Department of Neuroscience, Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA; Stanford Bio-X, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
Dr. Fahey studies how students can enhance public understanding of scientific topics, especially chronobiology, which deals with biological clocks and daily rhythms. He emphasizes the importance of students not only learning scientific concepts but also applying their knowledge to create accessible content for a broader audience. By guiding students to edit and improve Wikipedia articles on chronobiology, he showcases their ability to engage with scientific literature and communicate findings effectively to non-scientists.
Key findings
University students created and improved 15 Wikipedia articles on chronobiology, significantly enhancing the quality and accessibility of the information.
The project reached millions of readers worldwide, indicating the broad impact of student contributions to public knowledge.
Students spent approximately 9 hours each developing skills to read and evaluate scientific papers, leading to a marked improvement in their ability to communicate complex scientific ideas.
Frequently asked questions
Does Dr. Fahey study chronobiology?
Yes, he focuses on chronobiology, which explores biological clocks and daily rhythms.
What is Dr. Fahey's main research method?
He involves university students in enhancing Wikipedia articles to improve public understanding of scientific topics.
How does Dr. Fahey's work benefit the public?
His research helps make complex scientific information more accessible by training students to communicate effectively through widely-used platforms like Wikipedia.
Publications in plain English
Functional bipartite invariance in mouse primary visual cortex receptive fields.
2026
Nature neuroscience
Ding Z, Tran D, Ponder K, Ding Z, Froebe R +26 more
Plain English This study looked at how certain neurons in the mouse brain process visual information by identifying patterns that remain stable even when the visual input changes. Researchers discovered that these neurons have a dual approach: one set responds to detailed textures that can shift position, while another focuses on broader patterns that don't change, which helps the brain distinguish between different objects. They found that neurons processing these stable features are closely linked, with some neurons showing more consistency than others, which contributes to better understanding how our brains perceive and segment visual scenes.
Who this helps: This benefits researchers studying visual processing and could ultimately improve treatments for visual perception disorders.
Statistics of natural scenes shape contextual modulation in the visual cortex.
2026
Neuron
Fu J, Shrinivasan S, Baroni L, Ding Z, Fahey PG +20 more
Plain English This study looked at how the context of a visual scene affects how our brain processes what we see. Researchers found that certain surround visuals can enhance or reduce responses in the brain's visual cortex. Specifically, they observed that when the surrounding images looked like natural extensions of the center image, brain activity increased, while unrelated surrounds decreased it. This matters because understanding how our brain interprets complex scenes can improve treatments for visual disorders.
Who this helps: This benefits patients with vision problems and researchers working on visual processing.
An unsupervised map of excitatory neuron dendritic morphology in the mouse visual cortex.
2025
Nature communications
Weis MA, Papadopoulos S, Hansel L, Lüddecke T, Celii B +43 more
Plain English This study looked at the shapes of excitatory neurons in the visual cortex of mice, examining over 30,000 neurons using advanced imaging techniques. Researchers found that instead of fitting neurons into specific categories, it's more accurate to see them as part of a continuous range of shapes, with some differences in certain layers of the brain. For example, neurons in layer 2-3 became narrower and had smaller branches as you went deeper into the cortex, and layer 4 of the primary visual area (V1) had more unique neuron shapes compared to other areas.
Who this helps: This research benefits neuroscientists and medical researchers working on understanding brain function and disorders.
NEURD offers automated proofreading and feature extraction for connectomics.
2025
Nature
Celii B, Papadopoulos S, Ding Z, Fahey PG, Wang E +53 more
Plain English This study introduces NEURD, a new software tool that helps researchers analyze detailed images of brain cells taken with advanced electron microscopy. NEURD automates the process of correcting errors in cell reconstructions and extracts critical data about the structure of neurons, such as their shape and connections, making it easier for scientists to work with large amounts of complex data. This is important because it streamlines research, ultimately improving our understanding of brain connections and could lead to advances in neurological studies.
Who this helps: Neuroscience researchers.
Functional connectomics reveals general wiring rule in mouse visual cortex.
