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:

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
Understanding cells as natural sensors and repurposing them into living therapeutics to detect and treat diseases, maintain health and prevent infections
Developing living electronics to convert biochemical information into information-dense electronic signals in real-time at the cell-material interface
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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Here’s where wages grew the most in Houston since 2021, according to new report

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Bolstered by a thriving manufacturing sector, Waller County—the country’s second-fastest-growing county—leads all Houston-area counties for the growth of pay from 2021 to 2026, according to a new study.

The study, conducted by personal finance website SmartAsset, found average pay in Waller County rose 48 percent from 2021 to 2026. The county’s average weekly pay climbed from $891 to $1,323 during that period.

Manufacturing ranks as the No. 1 employment sector in Waller County, accounting for about 4,500 workers, according to Executive Pulse. Those workers earn an average pay of $77,442 per year.

Waller County powers up its manufacturing hub

Waller County’s manufacturing economy keeps expanding, almost certainly contributing to the 48 percent spike in average pay from 2021 to 2026.

Grundfos, the world’s largest producer of water pumps, broke ground in June on a manufacturing plant at its Brookshire campus. The Danish company’s U.S. headquarters is in Brookshire. In conjunction with the groundbreaking, Grundfos opened the Grundfos Academy Americas training center.

The new 143,000-square-foot facility will make pump systems and water technology, primarily for water utilities and commercial real estate landlords.

Grundfos expects construction to be completed by Q3 2027, with the first production lines planned to start in Q4 of next year.

“Our growing presence in Brookshire reflects both our confidence in the U.S. market and our long‑term commitment to investing where our customers and partners need us most,” Grundfos CEO Poul Due Jensen said in a release.

Another manufacturer, TMEIC Corporation America, recently opened its third U.S. plant at Twinwood Business Park in Brookshire. The 280,000-square-foot facility, which eventually might employ 500 people, makes uninterruptible power supply units and medium-voltage power drives. The $65 million plant includes a customer training center and tech development labs.

The Twinwood facility is the largest of TMEIC’s 13 factories around the world.

TMEIC’s two other U.S. manufacturing plants are in the Houston area. The company’s North American headquarters is in the Houston Energy Corridor.

Perhaps the biggest recent manufacturing prize for Waller County: Austin-based electric vehicle maker Tesla’s new 1.65 million-square-foot factory at Brookshire’s Empire West Industrial Park. The $200 million plant, expected to employ up to 1,500 people by 2028, produces utility-scale batteries for energy storage.

Other major manufacturers in Waller County include Daikin North America and Igloo.

Pay growth around the region

Here’s a rundown of 2021-26 pay growth in the Houston metro’s eight other counties, according to SmartAsset.

Austin County — 42 percent
Chambers County — 37 percent
Harris County — 33 percent
Liberty County — 31 percent
Montgomery County — 29 percent
Fort Bend County — 28 percent
Galveston County — 26 percent
Brazoria County — 23 percent

Statewide, Dickens County, outside of Lubbock, saw the most significant growth in wages. According to the study, wages grew by 212 percent over the five years, from $707 per week in 2021 to $2,204 per week in 2026.

Among all Texas counties, Waller was ranked No. 44 on the report.

Small counties in the High Plains and West Texas regions saw the largest percent changes in average weekly wage, according to the report. See the full findings here.

Houston team’s breakthrough device leads innovation news to know

10+ can't-miss Houston business and innovation events for October

where to be

Editor's note: Healthcare and energy conferences headline this month's slate of innovation events in Houston. But there's also time for family-friendly gatherings and pickleball socials. Here’s what not to miss in October and how to register. Please note: this article may be updated to add more events.

Oct. 2 — Joy in Medicine Initiative Symposium

The Houston Methodist Joy in Medicine Initiative Symposium will explore the power of connection in enhancing professional fulfillment for clinicians and healthcare teams, this year with the theme of "Forging New Paths: Leadership, Connection & Innovation to Sustain Joy in Medicine." Hear from Dr. Shlomit Schall, Houston Methodist Physician Organization president and CEO and chief physician executive; Houston Methodist CEO Marc Boom; and Dr. Albert Wu, from Johns Hopkins, author of Therefore, Let us Rejoice: Sustaining Joy in Medicine. Stick around for a networking happy hour.

This event is Friday, Oct. 2, from 8:30 a.m.-4:30 p.m. at Thompson Houston on Allen Parkway. Find more information here.

