publications

If you want to acquaint yourself with the nitty-gritties of our research, check out the links to our materials below.

In most cases we are happy to share our code and data, and we hope that you'll get in touch if you want to learn more! (If you're looking for a high-level overview of our lab's research, take a look at our research page instead.)

Papers

Text embedding models yield high-resolution insights into conceptual knowledge from short multiple-choice quizzes

Fitzpatrick PC, Heusser AC, Manning JR (2025). Text embedding models yield high-resolution insights into conceptual knowledge from short multiple-choice quizzes. Nature Communications: In press.

[PDF] [CODE + DATA]

A stylometric application of large language models

Stropkay HF, Chen J, Latifi MJ, Rockmore DN, Manning JR (2025). A stylometric application of large language models. arXiv: 2510.21958.

[PDF] [CODE + DATA]

High-level cognition is supported by information-rich but compressible brain activity patterns

Owen LLW, Manning JR (2024). High-level cognition is supported by information-rich but compressible brain activity patterns. Proceedings of the National Academy of Sciences, USA: 121(35): e2400082121.

[PDF] [CODE + DATA]

The psychological arrow of time drives temporal asymmetries in inferring unobserved past and future events

Xu X, Zhu Z, Manning JR (2024) The psychological arrow of time drives temporal asymmetries in inferring unobserved past and future events. Nature Communications: in press.

[PDF] [CODE + DATA]

Davos: a Python "smuggler" for constructing lightweight reproducible notebooks

Fitzpatrick PC, Manning JR (2024) Davos: a Python "smuggler" for constructing lightweight reproducible notebooks. SoftwareX: 25: 101614.

[PDF] [CODE]

High-level cognition during story listening is reflected in high-order dynamic correlations in neural activity patterns

Owen LLW, Chang TH, Manning JR (2021) High-level cognition during story listening is reflected in high-order dynamic correlations in neural activity patterns. Nature Communications, 12(5728).

[PDF] [CODE + DATA]

HyperTools: A Python toolbox for gaining geometric insights into high-dimensional data

Heusser AC, Ziman K, Owen LW, Manning JR (2018) HyperTools: A Python toolbox for gaining geometric insights into high-dimensional data. Journal of Machine Learning Research, 18(152): 1 - 6.

[PDF] [CODE]

Quail: A Python toolbox for analyzing and plotting free recall data

Heusser AC, Fitzpatrick PC, Field CE, Ziman K, Manning JR (2017) Quail: A Python toolbox for analyzing and plotting free recall data. The Journal of Open Source Software: 2(18): 224.

[PDF] [CODE]

People are represented and remembered through their relationships with others

Jolly E, Sadhukha S, Iqbal M, Molani Z, Walsh T, Manning JR, Chang LJ (2023) People are represented and remembered through their relationships with others. PsyArXiv: 10.31234/osf.io/bw9r2.

[PDF] [CODE + DATA]

Category-based and location-based volitional covert attention affect memory at different timescales

Ziman K, Lee MR, Martinez AR, Adner ED, Manning JR (2023) Category-based and location-based volitional covert attention affect memory at different timescales. PsyArXiv: 10.31234/osf.io/2ps6e.

[PDF] [CODE + DATA]

Feature and order manipulations in a free recall task affect memory for current and future lists

Manning JR, Whitaker EC, Fitzpatrick PC, Lee MR, Frantz AM, Bollinger BJ, Romanova D, Field CE, Heusser AC (2023). Feature and order manipulations in a free recall task affect memory for current and future lists. PsyArXiv: 10.31234/osf.io/erzfp.

[PDF] [CODE + DATA]

Fitness tracking reveals task-specific associations between memory, mental health, and physical activity

Manning JR, Notaro GM, Chen E, Fitzpatrick PC (2022) Fitness tracking reveals task-specific associations between memory, mental health, and exercise. Scientific Reports: 12(13822): doi.org/10.1038/s41598-022-17781-0.

