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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New findings from a team of Rice University researchers could enhance MRI clarity. Photo via Unsplash.

Rice University researchers unveil new model that could sharpen MRI scans

MRI innovation

Researchers at Rice University, in collaboration with Oak Ridge National Laboratory, have developed a new model that could lead to sharper imaging and safer diagnostics using magnetic resonance imaging, or MRI.

In a study recently published in The Journal of Chemical Physics, the team of researchers showed how they used the Fokker-Planck equation to better understand how water molecules respond to contrast agents in a process known as “relaxation.” Previous models only approximated how water molecules relaxed around contrasting agents. However, through this new model, known as the NMR eigenmodes framework, the research team has uncovered the “full physical equations” to explain the process.

“The concept is similar to how a musical chord consists of many notes,” Thiago Pinheiro, the study’s first author, a Rice doctoral graduate in chemical and biomolecular engineering and postdoctoral researcher in the chemical sciences division at Oak Ridge National Laboratory, said in a news release. “Previous models only captured one or two notes, while ours picks up the full harmony.”

According to Rice, the findings could lead to the development and application of new contrast agents for clearer MRIs in medicine and materials science. Beyond MRIs, the NMR relaxation method could also be applied to other areas like battery design and subsurface fluid flow.

“In the present paper, we developed a comprehensive theory to interpret those previous molecular dynamics simulations and experimental findings,” Dilipkumar Asthagiri, a senior computational biomedical scientist in the National Center for Computational Sciences at Oak Ridge National Laboratory, said in the release. ”The theory, however, is general and can be used to understand NMR relaxation in liquids broadly.”

The team has also made its code available as open source to encourage its adoption and further development by the broader scientific community.

“By better modeling the physics of nuclear magnetic resonance relaxation in liquids, we gain a tool that doesn’t just predict but also explains the phenomenon,” Walter Chapman, a professor of chemical and biomolecular engineering at Rice, added in the release. “That is crucial when lives and technologies depend on accurate scientific understanding.”

The study was backed by The Ken Kennedy Institute, Rice Creative Ventures Fund, Robert A. Welch Foundation and Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory.

Vicky Yao and Qiliang Lai. Photo courtesy of Rice University

Rice University scientists invent new algorithm to fight Alzheimer's

A Seismic Breakthrough

A new breakthrough from researchers at Rice University could unlock the genetic components that determine several human diseases such as Parkinson's and Alzheimer's.

Alzheimer's disease affected 57 million people worldwide in 2021, and cases in the United States are expected to double in the next couple of decades. Despite its prevalence and widespread attention of the condition, the full mechanisms are still poorly understood. One hurdle has been identifying which brain cells are linked to the disease.

For years, it was thought that the cells most linked with Alzheimer's pathology via DNA evidence were microglia, infection-fighting cells in the brain. However, this did not match with actual studies of Alzheimer's patients' brains. It's the memory-making cells in the human brain that are implicated in the pathology.

To prove this link, researchers at Rice, alongside Boston University, developed a computational algorithm called “Single-cell Expression Integration System for Mapping Genetically Implicated Cell Types," or SEISMIC. It allows researchers to zero in on specific neurons linked to Alzheimer's, the first of its kind. Qiliang Lai, a Rice doctoral student and the lead author of a paper on the discovery published in Nature Communications, believes that this is an important step in the fight against Alzheimer's.

“As we age, some brain cells naturally slow down, but in dementia — a memory-loss disease — specific brain cells actually die and can’t be replaced,” said Lai. “The fact that it is memory-making brain cells dying and not infection-fighting brain cells raises this confusing puzzle where DNA evidence and brain evidence don’t match up.”

Studying Alzheimer's has been hampered by the limitations of computational analysis. Genome-wide association studies (GWAS) and single-cell RNA sequencing (scRNA-seq) map small differences in the DNA of Alzheimer's patients. The genetic signal in these studies would often over-emphasize the presence of infection fighting cells, essentially making the activity of those cells too "loud" statistically to identify other factors. Combined with greater specificity in brain regional activity, SEISMIC reduces the data chatter to grant a clearer picture of the genetic component of Alzheimer's.

“We built our SEISMIC algorithm to analyze genetic information and match it precisely to specific types of brain cells,” Lai said. “This enables us to create a more detailed picture of which cell types are affected by which genetic programs.”

