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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.

Our grants advance knowledge and strengthen connections between science and society.

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Founded by Jim and Marilyn Simons, we’re a private philanthropy advancing mathematics and basic 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. Overexpression of CD47 is associated with brain overgrowth and 16p11.2 deletion syndrome.

    Publication
  2. Assessment of medical morbidities in a rhesus monkey model of naturally occurring low sociality.

    Publication
  3. Neural Anatomy and Optical Microscopy (NAOMi) Simulation for evaluating calcium imaging methods

    Publication
    Background: The past decade has seen a multitude of new in vivo functional imaging methodologies. However, the lack of ground-truth comparisons or evaluation metrics makes the large …
  4. A cross-species neural integration of gravity for motor optimization

    Publication
    Recent kinematic results, combined with model simulations, have provided support for the hypothesis that the human brain shapes motor patterns that use gravity effects to minimize muscle effort …
  5. deepregression: a Flexible Neural Network Framework for Semi-Structured Deep Distributional Regression

    Publication
    This paper describes the implementation of semi-structured deep distributional regression, a flexible framework to learn distributions based on a combination of additive regression models and deep neural …
  6. Ab initio Full Cell GW+DMFT for Correlated Materials

    Publication
  7. Genotype and defects in microtubule-based motility correlate with clinical severity in KIF1A-associated neurological disorder.

    Publication
  8. Diagnostic classification and prognostic prediction using common genetic variants in autism spectrum disorder: Genotype-based deep learning.

    Publication
  9. Autism spectrum disorders classification using genotype data: A deep learning-based predictive classifier.

    Publication
  10. High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo

    Publication
    The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising …
  11. Classification of Magnetohydrodynamic Simulations Using Wavelet Scattering Transforms

    Publication
    The complex interplay of magnetohydrodynamics, gravity, and supersonic turbulence in the interstellar medium (ISM) introduces non-Gaussian structure that can complicate comparison between theory and observation. We show …
  12. Comment on “Stepped pressure profile equilibria in cylindrical plasmas via partial Taylor relaxation” [J. Plasma Physics (2006), vol. 72, part 6, pp. 1167–1171]

    Publication
    In an early study of the properties and capabilities of the multiregion, relaxed magnetohydrodynamic model, Hole, Hudson & Dewar claim that they are able to construct a multiregion stepped …
  13. Synaptic plasticity as Bayesian inference

    Publication
    of synaptic weights must be set based on noisy, often ambiguous, sensory information. In such a high-noise regime, keeping track of probability distributions over weights is the …
  14. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

    Publication
    Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional …
  15. Microglia complement signaling promotes neuronal elimination and normal brain functional connectivity.

    Publication
  16. Constrained non-negative matrix factorization enabling real-time insights of in situ and high-throughput experiments

    Publication
    Non-negative Matrix Factorization (NMF) methods offer an appealing unsupervised learning method for real-time analysis of streaming spectral data in time-sensitive data collection, such as in …
  17. Measuring depression in autistic adults: Psychometric validation of the Beck Depression Inventory-II.

    Publication
  18. An Implicit Finite Volume Scheme to Solve the Time-dependent Radiation Transport Equation Based on Discrete Ordinates

    Publication
    We describe a new algorithm to solve the time dependent, frequency integrated radiation transport (RT) equation implicitly, which is coupled to an explicit solver for equations of magnetohydrodynamics …
  19. Spontaneous neural activity relates to psychiatric traits in 16p11.2 CNV carriers: An analysis of EEG spectral power and multiscale entropy.

    Publication
  20. Comparison of Full-Reference Image Quality Models for Optimization of Image Processing Systems

    Publication
    The performance of objective image quality assessment (IQA) models has been evaluated primarily by comparing model predictions to human quality judgments. Perceptual datasets gathered for this purpose have …
  21. Fast periodic Gaussian density fitting by range separation

    Publication
  22. Filling anomaly for general 2D and 3D C

    Publication
  23. Improving scalability in systems neuroscience

    Publication
    Emerging technologies to acquire data at increasingly greater scales promise to transform discovery in systems neuroscience. However, current exponential growth in the scale of data acquisition is a …
  24. Computation of the electroencephalogram (EEG) from network models of point neurons.