[PDF] [CODE + DATA]

BrainIAK: The Brain Imaging Analysis Kit

Kumar M, Anderson MJ, Antony JW, Baldassano C, Brooks PP, Cai MB, Chen P-HC, Ellis CT, Henselman-Petrusek G, Huberdeau D, Hutchinson BJ, Li PY, Lu Q, Manning JR, Mennen AC, Nastase SA, Richard H, Schapiro AC, Schuck NW, Suo D, Turek JS, Vo VA, Wallace G, Wang Y, Zhang H, Zhu X, Capotă M, Cohen JD, Hasson U, Li K, Ramadge PJ, Turk-Browne NB, Willke TL, Norman KA (2022) BrainIAK: The Brain Imaging Analysis Kit. Aperture, 1(4): 1—19.

[PDF] [CODE + DATA]

Biomarkers of Depression Symptoms Defined by Direct Intracranial Neurophysiology

Scangos KW, Khambhati AN, Daly PM, Owen LW, Manning JR, Ambrose JB, Austin E, Dawes HE, Krystal AD, Chang EF (2021) Biomarkers of depression symptoms defined by direct intracranial neurophysiology. Frontiers in Human Neuroscience: doi.org/10.3389/fnhum.2021.746499.

[PDF] [CODE] [DATA]

Between-subject prediction reveals a shared representational geometry in the rodent hippocampus

Chen H-T, Manning JR, van der Meer MAA (2021) Between-subject prediction reveals a shared representational geometry in the rodent hippocampus. Current Biology, 31(19): 4293—4304.

[PDF] [CODE + DATA]

Episodic memory: mental time travel or a quantum 'memory wave' function?

Manning JR (2021) Episodic memory: mental time travel or a quantum 'memory wave' function? Psychological Review, 128(4): 711—725.

[PDF] [CODE] [DATA]

Minimal functional alignment of ventromedial prefrontal cortex intracranial EEG signals during naturalistic viewing

Xie T, Cheong JH, Manning JR, Brandt AM, Aronson JP, Jobst BC, Bujarski KA, Chang LJ (2021) Minimal functional alignment of ventromedial prefrontal cortex intracranial EEG signals during naturalistic viewing. bioRxiv: 2021.05.10.443308v1.

[PDF] [CODE]

Endogenous variation in ventromedial prefrontal cortex state dynamics during naturalistic viewing reflects affective experience

Chang LJ, Jolly E, Cheong JH, Rapuano K, Greenstein N, Chen P-HA, Manning JR (2021) Endogenous variation in ventromedial prefrontal cortex state dynamics during naturalistic viewing reflects affective experience. Science Advances, 7(17): doi.org/10.1126/sciadv.abf7129.

[PDF] [CODE + DATA]

Unexpected false feelings of familiarity about faces are associated with increased pupil dilations

Ziman K, Manning JR (2021) Unexpected false feelings of familiarity about faces are associated with increased pupil dilations. bioRxiv: 10.1101/2021.02.22.432360v1

[PDF] [CODE + DATA]

Geometric models reveal behavioral and neural signatures of transforming naturalistic experiences into episodic memories

Heusser AC, Fitzpatrick PC, Manning JR (2021) Geometric models reveal behavioral and neural signatures of transforming naturalistic experiences into episodic memories. Nature Human Behaviour: https://doi.org/10.1038/s41562-021-01051-6.

[PDF] [CODE] [DATA]

A Gaussian process model of human electrocorticographic data

Owen LLW, Muntianu TA, Heusser AC, Daly P, Scangos KW, Manning JR (2020) A Gaussian process model of human electrocorticographic data. Cerebral Cortex, 30(10): 5333—5345.

[PDF] [CODE] [DATA]

Capturing the geometric structure of episodic memories for naturalistic experiences

Heusser AC, Manning JR (2018) Capturing the geometric structure of episodic memories for naturalistic experiences. Conference on Cognitive Computational Neuroscience, PS-2B.16.

