New Wyss Catalyst Embraces AI Landscape to Advance Innovation and Collaboration
By Seth Kroll
(BOSTON) – Artificial intelligence (AI) is rapidly permeating the modern technological landscape. While its rise often sparks debate and caution in broader society, many in the life sciences view AI as a wellspring of opportunity. Researchers and innovators are increasingly eager to harness its potential to accelerate the development of transformative drugs, diagnostics, and medical devices, ushering in a new era of accuracy and efficiency in healthcare. For more than 16 years, the Wyss Institute for Biologically Inspired Engineering has pushed the boundaries of life-science innovation, often building the necessary tools needed to enable new discoveries and progress in many biomedical areas. In this spirit, Wyss scientists and engineers have been harnessing AI’s early potential for drug discovery and development, some of which are now being advanced towards clinics and patients by our in-house research teams and startups. At the Wyss, as new projects develop through our Innovation Funnel, we continue to push the boundaries to explore how AI can bring more patients closer to effective treatments.
Introducing the Translational AI Catalyst
Recognizing both the immense potential and real challenges surrounding AI in biomedicine, the Wyss has honed our approach to AI and launched the Translational AI Catalyst – an institute-wide effort designed to enable and accelerate innovation through effective and responsible application of new computational approaches while leveraging machine learning algorithms to generate unique biological datasets. We will apply AI to enhance application-driven science and address challenges in healthcare ranging from identifying new therapies to developing new diagnostic capabilities, as well as environmental challenges standing in the way of a more sustainable future.
The Translational AI Catalyst is led by Wyss Core Faculty member Jim Collins, Ph.D., whose labs at the Wyss and MIT have long used AI to advance science, as well as Wyss Computational Biologist Megan Sperry, Ph.D., and Wyss Business Development Director Ally Chang, Ph.D., M.B.A.
“The Wyss is a unique place to do this kind of work because our bioengineers and life scientists are generating and providing incredible amounts of data about relevant disease models and chemical interactions with computational scientists, enabling us to unlock new discoveries,” Collins said. “No one is working in a vacuum or in isolation.” Collins is also the Termeer Professor of Medical Engineering & Science at MIT.
“AI has the potential to transform how we understand and tackle complex challenges. At the Wyss we are exploring its capabilities to drive innovation and create impactful solutions, with a strong commitment to using it in ethical and meaningful ways,” said Sperry.
AI has the potential to transform how we understand and tackle complex challenges.
A Unique Ecosystem for AI-Enabled Science
Building on the Wyss Institute’s strong legacy of collaboration – which has produced numerous comprehensive datasets from sources such as human Organ Chips, organoid cultures, and small animal models, all with diverse patient populations in mind – we are now using these rich datasets with cutting-edge computational approaches. These approaches are bolstered by state-of-the-art multi-omics capabilities within the Wyss and clinical collaboration housed within the Biomarker Discovery Laboratory. This integration is driving innovation across all six of Wyss Grand Challenges: Brain Health, Cancer Solutions, Healthy Aging, Infectious Disease Control, Sustainable Futures, and Women’s Health Innovation.
“Our community and project teams are diverse in terms of experiences, skill sets, and areas of disease research. We include experts from both the wet lab, those generating experimental data, and the dry lab, those analyzing and modeling that data, as well as team members who work across both spaces. By fostering open communication and encouraging collaboration from the earliest stages of each project, we actively bridge the gap between disciplines and enable fast iteration between the dry and wet lab scientists. This kind of integration allows us to rapidly test hypotheses, adapt approaches, and tackle complex challenges more efficiently and creatively,” said Sperry, who joined the Wyss in 2019 as a Research Fellow in Wyss Associate Faculty member Michael Levin’s team, to work on a collaborative project with Wyss Founding Director Donald Ingber’s team before becoming a member of the Wyss’ Advanced Technology Team.
Powered by AI
As AI becomes increasingly embedded in life science research, a wave of Wyss projects is emerging that harness AI, machine learning, and other computational tools to address specific diseases and market applications. Some examples, which span the development of therapeutic and diagnostic proteins with novel capabilities, aging research, chronomedicine, and environmental sensing, include:
- A multidisciplinary team of computational biologists along with infectious disease, medical chemistry, and drug development experts formed at the Wyss Institute at the beginning of the COVID-19 pandemic to develop a broad-spectrum antiviral drug against multiple members of the coronavirus family. The team, with early support from the Defense Advanced Research Agency (DARPA) and led by Donald Ingber, created a cohesive AI-enabled and physics-based molecular modeling and drug discovery pipeline built around film industry procedural animation software that enabled them to identify the orally available, FDA-approved drug bemcentinib as a potential antiviral agent. To further optimize its activity, with follow up support from Open Philanthropy-Good Ventures Foundation, they used this chemical compound as a launch pad for developing a more specific and effective antiviral drug with efficacy against a broad range of coronaviruses and great potential for global biopreparedness.
- AminoX uses machine learning to design proteins containing new non-standard amino acids, laying the foundation for novel protein-based drugs with enhanced or entirely new functions, revolutionizing the synthesis of protein-based therapeutics. This project team is comprised of researchers from Wyss Core Faculty members George Church, Ph.D., andJim Collins’ labs and is supported through our strategic alliance with Northpond Labs. Church is also a Professor of Genetics at Harvard Medical School and Professor of Health Sciences and Technology at Harvard and MIT.