Though the algorithm is not in and of itself likely to lead to a cure or treatment for Alzheimer's any time soon, the researchers say that SEISMIC is already performing significantly better than existing tools at identifying important disease-relevant cellular signals more clearly.

“We think this work could help reconcile some contradicting patterns in the data pertaining to Alzheimer’s research,” said Vicky Yao, assistant professor of computer science and a member of the Ken Kennedy Institute at Rice. “Beyond that, the method will likely be broadly valuable to help us better understand which cell types are relevant in different complex diseases.”

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This article originally appeared on CultureMap.com.

Rice University's new Bachelor of Science in AI will be one of only a few in the country. Photo via Getty Images.

Houston university to launch artificial intelligence major, one of first in nation

BS in AI

Rice University announced this month that it plans to introduce a Bachelor of Science in AI in the fall 2025 semester.

The new degree program will be part of the university's department of computer science in the George R. Brown School of Engineering and Computing and is one of only a few like it in the country. It aims to focus on "responsible and interdisciplinary approaches to AI," according to a news release from the university.

“We are in a moment of rapid transformation driven by AI, and Rice is committed to preparing students not just to participate in that future but to shape it responsibly,” Amy Dittmar, the Howard R. Hughes Provost and executive vice president for academic affairs, said in the release. “This new major builds on our strengths in computing and education and is a vital part of our broader vision to lead in ethical AI and deliver real-world solutions across health, sustainability and resilient communities.”

John Greiner, an assistant teaching professor of computer science in Rice's online Master of Computer Science program, will serve as the new program's director. Vicente Ordóñez-Román, an associate professor of computer science, was also instrumental in developing and approving the new major.

Until now, Rice students could study AI through elective courses and an advanced degree. The new bachelor's degree program opens up deeper learning opportunities to undergrads by blending traditional engineering and math requirements with other courses on ethics and philosophy as they relate to AI.

“With the major, we’re really setting out a curriculum that makes sense as a whole,” Greiner said in the release. “We are not simply taking a collection of courses that have been created already and putting a new wrapper around them. We’re actually creating a brand new curriculum. Most of the required courses are brand new courses designed for this major.”

Students in the program will also benefit from resources through Rice’s growing AI ecosystem, like the Ken Kennedy Institute, which focuses on AI solutions and ethical AI. The university also opened its new AI-focused "innovation factory," Rice Nexus, earlier this year.

“We have been building expertise in artificial intelligence,” Ordóñez-Román added in the release. “There are people working here on natural language processing, information retrieval systems for machine learning, more theoretical machine learning, quantum machine learning. We have a lot of expertise in these areas, and I think we’re trying to leverage that strength we’re building.”

The new Rice Nexus is partnering with Google Public Sector and Non Sibi Ventures to support high-potential AI-focused startups. Image via Rice University.

Google teams up with Rice University to launch AI-focused accelerator

eyes on AI

Google Public Sector is teaming up with Rice University to drive early-stage artificial intelligence innovation and commercialization via the new Rice AI Venture Accelerator, or RAVA.

RAVA will use Google Cloud technology and work with venture capital firm Non Sibi Ventures to connect high-potential AI-focused startups with public and private sector organizations. The incubator will be led by Rice Nexus, which launched earlier this year in the Ion District as an AI-focused "innovation factory.”

“Google Public Sector is proud to partner with a leading institution like Rice University to launch the Rice AI Venture Accelerator,” Reymund Dumlao, director of state and local government and education at Google Public Sector, said in a news release. “By providing access to Google Cloud’s cutting-edge AI, secure cloud infrastructure and expertise, we’re enabling the next generation of AI pioneers to develop solutions that address critical challenges across industries and within the public sector. This unique partnership between education and industry will give participants access to cutting-edge research, leading technologists, specialized resources and a collaborative academic ecosystem, fostering an environment for rapid innovation and growth.”

Participants will have access to Google Public Sector’s AI leadership as well as experts from Rice’s Ken Kennedy Institute, which focuses on AI and computing research. It will be led by Sanjoy Paul, Rice Nexus’ inaugural executive director. Paul previously worked at Accenture LLC as a managing director of technology and is a lecturer in Rice's Department of Computer Science.

Rice Nexus will serve as the physical hub for RAVA, but the program will support AI startups from across the U.S., as part of Rice’s Momentous strategic plan, according to the university.