[PDF] [CODE] [DATA]

Is automatic speech-to-text transcription ready for use in psychological experiments?

Ziman K, Heusser AC, Fitzpatrick PC, Field CE, Manning JR (2018) Is automatic speech-to-text transcription ready for use in psychological experiments? Behavior Research Methods, https://doi.org/10.3758/s13428-018-1037-4.

[PDF] [CODE] [DATA]

A probabilistic approach to discovering dynamic full-brain functional connectivity patterns

Manning JR, Zhu X, Willke T, Ranganath R, Stachenfeld K, Hasson U, Blei DM, Norman KA (2018) A probabilistic approach to discovering dynamic full-brain functional connectivity patterns. NeuroImage, 180: 243 - 252.

[PDF] [CODE] [DATASET 1] [DATASET 2]

Enabling Factor Analysis on Thousand-Subject Neuroimaging Datasets

Anderson MJ, Capota M, Turek JS, Zhu X, Wilke TL, Chen PH, Manning JR, Ramadge PJ, Norman KA (2016, December). Enabling factor analysis on thousand-subject neuroimaging datasets. In Big Data (Big Data), 2016 IEEE International Conference on (pp. 1151 - 1160). IEEE.

[PDF] [CODE]

A neural signature of contextually mediated intentional forgetting

Manning JR, Hulbert JC, Williams J, Piloto L, Sahakyan L, Norman KA (2016) A neural signature of contextually mediated intentional forgetting. Psychonomic Bulletin and Review, 23(5): 1534 - 1542.

[PDF] [DATA]

Unsupervised learning of cone spectral classes from natural images

Benson NC, Manning JR, Brainard DH (2014) Unsupervised learning of cone spectral classes from natural images. PLoS Computational Biology, 10(6): e1003652.

[PDF] [CODE]

Hierarchical Topographic Factor Analysis

Manning JR, Ranganath R, Keung W, Turk-Browne NB, Cohen JD, Norman KA, Blei DM (2014) Hierarchical Topographic Factor Analysis. IEEE Xplore, 4th International Workshop on Pattern Recognition in Neuroimaging: 113 - 116.

[PDF] [CODE]

Topographic Factor Analysis: a Bayesian model for inferring brain networks from neural data

Manning JR, Ranganath R, Norman KA, Blei DA (2014) Topographic Factor Analysis: a Bayesian model for inferring brain networks from neural data. PLoS One, 9(5): e94914.

[PDF] [CODE]

MAGELLAN: a cognitive map-based model of human wayfinding

Manning JR, Lew TF, Li N, Kahana MJ, Sekuler RW (2013) MAGELLAN: a cognitive map-based model of human wayfinding. Journal of Experimental Psychology: General, 143(3): 1314 - 1330.

[PDF] [DATA]

Factor topographic latent source analysis: factor analysis for brain images

Manning JR, Gershman SJ, Norman KA, Blei DM (2012) Factor topographic latent source analysis: factor analysis for brain images. Proceedings of the NIPS Workshop on Machine Learning and Interpretation in Neuroimaging, 2: Online.

[PDF] [CODE]

Spontaneously reactivated patterns in frontal and temporal lobe predict semantic clustering during memory search

Manning JR, Sperling MR, Sharan A, Rosenberg EA, Kahana MJ (2012) Spontaneously reactivated patterns in frontal and temporal lobe predict semantic clustering during memory search. The Journal of Neuroscience, 32(26): 8800 - 8816.

[PDF]

Interpreting semantic clustering effects in free recall

Manning JR, Kahana MJ (2012) Interpreting semantic clustering effects in free recall. Memory, 20(5): 511 - 517.

[PDF]

Oscillatory patterns in temporal lobe reveal context reinstatement during memory search

Manning JR, Polyn SM, Baltuch G, Litt B, Kahana MJ (2011) Oscillatory patterns in temporal lobe reveal context reinstatement during memory search. Proceedings of the National Academy of Sciences of the United States of America, 108(31), 12893 - 12897.

