About

Richard Daniel Mooney is the George Barth Geller Distinguished Professor for Research in Neurobiology and a Professor of Neurobiology at Duke University. He also serves as the Director of the T32 Neurobiology Training Program and is a Professor of Cell Biology. He is a faculty member at the Duke Institute for Brain Sciences. His research focuses on neurobiology, and he is affiliated with the Bryan Research Building in Durham, North Carolina.

Research topics

• Computer Science
• Artificial Intelligence
• Machine Learning
• Psychology
• Biology
• Neuroscience

Selected publications

• Data from: Pose Splatter: A 3D Gaussian Splatting Model for Quantifying Animal Pose and Appearance

  Research Data Repository, Duke University · 2026-01-08

  datasetOpen accessSenior author

  This repository contains two datasets of freely moving laboratory animals. The first dataset contains 6 synchronous 30-minute videos of a freely moving mouse in a 28 cm diameter plastic cylinder. The RGB videos are captured at a resolution of 1536 x 2048 at 30 fps. The second dataset contains 6 synchronous 20-minute videos of a freely moving zebra finch, and is obtained in the same manner. Videos were obtained using 6 externally-triggered Basler cameras with campy v2.0.0 (https://github.com/ksseverson57/campy). Mask videos were obtained using Segment Anything Model 2 (SAM2; https://github.com/facebookresearch/sam2, https://github.com/heyoeyo/muggled_sam). See the README for more detailed usage information.

  PublisherDOI

• Brain-wide mapping of neuroanatomical connections to the auditory cortex of hearing and deaf mice

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-16

  articleOpen accessSenior author

  Summary Remarkable therapeutic innovations have made it possible to establish hearing in congenitally deaf subjects. Despite these advances, a potential obstacle to restoring auditory function is that the absence of auditory experience alters the connectivity of the auditory cortex, a region that contributes to auditory perception and cognition. Here we used an intersectional genetic approach to map the brainwide inputs to the primary auditory cortex of congenitally deaf mice and their hearing littermates. We found that deaf mice displayed a significant reduction in afferents arising from the basomedial amygdala, the core of the medial geniculate nucleus, and anterior auditory thalamic nuclei. Nonetheless, major aspects of auditory cortical connectivity, including input from other thalamic nuclei and from non-auditory regions of the cortex, were unaffected by deafness. These findings highlight altered and preserved connectivity of the auditory cortex in the absence of auditory experience, which may inform therapies designed to establish hearing in congenitally deaf subjects.

  PublisherOA PDFDOI

• A synaptic locus of song learning

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-21

  articleSenior authorCorresponding

  Learning by imitation is the foundation for verbal and musical expression, but its underlying neural basis remains obscure. A juvenile male zebra finch imitates the multisyllabic song of an adult tutor in a process that depends on a song-specialized cortico-basal ganglia circuit, affording a powerful system to identify the synaptic substrates of imitative motor learning. Plasticity at a particular set of cortico-basal ganglia synapses is hypothesized to drive rapid learning-related changes in song before these changes are subsequently consolidated in downstream circuits. Nevertheless, this hypothesis is untested and the synaptic locus where learning initially occurs is unknown. By combining a computational framework to quantify song learning with synapse-specific optogenetic and chemogenetic manipulations within and directly downstream of the cortico-basal ganglia circuit, we identified the specific cortico-basal ganglia synapses that drive the acquisition and expression of rapid vocal changes during juvenile song learning and characterized the hours-long timescale over which these changes consolidate. Furthermore, transiently augmenting postsynaptic activity in the basal ganglia briefly accelerates learning rates and persistently alters song, demonstrating a direct link between basal ganglia activity and rapid learning. These results localize the specific cortico-basal ganglia synapses that enable a juvenile songbird to learn to sing and reveal the circuit logic and behavioral timescales of this imitative learning paradigm.

  PublisherDOI

• The mouse posterior insular cortex encodes expressive and receptive aspects of courtship vocalizations

  Cell Reports · 2025-06-01 · 1 citations

  articleOpen accessSenior author

  Socially effective vocal communication requires brain regions that encode expressive and receptive aspects of vocal communication in a social context-dependent manner. Here, we combined a novel behavioral assay with microendoscopic calcium imaging to interrogate neuronal activity (regions of interest [ROIs]) in the posterior insula (pIns) in socially interacting mice as they switched rapidly between states of vocal expression and reception. We found that largely distinct subsets of pIns ROIs were active during vocal expression and reception. Notably, pIns activity during vocal expression increased prior to vocal onset and was also detected in congenitally deaf mice, pointing to a motor signal. Furthermore, receptive pIns activity was modulated strongly by social context. Lastly, tracing experiments reveal that deep-layer neurons in the pIns directly bridge the auditory thalamus to a midbrain vocal gating region. Therefore, the pIns is a site that encodes vocal expression and reception in a manner that depends on social context.

  PublisherOA PDFDOI

• Correctness is its own reward: bootstrapping error signals in self-guided reinforcement learning

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-23

  preprintOpen access

  Reinforcement learning (RL) offers a compelling account of how agents learn complex behaviors by trial and error, yet RL is predicated on the existence of a reward function provided by the agent's environment. By contrast, many skills are learned without external guidance, posing a challenge to RL's ability to account for self-directed learning. For instance, juvenile male zebra finches first memorize and then train themselves to reproduce the song of an adult male tutor through extensive practice. This process is believed to be guided by an internally computed assessment of performance quality, though the mechanism and development of this signal remain unknown. Here, we propose that, contrary to prevailing assumptions, tutor song memorization and performance assessment are subserved by the same neural circuit, one trained to predictively cancel tutor song. To test this hypothesis, we built models of a local forebrain circuit that learns to use contextual input from premotor regions to cancel tutor song auditory input via plasticity at different synaptic loci. We found that, after learning, excitatory projection neurons in these circuits exhibited population error codes signaling mismatches between the tutor song memory and birds' own performance, and these signals best matched experimental data when networks were trained with anti-Hebbian plasticity in the recurrent pathway through inhibitory interneurons. We also found that model learning proceeds in two stages, with an initial phase of sharpening error sensitivity followed by a fine-tuning period in which error responses to the tutor song are minimized. Finally, we showed that the error signal produced by this model can train a simple RL agent to replicate the spectrograms of adult bird songs. Together, our results suggest that purely local learning via predictive cancellation suffices for bootstrapping error signals capable of guiding self-directed learning of natural behaviors.

