Nicholas Hutchins

PhD Student · MIT & Whitehead Institute

Nicholas Hutchins

Biological AI/ML · Stem cell engineering · Uncertainty quantification

MIT Presidential Fellowship NSF GRFP Brill Fellowship Whitehead Innovation Award

I am a current PhD student at MIT advised by Pulin Li, a member of the Whitehead Institute. My research focuses on how we represent biological perturbation problems meaningfully in AI/ML approaches and create tools that illuminate aspects of biology that were not previously possible.

Much of my graduate work has focused on predictively modeling stem cell engineering and identifying which combinations of perturbations drive cells into desired states. I am broadly interested in expanding and using the uncertainty quantification toolbox to better understand the properties of ML models in biology.

I have enjoyed working with many collaborators throughout my PhD, most notably at Kira Learning, GC Therapeutics, and Microsoft Research New England.

Before starting my PhD, I was a research associate at Twist Bioscience and received my BS from Caltech.

2026
Nicholas T. Hutchins, Miram Meziane, Claire Lu, Maisam Mitalipova, David S. Fischer, Pulin Li
Nature Methods · Published online Sep. 8, 2026
Nature Methods Figure 1 — overview of the IRIS framework
Fig. 1 — IRIS learns signaling response signatures from in vitro perturbation screens to infer signaling histories in vivo.
2026
Nicholas T. Hutchins*, Alexandra Cao*, Pulin Li
Cell Systems · 17(8) 101619 · Aug. 19, 2026
Cell Systems Figure 2 — bottom-up reconstitution of cell sorting
Fig. 1 — Synthetic biology enables reconstitution across multiple scales of development.
2018
Timothy M. Wannier, Sarah Gillespie, Nicholas Hutchins, R. Scott McIsaac, Sheng-Yi Wu, Yi Shen, Robert E. Campbell, Kevin S. Brown, Stephen L. Mayo
Proceedings of the National Academy of Sciences · 115(48) E11294–E11301 · Nov. 13, 2018
PNAS figure 3
Fig. 3 — Bright, far-red monomeric RFP variants (mGinger, mKelly series).
AIChE
Annual Meeting · Boston, MA
abstract · 2025
ISSCR
AI and Digital Biology Symposium · Seattle, WA
abstract · 2025
Keystone
AI in Molecular Biology · Santa Fe, NM
abstract · 2025
AIChE
Annual Meeting · San Diego, CA
abstract · 2024
BioTM
Bioengineering and Translational Medicine · San Diego, CA
abstract · 2024
SCDBM
Santa Cruz Developmental Biology Meeting · Santa Cruz, CA
abstract · 2024
IMSBW
International Mammalian Synthetic Biology Workshop · Boston, MA
abstract · 2024
Whitehead
Whitehead Institute Forum · Boston, MA
dept. · 2024
MIT BTS
Bioengineering and Toxicology Seminar · Boston, MA
dept. · 2023–24
Lucy Xu*, Dagney Cooke, Nicholas Hutchins, Tony Cox. A New Twist on Antibody Library Engineering. PEGS 2019 Boston · Apr. 8, 2019
Xiaozhe Ding*, Claire N. Bedbrook, Nicholas Hutchins, Viviana Gradinaru. Engineering Prokaryotic Repressors for Optical Sensing of Neurotransmitters. Society for Neuroscience Conference · 2017

* presenter

Sam Maffa
PhD Student · MIT Computational Biology
2026
Claire Lu
Masters · Now Engineer at Databricks
2024–2025
Lauren Tso
PhD Student · MIT Computational Biology
2024
Hariharan Jayaraman
PhD Student · MIT Biology
2023
Alex Cao
PhD Student · MIT Biology
2022