I am a researcher and software engineer residing in Boston, Massachusetts.
Currently, I am working at a stealth startup company in Cambridge, MA.
Prior to this, I was a postdoctoral research fellow at Brigham and Women's Hospital / Harvard Medical School (Computational Pathology - Gibson Lab).
I received my Ph.D. from MIT in Applied Mathematics in 2023.
As a Postdoc, I worked on Bayesian models for performing inference on microbiome time-series data, and deep-learning representations of microbial genomcs.
For my Ph.D., I specialized in probabilistic inference for computational biology (specifically, population genetics and gut metagenomics).
Prior to that, I received a Bachelor of Science degree in May 2016 from Brown University in Mathematics and Computer Science.
Please note that my MIT email (younhun@mit.edu) is outdated, and so is my BWH email (ykim78@bwh.harvard.edu).
Please contact me at youn.kim.3181@gmail.com for all research/work-related messages.
My CV is available upon request.
My first name (Kor: 김연훈) is pronounced "Young Hoon", without the g. My colleagues simply call me "Youn".
Research
- 2025 Gibson TE*, Kim Y*, et al. Learning ecosystem-scale dynamics from microbiome data with MDSINE2. [Nature Microbiology]
- 2025 Kim Y, (...), Berger B, Gibson TE. Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain. [Nature Microbiology] [Github]
- 2021 Gibson TE, Kim Y, et al. Intrinsic instability of the dysbiotic microbiome revealed through dynamical systems inference at scale. [bioRxiv]
- 2020 Kim Y, Acharya S, Alfonsetti D, Gerber G, Berger B, Gibson T. Strain Tracking from Time-Series Data. (Workshop poster, ICML Compbio 2020)
- 2020 Kim Y, Mossel E, Ramnarayan G, Turner P. Efficient Reconstruction of Stochastic Pedigrees. [arxiv]
- 2019 Kim Y, Koehler F, Moitra A, Mossel E, Ramnarayan G. How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories. RECOMB 2019, Journal of Computational Biology Special Issue. [arxiv] [journal]
- 2014 Leiserson MD, Vandin F, Wu HT, Dobson JR, Eldridge JV, Thomas JL, Papoutsaki A, Kim Y, Niu B, McLellan M, Lawrence MS. Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nature genetics 2015. [article]
Teaching & Mentorship
- Recitation Instructor, 18.650 (Statistics) - Spring 2020
- Recitation Instructor, 18.600 (Probability) - Fall 2019
- Recitation Instructor, 6.431x (Probability, edX Micromasters Program in Statistics and Data Science)
- TA, 18.6501x (Fundamentals of Statistics, edX Micromasters Program in Statistics and Data Science)
- Grader, 18.404 (Theory of Computation, Prof. Sipser)
- TA, 18.085 (Computational Science and Engineering, Prof. Gil Strang)
- TA, 18.418 (Topics in Computational Bio, Prof. Bonnie Berger)
