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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Houston e-commerce giant Cart.com launches government-focused subsidiary

government branch

Houston e-commerce and logistics unicorn Cart.com has launched a new subsidiary.

Cart Government Solutions (CGS), which was announced earlier this week, will provide supply chain and logistics services and software for the federal and state government sectors. The new subsidiary will be headquartered in Washington, D.C., and operate out of about 6 million square feet of secure warehouse space across 14 U.S. facilities, according to a news release from Cart.com. It will support both domestic and overseas logistics.

Industry veteran Gregg Zegras will lead the new entity as president. Zegras previously served as Cart.com's chief revenue officer, according to LinkedIn. Before that, he served as president of Connecticut-based Pitney Bowes Global eCommerce, a digital shipping solutions company.

Remington Tonar, Cart.com's co-founder, will serve as CGS's chief innovation officer.

“Government agencies face procurement and logistics challenges that many commercial platforms simply weren’t built to solve,” Zegras said in the news release. “Cart Government Solutions exists to change that. We’re combining the speed and innovation of a technology company with the compliance rigor, security, and operational depth that federal and state customers require, and we’re doing it with a team that has spent careers working alongside and inside these agencies.”

According to the company, CGS will focus on meeting compliance and security requirements in the public sector. Some of the services the new entity will offer include:

Inventory management
Cold-chain and specialty storage for pharmaceuticals, medical devices and regulated goods
Enterprise-grade supply chain software
Government-compliant webstores and online ordering portals
Cybersecurity operations

Cart.com has been serving the public sector since 2022, when the company began distributing COVID-19 health supplies nationwide, according to the news release. Through that pandemic-era contract, the company reports it moved more than 725 million units, with an average of under two days per shipment.

Cart.com was founded in Houston in 2020, though it briefly moved its headquarters to Austin. The company reached unicorn status with its $60 million Series C raise in 2023. It most recently raised $180 million in growth capital from private equity firm Springcoast Partners in March, which put the startup over the $1 billion in fundraising mark in just six years.

At the time, Cart.com said it planned to scale its logistics network, expand AI capabilities and develop workflow automation tools.

Houston-based KBR Inc. also recently launched a government services spinoff. Read more here.

2 Houston universities named best colleges of 2027 by Princeton Review

A-Plus Ratings

Back-to-school season is has returned in full force, and that means it's time for college rankings. Two Houston universities in particular are being hailed as the top of the class for 2027.

The high caliber schools — Rice University and University of Houston — earned new acclaim in The Princeton Review's ranking of the "Best 392 Colleges" for 2027.

The Princeton Review's 35th annual "Best Colleges" rankings are determined by a survey of 172,000 current college students that gave "candid feedback" about their schools and their experiences. The flagship guide does not rank the schools overall, but it does rank them across 50 different categories, including best-run colleges, best quality of life, happiest students, best athletic facilities, among others.

In all, 14 Texas institutions were highlighted in the overall list of the 392 best colleges.

Schools don't pay to be included in the guide, but The Princeton Review clarified that schools could pay for a "featured" designation. No Houston university paid to be featured in this year's guide. Trinity University in San Antonio and Southwestern University, a private school in the Austin suburb Georgetown, were the only two Texas schools that paid to be "featured."

Rice and UH have been on a winning streak in separate reports of the best universities worldwide, best graduate schools, and best online degree programs.

In addition to being included in the overall list, Rice was highlighted as one of the Best Value Colleges, Colleges That Create Futures, and it earned high marks in Princeton Review's Mental Health Honor Roll 2026. The home of the Rice Owls also starred in the regional Best Southwest list that contained 41 universities across Arizona, Colorado, New Mexico, Oklahoma, and Texas.

"Rice University stands out as a leading research university where academic diversity and a wide array of interdisciplinary institutes and centers make it easy for students to explore multiple areas of interest," the school's profile says. "At Rice, 'knowledge isn’t siloed — students are constantly crossing disciplines and interests in ways that feel natural rather than exceptional.'"

