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.”

From Your Site Articles
The Texas Medical Center and KBIOHealth have launched the TMC Republic of Korea BioBridge. Photo via LinkedIn.

TMC launches new biotech partnership with Republic of Korea

international collaboration

Houston's Texas Medical Center has launched its new TMC Republic of Korea BioBridge.

The new partnership brings together the TMC with the Osong Medical Innovation Foundation, or KBIOHealth. The Biobridge aims to support the commercialization of Korean biotech and life science startups in the U.S., foster clinical research, and boost collaboration in the public, private and academic sectors.

Through the partnership, TMC will also develop a Global Innovators Launch Pad to foster U.S. market entry for international health care companies. Founders will be selected to participate in the 10-week program at the TMC Innovation Factory in Houston.

“Gene and cell therapies are driving biotech innovation, opening possibilities for treating diseases once thought untreatable," William McKeon, president and CEO of the Texas Medical Center, said in a news release. "Expanding biomanufacturing capacity is essential to delivering the next wave of these therapies, and partnerships with leading innovators will strengthen our efforts in Houston and internationally.”

McKeon officially signed the TMC Korea BioBridge Memorandum of Understanding with Myoung Su Lee, chairman of KBIOHealth, in South Korea in October.

"This collaboration marks a significant milestone for Korea’s biohealth ecosystem, creating a powerful bridge between Osong and Houston," Lee added in the release. "By combining KBIOHealth’s strength in research infrastructure and Korea’s biotech talent with TMC’s global network and accelerator platform, we aim to accelerate innovation and bring transformative solutions to patients worldwide.”

This is the seventh international strategic partnership for the TMC. It launched its first BioBridge with the Health Informatics Society of Australia in 2016. It launched its TMC Japan BioBridge, focused on advancing cancer treatments, last year. It also has BioBridge partnerships with the Netherlands, Ireland, Denmark and the United Kingdom.

Pete O'Heeron leads FibroBiologics as CEO and chairman. Photo via Fibrobiologics.com

Houston founder on shaping the future of medicine through biotechnology and resilience

Guest Column

Living with chronic disease has shaped my life in profound ways. My journey began in 5th grade when I was diagnosed with Scheuermann’s disease, a degenerative disc condition that kept me sidelined for an entire year. Later, I was diagnosed with hereditary neuropathy with liability to pressure palsies (HNPP), a condition that significantly impacts nerve recovery. These experiences didn’t just challenge me physically, they reshaped my perspective on healthcare — and ultimately set me on my path to entrepreneurship. What started as personal health struggles evolved into a mission to transform patient care through innovative biotechnology.

A defining part of living with these conditions was the diagnostic process. I underwent nerve tests that involved electrical shocks to my hands and arms — without anesthesia — to measure nerve activity. The pain was intense, and each test left me thinking: There has to be a better way. Even in those difficult moments, I found myself thinking about how to improve the tools and processes used in healthcare.

HNPP, in particular, has been a frustrating condition. For most people, sleeping on an arm might cause temporary numbness that disappears in an hour. For me, that same numbness can last six months. Even more debilitating is the loss of strength and fine motor skills. Living with this reality forced me to take an active role in understanding my health and seeking solutions, a mindset that would later shape my approach to leadership.

Growing up in Houston, I was surrounded by innovation. My grandfather, a pioneering urologist, was among the first to introduce kidney dialysis in the city in the 1950s. His dedication to advancing patient care initially inspired me to pursue medicine. Though my path eventually led me to healthcare administration and eventually biotech, his influence instilled in me a lifelong commitment to medicine and making a difference.

Houston’s thriving medical and entrepreneurial ecosystems played a critical role in my journey. The city’s culture of innovation and collaboration provided opportunities to explore solutions to unmet medical needs. When I transitioned from healthcare administration to founding biotech companies, I drew on the same resilience I had developed while managing my own health challenges.

My experience with chronic disease also shaped my leadership philosophy. Rather than accepting diagnoses passively, I took a proactive approach questioning assumptions, collaborating with experts, and seeking new solutions. These same principles now guide decision-making at FibroBiologics, where we are committed to developing groundbreaking therapies that go beyond symptom management to address the root causes of disease.

