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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Telsa targets Houston area for new $10 billion manufacturing plant

Project Sun City

Electric vehicle and clean energy company Tesla is considering building a new $10.1 billion solar cell manufacturing facility in Fort Bend County, according to documents filed with the Texas Comptroller’s Office.

If approved, the plant, called Project Sun City, would be located on a 3,050-acre site off FM 762 and FM 1994 in Richmond, Texas. Tesla aims to finish construction in 2028, with the plant being operational by early 2029.

The plant will manufacture photovoltaic (PV) solar cells and modules that can convert sunlight into electricity. PV Magazine reports that the facility is "the largest single manufacturing investment Tesla has proposed on paper."

Advisory and consulting firm Kroll submitted the documents to the Texas Comptroller of Public Accounts and noted if an agreement regarding tax incentives isn't reached, the project will exit Texas.

Tesla has requested credits under the Jobs, Energy, Technology, and Innovation (JETI) Act. The incentive program aims to attract large, capital-intensive economic development projects by lowering the property taxes an entity must pay over 10 years if it meets requirements related to job creation and investment. For example, pharmaceutical giant Bristol Myers Squibb Co. recently announced that its forthcoming $2.3 billion Houston-area manufacturing site is a qualified project under the JETI program.

Kroll predicts that the facility would create 9,712 new full-time jobs, over 1,100 construction jobs and billions of dollars in future property tax revenue, the documents show. Additionally, it says the project will spur $1.1 billion in local business expenditures and that Texas would increase its GDP by approximately $107 billion as a result of the project activities.

Tesla opened its $200 million Megafactory in Brookshire, Texas, last year. The company is continuing its goal to deploy 100 gigawatts of solar manufacturing in the U.S before the end of 2028. According to the U.S. Energy Information Administration, 100 gigawatts is equal to about 8 percent of the country's power grid capacity.

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This article originally appeared on EnergyCapitalHTX.com.

Tech giant Apple opens Advanced Manufacturing Center at massive Houston facility

up and running

Cupertino, California-based Apple Inc. unveiled its Advanced Manufacturing Center in the Houston area last week, marking the completion of the second of three facilities the tech giant plans to launch in the city by the end of this year.

The 20,000-square-foot training center will welcome small- and medium-sized businesses for free training and educational sessions to "help accelerate smart manufacturing across America," according to a release from Apple. Apple opened a similar Apple Manufacturing Academy in Detroit last year.

The AMC is part of Apple's 500,000-square-foot site in northwest Harris County. It also features a massive manufacturing site for Apple’s advanced AI servers and Mac mini. The facility was originally slated to open in 2026, but Apple began producing its advanced AI servers ahead of schedule in 2025.

The company said it plans to begin manufacturing its Mac mini at the site this year. The move will bring production of the compact desktop computer to the U.S. for the first time.

“In less than nine months, we have invested hundreds of millions of dollars into this Houston facility. We stood up a factory, started production, and shipped the first advanced AI servers off the line. Today, we’re thrilled to open our new Advanced Manufacturing Center, a place where businesses, workers, and students can learn the same innovative processes that we use to make Apple’s most groundbreaking products. And we’re pleased to begin Mac mini production later this year,” Tim Cook, Apple’s CEO, said in the news release. “We believe in American workers and American ingenuity, and we are moving at an incredible pace because we want to build more than great products. We want to build the future of American manufacturing.”

Apple's Advanced Manufacturing Center. Photos courtesy Apple

Apple's Houston expansion is part of a $600 billion commitment the company made to the U.S. in 2025.

The company originally announced plans in February 2025 to open a 250,000-square-foot Houston factory, but doubled the facility's planned size about a year later. Apple has reported that the factory will employ thousands of workers.

“Houston is grateful to Apple for this significant investment in our city. The Advanced Manufacturing Center will create local jobs and will continue improving the quality of life of Houston residents," Houston Mayor John Whitmire added in the release. "The AMC also recognizes our city as a growing technology hub and solidifies Houston’s leadership in the manufacturing sector of the United States.”

The opening comes on the heels of New Jersey-based pharmaceutical giant Bristol Myers Squibb Co. officially naming Houston home of its new $2.3 billion, state-of-the-art manufacturing site. Read more here.

Nominations for the 2026 Houston Innovation Awards are due by Aug. 27

Calling All Innovators

Calling all Houston innovators: The 2026 Houston Innovation Awards, presented by InnovationMap, return this fall to celebrate the best and brightest in the Houston innovation ecosystem right now.

We're asking you to nominate Houston's top innovators and startups for this year's awards. Nominations are open now through August 27 and can be made on behalf of yourself, your organization, and other influential leaders in the local innovation scene.

The annual awards program recognizes the most innovative individuals and companies in Houston across 10 prestigious categories.

This year's awards will honor the following categories:

  • Minority-founded Business, honoring an innovative startup founded or co-founded by BIPOC or LGBTQ+ representation.
  • Female-founded Business, honoring an innovative startup founded or co-founded by a woman.
  • Energy Transition Business, honoring an innovative startup providing a solution within renewables, climatetech, clean energy, alternative materials, circular economy, and beyond.
  • Health Tech Business, honoring an innovative startup within the health and medical technology sectors.
  • Deep Tech Business, honoring an innovative startup providing technology solutions based on substantial scientific or engineering challenges, including those in the AI, robotics, and space sectors.
  • Startup of the Year (People's Choice), honoring a startup celebrating a recent milestone or success. The winner will be selected by the community via an interactive voting experience.
  • Scaleup of the Year, honoring an innovative later-stage startup that's recently reached a significant milestone in company growth.
  • Incubator/Accelerator of the Year, honoring a local incubator or accelerator that is championing and fueling the growth of Houston startups.
  • Mentor of the Year, honoring an individual who dedicates their time and expertise to guide and support budding entrepreneurs.
  • Trailblazer, honoring an innovator who's made a lasting impact on the Houston innovation community.

You have three weeks to submit nominees, so don't delay — nominate today at this link or fill out the form below. Qualified nominees will receive a formal application to complete, which will be reviewed by our esteemed panel of judges to determine the finalists and winners.

More announcements about the 2026 Houston Innovation Awards are coming soon, including an introduction to this year's panel of judges. Interested in sponsoring the 2026 Houston Innovation Awards? Please contact sales@innovationmap.com.

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