Neuroscience | Ellie Beam

Data-driven ontology of brain function

In modern healthcare, there is no accepted system for diagnosing disorders of mental function based on the altered brain systems that cause them. In neuroscience, there is no consensus on what a brain system is. My PhD thesis took a data-driven approach to mapping domains of brain function across the human neuroimaging literature. Neural circuits and associated mental functions were mapped from the brain coordinate data and full texts of nearly 20,000 studies. The resulting domains characterize several novel brain circuits that are absent from the conceptually dominant expert-determined frameworks in the field. The ontology can be viewed in an interactive format at neuro-knowledge.org.

Brain network disruption in mental illness

Mood disorders affect not only the way people feel, but also the way they plan and process information. The frontoparietal control network is believed to play a crucial role in support of goal-directed planning and adaptive behavioral adjustments. As part of my post-undergraduate work, I examined the integrity of the frontoparietal circuitry in young adults showing signs of depressive illness onset. Deficits in executive functioning were found to predict a decline in frontoparietal network integrity.

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The semantic structure of neuroscience

Human neuroscience is a linking discipline that seeks to understand relationships between the systems of the brain and the processes of the mind. As an undergraduate, I visualized the semantic structure of human neuroscience by mapping co-occurrences of anatomical and psychological terms in fMRI article abstracts. Graph theoretical analyses identified topics that were likely to advance the integrative goal of the field.

Bibliography

Peer-Reviewed Articles

Tu, J., Tran, D., Beam, E.H. (2022). Neurocysticercosis. RSNA Case Collection. DOI: 10.1148/cases.20226020.
Beam, E.H., Potts, C., Poldrack, R.A., & Etkin, A. (2021). A data-driven framework for mapping domains of human neurobiology. Nature Neuroscience. DOI: 10.1038/s41593-021-00948-9.
Siless, V., Davidow, J.Y., Nielsen, J., Fan, Q., Hedden, T., Hollinshead, M., Beam, E.H., Vidal Bustamante, C.M., Garrad, M.C., Santillana, R., Smith, E.E., Hamadeh, A., Snyder, J., Drews, M.K., Van Dijk, K.R.A., Sheridan, M., Somerville, L.H., Yendiki, A. (2020). Registration-free analysis of diffusion MRI tractography data across subjects through the human lifespan. NeuroImage 214(116703). DOI: 10.1016/j.neuroimage.2020.116703.
Beam, E.H.,* Appelbaum, L.G.,* Jack, J., Moody, J., & Huettel, S.A. (2014). Mapping the semantic structure of cognitive neuroscience. Journal of Cognitive Neuroscience 26(9). DOI: 10.1162/jocn_a_00604.

Community Articles

Beam, E.H. (2022). Multiple immune cell types and a checkpoint implicated in myasthenia gravis. Rare Disease Advisor.
Beam, E.H. & Ballon, J. (2022). A decade of drug discovery for schizophrenia: TAAR1 and muscarinic agonists. CureSZ Foundation Newsletter.
Beam, E.H. (2020). A brief history of our language for the brain: Vocabulary, dictionary, and poetry. NeuWrite West Blog.
Beam, E.H. (2019). How the brain learns to learn. NeuWrite West Blog.
Beam, E.H. (2018). Resolving conflict in the medial frontal cortex. NeuWrite West Blog.
Beam, E.H. (2014). Brain and language on the fly: The neuroscience of linguistic improvisation. Harvard Science Review 27(2).
Beam, E.H. (2013). Data: The bigger the better? Harvard Science Review 27(1).
Beam, E.H. (2012). Creativity and the default network. Neurogenesis: The Undergraduate Journal of Neuroscience 2(1).
Beam, E.H. (2010). Sylvia Plath on edge: A case for the correlation of bipolar disorder and exceptional poetic creativity. Eruditio: Duke Humanities Journal 30(1).

