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

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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. 'There and back again'-forward genetics and reverse phenotyping in pulmonary arterial hypertension.

    Publication
  2. An Asymmetric Eclipse Seen Towards the Pre-Main Sequence Binary System V928 Tau

    Publication
    K2 observations of the weak-lined T Tauri binary V928 Tau A+B show the detection of a single, asymmetric eclipse which may be due to a previously …
  3. CHD8 haploinsufficiency alters the developmental trajectories of human excitatory and inhibitory neurons linking autism phenotypes with transient cellular defects

    Publication
    Chromodomain helicase DNA-binding 8 (CHD8) is one of the most frequently mutated genes causative of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly and …
  4. Efficient Inference in Structured Spaces

    Publication
    Whittington et al. demonstrate how network architectures defined in a spatial context may be useful for inference on different types of relational knowledge. These architectures allow for learning …
  5. Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

    Publication
    Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this …
  6. A Unified Framework for Dopamine Signals across Timescales

    Publication
    Rapid phasic activity of midbrain dopamine neurons is thought to signal reward prediction errors (RPEs), resembling temporal difference errors used in machine learning. However, recent studies describing slowly …
  7. Tau and other proteins found in Alzheimer's disease spinal fluid are linked to retromer-mediated endosomal traffic in mice and humans

    Publication
    ndosomal trafficking has emerged as a defective biological pathway in Alzheimer's disease (AD), and the pathway is a source of cerebrospinal fluid (CSF) protein accumulation. Nevertheless, the …
  8. Distinct prefrontal top-down circuits differentially modulate sensorimotor behavior.

    Publication
  9. Low rank mechanisms underlying flexible visual representations

    Publication
    Neuronal population responses to sensory stimuli are remarkably flexible. The responses of neurons in visual cortex have heterogeneous dependence on stimulus properties (e.g., contrast), processes that affect …
  10. Rational thoughts in neural codes

    Publication
    Complex behaviors are often driven by an internal model, which integrates sensory information over time and facilitates long-term planning to reach subjective goals. A fundamental challenge in …
  11. Common diseases alter the physiological age-related blood microRNA profile

    Publication
    Aging is a key risk factor for chronic diseases of the elderly. MicroRNAs regulate post-transcriptional gene silencing through base-pair binding on their target mRNAs. We identified …
  12. The Stellar Merger Scenario for Black Holes in the Pair-instability Gap

    Publication
    The recent detection of GW190521 stimulated ideas on how to populate the predicted black hole (BH) pair-instability (PI) mass gap. One proposal is the dynamical merger of …
  13. DNMT3A haploinsufficiency results in behavioral deficits and global epigenomic dysregulation shared across neurodevelopmental disorders.

    Publication
  14. The stability flexibility tradeoff and the dark side of detail.

    Publication
  15. Real-Time Point Process Filter for Multidimensional Decoding Problems Using Mixture Models

    Publication
    … decoding a rat position only drops by less than 9% and 4% in RMSE and 95% highest probability coverage area (HPD) performance metrics. Though the marked-point …
  16. Meta Variational Monte Carlo

    Publication
    An identification is found between meta-learning and the problem of determining the ground state of a randomly generated Hamiltonian drawn from a known ensemble. A model-agnostic …
  17. Poisson balanced spiking networks

    Publication
    An important problem in computational neuroscience is to understand how networks of spiking neurons can carry out various computations underlying behavior. Balanced spiking networks (BSNs) provide a powerful …
  18. Approaches to inferring multi-regional interactions from simultaneous population recordings: Inferring multi-regional interactions from simultaneous population recordings

    Publication
    Most past studies of neural representations and dynamics have focused on recordings from single brain areas. However, growing evidence of brain-wide, parallel representations of cognitive variables suggests …
  19. Inferring the molecular and phenotypic impact of amino acid variants with MutPred2.

    Publication
  20. Identifying cell type specific driver genes in autism-associated copy number loci from cerebral organoids.

    Publication
  21. Young adult-born neurons improve odor coding by mitral cells

    Publication
    New neurons are continuously generated in the adult brain through a process called adult neurogenesis. This form of plasticity has been correlated with numerous behavioral and cognitive phenomena …
  22. 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 …
  23. The Geometry of Abstraction in the Hippocampus and Prefrontal Cortex

    Publication
    The curse of dimensionality plagues models of reinforcement learning and decision making. The process of abstraction solves this by constructing variables describing features shared by different instances, reducing …
  24. Spatial connectivity matches direction selectivity in visual cortex

    Publication
    The selectivity of neuronal responses arises from the architecture of excitatory and inhibitory connections. In the primary visual cortex, the selectivity of a neuron in layer 2/3 …
  25. SARS-CoV-2 Transmission among Marine Recruits during Quarantine

    Publication
    … previously had negative results for SARS-CoV-2 at the beginning of supervised quarantine, and less than 2% of recruits with unknown previous status, tested positive by …
  26. A new no-report paradigm reveals that face cells encode both consciously perceived and suppressed stimuli

    Publication
    A powerful paradigm to identify neural correlates of consciousness is binocular rivalry, wherein a constant visual stimulus evokes a varying conscious percept. It has recently been suggested that …
  27. Lower airway dysbiosis affects lung cancer progression

    Publication
    In lung cancer, enrichment of the lower airway microbiota with oral commensals commonly occurs and ex vivo models support that some of these bacteria can trigger host transcriptomic …
  28. Phenotypic subtyping and re-analyses of existing transcriptomic data from autistic probands in simplex families reveal differentially expressed and ASD trait-associated genes.

