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<!DOCTYPE html>
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<title>Publications — Contextual Dynamics Lab</title>
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<h1>publications</h1>
<h3>If you want to acquaint yourself with the nitty-gritties of our research, check out the links to our materials below.</h3>
<p class="page-intro">In most cases we are happy to share our code and data, and we hope that you'll <a href="contact.html">get in touch</a> 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 <a href="research.html">research page</a> instead.)</p>
<p class="jump-links"><a href="#papers">papers</a> | <a href="#chapters">book chapters</a> | <a href="#dissertations">dissertations</a> | <a href="#talks">talks</a> | <a href="#course-mats">course materials</a> | <a href="#posters">abstracts + posters</a></p>
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<!-- Papers Section -->
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<h2>Papers</h2>
<div class="publications-grid">
<div class="publication-card">
<img src="images/publications/FitzEtal26b.png" alt="Publication thumbnail">
<div>
<h4><a href="https://osf.io/preprints/psyarxiv/mhxtd" target="_blank">Delayed recountings preserve but simplify the semantic geometry of earlier recountings</a></h4>
<p>Fitzpatrick PC, Tahir A, Xu J, Park SH, Manning JR (2026). Delayed recountings preserve but simplify the semantic geometry of earlier recountings. <em>PsyArXiv</em>: mhxtd.</p>
<p class="publication-links">[<a href="https://osf.io/preprints/psyarxiv/mhxtd" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/memory-dynamics" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/SiuEtal26.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.biorxiv.org/content/10.64898/2026.04.30.722005v1" target="_blank">Global topology of brain-wide co-fluctuations links task states, personality, and behavioral symptom dimensions</a></h4>
<p>Siu C, Pirzada ST, Glick CC, Betzel R, Petri G, Manning JR, Williams L, Saggar M (2026). Global topology of brain-wide co-fluctuations links task states, personality, and behavioral symptom dimensions. <em>Communications Biology</em>: In press.</p>
<p class="publication-links">[<a href="https://www.biorxiv.org/content/10.64898/2026.04.30.722005v1" target="_blank">PDF</a>] [<a href="https://github.com/braindynamicslab/demapper" target="_blank">CODE</a>] [<a href="https://db.humanconnectome.org" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/text-embedding-quizzes.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.nature.com/articles/s41467-026-69746-w" target="_blank">Text embedding models yield detailed conceptual knowledge maps derived from short multiple-choice quizzes</a></h4>
<p>Fitzpatrick PC, Heusser AC, Manning JR (2026). Text embedding models yield detailed conceptual knowledge maps derived from short multiple-choice quizzes. <em>Nature Communications</em>, 17: 2055.</p>
<p class="publication-links">[<a href="https://www.nature.com/articles/s41467-026-69746-w.pdf" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/efficient-learning-khan" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/bookshelf.png" alt="Publication thumbnail">
<div>
<h4><a href="https://arxiv.org/abs/2510.21958" target="_blank">A stylometric application of large language models</a></h4>
<p>Stropkay HF, Chen J, Latifi MJ, Rockmore DN, Manning JR (2025). A stylometric application of large language models. <em>arXiv</em>: 2510.21958.</p>
<p class="publication-links">[<a href="https://arxiv.org/pdf/2510.21958" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/llm-stylometry" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/sciam-past.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.scientificamerican.com/article/why-were-so-preoccupied-by-the-past/" target="_blank">Why we're so preoccupied by the past</a></h4>
<p>Manning JR (2025). Why we're so preoccupied by the past. <em>Scientific American</em>: Online.</p>
<p class="publication-links">[<a href="https://www.scientificamerican.com/article/why-were-so-preoccupied-by-the-past/" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/high-level-cognition-pnas.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.pnas.org/doi/10.1073/pnas.2400082121" target="_blank">High-level cognition is supported by information-rich but compressible brain activity patterns</a></h4>
<p>Owen LLW, Manning JR (2024). High-level cognition is supported by information-rich but compressible brain activity patterns. <em>Proceedings of the National Academy of Sciences, USA</em>, 121(35): e2400082121.</p>
<p class="publication-links">[<a href="https://biorxiv.org/cgi/content/short/2023.03.17.533152v1" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/pca_paper" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/psychological-arrow-time.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.nature.com/articles/s41467-024-52627-5" target="_blank">Temporal asymmetries in inferring unobserved past and future events</a></h4>
<p>Xu X, Zhu Z, Zheng X, Manning JR (2024). Temporal asymmetries in inferring unobserved past and future events. <em>Nature Communications</em>, 15: 8502.</p>
<p class="publication-links">[<a href="https://psyarxiv.com/yp2qu" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/prediction-retrodiction-paper" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/davos.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.sciencedirect.com/science/article/pii/S2352711023003102" target="_blank">Davos: a Python package "smuggler" for constructing lightweight reproducible notebooks</a></h4>
<p>Fitzpatrick PC, Manning JR (2024). Davos: a Python package "smuggler" for constructing lightweight reproducible notebooks. <em>SoftwareX</em>, 25: 101614.</p>
<p class="publication-links">[<a href="https://www.sciencedirect.com/science/article/pii/S2352711023003102/pdfft" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/davos" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/people-relationships.png" alt="Publication thumbnail">
<div>
<h4><a href="https://psyarxiv.com/bw9r2/" target="_blank">People are represented and remembered through their relationships with others</a></h4>
<p>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. <em>PsyArXiv</em>: bw9r2.</p>
<p class="publication-links">[<a href="https://psyarxiv.com/bw9r2/" target="_blank">PDF</a>] [<a href="https://github.com/ejolly/social_mem" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/ZimaEtAl19-34.png" alt="Publication thumbnail">
<div>
<h4><a href="https://psyarxiv.com/2ps6e/" target="_blank">Category-based and location-based volitional covert attention are mediated by different mechanisms and affect memory at different timescales</a></h4>
<p>Ziman K, Lee MR, Martinez AR, Adner ED, Manning JR (2023). Category-based and location-based volitional covert attention are mediated by different mechanisms and affect memory at different timescales. <em>PsyArXiv</em>: 2ps6e.</p>