  PublisherDOI

• Dual neuromodulatory dynamics underlie birdsong learning

  Nature · 2025-03-12 · 8 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Author Correction: Dual neuromodulatory dynamics underlie birdsong learning

  Nature · 2025-08-29

  erratumOpen accessSenior author
  PublisherOA PDFDOI

• Vocalization modulates the mouse auditory cortex even in the absence of hearing

  Cell Reports · 2024-08-01 · 10 citations

  articleOpen accessSenior author

  Vocal communication depends on distinguishing self-generated vocalizations from other sounds. Vocal motor corollary discharge (CD) signals are thought to support this ability by adaptively suppressing auditory cortical responses to auditory feedback. One challenge is that vocalizations, especially those produced during courtship and other social interactions, are accompanied by other movements and are emitted during a state of heightened arousal, factors that could potentially modulate auditory cortical activity. Here, we monitor auditory cortical activity, ultrasonic vocalizations (USVs), and other non-vocal courtship behaviors in a head-fixed male mouse while he interacts with a female mouse. This approach reveals a vocalization-specific signature in the auditory cortex that suppresses the activity of USV playback-excited neurons, emerges before vocal onset, and scales with USV band power. Notably, this vocal modulatory signature is also present in the auditory cortex of congenitally deaf mice, revealing an adaptive vocal CD signal that manifests independently of auditory feedback or auditory experience.

  PublisherOA PDFDOI

• A Cortical Site that Encodes Vocal Expression and Reception

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-16

  preprintOpen accessSenior author

  Socially effective vocal communication requires brain regions that encode expressive and receptive aspects of vocal communication in a social context-dependent manner. Here, we combined a novel behavioral assay with microendoscopy to interrogate neuronal activity in the posterior insula (pIns) in socially interacting mice as they switched rapidly between states of vocal expression and reception. We found that distinct but spatially intermingled subsets of pIns neurons were active during vocal expression and reception. Notably, pIns activity during vocal expression increased prior to vocal onset and was also detected in congenitally deaf mice, pointing to a motor signal. Furthermore, receptive pIns activity depended strongly on social cues, including female odorants. Lastly, tracing experiments reveal that deep layer neurons in the pIns directly bridge the auditory thalamus to a midbrain vocal gating region. Therefore, the pIns is a site that encodes vocal expression and reception in a manner that depends on social context.

  PublisherOA PDFDOI

• Nested circuits mediate the decision to vocalize

  eLife · 2023-06-14 · 14 citations

  articleOpen accessSenior author

  Vocalizations facilitate mating and social affiliation but may also inadvertently alert predators and rivals. Consequently, the decision to vocalize depends on brain circuits that can weigh and compare these potential benefits and risks. Male mice produce ultrasonic vocalizations (USVs) during courtship to facilitate mating, and previously isolated female mice produce USVs during social encounters with novel females. Earlier we showed that a specialized set of neurons in the midbrain periaqueductal gray (PAG-USV neurons) are an obligatory gate for USV production in both male and female mice, and that both PAG-USV neurons and USVs can be switched on by their inputs from the preoptic area (POA) of the hypothalamus and switched off by their inputs from neurons on the border between the central and medial amygdala (Amg C/M-PAG neurons) (Michael et al., 2020). Here, we show that the USV-suppressing Amg C/M-PAG neurons are strongly activated by predator cues or during social contexts that suppress USV production in male and female mice. Further, we explored how vocal promoting and vocal suppressing drives are weighed in the brain to influence vocal production in male mice, where the drive and courtship function for USVs are better understood. We found that Amg C/M-PAG neurons receive monosynaptic inhibitory input from POA neurons that also project to the PAG, that these inhibitory inputs are active in USV-promoting social contexts, and that optogenetic activation of POA cell bodies that make divergent axonal projections to the amygdala and PAG is sufficient to elicit USV production in socially isolated male mice. Accordingly, Amg C/M-PAG neurons, along with POA PAG and PAG-USV neurons, form a nested hierarchical circuit in which environmental and social information converges to influence the decision to vocalize.

  PublisherDOI

Recent grants

• NIH Grant R01DC004691

  NIH · $1.2M · 2006

• NIH Grant R01DC005671

  NIH · $1.4M · 2009

• NIH Grant R21NS079929

  NIH · $376k · 2014

• NIH Grant R01EY008015

  NIH · $389k · 1993

• NIH Grant R21NS046583

  NIH · $363k · 2006

Frequent coauthors

• Fan Wang

  Shanghai Hospital Development Center

  56 shared

• Valerie Michael

  Duke University

  50 shared

• Frederick S. Livingston

  Molecular Devices

  36 shared

• Stephen Nowicki

  Emory University

  34 shared

• Robert W. Rhoades

  32 shared

• Jonathan F. Prather

  University of Wyoming

  31 shared

• Katherine Tschida

  Cornell University

  30 shared

• Jonnathan Singh Alvarado

  Beth Israel Deaconess Medical Center

  28 shared

Labs

• Mooney LabPI

Awards & honors

• George Barth Geller Distinguished Professor for Research in…