- Ichor has developed an AI-driven platform that predicts cellular responses to genetic perturbations, enabling the discovery of interventions that reverse the effects of chronic disease and aging. By embedding AI at the core of its R&D pipeline, Ichor significantly accelerates discovery while increasing experimental throughput. The team has uncovered gene networks strongly implicated in aging processes and is now translating these insights into RNA-based therapies designed to restore youthful function in aging cells. Currently supported as an Institute Project, Ichor is preparing to launch a startup.
- CircaVent uses an AI-powered platform developed at the Wyss to uncover circadian rhythm-related mechanisms that influence drug efficacy and side effects. By integrating biological omics data obtained over the course of entire day-night cycles with pharmacological drug profiles, CircaVent identifies optimal dosing windows and drug repurposing opportunities based on the body’s internal clock. The team’s approach aims to enhance therapeutic effectiveness while minimizing adverse effects and applied to patient-specific organoids, could enable personalized and time-sensitive treatments across a range of diseases, starting with bipolar disorder. The team, which is led by Church, is supported by a philanthropic BD2 grant.
- SNIFFIA is developing an advanced, bioinspired indoor air quality monitoring system that mimics the natural sniffing patterns of animals to detect and distinguish specific volatile organic compounds (VOCs) in real time. Led by Joanna Aizenberg, Ph.D., the highly collaborative platform integrates distributed sensors with machine learning algorithms to provide highly accurate, time-sensitive measurements of air quality that, in the future, can be used to trigger air ventilation and purification actions in buildings. Project Air is supported through the National Science Foundation and the Wyss’ strategic alliance with Collaborative Fund.
Collaborating with External Partners
Adding to building a strong foundation for the Translational AI Catalyst, various Wyss teams are working in close collaboration with industry and government agencies. One such collaboration, led by Don Ingber, M.D., Ph.D. is working with the Defense Advanced Research Projects Agency (DARPA)’s “Anesthetics for Battlefield Care” (ABC) program. Using computational drug prediction, combined with AI-powered analysis of animal behavior, the team is identifying compounds that can induce safe and reversible anesthesia without the need for extensive monitoring. The project aims to enable life-saving anesthesia for battlefield and disaster situations. Ingber is also the Wyss Institute Founding Director.
Rooted in Responsibility
As with any powerful new technology, responsible use and implementation of AI is paramount, especially when exploring new frontiers of the technology. At the Wyss , we are committed to ensuring that all our research and technology development is both ethical and beneficial to society. Our approach is grounded in our proven Collaborative Ethics framework, which emphasizes continuous collaboration between scientists and ethicists. This close collaboration helps us navigate the complexities of open-source AI, adhere to emerging regulations, and address ethical dilemmas, all while maintaining a focus on patient outcomes and ethical integrity.
Moreover, our commitment to responsible AI use extends beyond our internal practices. We actively engage with industry partners and the broader scientific community to share our insights and promote best practices. This collaborative effort helps create a more robust and ethical AI ecosystem, ultimately benefiting society as a whole.
From the Wyss to the World: AI-enabled startups
Our current AI efforts build upon a foundation created by several successful Wyss startup teams. Wyss Lumineers, entrepreneurial scientists who have translated their Wyss innovations into startup companies, have used AI to gain new, previously unachievable insights that are posed to vastly improve the lives of patients.
Dyno Therapeutics and Manifold Bio, both co-founded by Church, are using AI to, respectively, design gene vectors for tissue targeted delivery of therapeutics and tissue-specific antibodies. Dyno currently has active collaborations with Roche, Novartis, and Sarepta Therapeutics, as well as NVIDIA, the leader in developing AI processers.
Pluto Biosciences is harnessing AI to streamline bioinformatics research through a cloud-based platform that simplifies the analysis, visualization, and sharing of complex biological data, including RNA-seq and microbiome data. Designed to make advanced analytics accessible to researchers at all levels, Pluto combines intuitive interfaces with powerful AI tools to accelerate discovery and collaboration across academia and industry.
Unravel Biosciences is using AI to identify entire gene expression networks that are changed in complex diseases. With an initial focus on rare genetic disorders like Rett syndrome, Unravel’s platform can model complex disease biology in living systems to uncover actionable gene network changes and drug candidates that can normalize those changes across multiple tissues. Within four years of launching, following collaborative research between teams of Ingber and Michael Levin, Ph.D., a Wyss Associate Faculty member, Unravel has already initiated clinical trials to treat patients with Rett syndrome with an identified drug. Levin is also a Distinguished Professor and Vannevar Bush Chair at Tufts University and Director of the Allen Discovery Center at Tufts University.
Looking Ahead
AI empowers scientists to analyze vast amounts of data, uncover hidden patterns, and make decisions that drive projects forward in new directions at unprecedented speed. Through the Translational AI Catalyst, the Wyss is committed to providing comprehensive AI resources to its community, while attracting and collaborating with AI computational scientists, ensuring that AI continues to serve as a bridge between scientific discovery and real-world impact on patients and the environment by unlocking entirely new opportunities.
We invite industry collaborators, investors, and policymakers to engage with us in this shared mission –to transform breakthrough ideas into impactful solutions that advance human health and environmental sustainability. Together, we can shape an AI-powered future grounded in scientific excellence, ethical responsibility, and meaningful global impact.
“Everyone is data-hungry, and we’re generating incredible multimodal and multiomics datasets. We welcome collaborations with industry partners who will help translate these discoveries into real-world impact,” said Chang. “We invite industry collaborators and donors to join us in our mission to harness the power of AI for life-changing innovations for healthcare and the environment.”
We invite industry collaborators and donors to join us in our mission to harness the power of AI for life-changing innovations for healthcare and the environment.