The resilience I built through my health struggles has been invaluable in navigating business challenges. While my early career in healthcare administration provided industry insights, launching and leading companies required the same determination I had relied on in my personal health journey.

I believe the future of healthcare lies in curative treatments, not just symptom management. Fibroblast cells hold the promise of engaging the body’s own healing processes — the most powerful cure for chronic diseases. Cell therapy represents both a scientific breakthrough and a significant business opportunity, one that has the potential to improve patient outcomes while reducing long-term healthcare costs.

Innovation in medicine isn’t just about technology; it’s about reimagining what’s possible. The future of healthcare is being written today. At FibroBiologics, our mission is driven by more than just financial success. We are focused on making a meaningful impact on patients’ lives, and this purpose-driven approach helps attract talent, engage stakeholders, and differentiate in the marketplace. Aligning business goals with patient needs isn’t just the right thing to do, it’s a powerful model for sustainable growth and lasting innovation in biotech.

---

Pete O’Heeron is the CEO and founder of FibroBiologics, a Houston-based regenerative medicine company.


CellChorus announced that the company, along with The University of Houston, has been awarded up to $2.5 million in funding. Photo via Getty Images

University of Houston-founded company secures $2.5M in NIH grant funding

all in the timing

You could say that the booming success of Houston biotech company CellChorus owes very much to auspicious TIMING. Those six letters stand for Time-lapse Imaging Microscopy In Nanowell Grids, a platform for dynamic single-cell analysis.

This week, CellChorus announced that the company, along with The University of Houston, has been awarded up to $2.5 million in funding from the National Center for Advancing Translational Sciences (NCATS) at the National Institute of Health. A $350,000 Phase I grant is already underway. Once predetermined milestones are achieved, this will lead to a two-year $2.1 million Phase II grant.

The TIMING platform was created by UH Single Cell Lab researchers Navin Varadarajan and Badri Roysam. TIMING generates high-throughput in-vitro assays that quantitatively profile interactions between cells on a large scale, particularly what happens when immune cells confront target cells. This has been especially useful in the realm of immuno-oncology, where it has demonstrated its power in designing novel therapies, selecting lead candidates for clinical trials and evaluating the potency of manufactured cells.

“By combining AI, microscale manufacturing and advanced microscopy, the TIMING platform yields deep insight into cellular behaviors that directly impact human disease and new classes of therapeutics,” says Rebecca Berdeaux, chief scientific officer at CellChorus. “The generous support of NCATS enables our development of computational tools that will ultimately integrate single-cell dynamic functional analysis of cell behavior with intracellular signaling events.”

Houston’s CellChorus Innovation Lab supports both the further development of TIMING and projects for early-access customers. Those customers include top-25 biopharmaceutical companies, venture-backed biotechnology companies, a leading comprehensive cancer center and a top pediatric hospital, says CEO Daniel Meyer.

CellChorus’s publications include papers written in collaboration with researchers from the Baylor College of Medicine, Houston Methodist, MD Anderson, Texas Children’s Hospital, the University of Texas and UTHealth in journals including Nature Cancer, Journal of Clinical Investigation and The Journal for ImmunoTherapy of Cancer.

The new Small Business Technology Transfer (STTR) award will specifically support the development of a scalable integrated software system conceived with the goal of analyzing cells that are not fluorescently labeled. This label-free analysis will be based on new AI and machine learning (ML) models trained on tens of millions of images of cells.

“This is an opportunity to leverage artificial intelligence methods for advancing the life sciences,” says Roysam. “We are especially excited about its applications to advancing cell-based immunotherapy to treat cancer and other diseases.”

The Houston-born-and-bred company couldn’t have a more appropriate home, says Meyer.

“Houston is a premier location for clinical care and the development of biotechnology and life sciences technologies. In particular, Houston has established itself as a leader in the development and delivery of immune cell-based therapies,” the CEO explains. “As a spin-out from the Single Cell Lab at the University of Houston, we benefit from working with world-class experts at local institutions.”

