Repetition-related reductions in neural activity support improved behavior through increases in oscillatory power
Gilmore A.W., Claudino L., Levesque C.M., Agron A.M., Molfese P.J. et al. Communications Biology, in press
Recent Publications
Publication entries are Markdown files so papers can be added one at a time.
2026
A unitary representational space for abstract and concrete concepts derived from human similarity judgments
Persichetti A., Zheng C., Li T., Gotts S., Pereira F., Martin A.
Brain age prediction in generalized anxiety disorder using a convolutional neural network
Richier C., Zugman A., Harrewijn A., Cardinale E. M., Khosravi P. (...) Winkler A. M., Pine D. S., Sawyers C. K. - Translational Psychiatry, 16:368, 2026
Capturing instantaneous neural signal-behavior relationships with concurrent functional mixed models
Xin A.W., Cui E., Pereira F., Loewinger G.
Causal Inference in Studies with Functional Unmasking: Psychedelics and Beyond
Loewinger G., Stensrud M.J., Nayak S.M., Yaden D., Levis A.
Characterizing Universal Object Representations Across Vision Models
Mahner F. P., Roth J., Lam K. C., Bonner M. F., Pereira F., Hebart M. N.
Experimenter-free pain assessment in mice using a thermal gradient ring and functional linear models
Garcia A., Siemian J. N., Loewinger G., Yadav P. M., Sarsfield S. - Pain Reports 11 (4), e1469, 2026
Fast Penalized Generalized Estimating Equations for Large Longitudinal Functional Datasets
Loewinger G., Levis A., Cui E., Pereira F. Biometrics 82
Format-invariant semantic dimensions structure food similarity judgments
Avery J., Zheng C., Candy C., Persichetti A., Martin A.
In-Scanner Thoughts shape Resting-state Functional Connectivity: how participants "rest" matters
Gonzalez-Castillo J., Spurney M., Lam K.C., Gephart I. S., Pereira F., Handwerker D. A., Kam J. W. Y., Bandettini P. - in press at Nature Communications, 2026
Interpretable factorization of clinical questionnaires to identify latent factors of psychopathology
Lam K.C., Pereira F., Mahony B.W., Raznahan A. Transactions on Machine Learning Research 2026
Mood and Behaviors of Adolescents With Depression in a Longitudinal Study Before and During the COVID-19 Pandemic
"Mood and Behaviors of Adolescents With Depression in a Longitudinal Study Before and During the COVID-19 Pandemic" Sadeghi N., Fors P.Q., Eisner L., Taigman J., Qi K., Gorham L.S., Camp C.C., O'Callaghan G., Rodriguez D., McGuire J., Garth E.M., Engel C., Davis M., Towbin K.E., Stringaris A., Nielson D.M.
Nonparametric causal inference for optogenetics: sequential excursion effects for dynamic regimes
Loewinger G., Levis A., Pereira F. Journal of the American Statistical Association, 2026
Origins of Anhedonia in Childhood and Adolescence
"Origins of Anhedonia in Childhood and Adolescence" Prabhakar J., Nielson D.M., Stringaris A.
Similarity-based representation factorization for revealing interpretable dimensions in representational data
Mahner F. P., Lam K. C., Pereira F., Hebart M. N.