“This hub enables AI startups to go beyond building minimum viable products that meet industry privacy standards by utilizing the latest AI technologies from Google Cloud,” Paul said in the news release. “Our goal is to maximize the return on investment for our corporate partners, driving meaningful innovation that will have lasting impact on their industries.”

The 10,000-square-foot Rice Nexus space currently serves as home base for several startups with ties to Rice, including Solidec, BeOne Sports and others. Read more about the new incubation space here.

OpenSafe.AI, a new platform that utilizes AI, data, and hazard and resilience models to support storm response decision makers, has secured an NSF grant. Photo by Eric Turnquist

Houston-area researchers score $1.5M grant to develop storm response tech platform

fresh funding

Researchers from Rice University have secured a $1.5 million grant from the National Science Foundation to continue their work on improving safety and resiliency of coastal communities plagued by flooding and hazardous weather.

The Rice team of engineers and collaborators includes Jamie Padgett, Ben Hu, and Avantika Gori along with David Retchless at Texas A&M University at Galveston. The researchers are working in collaboration with the Severe Storm Prediction, Education and Evacuation from Disasters (SSPEED) Center and the Ken Kennedy Institute at Rice and A&M-Galveston’s Institute for a Disaster Resilient Texas.

Together, the team is developing and hopes to deploy “Open-Source Situational Awareness Framework for Equitable Multi-Hazard Impact Sensing using Responsible AI,” or OpenSafe.AI, a new platform that utilizes AI, data, and hazard and resilience models "to provide timely, reliable and equitable insights to emergency response organizations and communities before, during and after tropical cyclones and coastal storm events," reads a news release from Rice.

“Our goal with this project is to enable communities to better prepare for and navigate severe weather by providing better estimates of what is actually happening or might happen within the next hours or days,” Padgett, Rice’s Stanley C. Moore Professor in Engineering and chair of the Department of Civil and Environmental Engineering, says in the release. “OpenSafe.AI will take into account multiple hazards such as high-speed winds, storm surge and compound flooding and forecast their potential impact on the built environment such as transportation infrastructure performance or hazardous material spills triggered by severe storms.”

OpenSafe.AI platform will be developed to support decision makers before, during, and after a storm.

“By combining cutting-edge AI with a deep understanding of the needs of emergency responders, we aim to provide accurate, real-time information that will enable better decision-making in the face of disasters,” adds Hu, associate professor of computer science at Rice.

In the long term, OpenSafe.AI hopes to explore how the system can be applied to and scaled in other regions in need of equitable resilience to climate-driven hazards.

“Our goal is not only to develop a powerful tool for emergency response agencies along the coast but to ensure that all communities ⎯ especially the ones most vulnerable to storm-induced damage ⎯ can rely on this technology to better respond to and recover from the devastating effects of coastal storms,” adds Gori, assistant professor of civil and environmental engineering at Rice.

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This article originally ran on EnergyCapital.

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KBR names C-suite duo to lead $5.3B government services spinoff

new leaders

In advance of the spinoff of its Mission Technology Solutions unit, Houston-based KBR has made two C-suite hires for the new business.

Michael LaRouche is coming aboard as president and CEO of the spinoff, currently called SpinCo, on Sept. 26. Nicholas Veasey is joining as executive vice president and chief financial officer on July 1.

“Michael and Nick bring a highly complementary combination of operational leadership, financial expertise, and mission-driven experience, and together they will accelerate our impact for stakeholders,” Stuart Bradie, chairman, president and CEO of publicly traded KBR, said in a news release.

LaRouche currently is CEO of Serco North America, a Herndon, Virginia-based government services contractor. Veasey most recently was CFO of MAG Aerospace, a Fairfax, Virginia-based defense contractor.

SpinCo, a government services contractor, will launch with more than $5.3 billion in annual revenue and 20,000 employees. KBR’s total headcount is around 36,000. Branding for SpinCo, including a formal name, will be revealed in July.

“SpinCo is positioned as a top-tier provider of differentiated technology solutions, anchored by deep mission expertise, global scale, and a relentless commitment to delivering for our customers,” LaRouche says.

After the spinoff, the slimmed-down KBR will focus on its Sustainable Technology Solutions business, a provider of energy and industrial technology that generated $2.5 billion in revenue in 2025. Bradie will remain chairman, president and CEO of the business.

Both SpinCo and the new KBR will be public companies. The spinoff is scheduled to be completed in January.