[PDF]

Response to Miller: "broadband" vs. "high gamma" electrocorticographic signals

Jacobs J, Manning JR, Kahana MJ (2010) Response to Miller: "Broadband" vs. "high gamma" electrocorticographic signals. The Journal of Neuroscience, 30: Online.

[PDF]

Broadband shifts in local field potential power spectra are correlated with single-neuron spiking in humans

Manning JR, Jacobs J, Fried I, Kahana MJ (2009) Broadband shifts in local field potential power spectra are correlated with single-neuron spiking in humans. The Journal of Neuroscience, 29(43): 13613 - 13620.

[PDF]

Optimal design of photoreceptor mosaics: why we do not see color at night

Manning JR, Brainard DB (2009) Optimal design of photoreceptor mosaics: why we do not see color at night. Visual Neuroscience, 26: 5 - 19.

[PDF]

^ REINSTATE CONTEXT (BACK TO TOP) ^

Book Chapters

Identifying stimulus-driven neural activity patterns in multi-patient intracranial recordings

Manning JR (2022) Identifying stimulus-driven neural activity patterns in multi-patient intracranial recordings. Appears in Axmacher N, Ed. Intracranial EEG for Cognitive Neuroscience. New York, NY: Springer.

[PDF]

Context reinstatement

Manning JR (2020) Context reinstatement. Appears in Kahana MJ and Wagner AD, Eds. Handbook of Human Memory: Foundations and Applications. Oxford, UK: Oxford University Press.

[PDF]

The role of context in episodic memory

Manning JR, Norman KA, Kahana MJ (2015) The role of context in episodic memory. Appears in Gazzaniga M, Ed. The Cognitive Neurosciences, 5th Edition. Cambridge, MA: MIT Press.

[PDF]

^ REINSTATE CONTEXT (BACK TO TOP) ^

Dissertations

Acquisition, storage, and retrieval in digital and biological brains

Manning JR (2011) Acquisition, storage, and retrieval in digital and biological brains. Doctoral dissertation: University of Pennsylvania, Philadelphia, PA.

[PDF]

Modeling human spatial navigation using a degraded ideal navigator

Manning JR (2006) Modeling human spatial navigation using a degraded ideal navigator. Senior thesis: Brandeis University, Waltham, MA.

[PDF]

^ REINSTATE CONTEXT (BACK TO TOP) ^

talks

Towards an exercise recommendation system for optimizing mental fitness

Manning (2021) Towards an exercise recommendation system for optimizing mental fitness. Talk given at the Center for Technology and Behavioral Health.

Dynamic geometries of thoughts, memories, and conversations

Manning (2020) Dynamic geometries of thoughts, memories, and conversations. Talk given at the Human Cognition Colloquium at Berkeley.

Can we improve real-world learning using scalable AI teachers?

Manning (2019) Can we improve real-world learning using scalable AI teachers? Talk given at the MIND Summer School at Dartmouth.

Coding like a rock star

Manning (2019) Coding like a rock star. Talk given at the MIND Summer School at Dartmouth.

How is experience transformed into memory?

Manning (2018) How is experience transformed into memory? Talk given at Northeastern University.

[PAPER] [CODE] [DATA]

Contextual Dynamics

Manning (2018) Contextual Dynamics. Talk given at the MIND Summer School at Dartmouth.

SuperEEG and Gaussian Process Regression

Manning (2018) SuperEEG and Gaussian Process Regression. Talk given at the MIND Summer School at Dartmouth.

[TUTORIAL] [CODE]

Coding like a science hacker

Manning (2018) Coding like a science hacker. Talk given at the MIND Summer School at Dartmouth.

HyperTools and data visualization in Python

Manning (2017) HyperTools and data visualization in Python. Talk given at the MIND Summer School at Dartmouth.