<p class="publication-links">[<a href="https://psyarxiv.com/2ps6e/" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/attention-memory-task" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/feature-order-recall.png" alt="Publication thumbnail">
<div>
<h4><a href="https://psyarxiv.com/erzfp" target="_blank">Feature and order manipulations in a free recall task affect memory for current and future lists</a></h4>
<p>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. <em>PsyArXiv</em>: erzfp.</p>
<p class="publication-links">[<a href="https://psyarxiv.com/erzfp" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/FRFR-analyses" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/fitness-tracking.png" alt="Publication thumbnail">
<div>
<h4><a href="https://doi.org/10.1038/s41598-022-17781-0" target="_blank">Fitness tracking reveals task-specific associations between memory, mental health, and physical activity</a></h4>
<p>Manning JR, Notaro GM, Chen E, Fitzpatrick PC (2022). Fitness tracking reveals task-specific associations between memory, mental health, and physical activity. <em>Scientific Reports</em>, 12: 13822.</p>
<p class="publication-links">[<a href="https://trebuchet.public.springernature.app/get_content/36d8a20c-775b-49b5-a60e-2e7339f2a396" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/brainfit-paper" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/brainiak.png" alt="Publication thumbnail">
<div>
<h4><a href="https://apertureneuropub.cloud68.co/articles/42/index.html" target="_blank">BrainIAK: The Brain Imaging Analysis Kit</a></h4>
<p>Kumar M, Anderson MJ, Antony JW, Baldassano C, Brooks PP, Cai MB, Chen P-HC, Ellis CT, Henselman-Petrusek G, Huberdeau D, Hutchinson JB, Li YP, Lu Q, Manning JR, Mennen AC, Nastase SA, Richard H, Schapiro AC, Schuck NW, Shvartsman M, Sundaram N, Suo D, Turek JS, Turner D, Vo VA, Wallace G, Wang Y, Williams JA, 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. <em>Aperture</em>, 1(4): 1—19.</p>
<p class="publication-links">[<a href="https://osf.io/db2ev/" target="_blank">PDF</a>] [<a href="https://github.com/brainiak/brainiak-aperture" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/timecorr.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.nature.com/articles/s41467-021-25876-x" target="_blank">High-level cognition during story listening is reflected in high-order dynamic correlations in neural activity patterns</a></h4>
<p>Owen LLW, Chang TH, Manning JR (2021). High-level cognition during story listening is reflected in high-order dynamic correlations in neural activity patterns. <em>Nature Communications</em>, 12: 5728.</p>
<p class="publication-links">[<a href="https://www.biorxiv.org/content/10.1101/763821v3" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/timecorr-paper" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/ScangosEtAl20-01.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.frontiersin.org/articles/10.3389/fnhum.2021.746499/full" target="_blank">Distributed subnetworks of depression defined by direct intracranial neurophysiology</a></h4>
<p>Scangos KW, Khambhati AN, Daly PM, Owen LLW, Manning JR, Ambrose JB, Austin E, Dawes HE, Krystal AD, Chang EF (2021). Distributed subnetworks of depression defined by direct intracranial neurophysiology. <em>Frontiers in Human Neuroscience</em>, 15: 746499.</p>
<p class="publication-links">[<a href="https://www.frontiersin.org/articles/10.3389/fnhum.2021.746499/full" target="_blank">PDF</a>] [<a href="https://supereeg.readthedocs.io/en/latest/" target="_blank">CODE</a>] [<a href="https://zenodo.org/record/5540172#.YXQQunkpDS5" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/rodent-hippocampus.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.sciencedirect.com/science/article/pii/S0960982221010514" target="_blank">Between-subject prediction reveals a shared representational geometry in the rodent hippocampus</a></h4>
<p>Chen HT, Manning JR, van der Meer MAA (2021). Between-subject prediction reveals a shared representational geometry in the rodent hippocampus. <em>Current Biology</em>, 31(19): 4293—4304.e5.</p>
<p class="publication-links">[<a href="https://authors.elsevier.com/c/1ddOZ3QW8RwpPI" target="_blank">PDF</a>] [<a href="https://github.com/vandermeerlab/hc_hyperalign/tree/v1.0.0" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/mental-time-travel.png" alt="Publication thumbnail">
<div>
<h4><a href="https://psycnet.apa.org/record/2021-47824-001" target="_blank">Episodic memory: mental time travel or a quantum 'memory wave' function?</a></h4>
<p>Manning JR (2021). Episodic memory: mental time travel or a quantum 'memory wave' function?. <em>Psychological Review</em>, 128(4): 711—725.</p>
<p class="publication-links">[<a href="https://psyarxiv.com/6zjwb" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/mental-time-travel-paper" target="_blank">CODE</a>] [<a href="https://dataspace.princeton.edu/jspui/handle/88435/dsp01nz8062179" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/XieEtAl21-08.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.biorxiv.org/content/10.1101/2021.05.10.443308v1" target="_blank">Minimal functional alignment of ventromedial prefrontal cortex intracranial EEG signals during naturalistic viewing</a></h4>
<p>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. <em>bioRxiv</em>: 2021.05.10.443308.</p>
<p class="publication-links">[<a href="https://www.biorxiv.org/content/10.1101/2021.05.10.443308v1" target="_blank">PDF</a>] [<a href="https://github.com/cosanlab/naturalistic_iEEG_func_align" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/vmPFC-dynamics.png" alt="Publication thumbnail">
<div>
<h4><a href="https://advances.sciencemag.org/content/7/17/eabf7129" target="_blank">Endogenous variation in ventromedial prefrontal cortex state dynamics during naturalistic viewing reflects affective experience</a></h4>
<p>Chang LJ, Jolly E, Cheong JH, Rapuano KM, Greenstein N, Chen PHA, Manning JR (2021). Endogenous variation in ventromedial prefrontal cortex state dynamics during naturalistic viewing reflects affective experience. <em>Science Advances</em>, 7(17): eabf7129.</p>
<p class="publication-links">[<a href="https://www.biorxiv.org/content/10.1101/487892v3" target="_blank">PDF</a>] [<a href="https://github.com/cosanlab/vmPFC_dynamics" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/false-familiarity.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.biorxiv.org/content/10.1101/2021.02.22.432360v1" target="_blank">Unexpected false feelings of familiarity about faces are associated with increased pupil dilations</a></h4>
<p>Ziman K, Manning JR (2021). Unexpected false feelings of familiarity about faces are associated with increased pupil dilations. <em>bioRxiv</em>: 2021.02.22.432360.</p>