TONI-NLP at PsyDefDetect: Defense Mechanism Detection via LLM-based Ensemble Methods
Paul D., Basavaraj A., Chan C. Perez-Rosas V., Inkpen D., Pereira F., Lossio-Ventura J. A. - Proceedings of the BioNLP 2026 (Shared Tasks)
2025
Neuroimaging findings for overnight consolidation of learned non-native speech sounds
Earle F.S., Molfese P.J., Myers E.B. Neurobiology of Language, 2025
A Statistical Framework for Analysis of Trial-Level Temporal Dynamics in Fiber Photometry Experiments
Loewinger G., Cui E., Lovinger D., Pereira F. in press at eLife, 2025
Automated classification of exposure and encourage events in speech data from pediatric OCD treatment
Lossio-Ventura J.A., Frank S., Ringlein G., Bonson K., Olszko A., Knobel A., Pine D.S., Freeman J., Benito K., Jangraw D.C, in JAMIA Open 8 (6), 2025
Brain-wide presynaptic networks of functionally distinct cortical neurons
Inacio A. R., Lam K. C., Zhao Y., Pereira F., Gerfen C. R., Lee S. in Nature 1-11, 2025
Detecting Cry in Daylong Audio Recordings using Machine Learning: The Development and Evaluation of Binary Classifiers
Henry L.M., Lee K., Hansen E., Tandilashvili E., Rozsypal J., Erjo T., Raven J. G., Reynolds H. M., Curtis P., Haller S.,Pine D., Norton E., Wakschlag K.S., Pereira F., Brotman M.A. in press at Assessment, 2025
Distinct prelimbic cortex ensembles encode response execution and inhibition
Madangopal R., Zhao Y., Heins C., Zhou U., Liang B., Barbera G., Lam K.C., Komer L.E., Weber S.J., Thompson D. J., Gera Y., Pham D.Q., Savell K.E., Warren B.L., Caprioli D., Venniro M., Bossert J.M., Ramsey L.A., Jedema H.P., Schoenbaum G., Lin D.T., Shaham Y., Pereira F., Hope B.T. in Proceedings of the National Academy of Sciences 122 (37), 2025
More Experts Than Galaxies: Conditionally-overlapping Experts With Biologically-Inspired Fixed Routing
Shaier S., Pereira F., K von der Wense, LE Hunter, M Jones in International Conference on Learning Representations, 2025
Multivariate prediction of temper outbursts in a sample of youth enriched for irritability using ecological momentary assessment data: A registered report
Saha D., Naim R., Pereira F., Brotman M.A., Zheng C.Y. in PLoS one, vol. 30 (3), 2025
Neural and behavioral reinstatement jointly reflect retrieval of narrative events
Nau M., Greene A., Tarder-Stoll H., Lossio-Ventura J.A., Pereira F., Chen J., Baldassano C., Baker C.I. in press at Nature Communications, 2025
Persistent representation of a prior schema in the orbitofrontal cortex facilitates learning of a conflicting schema
Maor I., Atwell J., Ascher I., Zhao Y., Takahashi Y.K., Hart E., Pereira F., Schoenbaum G. in press at Nature Communications, 2025
The encoding of interoceptive-based predictions by the paraventricular nucleus of the thalamus D2+ neurons
Machen B., Miller S., Xin A., Lampert C., Assaf L., Tucker J., Pereira F., Loewinger G., Beas S. in press at iScience, 2025
2024
Will you read how I read? Naturalistic fMRI predictors of early reading
Wat E.K., Jangraw D.C., Finn E.S., Bandettini P.A., Preston J.L., Landi N., Hoeft F., Frost S.J., Lau A., Chen G., Pugh K.R., Molfese P.J. Neuropsychologia, 2024
A Comparison of ChatGPT and Fine-Tuned Open Pre-Trained Transformers (OPT) Against Widely Used Sentiment Analysis Tools: Sentiment Analysis of COVID-19 Survey Data
Lossio-Ventura J. A., Weger R., Lee A., Guinee E., Chung J. Y., Atlas L. Y., Linos E., Pereira F. JMIR Mental Health Vol 11, 2024
Causal Inference in the Closed-Loop: Marginal Structural Models for Sequential Excursion Effects
"Causal Inference in the Closed-Loop: Marginal Structural Models for Sequential Excursion Effects" Levis A., Loewinger G., Pereira in Neural Information Processing Systems, 2024
Dissociable encoding of motivated behavior by parallel thalamo-striatal projections
Beas S., Khan I., Gao C., Loewinger G., Macdonald E., Bashford A., Rodriguez-Gonzalez S., Pereira F., Penzo M.A. in Current Biology, 2024
Dynamic effects of psychiatric vulnerability, loneliness, and social distancing on distress during the first year of the COVID-19 pandemic: Insights from a large-scale longitudinal study
Atlas L. Y., Farmer C., Shaw J., Gibbon A., Guinee E.P., Lossio-Ventura J. A., Ballard E., Ernst M., Japee S., Pereira F., Chung J. Y. in Nature Mental Health, 2024
Outcomes that matter to depressed adolescents can be identified with large language models
Xin A., Lossio-Ventura J. A., Krause, K. R., Fiorini, G., Midgley N., Pereira F., and Nielson D. M. in Journal of the American Medical Informatics Association, 2024
Subjective Affective Experience under threat is shaped by environmental affordances
Qi S., Nielson D.M., Marcotulli D., Pine D.S., Stringaris A. in Public Library of Science One, 2024