[TUTORIAL] [CODE]

Network dynamics of the world and our brains

Manning (2017) Network dynamics of the world and our brains. Talk given at the MIND Summer School at Dartmouth.

[TUTORIAL] [CODE]

Towards human SuperEEG

Manning JR (2017) Towards human SuperEEG. Virtual talk given to the EPSCoR Attention Consortium.

A neural signature of mental time travel

Manning JR (2015) A neural signature of mental time travel. Talk given at Dartmouth-Hitchcock Medical Center Grand Rounds, Hanover, NH.

^ REINSTATE CONTEXT (BACK TO TOP) ^

course materials

Laboratory in Psychological Science

An open course intended to introduce students to project development, experimental design, analysis, and interpretation.

[GitHub]

Human Memory

An open course based on Mike Kahana's Foundations of Human Memory. Covers classic experimental findings and experimental models.

[GitHub]

Naturalistic Data Analysis

An online book that includes a collection of state-of-the-art approaches to analyzing naturalistic data.

[LINK]

Introduction to Programming for Psychological Scientists

A self-directed open course intended to introduce students to fundamental computational tools used by modern psychological researchers.

[GitHub]

Lab tutorials

A collection of lab tutorials on a range of quantitative and computational topics.

[GitHub]

Methods in Neuroscience at Dartmouth (MIND)

A 10-day intensive summer course on cutting-edge computational methods.

[LINK]

Storytelling with Data

Data science course aimed at a general audience (no pre-requisites).

[GitHub]

Computational Neuroscience

A short University of Pennsylvania summer course that provides an introduction to programming in MATLAB, single-neuron models, ion channel models, basic neural networks, and neural decoding.

[GitHub]

^ REINSTATE CONTEXT (BACK TO TOP) ^

Abstracts + Posters

Volitional Attention Modulates Memory Encoding and Retrieval

Ziman K, Lee MR, Martinez AR, Manning JR (2019) Volitional Attention Modulates Memory Encoding and Retrieval. Society for Neuroscience. Chicago, IL

Exploring the evolving geometric structure of experiences and memories

Fitzpatrick PC, Heusser AC, Manning JR (2019) Exploring the evolving geometric structure of experiences and memories. Society for Neuroscience. Chicago, IL.

Understanding complexity and interactivity of brain patterns in naturalistic processing

Owen LLW, Manning JR (2019) Understanding complexity and interactivity of brain patterns in naturalistic processing. Society for Neuroscience. Chicago, IL.

Capturing the geometric structure of our experiences and how we remember them

Heusser AC, Manning JR (2018) Capturing the geometric structure of episodic memories for naturalistic experiences. Conference on Cognitive Computational Neuroscience, PS-2B.16.

Volitional Attention Modulates Memory Encoding and Retrieval

Ziman K, Lee MR, Martinez AR, Manning JR (2018) Volitional Attention Modulates Memory Encoding and Retrieval. Society for Neuroscience. San Diego, CA.

Mapping between naturalistic experience and verbal recall

Fitzpatrick PC, Heusser AC, Manning JR (2018) Mapping between naturalistic experience and verbal recall. Society for Neuroscience. San Diego, CA.

The utility of speech-to-text software for transcription of verbal response data

Fitzpatrick PC, Ziman K, Heusser AC, Field CE, Manning JR (2018) The utility of speech-to-text software for transcription of verbal response data. Wetterhan Science Symposium. Hanover, NH.

How does attention affect memory?

Pak EK, Ziman K, Manning JR (2018) How does attention affect memory? Wetterhan Science Symposium. Hanover, NH.

Adaptive Free Recall: Enhancing (Or Diminishing) Memory

Lee MR, Chacko RS, Whitaker EC, Fitzpatrick PC, Field CE, Ziman K, Bollinger BJ, Heusser AC, Manning JR (2018) Adaptive Free Recall: Enhancing (Or Diminishing) Memory. Wetterhan Science Symposium. Hanover, NH.