<p class="publication-links">[<a href="https://www.biorxiv.org/content/10.1101/2021.02.22.432360v1" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/attention-memory-task" target="_blank">CODE + DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/Sherlock-40.png" alt="Publication thumbnail">
<div>
<h4><a href="https://rdcu.be/cpMwZ" target="_blank">Geometric models reveal behavioural and neural signatures of transforming experiences into memories</a></h4>
<p>Heusser AC, Fitzpatrick PC, Manning JR (2021). Geometric models reveal behavioural and neural signatures of transforming experiences into memories. <em>Nature Human Behaviour</em>, 5(7): 905—919.</p>
<p class="publication-links">[<a href="https://rdcu.be/cpMwZ" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/sherlock-topic-model-paper" target="_blank">CODE</a>] [<a href="https://dataspace.princeton.edu/jspui/handle/88435/dsp01nz8062179" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/supereeg-gp.png" alt="Publication thumbnail">
<div>
<h4><a href="https://academic.oup.com/cercor/article/30/10/5333/5851264" target="_blank">A Gaussian process model of human electrocorticographic data</a></h4>
<p>Owen LLW, Muntianu TA, Heusser AC, Daly PM, Scangos KW, Manning JR (2020). A Gaussian process model of human electrocorticographic data. <em>Cerebral Cortex</em>, 30(10): 5333—5345.</p>
<p class="publication-links">[<a href="https://academic.oup.com/cercor/article/30/10/5333/5851264" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/supereeg_paper" target="_blank">CODE</a>] [<a href="http://memory.psych.upenn.edu/Request_EEG_access?paper=EzzyEtal17" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/naturalistic-data.png" alt="Publication thumbnail">
<div>
<h4><a href="https://naturalistic-data.org/" target="_blank">Naturalistic data analysis</a></h4>
<p>Chang L, Manning JR, Baldassano C, de la Vega A, Fleetwood G, Geerligs L, Haxby J, Lahnakoski J, Parkinson C, Shappell H, Shim WM, Wager T, Yarkoni T, Yeshurun Y, Finn E (2020). Naturalistic data analysis. <em>Zenodo</em>: 10.5281/zenodo.3937849.</p>
<p class="publication-links">[<a href="https://naturalistic-data.org/" target="_blank">PDF</a>] [<a href="https://github.com/naturalistic-data-analysis/naturalistic_data_analysis" target="_blank">CODE</a>]</p>
</div>
</div>
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<img src="images/publications/hypertools.png" alt="Publication thumbnail">
<div>
<h4><a href="http://jmlr.org/papers/v18/17-434.html" target="_blank">HyperTools: A Python toolbox for gaining geometric insights into high-dimensional data</a></h4>
<p>Heusser AC, Ziman K, Owen LLW, Manning JR (2018). HyperTools: A Python toolbox for gaining geometric insights into high-dimensional data. <em>Journal of Machine Learning Research</em>, 18(152): 1—6.</p>
<p class="publication-links">[<a href="http://jmlr.org/papers/volume18/17-434/17-434.pdf" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/hypertools" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/Sherlock-41.png" alt="Publication thumbnail">
<div>
<h4><a href="https://ccneuro.org/2018/proceedings/1267.pdf" target="_blank">Capturing the geometric structure of episodic memories for naturalistic experiences</a></h4>
<p>Heusser AC, Manning JR (2018). Capturing the geometric structure of episodic memories for naturalistic experiences. <em>Conference on Cognitive Computational Neuroscience</em>: PS-2B.16.</p>
<p class="publication-links">[<a href="https://ccneuro.org/2018/proceedings/1267.pdf" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/sherlock-topic-model-paper" target="_blank">CODE</a>] [<a href="https://dataspace.princeton.edu/jspui/handle/88435/dsp01nz8062179" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/SketchLogo_AutoFR-22.png" alt="Publication thumbnail">
<div>
<h4><a href="https://link.springer.com/article/10.3758/s13428-018-1037-4" target="_blank">Is automatic speech-to-text transcription ready for use in psychological experiments?</a></h4>
<p>Ziman K, Heusser AC, Fitzpatrick PC, Field CE, Manning JR (2018). Is automatic speech-to-text transcription ready for use in psychological experiments?. <em>Behavior Research Methods</em>, 50(6): 2597—2605.</p>
<p class="publication-links">[<a href="https://psyarxiv.com/psh48" target="_blank">PDF</a>] [<a href="https://github.com/ContextLab/autoFR" target="_blank">CODE</a>] [<a href="https://github.com/ContextLab/quail/tree/master/quail/data" target="_blank">DATA</a>]</p>
</div>
</div>
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<img src="images/publications/htfa-connectivity.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.sciencedirect.com/science/article/pii/S1053811918300715?via%3Dihub" target="_blank">A probabilistic approach to discovering dynamic full-brain functional connectivity patterns</a></h4>
<p>Manning JR, Zhu X, Willke TL, Ranganath R, Stachenfeld K, Hasson U, Blei DM, Norman KA (2018). A probabilistic approach to discovering dynamic full-brain functional connectivity patterns. <em>NeuroImage</em>, 180: 243—252.</p>
<p class="publication-links">[<a href="https://www.sciencedirect.com/science/article/pii/S1053811918300715?via%3Dihub" target="_blank">PDF</a>] [<a href="https://github.com/IntelPNI/brainiak" target="_blank">CODE</a>] [<a href="https://dataspace.princeton.edu/jspui/handle/88435/dsp01nz8062179" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/quail.png" alt="Publication thumbnail">
<div>
<h4><a href="http://joss.theoj.org/papers/10.21105/joss.00424" target="_blank">Quail: A Python toolbox for analyzing and plotting free recall data</a></h4>
<p>Heusser AC, Fitzpatrick PC, Field CE, Ziman K, Manning JR (2017). Quail: A Python toolbox for analyzing and plotting free recall data. <em>The Journal of Open Source Software</em>, 2(18): 424.</p>
<p class="publication-links">[<a href="https://github.com/openjournals/joss-papers/raw/master/joss.00424/10.21105.joss.00424.pdf" target="_blank">PDF</a>] [<a href="http://cdl-quail.readthedocs.io/en/latest/" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/AndeEtAl16-16.png" alt="Publication thumbnail">
<div>
<h4><a href="https://ieeexplore.ieee.org/document/7840719/" target="_blank">Enabling factor analysis on thousand-subject neuroimaging datasets</a></h4>
<p>Anderson MJ, Capota M, Turek JS, Zhu X, Willke TL, Wang Y, Chen P-H, Manning JR, Ramadge PJ, Norman KA (2016). Enabling factor analysis on thousand-subject neuroimaging datasets. <em>IEEE International Conference on Big Data (Big Data)</em>: 1151—1160.</p>
<p class="publication-links">[<a href="http://arxiv.org/pdf/1608.04647.pdf" target="_blank">PDF</a>] [<a href="https://github.com/IntelPNI/brainiak" target="_blank">CODE</a>]</p>
</div>
</div>
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<img src="images/publications/intentional-forgetting.png" alt="Publication thumbnail">
<div>
<h4><a href="http://link.springer.com/content/pdf/10.3758%2Fs13423-016-1024-7.pdf" target="_blank">A neural signature of contextually mediated intentional forgetting</a></h4>
