James Bole Pan 潘柏乐

Email: bole.pan (at) columbia.edu

I'm an incoming PhD student at MIT, through the Harvard-MIT Health Sciences and Technology (HST) program. I graduated from Columbia University in 2024 with a major in Computer Science. With strong background in data science, software engineering, and wet-lab research, I have a demonstrated interest understanding biology through computational lens.

My research interest lies at the intersection of genomics, systems biology, and machine learning. I'm specifically interested in leveraging computational approaches to study regulatory genomics and the mechanisms of cellular identity dysregulation, so as to understand molecular underpinnings of age-related diseases.

I'm have worked with Prof. Dana Pe'er, Prof. Ron Jachimowicz, Prof. Liam Paninski, and Prof. Darcy Kelley.

Selected Projects

Inferring Nucleosome Position Shifting with Single-cell Data from Prostate Cancer Neuroendocrine Transformation, 2023 - 2024
Explored the role of chromatin remodelers in prostate cancer's neuroendocrine transformation using single-cell multiomics data from mouse models. Identified significant chromatin landscape remodeling during transformation, with key regulatory regions showing nucleosome eviction and reassembly or position shifting.

Clusterless Decoding of Mouse Choices Based on Point-wise Neural Network, 2022 - 2023
Proposed and implemented a permutation-invariant deep neural network based on PointNet architecture to process mouse electrophysiology data. Achieved performances on par with the state-of-the-art decoding methods. Exploring further possibilities in neural-network-based clusterless decoding. (link)

Ethology and Evolution of Courtship Vocalization in Xenopus, 2022 - 2023
Investigated the evolution of vocal communication in African clawed frogs, Xenopus. Developed computational pipelines for speech identification using digital signaling and stochastic processes. Presented at Society for Integrative and Comparative Biology (SICB) Annual Meeting 2023. (link)

Synthesis of an Effective Flame-retardant Hydrogel for Skin Protection Using Xanthan Gum and Resorcinol Bis(diphenyl phosphate)-coated Starch, 2019 - 2021
Developed a flame-retardant hydrogel based on polysaccharide to protect firefighters from burns. Devised quantitative models to understand heat diffusion mechanisms. Presented at Materials Research Society (MRS) Fall 2019 Meeting, Stony Brook Fire Dept. and Israel Chemicals Ltd. (link)

Selected Publications

  1. Pan, B., Kwon, Y., Bagnato-Colin, E., Kelley, D. (2023). Ethology and evolution of courtship vocalization in Xenopus. Society for Integrative and Comparative Biology (SICB) Annual Meeting 2023. (Abstract ID: 815)    Abstract PDF   |   Poster

  2. Xue, Y., Yang, F., Li, J., Zuo, X., Pan, B., Li, M., Quinto, L., Mehta, J., Stiefel, L., Kimmey, C., Eshed, Y., Zussman, E., Simon, M., & Rafailovich, M. (2021). Synthesis of an effective flame-retardant hydrogel for skin protection using xanthan gum and resorcinol bis(diphenyl phosphate)-coated starch. Biomacromolecules, 22(11), 4535-4543.    PDF   |   Source   |   Poster

  3. Pan, B., Wang, Y., Li, H., Yi, W., & Pan, Y. (2020). Preparation and electrosorption desalination performance of peanut shell-based activated carbon and MOS2. Journal of Electrochemical Science , 15 , 1861-1880.    PDF   |   Source

  4. Islam, D., Uddin, M. H., Pan, B., & Joy, M. M. A. (2020). Flexible and high-energy dense yarn-shaped supercapacitor based on Ni-carbon nanotubes framework. Chemical Physics Letters, 760, 138007.   PDF   |   Source

  5. Xiao, X., Lin, Y., Pan, B., Fan, W., & Huang, Y. (2018). Photocatalytic degradation of methyl orange by BiOI/Bi4O5I2 microspheres under visible light irradiation. Inorganic Chemistry Communications, 93, 65-68.    PDF   |   Source

Experience

  • Research Intern, Max Plank Institute for Biology of Ageing (PI: Dr. Ron Jachimowicz), 05/2024 - 08/2024

  • Research Intern, Memorial Sloan Kettering Cancer Center (PI: Dr. Dana Pe'er), 09/2023 - 05/2024

  • Research Intern, Center for Theoretical Neuroscience, Columbia University (PI: Dr. Liam Paninski), 09/2022 - 08/2023

  • Software Engineering Intern, Amazon Web Services, Seattle, WA, 05/2023 - 08/2023

  • Undergraduate Researcher, Department of Biology, Columbia University (PI: Dr. Darcy Kelley), 10/2022 - 01/2023

Awards and Honors

  1. Recipient, Computer Science Scholarship Award, 2024

  2. Finalist, Rhodes Scholarship, 2023

  3. Recipient, Kraft Global Fellowship, 2022

  4. Invited Participant, Shanghai Science Festival, 2021

  5. Recipient, 12th China Youth Science and Technology Innovation Award, 2020.

  6. Finalist, Regeneron International Science and Engineering Fair, 2020

  7. Finalist, Stockholm Junior Water Prize, 2019

Others

Outside of academics:

  • I'm passionate about science communication and led the production of podcast series Bio Bytes and BioWorks as a part of Columbia University Systems Biology Initiative, which I served as Vice President.

  • I was an elected member of Columbia College Student Council. I served as the Representative for the Class of 2024.

  • I'm a basketball enthusiast and played for the Columbia Intramural team Brickeroos

  • I love reading and writing, and enjoy exploring diverse topics in literature, philospohy, arts, and music. Some of my writings can be found on my Medium page.