2025
Nature
Ding Z, Fahey PG, Papadopoulos S, Wang EY, Celii B +58 more
Plain English Researchers studied how neurons in the visual cortex of mice connect and work together to process visual information. They found that neurons that respond similarly are more likely to be connected to each other—both within different layers and across various areas of the cortex. This “like-to-like” connectivity helps the brain process visual signals more effectively, a principle that seems to apply to both natural brains and artificial systems.
Who this helps: This helps neuroscientists and researchers develop better models for understanding brain function and improving artificial intelligence.
Foundation model of neural activity predicts response to new stimulus types.
2025
Nature
Wang EY, Fahey PG, Ding Z, Papadopoulos S, Ponder K +18 more
Plain English This study looked at how well a new type of artificial intelligence model can predict brain activity in response to different kinds of visual stimuli in mice. The researchers found that their model not only accurately predicted how neurons responded to various natural videos but also adapted to new mice with little extra training. This advancement is important because it helps scientists better understand brain functions and could speed up research in neuroscience by making it easier to work with complex brain data.
Who this helps: This benefits researchers studying the brain and developing treatments for neurological conditions.
NEURD offers automated proofreading and feature extraction for connectomics.
2024
bioRxiv : the preprint server for biology
Celii B, Papadopoulos S, Ding Z, Fahey PG, Wang E +53 more
Plain English This research developed a new software called NEURD that simplifies the process of analyzing complex brain cell structures from high-resolution images. NEURD automates tasks like checking for errors in cell reconstructions and classifying different types of neurons, making it easier for scientists to work with large amounts of detailed data. This matters because it speeds up research in neuroscience, allowing for better understanding of how brain cells are connected and how they function, which could lead to advancements in treating neurological disorders.
Who this helps: Neuroscience researchers and, ultimately, patients with neurological conditions.
Pattern completion and disruption characterize contextual modulation in the visual cortex.
2024
bioRxiv : the preprint server for biology
Fu J, Shrinivasan S, Baroni L, Ding Z, Fahey PG +19 more
Plain English This study explored how our brain processes visual information by examining how the surrounding context affects our perception of images. Researchers discovered that certain surrounding patterns can actually enhance the brain's response to the main image, contrary to previous beliefs. For example, they found that when using mouse models, surrounding patterns that matched the main image made the response stronger than those that did not match, highlighting the importance of context in visual perception.
Who this helps: This benefits researchers and neuroscientists studying visual processing and perception.
Functional connectomics reveals general wiring rule in mouse visual cortex.
2024
bioRxiv : the preprint server for biology
Ding Z, Fahey PG, Papadopoulos S, Wang EY, Celii B +58 more
Plain English This study looked at how neurons in the mouse brain's visual area connect with each other and how this affects their function. Researchers found that neurons that respond similarly to visual stimuli are more likely to be connected, both within their own layer and with other layers. They discovered that this "like connects with like" pattern is a key principle in the brain and is also observed in artificial intelligence systems, suggesting it plays an important role in how we process visual information.
Who this helps: This helps researchers and engineers developing therapies and technologies for visual processing and learning.
Foundation model of neural activity predicts response to new stimulus types and anatomy.
2024
bioRxiv : the preprint server for biology
Wang EY, Fahey PG, Ding Z, Papadopoulos S, Ponder K +17 more
Plain English This study looked at how well a new type of artificial intelligence model can predict how brain cells respond to different visual stimuli. Researchers tested this model using data from various mice, and they found it could accurately predict brain responses to new kinds of videos, achieving at least 90% accuracy in some cases. This is important because it means we could better understand how the brain processes information and develop new tools for neuroscience research.
Who this helps: This benefits researchers in neuroscience and potentially patients related to brain disorders.
The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videos.
2024
ArXiv
Turishcheva P, Fahey PG, Vystrčilová M, Hansel L, Froebe R +9 more
Plain English Researchers organized a competition to better understand how mouse brains respond to moving images, or video, since this reflects real-world situations. They collected data from over 78,000 neurons in the brains of ten mice while exposing them to two hours of video stimuli. This work matters because it will help scientists create better models of how biological visual systems work, moving our understanding of brain activity closer to real-life vision processing.
