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

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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.”

These three entrepreneurs saw a need in their industries and created their own solutions. Photos courtesy

3 Houston innovators to know this week

Who's who

A true innovator is someone who's able to look past how something has been done for years — decades even — and be creative enough to find a better way to do it.

From redesigning conventional lab space to seeing a niche opportunity for luxury home rentals, these three innovators to know this week have made strides in changing the game.

Caleb Bashor, professor at Rice University

Photo courtesy of Caleb Bashor

Not all labs are created equal — or affordably. Caleb Bashor, a professor at Rice University, along with seven colleagues, created a DIY lab to further research efforts based at the university.

The DIY lab, eVOLVER, comprises three modules: a customizable "smart sleeve" housing and interface for each culture vessel, a fluidic module that controls movement of liquid in and out of each culture vessel, and a modular hardware infrastructure that simplifies high-volume bi-directional data flow by decoupling each parameter into individual microcontrollers.

"The prototype 16-chamber version of eVOLVER described in the new paper cost less than $2,000, cheaper than what a lab might pay for a single continuous culture bioreactor," Bashor says. Read more about the eVOLVER here.

Sébastien Long, founder and CEO of Lodgeur

Photo courtesy of Lodgeur

Sébastien Long ended up in Houston by chance, and the city ended up being a great place to take his luxe apartment rental business plan and turn it into a reality. Houston-based Lodgeur is a rental company that takes the convenience of Airbnb and adds in the luxury experience of a hotel.

Long identified stylish apartment complexes and built his business which now has a couple properties downtown that are attractive to a niche market of clientele.

"We're roughly split between leisure guests and business travelers," Long says. "They want to feel like they're staying in a home away from home." Read more about Lodgeur here.

Gustavo Sanchez, co-founder and CEO of Pandata Tech

Photo courtesy of Pandata Tech

In oil and gas, proper data management can be the difference of millions of dollars in savings. Pandata Tech can run a data quality check for its oil and gas clients — and even engages automation and machine learning for quicker, more thorough results.

Gustavo Sanchez, co-founder and CEO of the company, is looking to bring his data systems into new industries, like health care, where data management can be hectic, overwhelming, and crucial to life-saving opportunities.

"There's so much data, and it's so noisy, that it's hard to know whether the data can be trusted or not," Sanchez says. Read more about Pandata Tech here.

The DIY lab, called the eVOLVER, costs $2,000 less than a comparable setup. Photo courtesy of Rice University

Houston scientist creates a DIY lab concept for flexible and efficient work

Work space

Every scientist needs his or her own space, and each discipline calls for different types of tools and space requirements. Caleb Bashor, a professor at Rice University, along with seven colleagues, created a DIY lab to further research efforts based at the university.

Stemming from the need of a more customized study, Bashor and his team created a setup that combines the control of automated cell-culturing systems that can run continuously for months with the scale of high-throughput systems that grow dozens of cultures at once, according to a news release issued by Rice University.

Bashor, who has been at the university since 2017, has worked in science for 15 years and received his post doctorate from Massachusetts Institute of Technology, where he met many of his colleagues that collaborated on eVOLVER.

"If you don't have something to do the job in the lab, you go and you build it," says Bashor. "It might take a few rounds of building and rebuilding, but eventually you get around to having it be something that gives you what you want. In this case, it's something a lot of different academic labs want now, we have actually given this out to dozens of labs."

The DIY initiative has made waves throughout the Rice student body, Bashor shares with InnovationMap. One graduate student, Brandon Wong, tasked to help with the project has shared a how-to for the DIY lab online.

"It's a basic research tool, it's exciting," says Bashor. It's something that can be leveraged for a lot of great research projects inside of the university."

Bashor and his team in the bioengineering department support lead cellular and biomolecular engineering research, which led them to create the lab.

"We turned to DIY electronics and we decided to build it ourselves," Bashor tells InnovationMap. "The process took about three years. We had to learn all of the tools that were out there for doing DIY work and a lot of these tools have showed up in the last ten years."

Rice University's department of bioengineering is a member of the Texas Medical Center and hosts interdisciplinary training programs at MD Anderson Cancer Center and Baylor College of Medicine, according to the school's website.

"This is one of the biggest centers in the world for immunotherapy, particularly clinical immunotherapy, and so we're working with people who do immunotherapy using my special engineering techniques, which mostly involve engineering the way that cells behave to try to more effectively kill cancer," says Bashor.

Caleb Bashor and his associates created the lab. Photo courtesy of Rice University

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Axiom Space wins NASA contract for fifth private mission, lands $350M in financing

ready for takeoff

Editor's note: This story has been updated to include information about Axiom's recent funding.

Axiom Space, a Houston-based space infrastructure company that’s developing the first commercial space station, has forged a deal with NASA to carry out the fifth civilian-staffed mission to the International Space Station.

Axiom Mission 5 is scheduled to launch in January 2027, at the earliest, from NASA’s Kennedy Space Center in Florida. The crew of non-government astronauts is expected to spend up to 14 days docked at the International Space Station (ISS). Various science and research activities will take place during the mission.