Test-retest reliability of functional connectivity in adolescents with depression
Camp C., Noble S., Scheinost D., Stringaris A., Nielson D.M. in Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 2024
2023
Inter-subject correlation during long narratives reveals widespread neural correlates of reading ability
Jangraw D.C., Finn E.S., Bandettini P.A., Landi N., Sun H., Hoeft F., Chen G., Pugh K.R., Molfese P.J. NeuroImage, 282, 120390, 2023
A Highly Replicable Decline in Mood During Rest and Simple Tasks
"A Highly Replicable Decline in Mood During Rest and Simple Tasks" Jangraw D., Keren H., Sun H., Bedder R., Rutledge R., Pereira F., Thomas A., Pine D., Zheng C., Nielson D., Stringaris A. Nature Human Behaviour 7 (4), 596-610, 2023
Improving the Interpretability of fMRI Decoding using Deep Neural Networks and Adversarial Robustness
"Improving the Interpretability of fMRI Decoding using Deep Neural Networks and Adversarial Robustness" McClure P., Moraczewski D., Lam K. C., Thomas A., Pereira F. Aperture Neuro, 2023
Linear time GPs for inferring latent trajectories from neural spike trains
Linear time GPs for inferring latent trajectories from neural spike trains" Matthew Dowling, Yuan Zhao, Il Memming Park in International Conference on Machine Learning, 2023
Manifold learning for fMRI time-varying functional connectivity
"Manifold learning for fMRI time-varying functional connectivity" Gonzalez-Castillo J., Fernandez I., Lam K., Handwerker D., Pereira F., Bandettini P. Front Hum Neurosci. 2023; 17: 1134012
Real-time variational method for learning neural trajectory and its dynamics
"Real-time variational method for learning neural trajectory and its dynamics" Matthew Dowling, Yuan Zhao, Il Memming Park in International Conference on Learning Representations, 2023
Sensory and Choice Responses in MT Distinct from Motion Encoding
"Sensory and Choice Responses in MT Distinct from Motion Encoding" Aaron J. Levi, Yuan Zhao, Il Memming Park and Alexander C. Huk Journal of Neuroscience 22 March 2023, 43 (12) 2090-2103
Trends in Language Use During the COVID-19 Pandemic and Relationship Between Language Use and Mental Health: Text Analysis Based on Free Responses From a Longitudinal Study
Weger R., Lossio-Ventura J. A., Rose-McCandlish M., Shaw J., Sinclair S., Pereira F., Chung J., Atlas L. JMIR Mental Health 10 (1), e40899, 2023
Validation of CBCL depression scores of adolescents in three independent datasets
Zelenina M., Pine D.S., Stringaris A., Nielson D.M. JCPP Advances, 2023
2022
Layer-specific activation in human primary somatosensory cortex during tactile temporal prediction error processing
Yu Y., Huber L., Yang J., Fukunaga M., Chai Y., Jangraw D., Chen G., Handwerker D., Molfese P., Ejima Y., et al. NeuroImage, 248, 118867, 2022
Specific tractography differences in autism compared to developmental coordination disorder
Kilroy E., Gerbella M., Cao L., Molfese P., Butera C., Harrison L., Jayashankar A., Rizzolatti G., Ziz-Zadeh L. Scientific Reports, 12, 19246, 2022
Prediction of mental well-being from individual characteristics and circumstances during the COVID-19 pandemic
Harris C., Farmer C., Gibbon A., Shaw J., Thomas A., Atlas L. Y., Chung J. Y., Pereira F.
Semantic Projection: Recovering Human Knowledge of Multiple, Distinct, Object Features from Word Embeddings
Grand G., Blank I., Pereira F., Fedorenko E. Nature Human Behaviour, 2022
VICE: Variational Interpretable Concept Embeddings
"VICE: Variational Interpretable Concept Embeddings" Muttenthaler L., Zheng C., McClure P., Vandermeulen R., Hebart M., Pereira F. in Neural Information Processing Systems, 2022
Working memory and reward increase the accuracy of animal location encoding in the medial prefrontal cortex
"Working memory and reward increase the accuracy of animal location encoding in the medial prefrontal cortex" Ma X., Zheng C., Chen Y., Pereira F., Zheng L. Cerebral Cortex, 2022, 1-15
2021
Different activation signatures in the primary sensorimotor and higher-level regions for haptic three-dimensional curved surface exploration
Yang J., Molfese P., Yu Y., Handwerker D., Chen G., Taylor P., Ejima Y., Wu J., Bandettini P. NeuroImage, 231, 117754, 2021
Tracking second language immersion across time: Evidence from a bi-directional longitudinal cross-linguistic fMRI study
Brice H., Frost S., Bick A., Molfese P., Rueckl J., Pugh K., Frost R. Neuropsychologia, 154, 107796, 2021
Cell-type-specific recruitment of GABAergic interneurons in the primary somatosensory cortex by long-range inputs
Naskar S., Qi J., Pereira F., Gerfen, C., Lee, S. Cell Reports 34, 108774, 2021
Gauging facial feature viewing preference as a stable individual trait in autism spectrum disorder.
