating that 2.5 million surgical modules will be able to use the new tool. While starting out focused on biopsies, the company plans to evolve the system into other procedures, such as ablation, in the future. It is also planning for a controlled U.S. clinical rollout as it moves toward commercialization

Texas still ranks as No. 1 in U.S. for inbound moves, but growth dips

by the numbers

Texas continues to be the country’s No. 1 magnet for newcomers from other states, giving a boost to the state’s economy. However, Texas’ appeal weakened in 2024 compared with the previous year, due in large part to spiking home prices.

An analysis of U.S. Census Bureau data by self-storage platform StorageCafe shows Texas saw net interstate migration of 76,000 people in 2024. Texas’ net interstate migration dropped nearly 50 percent from 2023, according to the analysis. Net migration refers to the number of incoming residents minus the number of outgoing residents.

California remained the top source of newcomers for Texas, sending nearly 77,000 residents to the Lone Star State in 2024, the analysis says. Florida ranked second, followed by New York, Colorado and Illinois.

“These trends reveal Texas’ continued pull from both high-cost coastal markets and other large Sun Belt states, resulting in a mix of affordability-driven and job-driven relocation,” StorageCafe says.

Putting a damper on the influx of new residents: a roughly 124 percent surge in Texas home prices over the past decade, according to StorageCafe.

“While the state remains significantly more affordable than California, its top feeder state, the once-wide pricing gap has narrowed,” says StorageCafe. “For many movers, Texas is still a relative bargain, but no longer an undisputed one.”

Nonetheless, Texas keeps attracting young, highly educated people, which bodes well for the state’s long-term economic outlook, StorageCafe says. More than half of new arrivals to Texas in 2024 held at least a bachelor’s degree, and the age of newcomers averaged 32.

Where are most of these young, highly educated newcomers settling?

Lloyd Potter, former Texas state demographer, tells StorageCafe that population growth in Texas is happening most rapidly in suburban “ring counties” at the expense of slowing growth in urban cores. Ring counties are on the outskirts of major metro areas.

“Many people are moving from urban cores to suburban rings seeking lower costs, newer housing, better schools, and more space,” Potter says. “Typically, a move to a suburban county will be within commuting or hybrid‑commuting distance of major metro economies.”

Artemis II makes historic call to space station with help from Houston Mission Control

History in the making

Still aglow from their triumphant lunar flyby, the Artemis II astronauts made more history Tuesday, April 7: calling their friends aboard the International Space Station hundreds of thousands of miles away as they headed home from the moon.

It was the first moonship-to-spaceship radio linkup ever. NASA's Apollo crews had no off-the-planet company back in the 1960s and 1970s, the last time humanity set sail for deep space.

"We have been waiting for this like you can’t imagine,” Artemis II commander Reid Wiseman called out.

For Christina Koch on Artemis II and Jessica Meir aboard the space station, it marked a joyous space reunion despite being 230,000 miles (370,000 kilometers) apart. The two teamed up for the world's first all-female spacewalk in 2019 outside the orbiting lab.

Koch told her “astro-sister” that she'd hoped to meet up with her again in space “but I never thought it would be like this — it's amazing.”

“I'm so happy that we are back in space together,” Meir replied, “even if we are a few miles apart.”

Houston's Mission Control arranged the cosmic chitchat between the four lunar travelers and the space station's three NASA and one French residents.

Koch described being awe-struck by not just the beauty of Earth, “but how much blackness there was around it.”

“It just made it even more special. It truly emphasized how alike we are, how the same thing keeps every single person on planet Earth alive,” she told the space station crew. “The specialness and preciousness of that really is emphasized” when viewing the home planet from the moon.

By late Tuesday afternoon, the Artemis II astronauts had beamed back more than 50 gigabytes' worth of pictures and other data from the previous day's lunar rendezvous, which set a new distance record for humanity. The highlight: an Earthset photo reminiscent of Apollo 8's Earthrise shot from 1968.

"While they are inspirational and, I think, allow all of us to really feel a little bit of what they were feeling, there's also a lot of science hidden inside of those images," said Mission Control's lead lunar scientist Kelsey Young. “The conversations and the science lessons learned are just beginning."

During a debriefing with Young, the astronauts recounted how they spotted a cascade of pinpricks of light on the lunar surface from impacting cosmic debris. The flashes lasted mere milliseconds and coincided by chance with Monday evening's total solar eclipse.

Young said it was too soon to know whether the crew witnessed an actual meteor shower or more random, run-of-the-mill micrometeoroid hits. Either way, there were “audible screams of delight” in the science operations center, she said.

Koch described being awe-struck by not just the beauty of Earth, “but how much blackness there was around it.”

“It just made it even more special. It truly emphasized how alike we are, how the same thing keeps every single person on planet Earth alive,” she told the space station crew. “The specialness and preciousness of that really is emphasized” when viewing the home planet from the moon.

The first lunar explorers since Apollo 17 in 1972, Wiseman and his crew are aiming for a splashdown off the San Diego coast on Friday to wrap up the nearly 10-day test flight. The recovery ship USS John P. Murtha left port Tuesday for the target zone.

It sets the stage for next year's Artemis III, a lunar lander docking demo in orbit around Earth. Artemis IV will follow in 2028 with two astronauts attempting to land near the lunar south pole.

As for the Orion capsule’s pesky potty, Mission Control assured the astronauts that no maintenance was required Tuesday. The toilet has been on-and-off limits to the crew ever since last week’s launch, prompting them to rely on a backup bag-and-funnel system for urinating.

NASA Administrator Jared Isaacman told the crew following the lunar flyby Monday night: “We definitely have to fix some of the plumbing” ahead of the next Artemis mission. Engineers suspect a clogged filter in the overboard flushing system.

Aside from the toilet and other relatively minor matters, the mission has gone well, Isaacman noted at a news conference Tuesday, “but I'll breathe easier when we get through reentry and everybody's under chutes and in the water.”

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