<p>Manning JR, Hulbert JC, Williams J, Piloto L, Sahakyan L, Norman KA (2016). A neural signature of contextually mediated intentional forgetting. <em>Psychonomic Bulletin and Review</em>, 23(5): 1534—1542.</p>
<p class="publication-links">[<a href="http://link.springer.com/content/pdf/10.3758%2Fs13423-016-1024-7.pdf" target="_blank">PDF</a>] [<a href="https://openneuro.org/datasets/ds001745/versions/1.0.0" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/BensEtAl14-14.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/BensEtal14.pdf" target="_blank">Unsupervised learning of cone spectral classes from natural images</a></h4>
<p>Benson NC, Manning JR, Brainard DH (2014). Unsupervised learning of cone spectral classes from natural images. <em>PLoS Computational Biology</em>, 10(6): e1003652.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/BensEtal14.pdf" target="_blank">PDF</a>] [<a href="https://github.com/DavidBrainard/ReceptorLearning" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannEtAl14b-13.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal14b.pdf" target="_blank">Hierarchical Topographic Factor Analysis</a></h4>
<p>Manning JR, Ranganath R, Keung W, Turk-Browne NB, Cohen JD, Norman KA, Blei DM (2014). Hierarchical Topographic Factor Analysis. <em>IEEE International Workshop on Pattern Recognition in Neuroimaging</em>: 1—4.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal14b.pdf" target="_blank">PDF</a>] [<a href="https://github.com/IntelPNI/brainiak" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannEtAl14c-12.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal14c.pdf" target="_blank">Topographic Factor Analysis: a Bayesian model for inferring brain networks from neural data</a></h4>
<p>Manning JR, Ranganath R, Norman KA, Blei DM (2014). Topographic Factor Analysis: a Bayesian model for inferring brain networks from neural data. <em>PLoS One</em>, 9(5): e94914.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal14c.pdf" target="_blank">PDF</a>] [<a href="https://github.com/IntelPNI/brainiak" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannEtAl14a-11.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal14a.pdf" target="_blank">MAGELLAN: a cognitive map-based model of human wayfinding</a></h4>
<p>Manning JR, Lew TF, Li N, Sekuler R, Kahana MJ (2014). MAGELLAN: a cognitive map-based model of human wayfinding. <em>Journal of Experimental Psychology: General</em>, 143(3): 1314—1330.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal14a.pdf" target="_blank">PDF</a>] [<a href="http://memory.psych.upenn.edu/files/pubs/MannEtal14a.data.tgz" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannEtAl12b-10.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal12b.pdf" target="_blank">Factor topographic latent source analysis: factor analysis for brain images</a></h4>
<p>Manning JR, Gershman SJ, Norman KA, Blei DM (2012). Factor topographic latent source analysis: factor analysis for brain images. <em>Proceedings of the NIPS Workshop on Machine Learning and Interpretation in Neuroimaging</em>, 2: Online.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal12b.pdf" target="_blank">PDF</a>] [<a href="https://github.com/IntelPNI/brainiak" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannEtAl12a-09.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal12a.pdf" target="_blank">Spontaneously reactivated patterns in frontal and temporal lobe predict semantic clustering during memory search</a></h4>
<p>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. <em>The Journal of Neuroscience</em>, 32(26): 8871—8878.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal12a.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannKaha12-08.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannKaha12.pdf" target="_blank">Interpreting semantic clustering effects in free recall</a></h4>
<p>Manning JR, Kahana MJ (2012). Interpreting semantic clustering effects in free recall. <em>Memory</em>, 20(5): 511—517.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannKaha12.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannEtAl11-02.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal11.pdf" target="_blank">Oscillatory patterns in temporal lobe reveal context reinstatement during memory search</a></h4>
<p>Manning JR, Polyn SM, Baltuch G, Litt B, Kahana MJ (2011). Oscillatory patterns in temporal lobe reveal context reinstatement during memory search. <em>Proceedings of the National Academy of Sciences of the United States of America</em>, 108(31): 12893—12897.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal11.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/JacoEtAl10b-07.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/JacoEtal10b.pdf" target="_blank">Response to Miller: "Broadband" vs. "high gamma" electrocorticographic signals</a></h4>
<p>Jacobs J, Manning JR, Kahana MJ (2010). Response to Miller: "Broadband" vs. "high gamma" electrocorticographic signals. <em>The Journal of Neuroscience</em>, 30: Online.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/JacoEtal10b.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannEtAl09-05.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal09.pdf" target="_blank">Broadband shifts in local field potential power spectra are correlated with single-neuron spiking in humans</a></h4>
<p>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. <em>The Journal of Neuroscience</em>, 29(43): 13613—13620.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal09.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MannBrai09-06.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannBrai09.pdf" target="_blank">Optimal design of photoreceptor mosaics: why we do not see color at night</a></h4>
<p>Manning JR, Brainard DH (2009). Optimal design of photoreceptor mosaics: why we do not see color at night. <em>Visual Neuroscience</em>, 26(1): 5—19.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannBrai09.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
</div>
<p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
</section>
<hr>
<!-- Book Chapters -->
<section id="chapters" class="content-section">
<h2>Book Chapters</h2>
<div class="publications-grid">
<div class="publication-card">
<img src="images/publications/intracranial-chapter.png" alt="Publication thumbnail">
<div>
<h4><a href="https://arxiv.org/abs/2202.01933" target="_blank">How can I identify stimulus-driven neural activity patterns in multi-patient ECoG data?</a></h4>
<p>Manning JR (2023) How can I identify stimulus-driven neural activity patterns in multi-patient ECoG data?. Appears in Axmacher N, Ed. <em>Intracranial EEG: A Guide for Cognitive Neuroscientists.</em> Cham, Switzerland: Springer.</p>
<p class="publication-links">[<a href="https://arxiv.org/pdf/2202.01933.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/context-reinstatement.png" alt="Publication thumbnail">