Rice earned the following rankings on 14 other lists:

No. 1 – Lots of Race/Class Interaction
No. 3 – Best College Newspaper
No. 9 – Friendliest Students
No. 11 – Best Quality of Life
No. 13 – Great Financial Aid
No. 14 – Top 50 Best Value Private Colleges
No. 17 – Their Students Love These Colleges
No. 18 – Top 20 Best Value Private Colleges Without Aid
No. 18 – Best Student Support and Counseling Services
No. 19 – Best College Dorms
No. 21 – Students Study the Most
No. 24 – Best Campus Food
No. 24 – Best College Radio Station
No. 24 – Best-Run colleges

The University of Houston also appeared in the Best Southwest, Best Value Colleges, and Colleges That Create Futures lists, and it was named a top Green College, which examined schools that "share superb sustainability practices, a strong foundation in sustainability education, and a healthy quality of life for students on campus

UH earned five more accolades:

No. 1 – Top 50 Undergraduate Schools for Entrepreneurship Studies
No. 1 – Top Undergraduate Schools for Entrepreneurship Studies in the Southwest
No. 8 – Most Politically Moderate Students
No. 15 – Financial Aid Not So Great
No. 42 – Top 50 Best Value Public Colleges

In the school's profile, students say they had an overall positive experience thanks to UH's excellent academic offerings and dedicated faculty members.

"Students confirm that 'the research and other academic opportunities... are very accessible to students who seek it out,'" the profile says. "This includes taking advantage of UH’s vast alumni network (more than 325,000 and counting), not to mention its location in the corporate center of Houston, where 'the opportunities that are provided are immense.'"

The 12 other public and private universities in Texas included in The Princeton Review's 2027 guide are:

The University of Texas at Austin
Southwestern University, Georgetown
Baylor University, Waco
Texas A&M University - College Station
Trinity University, San Antonio
Texas State University, San Marcos
Angelo State University, San Angelo
Texas Christian University, Fort Worth
University of Dallas, Irving
Southern Methodist University, Dallas
The University of Texas at Dallas, Richardson
Austin College, Sherman

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A version of this story originally appeared on CultureMap.com.

Houston named the No.1 emerging city for biopharma in inaugural report

Biopharma Leader

Houston is ranked No.1 on the first-ever Next 10 U.S. Biopharma Clusters report published by Genetic Engineering & Biotechnology News (GEN).

The report, which ranks the best emerging hubs for life science activities, considered patents, NIH funding, lab space, venture capital investments, and the number of jobs in regions in cities, states and “clusters” across the U.S. GEN touts Houston as the top city for the biopharma industry due to a surge in funding, job creation, medical innovations and startup success.

Here’s how Houston ranked in the report’s different categories;

No. 1 for NIH funding with 2,262 awards totaling more than $1.25 billion
No. 2 for emerging regions for jobs, with 28,000 jobs
No. 2 for lab space, with roughly 8 million square feet in the market
No. 6 for patents, with 2,760 patent families

According to BioHouston chairman Jeff Wade, Houston secured half a billion dollars in venture capital funding in 2025 and 2026 to date.

The report called out major biopharm news out of Houston in the last few months, including Bristol Myers Squibb selecting Houston for its $1 billion, 600,000-square-foot manufacturing site and Eli Lily selecting Houston for its $6.5 billion, 236-acre manufacturing site. Both facilities will be located within Generation Park, a 4,300-acre, master-planned commercial district near Lake Houston.

Houston startups like CrossBridge Bio and Duracyte were also mentioned in the report. CrossBridge, which develops antibody-drug conjugates for cancer, was acquired by Eli Lily in April for $300 million. Duracyte, a “living pharmacy” company, was launched out of Rice University’s biotech venture studio RBL LLC this spring and is backed by up to a $45 million Advanced Research Projects Agency for Health (ARPA-H) award.

The startup is working to commercialize its Hybrid Advanced Molecular Manufacturing Regulator (HAMMR) technology, a rechargeable, implantable device that can sense biological signals, monitor tumor environments and adjust therapeutic output in real time.

“There’s a lot of great talent, but the unique advantage that we have is we are able to benefit from a lot of unique clinical infrastructure and clinician insights,” Omid Veiseh, Duracyte co-founder and managing partner of RBL LLC, told GEN. “There are a lot of clinicians here who are eager to partner on investigator-initiated trials.”

The report also touted Houston’s Texas Medical Center, home to the University of Texas MD Anderson Cancer Center and Baylor College of Medicine, and international partnerships like the recently expanded TMC Korea BioBridge.

Other cities to make the list include:

No. 2 Minneapolis-St. Paul
No. 3 Denver-Boulder
No. 4 St. Louis
No. 5 Dallas-Fort Worth

States to make the list include:

No. 1 Ohio (including Cincinnati, Cleveland, and Columbus)
No. 2 Indiana (including Indianapolis)
No. 3 Florida (including Jacksonville and Miami-Fort Lauderdale)
No. 4 Georgia (including Atlanta and Augusta)
No. 5 Wisconsin (including Madison and Kenosha)

Regional state clusters to watch include:

Phoenix
Pittsburgh
Greater Richmond, Virginia
South Carolina
Utah

See the full report here.

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