Publications — Living System Design Lab

2025

Science

Co-corresponding

389(6758)
386–391

Design of high-specificity binders for peptide–MHC-I complexes

Deep-learning protein design can build small proteins that clamp onto a specific peptide–MHC complex and tell apart antigens differing by a single amino acid. Several of the designs worked as CAR targeting domains, redirecting T cells against a chosen peptide.

Liu, B.*^#, Greenwood, N.F.*, Bonzanini, J.E.*, Motmaen, A., Meyerberg, J., Dao, T., … & Baker, D.^#

2024

Cell Systems

Co-first

15(12)
1264–1277

Regulators of intracellular STING trafficking, identified by genome-wide optical pooled screening

A genome-wide screen that reads out cell images, not just survival, mapped the genes that control where the immune sensor STING travels inside the cell — and sorted them into functional classes.

Gentili, M.*, Carlson, R.J.*, Liu, B.*, Hellier, Q., Andrews, J., Qin, Y., Blainey, P.C. & Hacohen, N.

2023

Science

Co-corresponding

381(6657)
508–514

Human STING is a proton channel

STING is famous as an innate-immune signaling hub. We found it also moves protons across membranes — and that channel activity, separate from its signaling role, is what triggers noncanonical autophagy and the NLRP3 inflammasome.

Liu, B.*^#, Carlson, R.J.*, Pires, I.S., Gentili, M., Feng, E., Hellier, Q., Schwartz, M.A., Blainey, P.C., Irvine, D.J.^# & Hacohen, N.^#

Nature Comms

14(1)
611

ESCRT-dependent STING degradation inhibits steady-state and cGAMP-induced signalling

The cell's ESCRT machinery actively degrades STING to keep innate immunity in check — setting both the resting tone and the off-switch after activation.

Gentili, M., Liu, B., Papanastasiou, M., Dele-Oni, D., Schwartz, M.A., Carlson, R.J., Al'Khafaji, A.M., Krug, K., Brown, A., Doench, J.G. & Carr, S.A.

Nature Immunol.

Human iPSC-derived microglia adopt diverse transcriptional states when exposed to brain substrates

Lab-grown human microglia shift into a range of brain-like states depending on what they're fed — giving a tunable model of how these immune cells behave in the brain.

Dolan, M.J., Therrien, M., Jereb, S., Kamath, T., Gazestani, V., … Liu, B., … & colleagues.

Earlier

bioRxiv

First · 2020

An efficient lentiviral CRISPRi approach to silence genes in primary human monocytes

A method paper: a lentiviral CRISPRi system that reliably knocks down genes in primary human monocytes — hard-to-engineer immune cells.

Liu, B., Gentili, M., Lieb, D., Eisenhaure, T., Irvine, D.J. & Hacohen, N.

Cell

168(5)
890–903 · 2017

Gene essentiality profiling reveals gene networks and synthetic-lethal interactions with oncogenic Ras

Genome-scale fitness screens across cancer cells mapped how genes depend on one another — and surfaced vulnerabilities specific to Ras-driven tumors.

Wang, T., Yu, H., Hughes, N.W., Liu, B., Kendirli, A., Klein, K., Chen, W.W., Lander, E.S. & Sabatini, D.M.

Titles link to the paper via Google Scholar. For the complete, current list, see Bingxu's Scholar profile.