The crew for the upcoming mission hasn’t been announced. Previous Axiom missions were commanded by retired NASA astronauts Michael López-Alegría, the company’s chief astronaut, and Peggy Whitson, the company’s vice president of human spaceflight.

“All four previous [Axiom] missions have expanded the global community of space explorers, diversifying scientific investigations in microgravity, and providing significant insight that is benefiting the development of our next-generation space station, Axiom Station,” Jonathan Cirtain, president and CEO of Axiom, said in a news release.

As part of Axiom’s new contract with NASA, Voyager Technologies will provide payload services for Axiom’s fifth mission. Voyager, a defense, national security, and space technology company, recently announced a four-year, $24.5 million contract with NASA’s Johnson Space Center in Houston to provide mission management services for the ISS.

Axiom also announced today, Feb. 12, that it has secured $350 million in a financing round led by Type One Ventures and Qatar Investment Authority.

The company shared in a news release that the funding will support the continued development of its commercial space station, known as Axiom Station, and the production of its Axiom Extravehicular Mobility Unit (AxEMU) under its NASA spacesuit contract.

NASA awarded Axiom a contract in January 2020 to create Axiom Station. The project is currently underway.

"Axiom Space isn’t just building hardware, it’s building the backbone of humanity’s next era in orbit," Tarek Waked, Founding General Partner at Type One Ventures, said in a news release. "Their rare combination of execution, government trust, and global partnerships positions them as the clear successor-architect for life after the ISS. This is how the United States continues to lead in space.”

Houston edtech company closes oversubscribed $3M seed round

fresh funding

Houston-based edtech company TrueLeap Inc. closed an oversubscribed seed round last month.

The $3.3 million round was led by Joe Swinbank Family Limited Partnership, a venture capital firm based in Houston. Gamper Ventures, another Houston firm, also participated with additional strategic partners.

TrueLeap reports that the funding will support the large-scale rollout of its "edge AI, integrated learning systems and last-mile broadband across underserved communities."

“The last mile is where most digital transformation efforts break down,” Sandip Bordoloi, CEO and president of TrueLeap, said in a news release. “TrueLeap was built to operate where bandwidth is limited, power is unreliable, and institutions need real systems—not pilots. This round allows us to scale infrastructure that actually works on the ground.”

True Leap works to address the digital divide in education through its AI-powered education, workforce systems and digital services that are designed for underserved and low-connectivity communities.

The company has created infrastructure in Africa, India and rural America. Just this week, it announced an agreement with the City of Kinshasa in the Democratic Republic of Congo to deploy a digital twin platform for its public education system that will allow provincial leaders to manage enrollment, staffing, infrastructure and performance with live data.

“What sets TrueLeap apart is their infrastructure mindset,” Joe Swinbank, General Partner at Joe Swinbank Family Limited Partnership, added in the news release. “They are building the physical and digital rails that allow entire ecosystems to function. The convergence of edge compute, connectivity, and services makes this a compelling global infrastructure opportunity.”

TrueLeap was founded by Bordoloi and Sunny Zhang and developed out of Born Global Ventures, a Houston venture studio focused on advancing immigrant-founded technology. It closed an oversubscribed pre-seed in 2024.

Texas space co. takes giant step toward lunar excavator deployment

Out of this world

Lunar exploration and development are currently hampered by the fact that the moon is largely devoid of necessary infrastructure, like spaceports. Such amenities need to be constructed remotely by autonomous vehicles, and making effective devices that can survive the harsh lunar surface long enough to complete construction projects is daunting.

Enter San Antonio-based Astroport Space Technologies. Founded in San Antonio in 2020, the company has become a major part of building plans beyond Earth, via its prototype excavator, and in early February, it completed an important field test of its new lunar excavator.

The new excavator is designed to function with California-based Astrolab's Flexible Logistics and Exploration (FLEX) rover, a highly modular vehicle that will perform a variety of functions on the surface of the moon.

In a recent demo, the Astroport prototype excavator successfully integrated with FLEX and proceeded to dig in a simulated lunar surface. The excavator collected an average of 207 lbs (94kg) of regolith (lunar surface dust) in just 3.5 minutes. It will need that speed to move the estimated 3,723 tons (3,378 tonnes) of regolith needed for a lunar spaceport.

After the successful test, both Astroport and Astrolab expressed confidence that the excavator was ready for deployment. "Leading with this successful excavator demo proves that our technology is no longer theoretical—it is operational," said Sam Ximenes, CEO of Astroport.

"This is the first of many implements in development that will turn Astrolab's FLEX rover into the 'Swiss Army Knife' of lunar construction. To meet the infrastructure needs of the emerging lunar economy, we must build the 'Port' before the 'Ship' arrives. By leveraging the FLEX platform, we are providing the Space Force, NASA, and commercial partners with a 'Shovel-Ready' construction capability to secure the lunar high ground."

"We are excited to provide the mobility backbone for Astroport's groundbreaking construction technology," said Jaret Matthews, CEO of Astrolab, in a release. "Astrolab is dedicated to establishing a viable lunar ecosystem. By combining our FLEX rover's versatility with Astroport's civil engineering expertise, we are delivering the essential capabilities required for a sustainable lunar economy."

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This article originally appeared on CultureMap.com.

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