In May, the company received a similar $2.5 million SBIR grant from NCATS at the NIH. Also this summer, CellChorus's technology was featured in Nature Cancer.

Prabhdeep Singh Sekhon, CEO of Gold H2, joins the Houston Innovators Podcast. Photo courtesy of Gold H2

Newly named CEO to lead Houston gold hydrogen biotech co. into high-growth phase

HOUSTON INNOVATORS PODCAST EPISODE 239

Using microbes to sustainably unlock low-cost hydrogen sounds like the work of science fiction, but one Houston company is doing just that.

Gold H2, a spin-off company from Cemvita, has bioengineered subsurface microbes to use in wells to consume carbon and generate clean hydrogen. The technology was piloted two years ago by Cemvita, and now, as its own company with a new CEO, it's safe to say Gold H2's on its way.

"First of all, that was groundbreaking," Prabhdeep Singh Sekhon, CEO of Gold H2, says of the 2022 pilot in the Permian Basin, "to be able to use bugs to produce hydrogen within a couple of days."

"2024 is supposed to be the year where Gold H2 takes off," Sekhon, who joined the company in April, tells the Houston Innovators Podcast. "It was one of those opportunities that I couldn't turn down. I had been following the company. I thought, 'here is this innovative tech that's on the verge of providing a ground-breaking solution to the energy transition — what better time to join the team.'"

Sekhon shares on the show how his previous roles at NextEra Energy Resources and Hess have prepared him for Gold H2. Specifically, as a leader on NextEra’s strategy and business development team, he says he was tasked with figuring out what the energy industry looks like in the next five, 10, and 20 years.

"Green hydrogen was a huge buzz, but one of the things I realized when I started looking at green hydrogen was that it's very expensive," Sekhon says. "I wanted to look at alternatives."

This journey led him to what Cemvita was doing with gold hydrogen, Sekhon says, explaining that the ability to use biotechnology to provide a new revenue stream from the mostly used up wells struck him as something with major potential.

"The idea of repurposing existing oil and gas assets to become hydrogen assets, leveraging current infrastructure to drive down overall deliver costs — to me I thought, 'wow, if they can make this works, that's brilliant,'" he says.

Now, as CEO, Sekhon gets to lead the company toward these goals, which include expanding internationally. He explains on the show that Gold H2 is interested in expanding to any part of the world where there's interest in implementing their biotech. In order to support the growth, Sekhon says they are looking to raise funding this year with plans for an additional round, if needed, in 2025.

"When we compare our tech to the rest of the stack, I think we blow the competition out of the water," Sekhon says, explaining that Gold H2's approach to gold hydrogen development is novel when you look at emerging technology in the space. "We're using a biological process — cheap bugs that eat oil for a living."

With its blend of biotechnology, conservation, and education, RioRaiz seeks to inspire a new generation of conservationists. Photo via RioRaiz/Instagram

Innovative Houston nonprofit taps into biotech to preserve ecological biodiversity

conservation tech

For centuries, humans have been negatively impacting the natural world around them. A Houston organization is looking to leave an impact on the environment — but this time for the better.

Based in Houston, RioRaiz is a 501c3 nonprofit organization charting a unique course in the world of conservation and education. Founded in March of 2021, RioRaiz – meaning "root of the river" in Spanish, a nod to its deep-rooted connection with South American culture – seeks to preserve biodiversity through biotechnology and offer transformative learning experiences to contribute to a healthier planet.

Led by Jeff Carlson, the president and CEO, RioRaiz's mission is driven by three core pillars: conservation, scientific discovery, and education.

Currently, the nonprofit's efforts are focused on regions on the edge of ecological disruption, specifically the East Texas area and the Tropical Andes. In Texas, the organization aims to expand the biome of the Big Thicket National Preserve in Kountze as well as engaging locals by hosting clean-up drives. In the Andes, RioRaiz aspires to establish biological corridors between national parks and natural reserves, diminishing potential disruptions to animal migration patterns.

The timeline for these critical initiatives, Carlson said, hinges on donations.

"We have a list of priorities that is cataloged from input from our scientific collaborators, as well as our ability to deliver on our promises to our donors and supporters,” Carlson said.