Experts: Houston's VC ecosystem has set the foundation — now we need scale

guest column

Fervo Energy went public earlier this summer. The Houston geothermal company priced its IPO at $27 per share, raised $1.89 billion, and opened the next morning at a market capitalization north of $10 billion. By most measures, it is the largest venture-backed cleantech IPO in history and an unambiguous win for Houston. It’s also a useful moment to look at where Houston's venture ecosystem stands and where it can go. The highlight: Houston's venture ecosystem has real foundations and, with increased company formation activity, can grow into the scale our city's ambitions deserve.

A Houston energy story in the national recovery

The recent uptick in Houston venture activity follows national trends. U.S. venture deal count contracted roughly 22 percent from its 2021 peak through 2024 before rebounding to about 16,700 rounds in 2025. Houston's 23 percent increase in VC funding from 2023 to 2024 is part of a national recovery of comparable magnitude over the same time window.

The energy sector is where Houston exhibits unique trends—and where the story turns clearly positive. (Houston's strong health and space sectors deserve their own separate consideration.) By deal count, energy-related rounds have accounted for 15 to 20 percent of Houston activity, roughly consistent over the past few years.

By capital, energy's share surged from about 14 percent in 2023 to over 60 percent in 2025, driven by a small number of large Houston-headquartered rounds, primarily in geothermal and related technologies. Fervo is the obvious anchor, but Sage Geosystems, Quaise Energy, Zeta Energy, Vaulted Deep, Applied Carbon and Mariana Minerals have all closed meaningful rounds. Houston is concentrated and accelerating as an energy capital market, an invaluable position to build upon.

From foundation to scale

The institutional pieces are in place. Greentown Labs, Activate, the Ion and others have built sector-specialized infrastructure most cities would struggle to assemble. Fervo itself is an alum of both Activate and Greentown Labs. Mercury Fund closed its $160 million Fund V, its largest ever. Houston Angel Network, GOOSE Capital, Fathom Fund, and broader pre-seed and seed capital coverage are here. The Houston $10 million-plus Series A list now includes 40 rounds since 2021, which break roughly into two eras. While 2021 to 2022 was biotech-heavy, with companies like Sporos Bioventures, RadioMedix, Cellenkos and Coya Therapeutics, 2024 to 2025 has tilted clearly toward energy, climate, and critical minerals, with Vaulted Deep, Applied Carbon, Mariana Minerals, Sage Geosystems and Ignis H2 Energy among them.

What’s less developed is the volume of seed-stage companies flowing into that capital. Imagine a dozen more Fervos coming out of that infrastructure over the next decade, each generating jobs, recycled founder capital, and the next wave of operators and angel investors. That is the kind of opportunity Houston has within reach if we build the company-formation pipeline to feed it. To be relevant on the national stage as a venture market, and to drive an economy the size of Houston's into the 2030s, the city needs to be doing closer to 20 Series A rounds per month rather than per year. That throughput implies roughly 1,000 seed rounds per year, feeding the funnel at a 20 percent to 30 percent graduation rate. Reaching such throughput depends on how many new founders Houston produces and how quickly our innovation ecosystem can help them achieve lift-off.

Houston in context

The comparative picture brings the scaling challenge into focus. Between 2021 and 2024, Houston-area startups closed between 126 and 153 disclosed venture rounds per year, against a national count between 9,854 and 14,125. That places Houston at a little over 1 percent of the U.S. deal count. For comparison, Austin ran about three times Houston's deal count each year.

At the Series A level, Houston closed between 12 and 24 rounds in any given year. The median Houston Series A across the period was about $10.7 million, compared with $15.4 million in San Francisco. Houston founders are raising fewer and smaller Series A rounds than founders in peer metros, which points directly to where Houston has the most room to grow.

The unicorn picture tells the same story. From 2021 through 2025, the U.S. produced 590 venture-backed unicorns. Four were Houston-based: Solugen and Axiom Space in 2021, Cart.com in 2023, and Fervo Energy in 2024. Adding HighRadius from 2020 brings Houston's all-time total to five. Austin added 19 over the same five-year window. The path from here is to make Houston's entries on lists like these less the exception and more the rule.

Where this leads

Houston has a real opportunity to become the deepest, most credible energy and climate capital market in the country, with the company formation, talent and operator density to support it. The data shows the foundation is already in place. Fervo, Solugen and the growing roster of energy-adjacent Series A graduates are proof. Fervo's IPO is the first of what should be many. Houston has not had a venture-backed cleantech liquidity event of this scale before, and the city now has one to reference, recruit against and build on. With increased company formation at the seed and pre-seed stages, a Fervo-scale outcome need not be a generational event in Houston, but instead, it can become part of a chain reaction powering the city's economy.