<div>
<h4><a href="https://psyarxiv.com/g2w73" target="_blank">Context reinstatement</a></h4>
<p>Manning JR (2024) Context reinstatement. Appears in Kahana MJ, Wagner AD, Ed. <em>The Oxford Handbook of Human Memory.</em> New York, NY: Oxford University Press.</p>
<p class="publication-links">[<a href="https://psyarxiv.com/g2w73/download" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/context-episodic.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal15.pdf" target="_blank">The role of context in episodic memory</a></h4>
<p>Manning JR, Kahana MJ, Norman KA (2014) The role of context in episodic memory. Appears in Gazzaniga MS, Mangun GR, Ed. <em>The Cognitive Neurosciences, Fifth Edition.</em> Cambridge, MA: MIT Press.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal15.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
</div>
<p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
</section>
<hr>
<!-- Dissertations -->
<section id="dissertations" class="content-section">
<h2>Dissertations</h2>
<div class="publications-grid">
<div class="publication-card">
<img src="images/publications/ZimaEtAl19-34.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/ziman_dissertation.pdf" target="_blank">Attending and remembering the external world</a></h4>
<p>Ziman K (2022) Attending and remembering the external world. <em>Doctoral dissertation: Dartmouth College</em>, Hanover, NH.</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/ziman_dissertation.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/timecorr.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/owen_dissertation.pdf" target="_blank">Modeling the fast-timescale network dynamics that underlie complex thought</a></h4>
<p>Owen LLW (2021) Modeling the fast-timescale network dynamics that underlie complex thought. <em>Doctoral dissertation: Dartmouth College</em>, Hanover, NH.</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/owen_dissertation.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/doctoral-dissertation.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/Manning_dissertation.pdf" target="_blank">Acquisition, storage, and retrieval in digital and biological brains</a></h4>
<p>Manning JR (2011) Acquisition, storage, and retrieval in digital and biological brains. <em>Doctoral dissertation: University of Pennsylvania</em>, Philadelphia, PA.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/Manning_dissertation.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/magellan-dissertation.png" alt="Publication thumbnail">
<div>
<h4><a href="http://caligari.dartmouth.edu/~jmanning/pubs/magellan_dissertation.pdf" target="_blank">Modeling human spatial navigation using a degraded ideal navigator</a></h4>
<p>Manning JR (2006) Modeling human spatial navigation using a degraded ideal navigator. <em>Senior thesis: Brandeis University</em>, Waltham, MA.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/magellan_dissertation.pdf" target="_blank">PDF</a>]</p>
</div>
</div>
</div>
<p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
</section>
<hr>
<!-- Talks -->
<section id="talks" class="content-section">
<h2>talks</h2>
<div class="publications-grid">
<div class="publication-card">
<img src="images/publications/exercise-recommendation.png" alt="Publication thumbnail">
<div>
<h4><a href="https://youtu.be/lnfBTjvVWKs" target="_blank">Towards an exercise recommendation system for optimizing mental fitness</a></h4>
<p>Manning (2021) Towards an exercise recommendation system for optimizing mental fitness. Talk given at the <a href="https://www.c4tbh.org" target="_blank"><em>Center for Technology and Behavioral Health</em></a>.</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/contextlab.github.io/blob/main/doi.org/10.1038/s41598-022-17781-0" target="_blank">PAPER</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/dynamic-geometries.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=yUCxk7sFny8" target="_blank">Dynamic geometries of thoughts, memories, and conversations</a></h4>
<p>Manning (2020) Dynamic geometries of thoughts, memories, and conversations. Talk given at the <a href="https://www.berkeley.edu/" target="_blank"><em>University of California, Berkeley</em></a>.</p>
<p class="publication-links">[<a href="https://doi.org/10.1038/s41562-021-01051-6" target="_blank">PAPER</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/scalable-ai-teachers.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=FMmPYcqS-iE" target="_blank">Can we improve real-world learning using scalable AI teachers? </a></h4>
<p>Manning (2019) Can we improve real-world learning using scalable AI teachers? . Talk given at the <a href="https://summer-mind.github.io/" target="_blank"><em>MIND Summer School at Dartmouth</em></a>.</p>
<p class="publication-links">[<a href="https://doi.org/10.31234/osf.io/dh3q2_v2" target="_blank">PAPER</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/coding-rock-star.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=148HoCOOG0M" target="_blank">Coding like a rock star</a></h4>
<p>Manning (2019) Coding like a rock star. Talk given at the <a href="https://summer-mind.github.io/" target="_blank"><em>MIND Summer School at Dartmouth</em></a>.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/northeaster_talk_2018.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=9rlUcsPC1rE&feature=youtu.be" target="_blank">How is experience transformed into memory?</a></h4>
<p>Manning (2018) How is experience transformed into memory?. Talk given at the <a href="https://www.northeastern.edu" target="_blank"><em>Northeastern University</em></a>.</p>
<p class="publication-links">[<a href="https://doi.org/10.1038/s41562-021-01051-6" target="_blank">PAPER</a>] [<a href="https://github.com/ContextLab/sherlock-topic-model-paper" target="_blank">CODE</a>] [<a href="https://dataspace.princeton.edu/jspui/handle/88435/dsp01nz8062179" target="_blank">DATA</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/contextual-dynamics-talk.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=8Pb9OXeKED0" target="_blank">Contextual Dynamics</a></h4>
<p>Manning (2018) Contextual Dynamics. Talk given at the <a href="https://summer-mind.github.io/" target="_blank"><em>MIND Summer School at Dartmouth</em></a>.</p>
<p class="publication-links">[<a href="https://psyarxiv.com/g2w73" target="_blank">PAPER</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/supereeg-gp-talk.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=Z0Lqeexr8v8" target="_blank">SuperEEG and Gaussian Process Regression</a></h4>
<p>Manning (2018) SuperEEG and Gaussian Process Regression. Talk given at the <a href="https://summer-mind.github.io/" target="_blank"><em>MIND Summer School at Dartmouth</em></a>.</p>