Reimann G., Walsh C., Csumitta K., McClure P., Pereira F., Martin A., Ramot M. Autism Research 14:1670–1683, 2021
Magnetoencephalographic Correlates of Mood and Reward Dynamics in Human Adolescents
"Magnetoencephalographic Correlates of Mood and Reward Dynamics in Human Adolescents" Liuzzi, L., Chang, K.K., Zheng, C., Keren, H., Saha, D., Nielson, D.M. and Stringaris, A. Cerebral Cortex, 2021
Mental representations of objects reflect the ways in which we interact with them
"Mental representations of objects reflect the ways in which we interact with them" Lam K. C., Pereira F., Vaziri-Pashkam M., Woodard K., McMahon E. Proceedings of the Cognitive Science Society Conference, 2021 [selected for oral presentation]
The temporal representation of experience in subjective mood
"The temporal representation of experience in subjective mood" Keren H., Zheng C., Jangraw D. C., Chang K., Vitale A., Nielson D., Rutledge R. B., Pereira F., Stringaris A. eLife 2021
The temporal representation of experience in subjective mood
"The temporal representation of experience in subjective mood" Keren H., Zheng C., Jangraw D. C., Chang K., Vitale A., Nielson D., Rutledge R. B., Pereira F., Stringaris A. eLife 2021
Validating the Representational Space of Deep Reinforcement Learning Models of Behavior with Neural Data
"Validating the Representational Space of Deep Reinforcement Learning Models of Behavior with Neural Data" Bruch S. N. , McClure P., Zhou J., Schoenbaum G., Pereira F. bioRxiv preprint
2020
The Haskins pediatric atlas: An MRI-based pediatric template and atlas
Molfese P.J., Glen D., Mesite L., Cox R.W., Hoeft F., Frost S.J., Mencl W.E., Pugh K., Bandettini P.A. Pediatric Radiology, 51(4), 628-639, 2020
Idiosynchrony: From shared responses to individual differences during naturalistic neuroimaging
Finn E.S., Glerean E., Khojandi A.Y., Nielson D., Molfese P.J., Handwerker D.A., Bandettini P.A. PsyArXiv, 2020
Thalamus is a common locus of reading, arithmetic, and IQ: Analysis of local intrinsic functional properties
Koyama M.S., Molfese P.J., Milham M.P., Mencl W.E., Pugh K.R. Brain and Language, 209, 104835, 2020
Untangling the relatedness among correlations, part III: Inter-subject correlation analysis through Bayesian multilevel modeling for naturalistic scanning
Chen G., Taylor P., Xianggui Q., Molfese P.J., Bandettini P.A., Cox R.W., Finn E.S. NeuroImage, 116474, 2020
A Deep Neural Network Tool for Automatic Segmentation of Human Body Parts in Natural Scenes
McClure P. , Reimann G., Ramot M., Pereira F. arXiv preprint
Revealing the multidimensional mental representations of natural objects underlying human similarity judgments
"Revealing the multidimensional mental representations of natural objects underlying human similarity judgments" Hebart, M., Zheng, C., Pereira, F., Baker, C. Nature Human Behaviour, 2020
2019
Brain-behavior relationships in incidental learning of non-native phonetic categories
Luthra S., Fuhrmeister P., Molfese P.J., Guediche S., Blumstein S.E., Myers E.B. Brain and Language, 198, 104692, 2019
Common neural basis of motor sequence learning and word recognition and its relation with individual differences in reading skill
Hung Y., Frost S.J., Molfese P., Malins J.G., Landi N., Mencl W.E., Rueckl J.G., Bogaerts L., Pugh K.R. Scientific Studies of Reading, 23, 89-100, 2019
Layer-dependent activity in human prefrontal cortex during working memory
Finn E.S., Huber L., Jangraw D.C., Molfese P.J., Bandettini P.A. Nature Neuroscience, 22(10), 1687-1695, 2019
Layer-specific activation of sensory input and predictive feedback in the human primary somatosensory cortex
Yu Y., Huber L., Yang J., Jangraw D.C., Handwerker D.A., Molfese P., Chen G., Ejima Y., Wu J., Bandettini P.A. Science Advances, 5, eaav9053, 2019
Visual temporal frequency preference shows a distinct cortical architecture using fMRI
Chai Y., Handwerker D.A., Marrett S., Gonzalez-Castillo J., Merriam E., Hall A., Molfese P.J., Bandettini P.A. NeuroImage, 197, 13-23, 2019