Who this helps: This benefits researchers and scientists studying brain function and vision.
Most discriminative stimuli for functional cell type clustering.
2024
ArXiv
Burg MF, Zenkel T, Vystrčilová M, Oesterle J, Höfling L +13 more
Plain English This study focused on finding efficient ways to identify different types of neurons in the retina and visual cortex of animals. Researchers developed a new method that uses optimized stimuli to quickly cluster neurons based on their functions, successfully applying it to mouse retina, marmoset retina, and macaque visual area V4. This method allows scientists to identify cell types much faster and more easily, which could significantly enhance our understanding of visual processing.
Who this helps: This benefits researchers and neuroscientists studying vision and brain function.
Retrospective for the Dynamic Sensorium Competition for predicting large-scale mouse primary visual cortex activity from videos.
2024
ArXiv
Turishcheva P, Fahey PG, Vystrčilová M, Hansel L, Froebe R +20 more
Plain English This study looked at how well different computer models can predict the activity of brain cells in the primary visual cortex of mice when exposed to videos. Researchers created a large dataset tracking responses from over 78,000 neurons while the mice experienced various visual stimuli, and they ran a competition where multiple teams submitted their predictive models. The best performing models improved predictions by 50% compared to earlier models, showing significant progress in understanding how mouse brains respond to visual information.
Who this helps: This benefits researchers in neuroscience and artificial intelligence, helping them improve models that simulate vision processing.
Bipartite invariance in mouse primary visual cortex.
2023
bioRxiv : the preprint server for biology
Ding Z, Tran DT, Ponder K, Cobos E, Ding Z +13 more
Plain English This study examined how specific neurons in the mouse brain's primary visual cortex respond to different visual patterns. Researchers found a new type of neuronal response called bipartite invariance, where some neurons reacted to texture-like patterns regardless of their phase, while others responded to fixed spatial patterns. This understanding helps explain how brains can recognize objects by detecting their edges, crucial for vision in dynamic environments.
Who this helps: This benefits neuroscientists and researchers working on visual processing and brain function.
A CRISPR toolbox for generating intersectional genetic mouse models for functional, molecular, and anatomical circuit mapping.
2022
BMC biology
Lusk SJ, McKinney A, Hunt PJ, Fahey PG, Patel J +11 more
Plain English This study explored a new toolkit that helps scientists create specialized genetic mouse models to better understand how specific cell types affect health and disease. The researchers successfully made 11 different mouse models and used some of them to study how respiratory control and hormone effects work at a cellular level. This is important because it makes it easier and cheaper for researchers to investigate complex cellular interactions, potentially leading to better insights into health issues.
Who this helps: This benefits scientists and researchers studying genetics and cell biology.
Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex.
2020
eLife
Cadwell CR, Scala F, Fahey PG, Kobak D, Mulherkar S +12 more
Plain English Researchers studied a specific group of brain cells called excitatory neurons in young mice to understand how they are organized and connected. They found that these neurons come from a common ancestor, usually two cells, and work together in processing information by connecting more vertically across different layers of the brain rather than side-to-side in the same layer. This matters because it gives insight into how brain circuits are formed and could influence our understanding of brain function and development.
Who this helps: This helps researchers and doctors studying brain development and neurological conditions.
Follicle-stimulating hormone and luteinizing hormone increase Ca2+ in the granulosa cells of mouse ovarian follicles†.
2019
Biology of reproduction
Egbert JR, Fahey PG, Reimer J, Owen CM, Evsikov AV +5 more
Plain English This study looked at how two hormones, follicle stimulating hormone (FSH) and luteinizing hormone (LH), affect calcium levels in specific cells of mouse ovaries. The researchers found that FSH raises calcium levels in certain ovarian cells within about 10 minutes and keeps them elevated for another 10 minutes, while LH causes calcium fluctuations that last over 6 hours. Understanding how these hormones influence calcium levels is important for grasping how ovarian functions like ovulation occur.