<p class="publication-links">[<a href="https://academic.oup.com/cercor/article/30/10/5333/5851264" target="_blank">PAPER</a>] [<a href="https://supereeg.readthedocs.io/en/latest/" target="_blank">CODE</a>] [<a href="https://github.com/Summer-MIND/mind_2018/blob/master/tutorials/supereeg/GP_demo_ECoG.ipynb" target="_blank">TUTORIAL</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/coding-science-hacker.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=Gin8_AITmS0" target="_blank">Coding like a science hacker</a></h4>
<p>Manning (2018) Coding like a science hacker. Talk given at the <a href="https://summer-mind.github.io/" target="_blank"><em>MIND Summer School at Dartmouth</em></a>.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/hypertools-talk.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=hb_ER9RGtOM" target="_blank">HyperTools and data visualization in Python</a></h4>
<p>Manning (2017) HyperTools and data visualization in Python. Talk given at the <a href="https://summer-mind.github.io/" target="_blank"><em>MIND Summer School at Dartmouth</em></a>.</p>
<p class="publication-links">[<a href="http://jmlr.org/papers/v18/17-434.html" target="_blank">PAPER</a>] [<a href="https://github.com/ContextLab/hypertools" target="_blank">CODE</a>] [<a href="http://hypertools.readthedocs.io/en/latest/tutorials.html" target="_blank">TUTORIAL</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/network-dynamics.png" alt="Publication thumbnail">
<div>
<h4><a href="https://youtu.be/DvzfPsOMvOw?t=2s" target="_blank">Network dynamics of the world and our brains</a></h4>
<p>Manning (2017) Network dynamics of the world and our brains. Talk given at the <a href="https://summer-mind.github.io/" target="_blank"><em>MIND Summer School at Dartmouth</em></a>.</p>
<p class="publication-links">[<a href="https://www.sciencedirect.com/science/article/pii/S1053811918300715?via%3Dihub" target="_blank">PAPER</a>] [<a href="http://brainiak.org/" target="_blank">CODE</a>] [<a href="https://github.com/Summer-MIND/mind_2017/tree/master/Tutorials/fMRI_NetworkDynamics" target="_blank">TUTORIAL</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/human-supereeg.png" alt="Publication thumbnail">
<div>
<h4><a href="https://www.youtube.com/watch?v=t6snLszEneA&feature=youtu.be&t=35" target="_blank">Towards Human SuperEEG</a></h4>
<p>Manning JR (2017) Towards Human SuperEEG. Talk given at the <a href="https://www.attentioninthebrain.com/" target="_blank"><em>EPSCoR Attention Consortium</em></a>.</p>
<p class="publication-links">[<a href="https://academic.oup.com/cercor/article/30/10/5333/5851264" target="_blank">PAPER</a>] [<a href="https://supereeg.readthedocs.io/en/latest/" target="_blank">CODE</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/mental-time-travel-talk.png" alt="Publication thumbnail">
<div>
<h4><a href="https://video.dartmouth-hitchcock.org/media/1_jl93ik1l" target="_blank">A neural signature of mental time travel</a></h4>
<p>Manning JR (2015) A neural signature of mental time travel. Talk given at the <a href="https://www.dartmouth-hitchcock.org/" target="_blank"><em>Dartmouth-Hitchcock Medical Center Grand Rounds</em></a>.</p>
<p class="publication-links">[<a href="http://caligari.dartmouth.edu/~jmanning/pubs/MannEtal11.pdf" target="_blank">PAPER</a>]</p>
</div>
</div>
</div>
<p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
</section>
<hr>
<!-- Course Materials -->
<section id="course-mats" class="content-section">
<h2>course materials</h2>
<div class="publications-grid">
<div class="publication-card">
<img src="images/publications/psych-lab.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/experimental-psychology" target="_blank">Laboratory in Psychological Science</a></h4>
<p>An open course intended to introduce students to project development, experimental design, analysis, and interpretation.</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/experimental-psychology" target="_blank">GitHub</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/human-memory.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/human-memory" target="_blank">Human Memory</a></h4>
<p>An open course based on Mike Kahana's <a href="https://www.amazon.com/Foundations-Human-Memory-Michael-Kahana/dp/0199387648" target="_blank">Foundations of Human Memory</a>. Covers classic experimental findings and experimental models.</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/human-memory" target="_blank">GitHub</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/programming-psych.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/cs-for-psych" target="_blank">Introduction to Programming for Psychological Scientists</a></h4>
<p>A self-directed open course intended to introduce students to fundamental computational tools used by modern psychological researchers.</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/cs-for-psych" target="_blank">GitHub</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/lab-tutorials.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/CDL-tutorials" target="_blank">Lab tutorials</a></h4>
<p>A collection of lab tutorials on a range of quantitative and computational topics.</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/CDL-tutorials" target="_blank">GitHub</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/mind-summer.png" alt="Publication thumbnail">
<div>
<h4><a href="http://mindsummerschool.org/" target="_blank">Methods in Neuroscience at Dartmouth (MIND)</a></h4>
<p>A 10-day intensive summer course on cutting-edge computational methods.</p>
<p class="publication-links">[<a href="https://github.com/Summer-MIND" target="_blank">GitHub</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/StorytellingWithData-23.webp" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/storytelling-with-data" target="_blank">Storytelling with Data</a></h4>
<p>Data science course aimed at a general audience (no pre-requisites).</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/storytelling-with-data" target="_blank">GitHub</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/MechanicalBrain_Edited.webp" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/computational-neuroscience" target="_blank">Computational Neuroscience</a></h4>
<p>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.</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/computational-neuroscience" target="_blank">GitHub</a>]</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/llm_course.jpg" alt="Publication thumbnail">
<div>
<h4><a href="https://context-lab.com/llm-course" target="_blank">Models of Language and Communication</a></h4>
<p>An open course on language models, chatbots, and natural language processing</p>
<p class="publication-links">[<a href="https://github.com/ContextLab/llm-course" target="_blank">GitHub</a>]</p>
</div>
</div>
</div>
<p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
</section>
<hr>
<!-- Abstracts + Posters -->
<section id="posters" class="content-section">