Partnerships form a critical role in RioRaiz's work, notably those with academic institutions in the United States and Colombia. One of these collaborations saw Carlson spend three months in Colombia, working with the local Páez tribe, also known as the Nasa, to explore the potential of their traditional medicines for modern treatments.

"We're really excited to learn and to share our techniques and our knowledge," Carlson said, underlining the organization's commitment to partnering with traditional and indigenous knowledge sources.

With its blend of biotechnology, conservation, and education, RioRaiz seeks to inspire a new generation of conservationists. By offering an intimate virtual glimpse into the world's biomes, the nonprofit aims to instill a deep-rooted respect for nature and encourage sustainable action.

"If you expose students to these different kinds of environments at an early age, that might inspire somebody to go into conservation," Carlson said.

With a progressive effort, RioRaiz is harnessing the power of virtual reality to redefine education. The organization uses specialized filming equipment during its expeditions, capturing moments like the discovery of new species or conducting bio surveys. RioRaiz's visually compelling stories will surpass language barriers, transporting students virtually to different biomes. In time, Carlson hopes to distribute pre-loaded systems to communities with limited internet access, taking the classroom to every corner of the world. These virtual reality experiences are expected to launch within the next year.

"We want to bring the rainforest into the classroom," Carlson said.

Through its work, RioRaiz aims to demonstrate that the route to a sustainable future lies not just in face-to-face interactions, but in a global, interconnected approach to education and conservation. Its vision is clear — to grow far beyond traditional reaches, preserving biodiversity and fostering a healthier world.

Ad Placement 300x100
Ad Placement 300x600

CultureMap Emails are Awesome

Property Showcase

Austin company to bring AI-powered school to The Woodlands

AI education

Austin-based Alpha School, which operates AI-powered private schools, is opening its first Houston-area location in The Woodlands.

The 8,000-square-foot school, scheduled to be ready for the 2026-27 academic year, initially will serve students in kindergarten through eighth grade. Alpha says the school will offer “open workshop spaces and innovative classrooms that support personalized instruction, core academics, leadership development, and real-world life skills.”

Alpha sets aside two hours each school day for the AI-driven, self-paced study of core subjects like math, reading and science. The rest of each school day consists of life-skills workshops focusing on topics such as leadership and financial literacy.

Alpha’s school in The Woodlands has begun accepting applications for the 2026-27 school year. Annual tuition costs $40,000.

“The Woodlands is one of the most dynamic, forward-thinking communities in Texas, and Alpha is proud to bring

an innovative educational model that complements its strong academic foundation,” says Rachel Goodlad, head

of expansion for Alpha.

Founded in 2014, Alpha School combines adaptive technology-driven instruction with immersive life-skills workshops. Its model emphasizes mastery-based learning in core subjects alongside development of communication, critical thinking, financial literacy and leadership skills. It operates more than 15 schools across the country.

Elsewhere in Texas, Alpha operates schools in Austin, Brownsville, Fort Worth and Plano. Alpha also operates 12 Texas Sports Academy campuses in Texas, including locations in Houston, Pearland and Richmond, along with a NextGen Academy esports school in Austin, a school for gifted students in Georgetown, and lower-cost Nova Academy campuses in Austin and Bastrop.

Alpha has fans and critics. While supporters tout students’ high achievement rates, detractors complain about the high tuition and the AI-influenced depersonalization of education.

“Students and our country need to be in relationship with other human beings,” Randi Weingarten, president of the American Federation of Teachers, a teachers union, tells The New York Times. “When you have a school that is strictly AI, it is violating that core precept of the human endeavor and of education.”

Alpha co-founder MacKenzie Price, a podcaster and social media influencer, doesn’t share Weingarten’s views.

“Parents and teachers: We need to embrace this change,” Price wrote after President Trump signed an executive order promoting AI in schools.

The Times notes that Alpha doesn’t employ AI as a tutor or a supplement. Rather, the newspaper says, AI is “the school’s primary educational driver to move students through academic content.”

