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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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.

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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.

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Rice Alliance names Houston healthtech exec as first head of platform

new hire

The Rice Alliance for Technology and Entrepreneurship has named its first head of platform.

Houston entrepreneur Laura Neder stepped into the newly created role last month, according to an email from Rice Alliance. Neder will focus on building and growing Houston’s Venture Advantage Platform.

The emerging platform, which is being promoted by Rice Alliance and the Ion, aims to connect founders with the "people, capital and expertise they need to scale."

"I’ve spent a lot of time thinking about what it takes to make an innovation ecosystem more navigable, more connected, and more useful for founders," Neder said in a LinkedIn post. "I’m grateful for the opportunity to do that work at Rice Alliance, alongside a team with a long history of supporting entrepreneurship and innovation."

"Houston has the talent, institutions, and industry base to create real advantage for founders," she added. "I’m looking forward to listening, learning, and building stronger pathways across the ecosystem."

Neder most recently served as CEO of Houston-based Careset, where she helped bring the Medicare data startup to commercialization. Prior to that, Neder served as COO of Houston-based telemedicine startup 2nd.MD, which was acquired for $460 million by Accolade in 2021.

"Laura brings a rare combination of founder empathy, operational experience and ecosystem leadership," Rice Alliance shared.

Neder and Rice Alliance also shared that the organization is hiring developers to design the new Venture Advantage Platform. Learn more here.

Elon Musk's SpaceX files initial paperwork to sell shares to the public

Incoming IPO

Elon Musk's space exploration company has filed preliminary paperwork to sell shares to the public, according to two sources familiar with the filing, a blockbuster offering that would likely rank as the biggest ever and could make its founder the world's first trillionaire.

A SpaceX IPO promises to be one of the biggest Wall Street events of the year, with several investment banks lining up to help raise tens of billions to fund Musk's ambitions to set up a base on the moon, put datacenters the size of several football fields in orbit and possibly one day send a man to Mars.

The sources spoke on condition of anonymity because they were not authorized to talk publicly about the confidential registration with the Securities and Exchange Commission.

SpaceX did not respond immediately to a request for comment.

Exactly how much SpaceX plans to raise has not been disclosed but the figure is reportedly as much as $75 billion. At that level, the offering would easily eclipse the $29 billion that Saudi Aramco raised in its IPO in 2019.

The offering, coming possibly in June, could value all the shares of SpaceX at $1.5 trillion, nearly double what the company was valued in December when some minority owners sold their stakes, according to research firm Pitchbook, before an acquisition that increased its size.

Musk owns 42% of the SpaceX now, according to Pitchbook, though that figure will change with the IPO when new owners are issued shares. In any case, he is likely to pierce the trillion dollar mark because he is already close. Forbes magazine estimates Musk's net worth at roughly $823 billion.

In addition to making reusable rockets to hurl astronauts and hardware into orbit, SpaceX owns Starlink, the world’s largest satellite communications company. The company also recently brought under its roof two other Musk businesses, social media platform X, formerly Twitter, and artificial intelligence business, xAI, in a controversial transaction because both the seller and the buyer were controlled by him.

SpaceX has become the biggest commercial launch company in its industry, responsible for sending payloads into orbit for customers across the globe, but has also benefited from big taxpayer spending. That has raised conflicts of interest issues given that Musk was the biggest donor to President Donald Trump's campaign and is still a big backer.

In the past five years, SpaceX won $6 billion in contracts from NASA, the Defense Department and other U.S. government agencies, according to USAspending.gov.

Among current SpaceX owners is Donald Trump Jr, the president's oldest son. He owns a shares through 1789 Capital. That venture capital firm made him a partner shortly after his father won the presidency for a second time and has been buying up federal contractors seeking to win taxpayer money ever since.

The White House and Trump himself have repeatedly denied there are any conflicts of interest between his role as president and his family's businesses.

8+ can't-miss Houston business and innovation events in April

where to be

Editor’s note: Houston's weeklong innovation festival kicks off April, followed by Rice University's globally recognized pitch competition returning for its 26th year. Plus, find coworking pop-ups, industry meetups, pitch battles and even a crawfish boil on the calendar. Here’s what not to miss and how to register. Please note: this article might be updated to add more events.

March 30-April 4 — H-Town Roundup

Celebrate innovation, entrepreneurship and collaboration at Houston Exponential's sixth-annual H-Town Roundup. During the free event series, previously known as Houston Tech Rodeo, attendees can expect insightful talks, workshops and networking events at venues across the city.

This event began March 30. Register here.

April 2 — Industrious Coworking Day

Enjoy a complimentary day of cowering at Industrious and network with professionals at the Ion. Breakfast, snacks, wifi and workspace tours are included. Following the cowering day, Industrious will host happy hour at Second Draught from 4-6 p.m.

This event is Thursday, April 2, from 8:30 a.m.-5 p.m. at the Ion. Register here.

April 2 — Technology Summit for Women

The fourth annual Women in Tech Cummil will feature speakers across three core tracks: Transformation + Digital strategy, Cyber + Risk + Resilience, and AI in Practice. Pearl Chu, director of technical domains and university relations at SLB, will give the opening remarks. Other panelists come from CenterPoint Energy, BP, Technip Energies and other leading companies.

This event is Thursday, April 2, from 2-5 p.m. at the Ion. Register here.

April 8 — Veterans Business Battle

Hear pitches from veterans and entrepreneurs as they compete for more than $10 million in investments at Rice Businesses' 12th annual Veterans Business Battle. This year, the two-day event will also feature a Small Business Expo, which invites Houston-based, veteran-owned businesses to participate in education, networking and the opportunity to showcase their business. Moonshots Capital and Mercury Fund will also host a fireside chat.

This event begins Wednesday, April 8, at 11 a.m. at the Ion. Click here to register.

April 9-11 — Rice Business Plan Competition

The Rice Alliance for Technology and Entrepreneurship will host the 26th annual Rice Business Plan Competition this month. Forty-two student-led teams from around the world, including one team from Rice, will present their plans before more than 300 angel, venture capital, and corporate investors to compete for more than $1 million in prizes.

This event begins Thursday, April 9. Find more information here.

April 10 — BioHouston Chili Cookoff

Connect with Houston's life sciences community at BioHouston's 21st annual chili cookout. This event is geared toward startup founders, researchers and industry veterans alike.

This event is Friday, April 10, from noon-4 p.m. at Bayou City Event Center. Register here.

April 14 — Mercury Fund Day at the Ion: Agentic Commerce

Don’t miss the latest installment of Mercury Fund Day at the Ion, previously known as Software Day. The recurring monthly event features office hours (by application), a keynote and networking opportunities. This month's topic focuses on agentic commerce.

This event is Tuesday, April 14, from 3:30-7 p.m. at the Ion. Register here.

April 19 – UH Energy Industry Crawfish Boil

Head to the UH Cullen College of Engineering Green Space for the 35th annual UH Energy Industry Crawfish Boil. The event will include a student showcase, STEM activities, a kids zone, live music, networking and, of course, crawfish. Proceeds from the event will support the multidisciplinary capstone fund that aims to increase professional readiness for Cullen College engineering and technology students.

This event is Sunday, April 19, from 1-5 p.m. at the Cullen College of Engineering Green Space. Find more information here.

April 24 — Rice Business Healthcare Conference

Leading experts, innovators and the next generation of healthcare leaders will converge at the Rice Business Healthcare Conference. Hosted by the Rice Business Healthcare Association, the conference will explore AI's potential impact on the sector.

This event is Friday, April 24, from 8 a.m.-2 p.m. at McNair Hall on Rice University's campus. Find more information here.

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