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Stephanie T. Schmidt, PhD, is the founder of a stealth startup, a Venture Fellow at Energy Transition Ventures, and an Executive MBA candidate at Rice University's Jones Graduate School of Business. Lawson Gow is the Chief Operating Officer of Greentown Labs. The full Houston VC landscape report is available at Energy Transition Ventures and CleanTech.Org.

Sources: Crunchbase, PitchBook-NVCA, Carta

8 can't-miss Houston business and innovation events for July

where to be

Editor's note: Summer is in full swing in Houston, but the city's innovation ecosystem isn't slowing down. This month brings AI workshops, energy and manufacturing discussions, entrepreneur-focused networking, and opportunities to connect with investors and industry leaders. Here’s what not to miss and how to register. Please note: this article may be updated to add more events.

July 7 — How Oil and Gas Professionals are Building Wealth Smarter

Hear from oil and gas professionals on how to preserve wealth at this event put on by Financial Advice Center. The conversation will touch on topics like investing, taxes and retirement planning.

This event is Tuesday, July 7, from noon-1 p.m. at the Ion. Register here.

July 7 — What AI, Cybersecurity, and Tequila Have in Common.

Join Blue People and Alpfa Houston for this engaging presentation on the advantages and risks associated with AI at the latest installment of Tech + Tequila Talk. Cybersecurity veteran Reynaldo Gonzalez will lead the conversation.

This event is Tuesday, July 7, from 5-7 p.m. at the Ion. Register here.

July 7 — Speed to Market: Houston’s Advanced Manufacturing Edge

The Greater Houston Partnership presents a forum that explores what allows advanced manufacturing projects in Houston to move from concept to operation, where delays and bottlenecks occur, and more. Industry leaders Jennifer Clement from CliftonLarsonAllen LLP and Sarah Janes from San Jacinto College will lead the discussion.

This event is Tuesday, July 7, from 11:30 a.m.-1 p.m. at the Partnership Tower. Register here.

July 9 — Capital Connections Summit

Houston City College Center for Entrepreneurship will host the Capital Connections Summit this month, with a panel discussion focused on access to capital and technical assistance for small businesses and entrepreneurs. The event will be moderated by the U.S. Small Business Administration Houston District Office and will feature lenders, nonprofit microlenders, business advisors, and entrepreneurial support organizations. A live Q&A will follow the panel.

This event is Thursday, July 9, from 11 a.m.-1:30 p.m. at Houston City College Central Campus. Register here.

July 9 — Upstream: Digital Tech Meetup at Second Draught

Join Timbergrove at this month's gathering of energy, operations and technology professionals from across the upstream ecosystem. Discuss challenges, explore new ideas and network over pizza and beer at Second Draught.

This event is Thursday, July 9, from 5:30–8 p.m. at the Ion. Register here.

July 14 — Why Networking Isn’t Turning Into Deals, And What To Do Instead

Jada Powell, founder of Powell Consulting Group, will break down why networking often fails to convert into deals and what companies can do differently to turn conversations into qualified opportunities. Powell works with oil and gas, energy, and industrial companies on business development solutions. This session is part of the monthly Pipeline Series: How Oil & Gas Companies Actually Grow Revenue.

This event is Tuesday, July 14, from noon-1 p.m. at the Ion. Register here.

July 15 — From Pilot to Performance: Building Your AI Procurement Roadmap

It's not too late to join in on the GHP's two-part AI series on moving from experimentation to implementation. In session two, explore how procurement and supply chain leaders can scale AI responsibly to create long-term business value. This event will be led by Cassye Cook Provost, founder and principal of RossGrigsby Consultancy.

This virtual event is Wednesday, July 15, from 8:30-10 a.m. Register here.

July 30 — Rice University Summer Engineering Innovation Program - Demo Day 2026

Meet the young minds and see the final team project presentations from Rice University’s Summer Engineering Innovation Program. The 10-week program challenges Rice students to solve real-world challenges using AI, digital engineering, model-based systems engineering and Industry 4.0 technologies.

This event is Thursday, July 30, from 6-8 p.m. at the Ion. Find more information here.

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