    Publication
  29. Dopamine signals as temporal difference errors: recent advances

    Publication
    In the brain, dopamine is thought to drive reward-based learning by signaling temporal difference reward prediction errors (TD errors), a 'teaching signal' used to train computers. Recent …
  30. A Framework for Multiphase Galactic Wind Launching Using TIGRESS

    Publication
    Galactic outflows have density, temperature, and velocity variations at least as large as that of the multiphase, turbulent interstellar medium (ISM) from which they originate. We have conducted …
  31. Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data

    Publication
    We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography–mass spectrometry (GC–MS) data. We then designed workflows to enable the community to …
  32. Modeling behaviorally relevant neural dynamics enabled by preferential subspace identification

    Publication
    Neural activity exhibits complex dynamics related to various brain functions, internal states and behaviors. Understanding how neural dynamics explain specific measured behaviors requires dissociating behaviorally relevant and irrelevant …
  33. 16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development.

    Publication
  34. TRAP-based allelic translation efficiency imbalance analysis to identify genetic regulation of ribosome occupancy in specific cell types in vivo.

    Publication
  35. Altered hippocampal-prefrontal communication during anxiety-related avoidance in mice deficient for the autism-associated gene Pogz.

    Publication
  36. Fractionating autism based on neuroanatomical normative modeling.

    Publication
  37. Protein Structural Alignments From Sequence

    Publication
    Computing sequence similarity is a fundamental task in biology, with alignment forming the basis for the annotation of genes and genomes and providing the core data structures for …
  38. Shear-induced dispersion in peristaltic flow

    Publication
    The effective diffusivity of a Brownian tracer in unidirectional flow is well known to be enhanced due to shear by the classic phenomenon of Taylor dispersion. At long …
  39. Reconstruction of natural images from responses of primate retinal ganglion cells

    Publication
    The visual message conveyed by a retinal ganglion cell (RGC) is often summarized by its spatial receptive field, but in principle also depends on the responses of other …
  40. A Fast, Two-dimensional Gaussian Process Method Based on Celerite: Applications to Transiting Exoplanet Discovery and Characterization

    Publication
    Gaussian processes (GPs) are commonly used as a model of stochastic variability in astrophysical time series. In particular, GPs are frequently employed to account for correlated stellar variability …
  41. Bayesian Workflow

    Publication
    The Bayesian approach to data analysis provides a powerful way to handle uncertainty in all observations, model parameters, and model structure using probability theory. Probabilistic programming languages make …
  42. Generalized co-sparse factor regression

    Publication
    Multivariate regression techniques are commonly applied to explore the associations between large numbers of outcomes and predictors. In real-world applications, the outcomes are often of mixed types …
  43. Cell types and neuronal circuitry underlying female aggression in Drosophila

    Publication
    Aggressive social interactions are used to compete for limited resources and are regulated by complex sensory cues and the organism's internal state. While both sexes exhibit aggression …
  44. Mapping the research domain criteria social processes constructs to the social responsiveness scale.

    Publication
  45. A Coupled Guiding Center–Boris Particle Pusher for Magnetized Plasmas in Compact-object Magnetospheres

    Publication
    We present a novel numerical scheme for simulating the motion of relativistic charged particles in magnetospheres of compact objects, typically filled with highly magnetized collisionless plasmas. The new …
  46. A Coupled Guiding Center–Boris Particle Pusher for Magnetized Plasmas in Compact-object Magnetospheres

    Publication
    We present a novel numerical scheme for simulating the motion of relativistic charged particles in magnetospheres of compact objects, typically filled with highly magnetized collisionless plasmas. The new …
  47. Anterolateral entorhinal cortex volume is associated with memory retention in clinically unimpaired older adults

    Publication
    The entorhinal cortex is subdivided into anterolateral entorhinal cortex (alERC) and posteromedial entorhinal cortex (pmERC) subregions, which are theorized to support distinct cognitive roles. This distinction is particularly …
  48. Constraining the Halo Mass of Damped Lyα Absorption Systems (DLAs) at z=2-3.5 using the Quasar-CMB Lensing Cross-correlation

    Publication
    We study the cross correlation of damped Ly\(alpha\) systems (DLAs) and their background quasars, using the most updated DLA catalog and the Planck 2018 CMB lensing convergence …
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