    Publication
  25. Flexible scaling and persistence of social vocal communication

    Publication
    Innate vocal sounds such as laughing, screaming or crying convey one's feelings to others. In many species, including humans, scaling the amplitude and duration of vocalizations is …
  26. Brain Endothelial Cells Are Exquisite Sensors of Age-Related Circulatory Cues

    Publication
    Brain endothelial cells (BECs) are key constituents of the blood-brain barrier (BBB), protecting the brain from pathogens and restricting access of circulatory factors. Yet, because circulatory proteins …
  27. Multivariate genome-wide analysis of education, socioeconomic status and brain phenome.

    Publication
  28. De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families.

    Publication
  29. Autism BrainNet.

    Publication
  30. Stellar Evolution in AGN Disks

    Publication
    Active galactic nuclei (AGNs) are powered by geometrically thin accretion disks surrounding a central supermassive black hole. Here we explore the evolution of stars embedded in these extreme …
  31. 3DeeCellTracker, a deep learning-based pipeline for segmenting and tracking cells in 3D time lapse images

    Publication
    Despite recent improvements in microscope technologies, segmenting and tracking cells in three-dimensional time-lapse images (3D + T images) to extract their dynamic positions and activities remains a …
  32. MTSplice predicts effects of genetic variants on tissue-specific splicing.

    Publication
  33. Comparison of explicit and mean-field models of cytoskeletal filaments with crosslinking motors

    Publication
    In cells, cytoskeletal filament networks are responsible for cell movement, growth, and division. Filaments in the cytoskeleton are driven and organized by crosslinking molecular motors. In reconstituted cytoskeletal …
  34. Learning is shaped by abrupt changes in neural engagement

    Publication
    Internal states such as arousal, attention and motivation modulate brain-wide neural activity, but how these processes interact with learning is not well understood. During learning, the brain …
  35. Combining Brain Perturbation and Neuroimaging in Non-human Primates

    Publication
    Brain perturbation studies allow detailed causal inferences of behavioral and neural processes. Because the combination of brain perturbation methods and neural measurement techniques is inherently challenging, research in …
  36. A biologically plausible neural network for multi-channel Canonical Correlation Analysis

    Publication
    Cortical pyramidal neurons receive inputs from multiple distinct neural populations and integrate these inputs in separate dendritic compartments. We explore the possibility that cortical microcircuits implement Canonical Correlation …
  37. Fast computation of latent correlations

    Publication
    Latent Gaussian copula models provide a powerful means to perform multi-view data integration since these models can seamlessly express dependencies between mixed variable types (binary, continuous, zero …
  38. The many behaviors of deformable active droplets

    Publication
    Active fluids consume fuel at the microscopic scale, converting this energy into forces that can drive macroscopic motions over scales far larger than their microscopic constituents. In some …
  39. The connectome predicts resting-state functional connectivity across the Drosophila brain

    Publication
    Anatomical connectivity can constrain both a neural circuit's function and its underlying computation. This principle has been demonstrated for many small, defined neural circuits. For example, connectome …
  40. Tracking the Footprints of Spin Fluctuations: A Multi-Method, Multi-Messenger Study of the Two-Dimensional Hubbard Model

    Publication
    The Hubbard model represents the fundamental model for interacting quantum systems and electronic correlations. Using the two-dimensional half-filled Hubbard model at weak coupling as testing grounds …
  41. Experience-dependent contextual codes in the hippocampus

    Publication
    The hippocampus contains neural representations capable of supporting declarative memory. Hippocampal place cells are one such representation, firing in one or few locations in a given environment. Between …
  42. Prefrontal cortex represents heuristics that shape choice bias and its integration into future behavior

    Publication
    Goal-directed behavior requires integrating sensory information with prior knowledge about the environment. Behavioral biases that arise from these priors could increase positive outcomes when the priors match …
  43. Directed information exchange between cortical layers in macaque V1 and V4 and its modulation by selective attention.

    Publication
  44. Exponential-family embedding with application to cell developmental trajectories for single-cell RNA-seq data.

    Publication
  45. Glia actively sculpt sensory neurons by controlled phagocytosis to tune animal behavior.

    Publication
  46. A Gravitational-wave Measurement of the Hubble Constant Following the Second Observing Run of Advanced LIGO and Virgo

    Publication
    This paper presents the gravitational-wave measurement of the Hubble constant (H0) using the detections from the first and second observing runs of the Advanced LIGO and Virgo …
  47. Nonequilibrium Green's Functions for Functional Connectivity in the Brain

    Publication
    A theoretical framework describing the set of interactions between neurons in the brain, or functional connectivity, should include dynamical functions representing the propagation of signal from one neuron …
  48. Evaluation of UBE3A antibodies in mice and human cerebral organoids.

    Publication
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