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  • Founded by Jim and Marilyn Simons, we’re a private philanthropy advancing mathematics and basic science.

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Bringing people and ideas together to fund, conduct, and share transformative science.

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The Flatiron Institute is a research center that uses computational science to advance fields like physics, biology, and astronomy.

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Featured

Dissecting mechanisms of hyperarousal in autism and related disorders using the Simons Sleep Project

Funded Work

Gravity Follows Newton’s and Einstein’s Rules, Even at Cosmic Scales

April 15, 2026

Scientists Capture Superconductivity’s ‘Dancing Pairs’ for First Time, Filling Gap in Decades-Old Theory

April 15, 2026

How SURFiN Fellowships Jump-Started These 3 Neuroscience Students’ STEM Careers

March 18, 2026

Results

  1. Estimating the dimensionality of the manifold underlying multi-electrode neural recordings

    Publication
    … for estimation was low. Based on the challenges we observed, we formulated a pipeline for estimating the dimensionality of experimental neural data.
  2. Exploring the genetic overlap of suicide-related behaviors and substance use disorders.

    Publication
  3. Autism severity aggregates with family psychiatric history in a community-based autism sample.

    Publication
  4. PTEN mutations in autism spectrum disorder and congenital hydrocephalus: Developmental pleiotropy and therapeutic targets.

    Publication
  5. Auditory hypersensitivity and processing deficits in a rat model of fragile X syndrome.

    Publication
  6. Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism.

    Publication
  7. Pre-treatment clinical and gene expression patterns predict developmental change in early intervention in autism.

    Publication
  8. Social behavior in prepubertal neurexin 1α deficient rats: A model of neurodevelopmental disorders.

    Publication
  9. Prediction of autism spectrum disorder diagnosis using nonlinear measures of language-related EEG at 6 and 12 months.

    Publication
  10. The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice.

    Publication
  11. A Convolutional Autoencoder-Based Pipeline for Anomaly Detection and Classification of Periodic Variables

    Publication
    The periodic pulsations of stars teach us about their underlying physical process. We present a convolutional autoencoder-based pipeline as an automatic approach to search for out-of …
  12. A high-resolution view of the filament of gas between Abell 399 and Abell 401 from the Atacama Cosmology Telescope and MUSTANG-2

    Publication
    We report a significant detection of the hot intergalactic medium in the filamentary bridge connecting the galaxy clusters Abell 399 and Abell 401. This result is enabled by …
  13. The PAIR-R24M dataset for multi-animal 3D pose estimation.

    Publication
  14. Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder.

    Publication
  15. Dynamics on the manifold: Identifying computational dynamical activity from neural population recordings

    Publication
    The question of how the collective activity of neural populations gives rise to complex behaviour is fundamental to neuroscience. At the core of this question lie considerations about …
  16. Meta-learning synaptic plasticity and memory addressing for continual familiarity detection

    Publication
    Over the course of a lifetime, we process a continual stream of information. Extracted from this stream, memories must be efficiently encoded and stored in an addressable manner …
  17. Patient brain organoids identify a link between the 16p11.2 copy number variant and the RBFOX1 gene.

    Publication
  18. A coarse-grained NADH redox model enables inference of subcellular metabolic fluxes from fluorescence lifetime imaging

    Publication
    Mitochondrial metabolism is of central importance to diverse aspects of cell and developmental biology. Defects in mitochondria are associated with many diseases, including cancer, neuropathology, and infertility. Our …
  19. Spatial organization of transcribing loci during early genome activation in Drosophila

    Publication
    The early Drosophila embryo provides unique experimental advantages for addressing fundamental questions of gene regulation at multiple levels of organization, from individual gene loci to the entire genome …
  20. Identification of disease-linked hyperactivating mutations in UBE3A through large-scale functional variant analysis.

    Publication
  21. Wide-field calcium imaging of cortex-wide activity in awake, head-fixed mice

    Publication
    Characterizing cortex-wide neural activity is essential for understanding large-scale interactions among distributed cortical regions. Here, we describe a protocol using wide-field calcium imaging to monitor …
  22. Single-cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss-of-function variants regulating glial cells.

