A dense block of serotonergic neurons in the DRN. Imaged in 2014, Warden Lab

Background

I am a passionate problem solver with broad interests spanning both the humanities and technology. Outside of work, I enjoy reading, cycling, swimming, meditating, examining both my own life and that of others (e.g. reading biographies), following various topics (such as American history, investing, macroeconomics, and law), and listening to music. I love working with people to solve challenging problems and learning about how different organizations—particularly businesses—grow and operate.

Recently, I completed my Ph.D. in the Department of Brain and Cognitive Sciences at the Massachusetts Institute of Technology. Under the guidance of my advisor, Steve Flavell, I investigated the neural circuits underlying behavior in C. elegans using cutting-edge optical, genetic, and computational tools (such as AI, deep learning, and Bayesian modeling). For more information on my main graduate work, please see the following news coverage: Scientific American and MIT News.

Before grad school, I spent a year conducting research in biomedical optics and systems neuroscience with Drew Robson and Jennifer Li at the Rowland Institute at Harvard. Prior to that, I was at Cornell, where I learned how to solve challenging problems, primarily in biological contexts (Biological Engineering). During my time at Cornell, I worked in Melissa Warden's lab, where I developed a deep interest in neuroscience.

Degrees

Ph.D. in Neuroscience, Brain and Cognitive Sciences, Massachusetts Institute of Technology

B.S. in Biological Engineering, College of Engineering, Cornell University

Thesis Project

Brain-wide representations of behavior spanning multiple timescales and states in C. elegans

I co-led a pioneering neuroscience project that was published in Cell and featured in Scientific American. Our work involved developing innovative hardware and software solutions to image neural activity in freely behaving C. elegans. We then used probabilistic modeling to create the first comprehensive neural encoding dictionary of an organism.

graphical abstract of the Cell 2023 paper

Simultaneous recordings of brain-wide activity and diverse behaviors in C. elegans
Using a custom-engineered microscope, we recorded brain-wide neural activity simultaneously with diverse motor behaviors in C. elegans. We developed a custom software to extract neural traces at the cellular level with high SNR.

Probabilistic encoder model describes how each neuron encodes behavior
We developed a probabilistic encoder model alongside tailored inference algorithms to analyze neural data. This approach provides detailed, interpretable descriptions of how individual neurons encode specific behaviors.

Results mapped to connectome, yielding encoding atlas of C. elegans nervous system
By integrating our models with the connectome, we generated a comprehensive encoding atlas illustrating how genetically identified neuron classes in C. elegans encode various behaviors.

Defined neurons flexibly change encoding in a state-dependent manner
Interestingly, we discovered that some neurons exhibit flexibility in encoding, dynamically changing these properties depending on the behavioral state.

Publications

Deep Neural Networks to Register and Annotate the Cells of the C. elegans Nervous System
bioRxiv, 2024
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Adam A. Atanas, Alicia Kun-Yang Lu, Jungsoo Kim, Saba Baskoylu, Di Kang, Talya S. Kramer, Eric Bueno, Flossie K. Wan, Steven W. Flavell

Brain-wide representations of behavior spanning multiple timescales and states in C. elegans
Cell, 2023
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Adam A. Atanas*, Jungsoo Kim*, Ziyu Wang, Eric Bueno, McCoy Becker, Di Kang, Jungyeon Park, Talya S. Kramer, Flossie K. Wan, Saba Baskoylu, Ugur Dag, Elpiniki Kalogeropoulou, Matthew A. Gomes, Cassi Estrem, Netta Cohen, Vikash K. Mansinghka, Steven W. Flavell

* equal contribution

Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale
Cell, 2023
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Ugur Dag*, Ijeoma Nwabudike*, Di Kang*, Matthew A. Gomes, Jungsoo Kim, Adam A. Atanas, Eric Bueno, Cassi Estrem, Sarah Pugliese, Ziyu Wang, Emma Towlson, Steven W. Flavell

* equal contribution

Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish
Nature Methods, 2017
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Dal Hyung Kim, Jungsoo Kim, João C. Marques, Abhinav Grama, David G. C. Hildebrand, Wenchao Gu, Jennifer M. Li, Drew N. Robson

* equal contribution