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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4 Houston health tech startups advancing medical innovation

meet the finalists

Houston has been driving medical innovation for decades. And thanks to leading hospitals, cutting-edge research and breakthrough technologies, the region’s healthcare ecosystem continues to improve how patients are diagnosed, treated and cared for.

The Health Tech Business category in our 2025 Houston Innovation Awards will honor an innovative startup within the health and medical technology sectors.

Four forward-thinking businesses have been named finalists for the 2026 award. This year's finalists, selected by our esteemed panel of judges, range from a startup developing miniaturized medical technologies for space to a company using AI to help develop cancer treatment plans.

Read more about these businesses, their innovative founders, and how they're shaping the future of health care below.. The 2026 winners will be announced on InnovationMap.com in mid-November.

Bairitone Health

Bairitone Health is bringing anatomy imaging for sleep apnea to the home environment. The company's platform maps users' anatomy during natural sleep using a facial patch to determine the root cause of airway obstruction. It then offers effective therapies for each patient.

The company was founded in 2022 in the Texas Medical Center's Biodesign program by CEO Meagan Pitcher, CTO Onur Kilic and chief medical officer Britt Cross. It was a member of Activate Houston's inaugural cohort and has participated in numerous accelerators and incubators. The company raised an oversubscribed seed round for $2.4 million earlier this year and received Breakthrough Device Designation from the Food and Drug Administration in April.

InformAI Inc.

InformAI Inc. develops fit-to-purpose AI solutions for the clinical setting. Its RadOncAI product recently received FDA 510(k) clearance. The product uses AI to create a first-pass radiation therapy dose plan for complex head and neck cancers in an effort to eliminate bottlenecks in radiation planning and ultimately cancer treatment. The company has also developed AI products for sinus disease detection and 3D organ reconstruction.

CEO Jim Havelka founded the company in 2017. It is participating in the Mayo Clinic Accelerate Platform. It has raised about $4 million in seed funding and has received numerous non-dilutive grants from the National Science Foundation, the National Institutes of Health and the Cancer Prevention and Research Institute of Texas. The company shared in its application that it plans to launch a Series A fundraising round and submit an FDA 510K application for its organ reconstruction product, Voluquant, by the end of 2026.

Prana Surgical

Prana Surgical is developing a minimally invasive surgical platform for small, hard-to-reach lung nodules that may be cancerous. The company's Prana System cleared U.S. Food and Drug Administration (FDA) approval earlier this year.

Prana Surgical was originally founded as Prana Thoracic in 2022. It has participated in numerous accelerators, including the Texas Medical Center Innovation Accelerator in 2023 and the IGNITE Health accelerator in 2022. It raised $6 million in Series A funding rounds in 2023 and 2024 , with a Series B currently ongoing. The company said in its application that it is currently moving into the next stage of clinical validation and revenue generation in the U.S., in addition to preparing its manufacturing and commercial infrastructure for broader use.

Skybound MedTech

Skybound MedTech develops technologies that aim to address the health risks of long-duration spaceflight. Its compact, miniaturized medical technologies can deliver complex therapies without a physician.

CEO Matthew Kuhn, who previously founded Taurus Vascular, founded Skybound last year. The company emerged from stealth in January after raising a $1.25 million Series A round. It plans to advance its lead dual-use platform into critical preclinical validation in November, the company shared in its application. It is currently raising a $25 million Series A round and is pursuing federal research partnerships with DARPA and ARPA-H.

Generation Park lands new facility to scale xeno-organ production

Organ innovation

Maryland-based United Therapeutics Corp. has opened a new 77,448-square-foot facility to manufacture xeno-organs in Northeast Houston’s growing biotech hub, Generation Park.

The new Houston location is United Therapeutics’ third Designated Pathogen-Free (DPF) site, named for transplant pioneers Dr. Bartley P. Griffith and Dr. Robert A. Montgomery. The company says the new facility will enable it to scale commercial production of its xeno-organs once they receive regulatory approval.

An existing DPF facility in Virginia is supporting clinical trials for the xeno-organs, and a third site in Minnesota will also focus on commercialization with the Houston site, according to the company.

Xeno-organs are organs taken from a non-human animal source and transplanted, implanted or infused into a human recipient.

Currently, United Therapeutics is advancing clinical trials to support a Biologics License Application with the U.S. Food and Drug Administration for its investigational-stage xenotransplantation, UKidney, UThymoKidney and UHeart products. The products all involve working with the genes from humans and pigs.

In 2025, Chron.com reported the company was working to construct an estimated $96 million facility to breed genetically engineered animals. Head of investor relations at United Therapeutics Dewey Steadman told the Houston Business Journal in 2025 that the pigs’ DNA will be edited. In November 2024, a 53-year-old woman in Alabama received a transplanted kidney from UKidney that had 10 gene edits. She had the transplant removed in April 2025, after her body rejected it.