    Publication
  23. Neural population geometry: An approach for understanding biological and artificial neural networks

    Publication
    Advances in experimental neuroscience have transformed our ability to explore the structure and function of neural circuits. At the same time, advances in machine learning have unleashed the …
  24. Context-dependent persistency as a coding mechanism for robust and widely distributed value coding

    Publication
    Task-related information is widely distributed across the brain with different coding properties, such as persistency. We found in mice that coding persistency of action history and value …
  25. A Normative and Biologically Plausible Algorithm for Independent Component Analysis

    Publication
    The brain effortlessly solves blind source separation (BSS) problems, but the algorithm it uses remains elusive. In signal processing, linear BSS problems are often solved by Independent Component …
  26. Flexible simultaneous mesoscale two-photon imaging of neural activity at high speeds

    Publication
    Understanding brain function requires monitoring local and global brain dynamics. Two-photon imaging of the brain across mesoscopic scales has presented trade-offs between imaging area and acquisition …
  27. Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry

    Publication
    Imaging the activity of neurons that are widely distributed across brain regions deep in scattering tissue at high speed remains challenging. Here, we introduce an open-source system …
  28. Shadow tomography based on informationally complete positive operator-valued measure

    Publication
    Recently introduced shadow tomography protocols use “classical shadows” of quantum states to predict many target functions of an unknown quantum state. Unlike full quantum state tomography, shadow tomography …
  29. The meaning of significant mean group differences for biomarker discovery.

    Publication
  30. Revealing nonlinear neural decoding by analyzing choices

    Publication
    Sensory data about most natural task-relevant variables are entangled with task-irrelevant nuisance variables. The neurons that encode these relevant signals typically constitute a nonlinear population code …
  31. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing.

    Publication
  32. Protocol for analysis of mouse neutrophil NETosis by flow cytometry

    Publication
    Studies involving neutrophils are steadily increasing, thus creating a need for more optimized and thorough protocols for studying neutrophil function. Here, we present our protocol for extracting mouse …
  33. Sequential and efficient neural-population coding of complex task information

    Publication
    Recent work has highlighted that many types of variables are represented in each neocortical area. How can these many neural representations be organized together without interference and coherently …
  34. Primary visual cortex straightens natural video trajectories

    Publication
    Many sensory-driven behaviors rely on predictions about future states of the environment. Visual input typically evolves along complex temporal trajectories that are difficult to extrapolate. We test …
  35. An oligomeric semiconducting nanozyme with ultrafast electron transfers alleviates acute brain injury

    Publication
  36. Accurate Localization of Linear Probe Electrode Arrays across Multiple Brains

    Publication
    Recently developed probes for extracellular electrophysiological recordings have large numbers of electrodes on long linear shanks. Linear electrode arrays, such as Neuropixels probes, have hundreds of recording electrodes …
  37. CD4 + T cells contribute to neurodegeneration in Lewy body dementia

    Publication
  38. All-sky search for long-duration gravitational-wave bursts in the third Advanced LIGO and Advanced Virgo run

    Publication
    After the detection of gravitational waves from compact binary coalescences, the search for transient gravitational-wave signals with less well-defined waveforms for which matched filtering is not …
  39. Pleiotropy between language impairment and broader behavioral disorders-an investigation of both common and rare genetic variants.

    Publication
  40. A Similarity-preserving Neural Network Trained on Transformed Images Recapitulates Salient Features of the Fly Motion Detection Circuit

    Publication
    Learning to detect content-independent transformations from data is one of the central problems in biological and artificial intelligence. An example of such problem is unsupervised learning of …
  41. Adaptive Denoising via GainTuning

    Publication
    Deep convolutional neural networks (CNNs) for image denoising are usually trained on large datasets. These models achieve the current state of the art, but they have difficulties generalizing …
  42. A Neural Network with Local Learning Rules for Minor Subspace Analysis

    Publication
    The development of neuromorphic hardware and modeling of biological neural networks requires algorithms with local learning rules. Artificial neural networks using local learning rules to perform principal subspace …
  43. Mapping Spatial Frequency Preferences Across Human Primary Visual Cortex

    Publication
    Neurons in primate visual cortex (area V1) are tuned for spatial frequency, in a manner that depends on their position in the visual field. Several studies have examined …
  44. Small brains for big science

    Publication
    As the study of the human brain is complicated by its sheer scale, complexity, and impracticality of invasive experiments, neuroscience research has long relied on model organisms. The …
  45. Unsupervised Deep Video Denoising

    Publication
    Deep convolutional neural networks (CNNs) for video denoising are typically trained with supervision, assuming the availability of clean videos. However, in many applications, such as microscopy, noiseless videos …
  46. How pushing the spatiotemporal resolution of fMRI can advance neuroscience

    Publication
  47. Unsupervised deep learning identifies semantic disentanglement in single inferotemporal face patch neurons

    Publication
    In order to better understand how the brain perceives faces, it is important to know what objective drives learning in the ventral visual stream. To answer this question …
  48. Discordant associations of educational attainment with ASD and ADHD implicate a polygenic form of pleiotropy.

    Publication
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