Houston space tech co. lands $175M and more innovation news to know

Trending News

Editor's note: The top Houston innovation news for the month includes major fundraising rounds for two Houston scaleups and local inductees into the National Academy of Inventors. Here are the five most-read InnovationMap headlines from March 1-15, 2026:

1. Intuitive Machines secures $175M equity investment to fuel growth

Intuitive Machines has landed a $175 million investment as it looks secure satellite deals and develop space-based data centers. Photo courtesy Intuitive Machines.

Houston-based space infrastructure and services company Intuitive Machines has secured a $175 million equity investment from unidentified institutional investors. The investors received shares of Class A stock in exchange for their funding. Publicly held Intuitive Machines (Nasdaq: LUNR) says it plans to use the capital to help build revenue and invest in technology, including communications and data-processing networks. Continue reading.

2. Houston e-commerce giant Cart.com raises $180M, surpasses $1B in funding

Cart.com has raised $180 million to scale its logistics network, expand AI capabilities and develop workflow automation tools. Photo courtesy of Cart.com

Houston-based commerce and logistics platform Cart.com has raised $180 million in growth capital from private equity firm Springcoast Partners, pushing the startup past the $1 billion funding mark since its founding in 2020. Cart.com says it will use the capital to scale its logistics network, expand AI capabilities and develop workflow automation tools. Continue reading.

3. Houston leads Texas with 7 new National Academy of Inventors senior members

The University of Houston has more faculty named to this year’s senior member class of the National Academy of Inventors than any other Texas institution. Photos courtesy UH.

The University of Houston is now home to seven new senior members of the National Academy of Inventors. According to UH, its seven new members represent the largest group from any single Texas institution this year, bringing the university's total senior member count to 46. Continue reading.

4. Booming Houston suburb launches innovation grant to attract startups

The City of Sugar Land is putting money on the table to support startups that relocate jobs to southwest Houston. Photo via Getty Images.

Think you’ve got a burgeoning startup? Consider moving it to southwest Houston. The City of Sugar Land announced the Sugar Land Starts Innovation Fund to support companies that move jobs to the area. Continue reading.

5. 6+ can't-miss Houston business and innovation events in March

From CERAWeek to H-Town Roundup, here's what not to miss this month and how to register. Photo courtesy of CERAWeek

March brings the return of some of Houston’s signature innovation events, plus insightful talks and celebrations in honor of Women's History Month. Here’s what not to miss and how to register. Continue reading.

Houston researcher secures $1.7M to develop drug for aggressive form of breast cancer

cancer research

A University of Houston researcher has joined a $3.2 million effort to develop a new drug designed to attack a cancer-driving protein commonly found in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is one of the most difficult-to-treat forms of cancer and accounts for 10 percent to 15 percent of all breast cancer cases. The disease gets its name because tumors associated with it test negative for estrogen receptors, progesterone receptors and excess HER2 protein, making it difficult to target. Due to this, TNBC is often treated with general chemotherapy, which can come with negative side effects and drug resistance, according to UH.

UH College of Pharmacy research associate professor Wei Wang is developing a drug that can target the disease more specifically. The drug will target MDM2, a protein often overproduced in TNBC that also contributes to faster tumor growth.

Wang is working on a team led by Wei Li, director of the University of Tennessee Health Science Center College of Pharmacy’s Drug Discovery Center. She has received $1.7 million to support the research.

Wang and UH professor of pharmacology and toxicology Ruiwen Zhang have discovered a compound that can break down MDM2. In early laboratory models, the compound has shown the ability to shrink tumors.

Wang and Zhang will focus on understanding how the treatment works and monitoring its effectiveness in models that closely mirror human disease.

“We will study how the drug targets MDM2 and evaluate the most promising drug candidates to determine effective dosing, understand how the drug behaves in the body, compare it with existing treatments and assess early safety,” Wang said in a news release.

Li’s team at the University of Tennessee will be working on the chemistry and drug design end of the project.

“This work could lead to an entirely new class of therapies for triple-negative breast cancer,” Li added in the release. “We’re hopeful that by directly removing the MDM2 protein from cancer cells, we can help more patients respond to treatment regardless of their tumor type.”

View All Listings