Publications

Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation.
Tamura T, Cheng C, Villasenor-Altamirano AB, Yamada K, Ikeda K, Hayashida K, Menon JA, Chen DX, Chung H, Varon J, Chen J, Choi J, Cullen AM, Guo J, Lin X, Olenchock BA, Pinilla-Vera MA, Manandhar R, Sheikh M, Hou PC, Lawler PR, Oldham WM, Seethala RR, Immunology of Cardiac Arrest Network (I-CAN), Baron RM, Bohula EA, Morrow DA, Blumberg RS, Chen F, Merriam LT, Weissman AJ, Brenner AB, Chen X, Ichinose F, Kim EY. Science Translational Medicine 2024, 16.

Contrastive Poincaré Maps for single-cell data analysis.
Bhasker N, Chung H, Boucherie L, Kim V, Speidel S, Weber M. International Conference on Learning Representations (ICLR), Workshop on Machine Learning for Genomics Explorations 2024 [PDF].

Joint single-cell measurements of nuclear proteins and RNA in vivo.
Chung H†, Parkhurst CP, Magee EM, Phillips D, Habibi E, Chen F, Yeung BZ, Waldman J, Artis D, Regev A†. Nature Methods 2021, 18. [PDF] [Nature Methods Technology Feature]

A multi-view generative model for molecular representations improves prediction tasks.
Yin J*, Chung H*†, Regev A†. Conference on Neural Information Processing Systems (NeurIPS), Workshop on Learning Meaningful Representations of Life 2020 [PDF].

Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections.
Chung H, Merakou C, Schaefers MM, Flett KB, Martini S, Lu R, Blumenthal JA, Webster SS, Cross AJ, Al Ahmar R, Halpin E, Anderson M, Moore NS, Snesrud EC, Yu HD, Goldberg JB, O’Toole GA, McGann P, Stam JA, Hinkle M, McAdam AJ, Kishony R, Priebe GP. Nature Communications 2022, 13. [PDF]

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus C*, Luecken MD*, Eraslan G*, Sikkema L*, Waghray A*, Heimberg G*, Kobayashi Y*, Vaishnav ED*, Subramanian A*, Smillie C*, Jagadeesh KA*, Duong ET*, Fiskin E*, Torlai Triglia E*, Ansari M*, Cai P*, Lin B*, Buchanan J*, Chen S*, Shu J*, Haber AL*, Chung H*, Montoro DT*, et al. Nature Medicine 2021, 27. [PDF]

The microbiota regulate neuronal function and fear extinction learning.
Chu C, Murdock MH, Jing D, Won TH, Chung H, Kressel AM, Tsaava T, Addorisio ME, Putzel GG, Zhou L, Bessman NJ, Yang R, Moriyama S, Parkhurst CN, Li A, Meyer HC, Teng F, Chavan SS, Tracey KJ, Regev A, Schroeder FC, Lee FS, Liston C, Artis D. Nature 2019, 574. [PDF]

Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung.
Chung H, Lieberman TD, Varags SO, Flett KB, McAdam AJ, Priebe GP, Kishony R. Nature Communications 2017, 8. [PDF]

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq.
Kelsic ED*, Chung H*, Cohen N, Park J, Wang HH, Kishony R. Cell Systems 2016, 3. [PDF]

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes.
Baym M*, Kryazhimskiy S*, Lieberman TD*, Chung H*, Desai MM, Kishony R. PLoS ONE 2015, 10. [PDF]

Isocost lines describe the cellular economy of genetic circuits.
Gyorgy A, Jimenez JI, Yazbek J, Huang HH, Chung H, Weiss R, Del Vecchio D. Biophysical Journal 2015, 109. [PDF]

Lipid-derived nanoparticles for immunostimulatory RNA adjuvant delivery.
Nguyen DN, Mahon KP, Chikh G, Kim P, Chung H, Vicari AP, Love KT, Goldberg M, Chen S, Krieg AM, Chen J, Langer R, Anderson DG. Proceedings of the National Academy of Sciences 2012, 109. [PDF]

Engineering novel synthetic biological systems.
Reza F, Chandran K, Feltz M, Heinz A, Josephs E, O’Brien P, Van Dyke B, Chung H, Indurkhya S, Lakhani N, Lee J, Lin S, Tang N, LaBean T, You L, Yuan F, Tian J. IET Synthetic Biology, 1.