Publications
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 | book chapters | dissertations | talks | course materials | abstracts + posters
Papers
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]
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]
Fitzpatrick PC, Manning JR (2024) Davos: a Python “smuggler” for constructing lightweight reproducible notebooks. SoftwareX: 25: 101614.
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]
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]
Fitzpatrick PC, Heusser AC, Manning JR (2023). Text embedding models yield high-resolution insights into conceptual knowledge from short multiple-choice quizzes. PsyArXiv: 10.31234/osf.io/dh3q2.
[PDF] [CODE + DATA]
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]
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]
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]
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.
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]
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): doi.org/10.1038/s41467-021-25876-x.
[PDF] [CODE + DATA]
Manning JR (2021) Episodic memory: mental time travel or a quantum ‘memory wave' function? Psychological Review, 128(4): 711—725.
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.
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]
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]
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.
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.
Heusser AC, Manning JR (2018) Capturing the geometric structure of episodic memories for naturalistic experiences. Conference on Cognitive Computational Neuroscience, PS-2B.16.
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.
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.
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.
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.
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.
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] [Public Radio] [Washington Post] [Dartmouth Press Release] [full press list...]
Benson NC, Manning JR, Brainard DH (2014) Unsupervised learning of cone spectral classes from natural images. PLoS Computational Biology, 10(6): e1003652.
[PDF] [CODE] [The Scientist]
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.
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.
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.
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.
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] [New Scientist] [Los Angeles Times] [UPenn Press Release]
Manning JR, Kahana MJ (2012) Interpreting semantic clustering effects in free recall. Memory, 20(5): 511 - 517.
[PDF]
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.
Jacobs J, Manning JR, Kahana MJ (2010) Response to Miller: "Broadband" vs. "high gamma" electrocorticographic signals. The Journal of Neuroscience, 30: Online.
[PDF]
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]
Manning JR, Brainard DB (2009) Optimal design of photoreceptor mosaics: why we do not see color at night. Visual Neuroscience, 26: 5 - 19.
[PDF]
Book Chapters
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]
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]
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]
Dissertations
Manning JR (2011) Acquisition, storage, and retrieval in digital and biological brains. Doctoral dissertation: University of Pennsylvania, Philadelphia, PA.
[PDF]
Manning JR (2006) Modeling human spatial navigation using a degraded ideal navigator. Senior thesis: Brandeis University, Waltham, MA.
[PDF]
talks
Manning (2021) Towards an exercise recommendation system for optimizing mental fitness. Talk given at the Center for Technology and Behavioral Health.
Manning (2020) Dynamic geometries of thoughts, memories, and conversations. Talk given at the Human Cognition Colloquium at Berkeley.
Manning (2019) Can we improve real-world learning using scalable AI teachers? Talk given at the MIND Summer School at Dartmouth.
Manning (2018) How is experience transformed into memory? Talk given at Northeastern University.
Manning (2018) SuperEEG and Gaussian Process Regression. Talk given at the MIND Summer School at Dartmouth.
Manning (2017) HyperTools and data visualization in Python. Talk given at the MIND Summer School at Dartmouth.
Manning (2017) Network dynamics of the world and our brains. Talk given at the MIND Summer School at Dartmouth.
Manning JR (2015) A neural signature of mental time travel. Talk given at Dartmouth-Hitchcock Medical Center Grand Rounds, Hanover, NH.
course materials
An open course intended to introduce students to project development, experimental design, analysis, and interpretation. Students engage in a series of guided laboratory exercises (each aimed at a different aspect of experimental psychology) and then carry out a full designed-from-scratch study that ties together all of the components of the course.
[GitHub]
An open course based on Mike Kahana’s Foundations of Human Memory (plus some more recent material). Covers a wide range of classic experimental findings and experimental models.
[GitHub]
An online book that includes a collection of state-of-the-art approaches to analyzing naturalistic data (and brain and behavioral responses to naturalistic stimuli).
A self-directed open course intended to introduce students to a set of fundamental computational tools used by modern psychological researchers.
[GitHub]
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]