Modeling the dynamic content, encoding, and retrieval of naturalistic stimuli

Heusser AC, Manning JR (2018) Modeling the dynamic content, encoding, and retrieval of naturalistic stimuli. Cognitive Neuroscience Society. Boston, MA.

Efficient Learning: Manipulating context to enhance (or diminish) memory

Manning JR, Ziman K, Heusser AC (2017) Efficient Learning: Manipulating context to enhance (or diminish) memory. Society for Neuroscience. Washington, DC.

HyperTools: A python toolbox for gaining geometric insights into high-dimensional data

Heusser AC, Ziman K, Owen LLW, Manning JR (2017) HyperTools: A python toolbox for gaining geometric insights into high-dimensional data. Society for Neuroscience. Washington, DC.

A Gaussian process model of human ECoG data

Owen LLW, Manning JR (2017) A Gaussian process model of human ECoG data. Society for Neuroscience. Washington, DC.

Effects of study context on recall organization

Ziman K, Heusser AC, Manning JR (2017) Effects of study context on recall organization. Society for Neuroscience. Washington, DC.

Harnessing the power of mnemonic fingerprints: Maximizing learning potential by personalizing stimulus organization during adaptive list learning

Ziman K, Heusser AC, Manning JR (2017) Harnessing the power of mnemonic fingerprints: Maximizing learning potential by personalizing stimulus organization during adaptive list learning. Context and Episodic Memory Symposium. Philadelphia, PA.

Towards human super EEG

Owen LLW, Manning JR (2017) Towards human super EEG. Context and Episodic Memory Symposium. Philadelphia, PA.

HyperTools: A python toolbox for visualizing and manipulating high-dimensional data

Heusser AC, Ziman K, Owen LLW, Manning JR (2017) HyperTools: A python toolbox for visualizing and manipulating high-dimensional data. Context and Episodic Memory Symposium. Philadelphia, PA.

Exploring connectivity patterns in storytelling data using Hierarchical Topographic Factor Analysis (HTFA)

Manning JR, Zhu Xia, Cohen J, Ranganath R, Stachenfeld K, Simony E, Regev M, Chen J, Hasson U, Willke T, Blei DM, Norman KA (2015) Exploring connectivity patterns in storytelling data using Hierarchical Topographic Factor Analysis (HTFA). Collaborative Research in Computational Neuroscience. Seattle, WA.

Efficient discovery of functional brain networks in large multi-subject fMRI datasets

Manning JR, Stachenfeld K, Ranganath R, Norman KA, Blei DM (2014) Efficient discovery of functional brain networks in large multi-subject fMRI datasets. Society for Neuroscience. Washington, DC.

Neural evidence for a context-change account of list-method directed forgetting

Manning JR, Hulbert JC, Williams JA, Piloto LR, Sahakyan L, Norman KA (2014) Neural evidence for a context-change account of list-method directed forgetting. Society for Neuroscience. Washington, DC.

Hierarchical Topographic Factor Analysis: a MATLAB toolbox for efficiently discovering brain networks in fMRI data

Manning JR, Ranganath R, Blei DM, Norman KA (2014) Hierarchical Topographic Factor Analysis: a MATLAB toolbox for efficiently discovering brain networks in fMRI data. Context and Episodic Memory Symposium. Philadelphia, PA.

Integrating neural and behavioral data into episodic memory models

Manning JR, Blei DM, Norman KA (2013) Integrating neural and behavioral data into episodic memory models. Society for Neuroscience. San Diego, CA.

A probabilistic temporal context model for tracking mental context using neural and behavioral data

Manning JR, Blei DM, Norman KA (2013) A probabilistic temporal context model for tracking mental context using neural and behavioral data. Context and Episodic Memory Symposium. Philadelphia, PA. (Also presented at Collaborative Research in Computational Neuroscience. Boston, MA)