The Dr. Bartley P. Griffith and Dr. Robert A. Montgomery Xenograft Production Facility requires a “strictly controlled, biosecure barrier environment, including air filtration, filtered water, filtered feed supplies, and state-of-the-art decontamination entryways,” according to the company. Being pathogen-free means it includes calibrated air and water conduits to support the transplantability of xenograft products and to prevent contamination. For energy considerations, the building also features solar arrays.

“With our third xenograft production facility now open and clinical trials underway, United Therapeutics is moving closer to its goal of providing transplantable organs to the people who need them,” Martine Rothblatt, chairperson and CEO of United Therapeutics, said in a news release. “It is fitting that this facility is named for Dr. Griffith and Dr. Montgomery, whose first-in-human surgeries turned xenotransplantation from a theoretical possibility into a clinical reality.”

The facility, which wrapped construction in August, is located at 11848 Common Dock Dr. in Generation Park, which will house manufacturing sites for pharmaceutical heavyweights Bristol Myers Squibb and Eli Lilly. Last fall, Eli Lilly tapped Generation Park for its $6.5 billion manufacturing plant, and Bristol Myers Squibb made a $2.3 billion investment in August to bring its state-of-the-art site to the master-planned commercial district.

Elon Musk's SpaceX reports profit as AI and satellite businesses booms

Booming Business

SpaceX reported a bigger quarterly profit than expected on Tuesday, October 20, as its satellite communications and artificial intelligence businesses boomed.

The company, run by Elon Musk, posted a profit for the three months through September 2026 of $4.4 billion, or 35 cents per share, reversing a year-ago loss and easily topping Wall Street's expectations. Revenue soared to $14.6 billion, up 161%.

On a conference call with analysts, Musk suggested a merger with his electric car company Tesla might be in the works, something that has been rumored for months. He said both companies formed “special committees” of independent directors to discuss the issue, though he played down the chances of an imminent deal.

“Some people out there assume that a SpaceX and Tesla merger is a certainty,” he said. “I think that would be overstating it.”

The AI business became SpaceX's largest by revenue in the third quarter, although the Starlink satellite service remains the biggest profit generator.

“They beat across all metrics and the Starlink business looks to be accelerating,” said Dan Ives, an analyst at Yorkville Ives. “This is just what (Wall) Street wanted.”

The stock rose 7.5% in after-hours trading.

Musk also told analysts that for next month's launch of its Starship rocket, SpaceX will attempt to grab both the booster and ship with mechanical arms upon return to base, a key step toward demonstrating it can reuse the massive spacecraft.

“The only way that we can extend consciousness beyond Earth on a sustained basis is with a fully reusable orbital launch vehicle,” Musk said, calling the attempt, if successful, “a massive technology milestone.”

SpaceX hopes to get Starship on a regular launch pattern in preparation for NASA's upcoming lunar missions.

The company already has huge contracts with the federal government, and House Democrats have called for investigations into those contracts and Musk’s work with the Department of Government Efficiency. Musk has spent $276 million since July in support of Republican candidates.

In a filing for its initial public offering in June, SpaceX warned that a change in control of Congress could have a “material and adverse impact on our growth and competitive position.”

Musk recently drew criticism from politicians in Washington after speeds for a military version of SpaceX's satellite communications service were slowed for Ukraine following President Donald Trump's deal to get more diesel oil from Russia amid a push to end the war. The Wall Street Journal reported Tuesday that it was Musk who ordered the slowdown, impeding Ukraine’s use of drones along the front. SpaceX did not immediately respond to an Associated Press request for comment on the Journal story.

Both Trump and Musk have denied responsibility for the slowdown.

As midterm elections near, Musk on Monday promised to give one share of SpaceX to “every kid in America” next year, though he provided no details on how the distribution would be carried out. With communities nationwide protesting the construction of large data centers and concerns about AI safety, AI companies are trying to build goodwill. Anthropic pledged to commit 5% of its shares to a new “public benefit” fund.

SpaceX shares have been under pressure over concerns that the company was spending too much on major projects to compete with rivals such as Anthropic. The company said capital expenditures totaled $19.6 billion last quarter, nearly triple the figure from a year earlier, and it forecast spending would grow to $35 billion to $40 billion in the current quarter.

Shares of SpaceX closed Tuesday at $147.79, down from a peak near $201 after its IPO, which made Musk the world’s first trillionaire at the time. But the share prices for SpaceX and Tesla have since dropped, reducing his net worth to $925 billion, according to Forbes magazine.

Tesla reports third-quarter financial results Wednesday. Last week, Tesla unveiled a new Roadster sports car that in some versions may include thrusters allowing it to briefly fly using SpaceX technology — though experts say anything usable for drivers is a long shot.

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