Who this helps: This helps patients undergoing fertility treatments and doctors working in reproductive health.
Froudarakis E, Fahey PG, Reimer J, Smirnakis SM, Tehovnik EJ +1 more
Plain English This research focused on how the mouse brain's primary visual cortex (V1) connects with other brain areas and how these connections influence visual processing. The study found that V1 has strong links to both higher and lower brain regions, which allows mice to process visual information based on their actions and goals. This understanding is crucial because it shows that visual processing is more complex than previously thought, affecting how we approach treatments for vision-related issues.
Who this helps: This helps researchers and doctors working on visual disorders in animals and potentially humans.
Inception loops discover what excites neurons most using deep predictive models.
2019
Nature neuroscience
Walker EY, Sinz FH, Cobos E, Muhammad T, Froudarakis E +5 more
Plain English This study explored how certain visual stimuli can trigger the strongest reactions in brain cells, specifically in the visual cortex of mice. Researchers created a system called "inception loops" that uses advanced computer models to predict how neurons respond to various stimuli. They found that the most effective visual patterns for exciting these neurons were complex and did not match traditional ideas of simple shapes, showing these patterns drove neuronal responses significantly better—up to 50% more effectively than standard stimuli.
Who this helps: This benefits researchers studying brain function and potentially leads to improved treatments for visual processing disorders.
Increased Axonal Bouton Stability during Learning in the Mouse Model of MECP2 Duplication Syndrome.
2018
eNeuro
Ash RT, Fahey PG, Park J, Zoghbi HY, Smirnakis SM
Plain English This study looked at how certain brain structures change when mice with a specific genetic condition, called MECP2 Duplication Syndrome, learn new motor skills compared to normal mice. The researchers found that while healthy mice lose more axonal boutons (tiny structures that help transmit signals between neurons) during training, the mice with MECP2 Duplication Syndrome do not have this same elimination of boutons, indicating a problem with the brain's ability to adapt and learn. This is important because it highlights a potential target for understanding and treating learning difficulties in this form of autism.
Who this helps: This helps researchers and doctors working with patients who have MECP2 Duplication Syndrome and related conditions.
Investigating the Limits of Neurovascular Coupling.
2016
Neuron
Denfield GH, Fahey PG, Reimer J, Tolias AS
Plain English This research studied how blood flow in the brain relates to nerve activity by examining the visual cortex in cats and rodents. The findings reveal that changes in blood flow do not always accurately reflect what neurons are doing, which means drawing conclusions about brain activity based on blood flow alone can be misleading. This is important for improving brain imaging techniques used in both research and medical diagnoses.
Who this helps: Patients and doctors who rely on brain imaging for diagnosis and treatment.
Activation of intracellular metabotropic glutamate receptor 5 in striatal neurons leads to up-regulation of genes associated with sustained synaptic transmission including Arc/Arg3.1 protein.
2012
The Journal of biological chemistry
Kumar V, Fahey PG, Jong YJ, Ramanan N, O'Malley KL
Plain English This study examined how a receptor called mGluR5 in brain cells affects gene activity related to communication between neurons. The researchers found that when they activated the mGluR5 inside the cells, it led to a rise in a specific protein called Arc/Arg3.1, which is important for the long-term efficiency of neuron connections. Specifically, they showed that this process requires calcium levels and certain protein activators, highlighting that proper functioning of this receptor is crucial for neuron communication.
Who this helps: This research benefits patients with neurological conditions by improving understanding of how brain signaling works.
Chiang CD, Lewis CL, Wright MD, Agapova S, Akers B +43 more
Plain English University students improved Wikipedia's coverage of chronobiology (the study of biological clocks and daily rhythms) by editing 15 articles and adding 3 new ones, citing nearly 350 scientific studies to back up the information. The students spent about 9 hours each evaluating scientific research and deciding which Wikipedia pages needed the most work, and their improvements made these pages rank at the top of search engine results. The project benefited both the public—who now have better access to accurate information about chronobiology—and the students themselves, who gained real skills in reading scientific papers, evaluating their quality, and writing clearly for a general audience.