† co-corresponding authors.
* co-first authors.


“How to build a bacterial cell: MreB as the foreman of E. coli construction”,

H Shi*, B Bratton*, Z Gitai†, KC Huang†,

Cell 172 1294-1305 (2018).

“RodZ modulates geometric localization of the bacterial actin MreB to regulate cell shape”,

 A Colavin*, H Shi*, KC Huang,

 Nature Communications, in press.

“Regulation of bacterial growth by turgor pressure”,

ER Rojas, KC Huang,

Current Opinion in Microbiology 42 62-70 (2018).

“The marine mammal microbiome yields a novel antibiotic with potent activity against Clostridium difficile”,

JL Ochoa, L Sanchez, B-M Koo, J Doherty, M Rajendram, KC Huang, CA Gross, RG Linington

ACS Infectious Diseases 4 59-67 (2018).


“An engineering design approach to systems biology“,

Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA.   

Integr. Biol. 9(7):574-583 (2017).

Pseudogenization of the secreted effector gene sseI confers rapid systemic dissemination of S. typhimurium ST313 within migratory dendritic cells,

Carden SE, Walker GT, Honeycutt J, Lugo K, Pham T, Jacobson A, Bouley D, Idoyaga J, Tsolis RM, Monack D,

Cell Host Microbe. 21(2):182-94. doi: 10.1016/j.chom.2017.01.009 (2017).

Combining comprehensive analysis of off-site lambda phage integration with a CRISPR-based means of characterizing downstream physiology,

Tanouchi Y, Covert MW, 

mBio.  Sep-Oct, 8(5): e01038-17, doi: 10.1128/mBio.01038-17 (2017).

Live-cell measurements of kinase activity in single cells using translocation reporters,

Kudo TJeknić SMacklin DNAkhter SHughey JJRegot SCovert MW, 

Nat Protoc. 2018 Jan;13(1):155-169. doi: 10.1038/nprot.2017.128. Epub 2017 Dec 21.

Measuring signaling and RNA-Seq in the same cell links gene expression to dynamic patterns of NF-kappa B activation,

Lane K*, Van Valen D*, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW,   

Cell Systems.  doi: 10.1016/j.cels.2017.03.010 (April 26, 2017)

“Deep phenotypic mapping of bacterial cytoskeletal mutants reveals physiological robustness to cell size”,

H Shi, A Colavin, M Bigos, C Tropini†, RD Monds†, KC Huang†,

Current Biology 27 3419-3429 (2017).

“Homeostatic cell growth is accomplished mechanically through membrane tension inhibition of cell-wall synthesis”,

ER Rojas, KC Huang†, JA Theriot†,

Cell Systems 5 578-590 (2017).

“Thinking big: The tunability of bacterial cell size”,

S Cesar, KC Huang,

FEMS Microbiology Reviews 41 672-678 (2017).

“Sizing up the bacterial cell cycle”,

L Willis†, KC Huang†,

Nature Rev Micro 15 606-620 (2017).

“The Gut Microbiome: Connecting spatial organization to function”,

C Tropini*, K Earle*, KC Huang†, J Sonnenburg†,

Cell Host & Microbe 21 433-442 (2017).

“GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ directs septal cell-wall synthesis”,

X Yang, Z Lyu*, A Miguel*, R McQuillen, KC Huang†, J Xiao†,

Science 355 744-747 (2017). Featured in Dispatch in Current Biology.

“Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library,

T Ursell*, TK Lee*, D Shiomi, H Shi, C Tropini, RD Monds, A Colavin, G Billings, I Bhaya-Grossman, M Broxton, BE Huang, H Niki, KC Huang,

BMC Biology 15 17 (2017).

“Staying in touch while on the go”,

KC Huang,

Cell 168 15-17 (2017).

“Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing”,

F Yu, L Willis, RMW Chau, A Zambon, MA Horowitz, D Bhaya†, KC Huang†, SR Quake†,

BMC Biology 15 11 (2017).

“Strain Library Imaging Protocol: high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates”,

H Shi*, A Colavin*, TK Lee, KC Huang,

Nature Protocols 12 429-438 (2017).


Deep learning automates the quantitative analysis of individual cells in live-cell imaging experiments,

Van Valen DKudo TLane KMacklin DN, Quach N, DeFelice MMaayan ITanouchi Y, Ashley E, Covert MW,  

PLOS Computational Biology. November 4, 2016. doi: 10.1371/journal.pcbi.1005177.

© 2018 Allen Center at Stanford University