Oct. 6-7 — Hydrogen Americas Summit and Exhibition

Hydrogen Americas delivers an unparalleled opportunity to explore how hydrogen integrates with CCUS and other energy solutions under the new U.S. and Americas energy paradigm. This event moves to Houston in 2026, providing unmatched access to industry leaders and opportunities. The summit will include CCUS-dedicated sessions integrated directly into the conference programming, providing deeper insights into carbon capture, utilization and storage. Look forward to networking opportunities to connect with global suppliers, regional developers and key policymakers.

This event begins Oct. 6 at George R. Brown Convention Center. Register here.

Oct. 6-7 — Annual Energy Summit — Energy, Risk, and Geopolitics

The 10th annual energy summit is co-hosted by Baker Botts and the Center for Energy Studies at Rice University's Baker Institute. This year's summit, “Energy, Risk, and Geopolitics,” will explore how a changing geopolitical landscape and shifts in supply chain risks are impacting investment, innovation and market dynamics. The two-day program will include discussions spanning petroleum and LNG markets, critical minerals, electricity reliability, AI and power demand.

This event begins Oct. 6 at 7:30 am at James A Baker III Hall. The event will also be livestreamed. Register here.

Oct. 7 – Rockets Get You to Orbit. Culture Gets You to Stay

The Ion will host a morning discussion exploring humanity’s future in space. The event will feature Rick Tumlinson, author of Why Space? The Purpose of People; Scott Solomon, author of Becoming Martian; and David Alexander and Alexander Regier of Rice University’s new Space Humanities Initiative. The conversations will be moderated by EarthLight Foundation Director Junaid Mian.

This event is Wednesday, Oct. 7, from 8:30-11 a.m. at the Ion. Register here.

Oct. 8 — Greentown Labs’ Fall Pickleball Social

Greentown Labs hosts its fall social at Pickle Lab HTX this month. Enjoy friendly matches, networking and light bites. All skill sets are welcome.

This event is Thursday, Oct. 8, from 5:30-7:30 p.m. at Pickle Lab HTX. Register here.

Oct. 10 – Ion Family Tech Festival

Bring the whole family out to the second Ion Family Tech Festival. Kids will get to participate in hands-on STEAM workshops and learn more about STEAM-related careers.

This event is Saturday, Oct. 10, from 9 a.m.-12 p.m. at the Ion. Register here.

Oct. 13 – Mercury Fund Day at the Ion

Don’t miss the latest installment of Mercury Fund Day at the Ion, previously known as Software Day. The recurring monthly event features office hours (by application), a keynote and networking opportunities.

This event is Tuesday, Oct. 13, from 3:30-7 p.m. at the Ion. Register here.

Oct. 14 — Future of Global Energy Conference

This October, the sixth annual Future of Global Energy Conference kicks off, convening influential leaders from across energy, technology, finance and public policy who will come together to explore the forces defining the next era of global energy and Houston’s role in shaping it. Ryan Lance, Executive Chairman of ConocoPhillips and 2027 Chair of the Greater Houston Partnership’s Board of Directors, is the keynote speaker for this year’s conference, bringing a global perspective on rising demand, market volatility and Houston’s role in the next era of energy growth.

This event takes place Oct. 14 at the Marriott Marquis. Register here.

Oct. 17 — Energy Day 2026

Energy Day Houston is the nation’s largest free, family-friendly STEM festival. It features over 50 interactive exhibits and live demonstrations focused on traditional and emerging energy career paths to power up your curiosity.

This event begins at 11 a.m. on Oct. 17 at Sam Houston Park. Get details here.

Oct. 22 — Rice360 Innovation for Healthcare Access Conference

Researchers and innovators from Rice University, the Texas Medical Center, non-profit organizations, healthcare providers and others will come together to explore gaps in healthcare at the Innovation for Healthcare Access Conference. The event will feature speakers, workshops and case study presentations and will focus on innovations for the health of women and children in underserved rural and urban communities across Texas.

This event is Thursday, Oct. 22, from 8 a.m.-5 p.m. at the Rice University BioScience Research Collaborative (BRC). Register here.

Oct. 28-29 – TiECon 2026

TiE Houston, TiE Dallas and TiE Austin are joining forces to host TiEcon Texas 2026 at the Ion this month. The event will focus on how automation, artificial intelligence and emerging technologies are reshaping Texas industries, the economy and daily life. The conference will feature keynotes, panels, fireside chats and the TiE Hatch Pitch Competition.

This event starts Thursday, Oct. 29, at the Ion. Register here.

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