Dr. Ellie Beam

Training Journey

	BS, BA. In 2013, Ellie graduated summa cum laude from Duke University with a BS in Neuroscience and a BA in English, earning distinction for theses in both majors. Her research in the lab of Scott Huettel applied network text analyses to map the semantic structure of human neuroimaging.
	Research. From 2013 to 2015, Ellie worked in the lab of Randy Buckner at Harvard University and Massachusetts General Hospital. In addition to coordinating studies of affective illness, she led an independent project investigating cognitive control network disruption in subthreshold depression.
	MD, PhD. In 2022, Ellie completed MD/PhD training at Stanford School of Medicine with mentorship by Amit Etkin and Russ Poldrack. Her PhD thesis in the Neurosciences developed a computational approach to mapping domains of brain function from the human neuroimaging literature. She was supported by the NRSA fellowship and recognized by the Leah J. Dickstein Award from the Association of Women Psychiatrists.
	Residency. Ellie is currently a resident physician in psychiatry at Stanford Health Care. As a member of the research track, she intends to combine natural language processing, machine learning, and other computational approaches to reconceptualize mental illness through the language of people living with it.

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© 2024 Elizabeth H. 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 above and 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.

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 11526808B2.

Book Chapters

• Beam, E.H. & Ballon, J. (2024). A decade of drug discovery for schizophrenia: TAAR1 and muscarinic agonists. In B. Yeiser & H.A. Nasrallah (Eds.), Awakenings: Stories of Recovery and Emergence from Schizophrenia (pp. 217-220). Seattle, WA: Amazon.
• 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. (2024, April). Natural language processing approaches to understanding psychosis. CURESZ Foundation. Virtual.
• Beam, E.H. (2023, March). Data-driven mapping and validation of a framework for human brain function. Symposium: The data science future of cognitive neuroscience. 30th Anniversary Meeting of the Cognitive Neuroscience Society. San Francisco, CA.
• Ballon, J., Beam, E.H. (2023, February). Medications in the pipeline for schizophrenia. CURESZ Foundation. Virtual.
• 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.​

Funding

© 2024 Elizabeth H. Beam