<h2>Abstracts + Posters</h2>
<div class="publications-grid">
<div class="publication-card">
<img src="images/publications/GoncMann26.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/GoncMann26.pdf" target="_blank">“Netflix” for lucid dreams: can preselected narrative cues during REM guide lucid dream content?</a></h4>
<p>Gonciulea CM, Manning JR (2026) “Netflix” for lucid dreams: can preselected narrative cues during REM guide lucid dream content?. <em>Cognitive Neuroscience Society Annual Meeting.</em> Vancouver, BC, Canada.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/PengEtal25.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/PengEtal25.pdf" target="_blank">Translating neurophysiological recordings into dynamic estimates of conceptual knowledge and learning</a></h4>
<p>Peng K, Carstensen D, Parigela S, Shah O, Wingo A, Liu A, Maina J, Dampal K, Manning JR (2025) Translating neurophysiological recordings into dynamic estimates of conceptual knowledge and learning. <em>Karen E. Wetterhahn Science Symposium.</em> Hanover, NH.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/XuMann25.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/XuMann25.pdf" target="_blank">Temporal asymmetries in cued recall of naturalistic events</a></h4>
<p>Xu X, Manning JR (2025) Temporal asymmetries in cued recall of naturalistic events. <em>Context and Episodic Memory Symposium.</em> Philadelphia, PA.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/CNS_2025.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/CNS_2025.pdf" target="_blank">Temporal (a)symmetries in cued recall of naturalistic events</a></h4>
<p>Xu X, Manning JR (2025) Temporal (a)symmetries in cued recall of naturalistic events. <em>Cognitive Neuroscience Society Annual Meeting.</em> Boston, MA.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/SfN_2025.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/SfN_2025.pdf" target="_blank">Probing temporal associations of naturalistic events with cued recall</a></h4>
<p>Xu X, Duncan CO, Manning JR (2025) Probing temporal associations of naturalistic events with cued recall. <em>Society for Neuroscience Annual Meeting.</em> San Diego, CA.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/CarsEtal24.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/CarsEtal24.pdf" target="_blank">Translating neurophysiological recordings into dynamic estimates of conceptual knowledge and learning</a></h4>
<p>Carstensen DL, Manning JR, Mucha P (2024) Translating neurophysiological recordings into dynamic estimates of conceptual knowledge and learning. <em>Wetterhahn Science Symposium.</em> Hanover, NH.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/CEMS_2024.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/CEMS_2024.pdf" target="_blank">Modeling the knowledge asymmetry of the past and the future</a></h4>
<p>Xu X (2024) Modeling the knowledge asymmetry of the past and the future. <em>Context and Episodic Memory Symposium.</em> Philadelphia, PA.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/JhaEtal23.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/JhaEtal23.pdf" target="_blank">Exploring high-order network dynamics in brains and stock markets</a></h4>
<p>Jha K, Carstensen DL, Patel A, Manning JR (2023) Exploring high-order network dynamics in brains and stock markets. <em>Wetterhahn Science Symposium.</em> Hanover, NH.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/XuMann23.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/XuMann23.pdf" target="_blank">Why we know more about the past: insights from statistical mechanics</a></h4>
<p>Xu X, Manning JR (2023) Why we know more about the past: insights from statistical mechanics. <em>Context and Episodic Memory Symposium.</em> Orlando, FL.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/CogSci_2023.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/CogSci_2023.pdf" target="_blank">Temporal asymmetries in inferring unobserved past and future events</a></h4>
<p>Xu X, Zhu Z, Manning JR (2023) Temporal asymmetries in inferring unobserved past and future events. <em>Annual Meeting of the Cognitive Science Society.</em> Sydney, Australia.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/CEMS_2022.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/CEMS_2022.pdf" target="_blank">A geometric approach to modeling knowledge and learning from Khan Academy course videos</a></h4>
<p>Fitzpatrick PC, Heusser AC, Manning JR (2022) A geometric approach to modeling knowledge and learning from Khan Academy course videos. <em>Context and Episodic Memory Symposium.</em> Philadelphia, PA.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/SaggEtal22.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/SaggEtal22.pdf" target="_blank">Higher-order interactions between brain regions are better at profiling tasks</a></h4>
<p>Saggar M, Betzel R, Manning JR, Liegeois R, Sporns O, Petri G (2022) Higher-order interactions between brain regions are better at profiling tasks. <em>Organization for Human Brain Mapping.</em> Glasgow, Scotland.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/JainEtal22.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/JainEtal22.pdf" target="_blank">Cognitive markers of mental health</a></h4>
<p>Jain S, Schreder N, Fitzpatrick PC, Ziman K, Manning JR (2022) Cognitive markers of mental health. <em>Conference on Cognitive Computational Neuroscience.</em> San Francisco, CA.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/XuEtal21.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/XuEtal21.pdf" target="_blank">Extrapolating the unobserved past and future in other people's autobiographical timelines</a></h4>
<p>Xu X, Zhu Z, Manning JR (2021) Extrapolating the unobserved past and future in other people's autobiographical timelines. <em>Context and Episodic Memory Symposium.</em> Philadelphia, PA.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/ZimaMann21.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/ZimaMann21.pdf" target="_blank">Unexpected false feelings of familiarity about faces are associated with increased pupil dilations</a></h4>
<p>Ziman K, Manning JR (2021) Unexpected false feelings of familiarity about faces are associated with increased pupil dilations. <em>Society for Neuroscience.</em> Virtual.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/SfN_GlobalConnectome_2021.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/SfN_GlobalConnectome_2021.pdf" target="_blank">Extrapolating the unobserved past and future in other people's autobiographical timelines</a></h4>
<p>Xu X, Zhu Z, Manning JR (2021) Extrapolating the unobserved past and future in other people's autobiographical timelines. <em>SfN Global Connectome.</em> Virtual.</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/OwenEtal20.png" alt="Publication thumbnail">
<div>