Pre-Print Article

Beam, E.H., Potts, C., Poldrack, R.A., & Etkin, A. (2019). A computational knowledge engine for human neuroscience. bioRxiv. DOI: 10.1101/701540.

Patent

Etkin, A. & Beam, E.H. (2020). Machine learning based generation of ontology for structural and functional mapping. US Patent App. 16/888,530. Pending.

Book Chapter

Jack, J., Appelbaum, L.G., Beam, E.H., Huettel, S.A., & Moody, J. (2017). Mapping rhetorical topologies in cognitive neuroscience. In L. Walsh & C. Boyle. (Eds.), Topologies as Techniques for a Post-Critical Rhetoric (pp. 125-150). New York, NY: Palgrave Macmillan.

Theses

Beam, E.H. (2020). A data-driven ontology of brain function: Engineered, interrogated, and clinically applied. In fulfillment of the requirements for a PhD in the Neurosciences. Stanford University.
Beam, E.H. (2013). Mapping the semantic structure of cognitive neuroimaging. In fulfillment of the requirements for Graduation with Distinction in Neuroscience. Duke University.

Talks

Beam, E.H. (2022, May). A data-driven ontology of brain function: Engineered, interrogated, and clinically applied. Stanford Psychology Department Friday Seminar Series. Stanford, CA.
Beam, E.H. (2019, May). A computational knowledge engine for human neuroscience. Stanford MSTP Retreat. Santa Cruz, CA.
Platt, M., Jenson, D., Harris, L., Beam, E.H., & Mooney, R. (2013, April). Brain science and our creative culture. Duke Forward. New York, NY.
Appelbaum, L.G. & Beam, E.H. (2012, November). Mapping disciplinary structures using network and semantic analysis. Text>Data Digital Scholarship Series. Durham, NC.

Posters

Beam, E.H. & Etkin, A. (2018, May). Toward a data-driven ontology of human brain function. Stanford MSTP Retreat, Santa Cruz, CA.
Beam, E.H., Maron-Katz, A., & Etkin, A. (2017, May). Discovery of post-traumatic stress disorder biotypes by clustering subcortical volumetrics. 34th Annual Stanford Medical Student Research Symposium.
Beam, E.H., Preston, S., & Jain, S. (2017, May). Preliminary outcomes of a novel protocol for phone-based management of antidepressant therapy initiated in primary care. 50th Annual Conference of the Society of Teachers of Family Medicine.
Barbour, T., DeCross, S.N., Holmes, A.J., Boeke, E.A., Beam, E.H., Wolthusen, R.P.F., Crowell, S., Coombs, G., Nyer, M., Buckner, R.L., Fava, M., Farabaugh, A.H., Holt, D.J. (2014, December). Insecure attachment in at-risk youth is associated with hyper-responsivity of a parietofrontal cortical network involved in social behavior. American College of Neuropsychopharmacology Annual Meeting.
Holt, D.J., DeCross, S.N., Holmes, A.J., Boeke, E.A., Beam, E.H., Wolthusen, R.P.F., Crowell, S., Coombs, G., Nyer, M., Buckner, R.L., Fava, M., Farabaugh, A.H. (2014, December). Abnormal amygdala functional connectivity in youth with subclinical delusions. American College of Neuropsychopharmacology Annual Meeting.
Beam, E.H., Coombs, G., Boeke, E., Crowell, S., Fava, M., Farabaugh, A., Holt, D.J., Buckner, R.L., & Holmes, A.J. (2014, September). Frontoparietal network connectivity associates with executive functioning deficits in young adults at risk for depression. Resting State and Brain Connectivity Conference.
Beam, E.H. & Huettel, S.A. (2013, April). Mapping the semantic structure of cognitive neuroscience. Atlantic Coast Conference Meeting of the Minds.
Beam, E.H., Appelbaum, L.G., Moody, J., & Huettel, S.A. (2011, November). Mapping the intrinsic structure of cognitive neuroscience. Society for Neuroscience Annual Meeting.