Data-driven identification of subtypes of executive function across typical development, attention deficit hyperactivity disorder, and autism spectrum disorders
Vaidya C., You X., Mostofsky S., Pereira F., Berl M., Kenworthy L. J Child Psychol Psychiatry 61(1): 51–61. 2019
Deep Neural Networks in Computational Neuroscience
"Deep Neural Networks in Computational Neuroscience" Kietzmann, T., McClure, P., Kriegeskorte, N. Oxford Research Encyclopedia of Neuroscience, 2019
Imaging the spontaneous flow of thought: Distinct periods of cognition contribute to dynamic functional connectivity during rest
Gonzalez-Castillo J., Caballero-Gaudes C., Topolski N., Handwerker D., Pereira F. , Bandettini P. Neuroimage 15; 202: 116129. 2019
Knowing What You Know in Brain Segmentation Using Bayesian Deep Neural Networks
"Knowing What You Know in Brain Segmentation Using Bayesian Deep Neural Networks" McClure, P., Rho, N., Lee, J., Kaczmarzyk, J., Zheng, C., Ghosh, S., Nielson, D., Thomas, A., Bandettini, P., Pereira, F. Frontiers in Neuroinformatics, 2019
Revealing interpretable object representations from human behavior
"Revealing interpretable object representations from human behavior" Zheng, C., Pereira, F., Baker, C., Hebart, M. International Conference on Learning Representations, 2019
Subtle predictive movements reveal actions regardless of social context
"Subtle predictive movements reveal actions regardless of social context" McMahon, E.G., Zheng, C.Y., Pereira, F., Gonzalez, R., Ungerleider, L.G. and Vaziri-Pashkam, M. Journal of vision 19 (7), 16-16, 2019
2018
Combined Resting State fMRI and EEG Investigation of Irritability
Michaels T., Ly M., Wang L., Chen C., Molfese P., Burke J. Biological Psychiatry, 83(9), S367, 2018
Individual differences in decoding skill, print exposure, and cortical structure in young adults
Johns C.L., Jahn A.A., Jones H.R., Kush D., Molfese P.J., Van Dyke J.A., Magnuson J.S., Tabor W., Mencl W.E., Shankweiler D.P., Braze D. Language, Cognition, and Neuroscience, 33, 1275-1295, 2018
Individual differences in reading skill are related to trial-by-trial neural activation variability in the reading network
Malins J.G., Pugh K.R., Buis B., Frost S.J., Hoeft F., Landi N., Mencl W.E., Kurian A., Staples R., Molfese P.J., Sevcik R., Morris R. Journal of Neuroscience, 38, 2981-2989, 2018
Neural representations for newly learned words are modulated by overnight consolidation, reading skill, and age
Landi N., Malins J.G., Frost S.J., Magnuson J.S., Molfese P., Ryherd K., Rueckl J.G., Mencl W.E., Pugh K.R. Neuropsychologia, 111, 133-144, 2018
Neurochemistry predicts convergence of written and spoken language: a proton magnetic resonance spectroscopy study of cross-modal language integration
Del Tufo S.N., Frost S.J., Hoeft F., Cutting L.E., Molfese P.J., Mason G.F., Rothman D.L., Fulbright R.K., Pugh K.R. Frontiers in Psychology, 9, 2018
Ventricular and Periventricular Anomalies in the Aging and Cognitively Impaired Brain
Todd K.L., Brighton T., Norton E.S., Schick S., Elkins W., Pletnikova O., Fortinsky R.H., Troncoso J.C., Molfese P.J., Resnick S.M., Conover J.C. Frontiers in Aging Neuroscience, 9, 445, 2018
Distributed Weight Consolidation: A Brain Segmentation Case Study
"Distributed Weight Consolidation: A Brain Segmentation Case Study" McClure P., Zheng C., Kaczmarzyk J., Rogers-Lee J., Ghosh S., Nielson D., Bandettini P., Pereira F. Neural Information Processing Systems, 2018
Extrapolating Expected Accuracies for Large Multi-Class Problems
"Extrapolating Expected Accuracies for Large Multi-Class Problems" Zheng, C., Achanta R., Benjamini. Y. Journal of Machine Learning Research vol. 19. 2018.
Toward a universal decoder of linguistic meaning from brain activation
"Toward a universal decoder of linguistic meaning from brain activation" Pereira F., Lou B., Pritchett B., Ritter S., Gershman S., Kanwisher N., Botvinick M., Fedorenko E. Nature Communications 9 (963), 2018