<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/OwenEtal20.pdf" target="_blank">A Gaussian process model of human ECoG data</a></h4>
<p>Owen LLW, Muntianu TA, Heusser AC, Manning JR (2020) A Gaussian process model of human ECoG data. <em>Context and Episodic Memory Symposium.</em> Philadelphia, PA (virtual).</p>
</div>
</div>
<div class="publication-card">
<img src="images/publications/OwenMann20.png" alt="Publication thumbnail">
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<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/OwenMann20.pdf" target="_blank">Understanding brain pattern complexity and interactivity in naturalistic processing</a></h4>
<p>Owen LLW, Manning JR (2020) Understanding brain pattern complexity and interactivity in naturalistic processing. <em>Context and Episodic Memory Symposium.</em> Philadelphia, PA (virtual).</p>
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<h4><a href="https://www.dropbox.com/s/3l5viwj0atiihae/SFN_2019c.pdf?dl=0" target="_blank">Volitional Attention Modulates Memory Encoding and Retrieval</a></h4>
<p>Ziman K, Lee MR, Martinez AR, Manning JR (2019) Volitional Attention Modulates Memory Encoding and Retrieval. <em>Society for Neuroscience.</em> Chicago, IL. 792.22/LLL18.</p>
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<h4><a href="https://github.com/ContextLab/contextlab.github.io/blob/main/data/pdfs/SFN_2019b.pdf" target="_blank">Exploring the evolving geometric structure of experiences and memories</a></h4>
<p>Fitzpatrick PC, Heusser AC, Manning JR (2019) Exploring the evolving geometric structure of experiences and memories. <em>Society for Neuroscience.</em> Chicago, IL. 423.16/BB14.</p>
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<h4><a href="https://www.dropbox.com/s/86osetoxu5uw6hg/SFN_2019a.pdf?dl=0" target="_blank">Understanding complexity and interactivity of brain patterns in naturalistic processing</a></h4>
<p>Owen LLW, Manning JR (2019) Understanding complexity and interactivity of brain patterns in naturalistic processing. <em>Society for Neuroscience.</em> Chicago, IL. 248.17/Z41.</p>
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<h4><a href="https://www.dropbox.com/s/zmcc74w6z6pow0t/CCN_2018.pdf?dl=0" target="_blank">Capturing the geometric structure of episodic memories for naturalistic experiences</a></h4>
<p>Heusser AC, Manning JR (2018) Capturing the geometric structure of episodic memories for naturalistic experiences. <em>Conference on Cognitive Computational Neuroscience.</em> Philadelphia, PA. PS-2B.</p>
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<h4><a href="https://www.dropbox.com/s/euj8p4csxa9qd9w/SFN_2018b.pdf?dl=0" target="_blank">Volitional Attention Modulates Memory Encoding and Retrieval</a></h4>
<p>Ziman K, Lee MR, Martinez AR, Manning JR (2018) Volitional Attention Modulates Memory Encoding and Retrieval. <em>Society for Neuroscience.</em> San Diego, CA. 792.22/LLL18.</p>
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<h4><a href="https://www.dropbox.com/s/rv86ve80zjis91t/SFN_2018a.pdf?dl=0" target="_blank">Mapping between naturalistic experience and verbal recall</a></h4>
<p>Fitzpatrick PC, Heusser AC, Manning JR (2018) Mapping between naturalistic experience and verbal recall. <em>Society for Neuroscience.</em> San Diego, CA. 086.10/HHH33.</p>
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<h4><a href="https://www.dropbox.com/s/kd72y0qh0bsm3mr/Wetterhahn_2018c.pdf?dl=0" target="_blank">The utility of speech-to-text software for transcription of verbal response data</a></h4>
<p>Fitzpatrick PC, Ziman K, Heusser AC, Field CE, Manning JR (2018) The utility of speech-to-text software for transcription of verbal response data. <em>Wetterhan Science Symposium.</em> Hanover, NH.</p>
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<h4><a href="https://www.dropbox.com/s/3gnsrfuve1ofztx/Wetterhahn_2018b.pdf?dl=0" target="_blank">How does attention affect memory?</a></h4>
<p>Pak EK, Ziman K, Manning JR (2018) How does attention affect memory?. <em>Wetterhahn Science Symposium.</em> Hanover, NH.</p>
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<h4><a href="https://www.dropbox.com/s/qmrzr0bc00p7hqv/Wetterhahn_2018a.pdf?dl=0" target="_blank">Adaptive Free Recall: Enhancing (Or Diminishing) Memory</a></h4>
<p>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. <em>Wetterhan Science Symposium.</em> Hanover, NH.</p>
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<h4><a href="https://www.dropbox.com/s/rpxv33fwsyd6xfp/CNS_2018.pdf?dl=0" target="_blank">Modeling the dynamic content, encoding, and retrieval of naturalistic stimuli</a></h4>
<p>Heusser AC, Manning JR (2018) Modeling the dynamic content, encoding, and retrieval of naturalistic stimuli. <em>Cognitive Neuroscience Society.</em> Boston, MA.</p>
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<h4><a href="https://www.dropbox.com/s/kdj8kdgoz8dqk1c/SFN_2017b.pdf?dl=0" target="_blank">Efficient Learning: Manipulating context to enhance (or diminish) memory</a></h4>
<p>Manning JR, Ziman K, Heusser AC (2017) Efficient Learning: Manipulating context to enhance (or diminish) memory. <em>Society for Neuroscience.</em> Washington, DC. 339.08/UU42.</p>
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<h4><a href="https://www.dropbox.com/s/n55irfqxxyyjbwy/SFN_2017c.pdf?dl=0" target="_blank">HyperTools: A python toolbox for gaining geometric insights into high-dimensional data</a></h4>
<p>Heusser AC, Ziman K, Owen LLW, Manning JR (2017) HyperTools: A python toolbox for gaining geometric insights into high-dimensional data. <em>Society for Neuroscience.</em> Washington, DC. 721.22/WW28.</p>
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<h4><a href="https://www.dropbox.com/s/xgb05okzcp0df47/SFN_2017a.pdf?dl=0" target="_blank">A Gaussian process model of human ECoG data</a></h4>
<p>Owen LLW, Manning JR (2017) A Gaussian process model of human ECoG data. <em>Society for Neuroscience.</em> Washington, DC. 093.04/UU78.</p>
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<h4><a href="https://www.dropbox.com/s/91jqthmj6ilplph/SFN_2017d.pdf?dl=0" target="_blank">Effects of study context on recall organization</a></h4>
<p>Ziman K, Heusser AC, Manning JR (2017) Effects of study context on recall organization. <em>Society for Neuroscience.</em> Washington, DC. 803.07/UU14.</p>
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<h4><a href="https://www.dropbox.com/s/f45pm5fl9fml1zj/CEMS2017a.pdf?dl=0" target="_blank">Harnessing the power of mnemonic fingerprints: Maximizing learning potential by personalizing stimulus organization during adaptive list learning</a></h4>
<p>Ziman K, Heusser AC, Manning JR (2017) Harnessing the power of mnemonic fingerprints: Maximizing learning potential by personalizing stimulus organization during adaptive list learning. <em>Context and Episodic Memory Symposium.</em> Philadelphia, PA.</p>
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