PUBLICATIONS

All students and postdocs in Huang lab are underlined below.

2024

Genome-scale resources in an infant gut symbiont reveal molecular determinants of colonization and host-microbe interactions
AL Shiver, J Sun, A Violette, R Culver, C Wynter, M Nieckarz, SP Mattiello, PK Sekhon, F Bottacini, L Friess, HK Carlson, D Wong, S Higginbottom, M Weglarz, W Wang, BD Knapp, E Guiberson, J Sanchez, P-H Huang, PA Garcia, CR Buie, B Good, B DeFelice, F Cava, J Scaria, J Sonnenberg, D Van Sinderen, AM Deutschbauer, KC Huang,
Cell, in press.

An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome
S Liu, C Ezran, MFZ Wang, Z Li, The Tabula Microcebus Consortium, JZ Long, I De Vlaminck, S Wang, C Kuo, J Epelbaum, J Terrien, MA Krasnow, JE Ferrell Jr.,
Nature Communications 15 2188 (2024).

Temporal profiling of Salmonella transcriptional dynamics during macrophage infection using a comprehensive reporter library
TH Nguyen, BW Wang, OR Diaz, M Ranjendram, JA McKenna, DSC Butler, K Hokamp, JCD Hinton, D Monack, KC Huang,
Nature Microbiol, in press.

A hot topic: how microbes adapt to temperature changes
KC Huang, BD Knapp,
Nature Microbiol, in press.

Complex state transitions of the bacterial cell division protein FtsZ
BD Knapp, H Shi, KC Huang,
Molec Biol of Cell, in press.

Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics
A Aranda-Díaz, L Willis, TH Nguyen, P-Y Ho, J Vila, T Thomsen, T Chavez, R Yan, FB Yu, N Neff, BC DeFelice, A Sanchez, S Estrela†, KC Huang,
Cell Systems, in press.

Metabolomic rearrangement as a basis for the intrinsic microbial response to temperature changes
BD Knapp, L Willis, C Gonzalez, H Vashistha, JJ Touma, M Tikhonov, J Ram, H Salman, JE Elias, KC Huang,
Nature Microbiol, in press.

Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics
S Tripathi, CGP Voogdt, SO Bassler, M Anderson, P-H Huang, N Sakenova, T Capraz, S Jain, A Koumoutsi, AM Bravo, V Trotter, M Zimmerman, J Sonnenburg, C Buie, A Typas, A Deutschbauer, AL Shiver, KC Huang,
Cell Reports 43 113517 (2024).

Randomly barcoded transposon mutant libraries for gut commensals I: strategies for efficient library construction
CGP Voogdt, S Tripathi, SO Bassler, M Anderson, SA McKeithen-Mead, ER Guiberson, A Koumoutsi, AM Bravo, C Buie, M Zimmerman, J Sonnenburg, A Typas, A Deutschbauer, AL Shiver, KC Huang,
Cell Reports 43 113519 (2024).

Resource competition predicts assembly of in vitro gut bacterial communities
P-Y Ho,T Nguyen, J Sanchez, B DeFelice, KC Huang
Nature Microbiol 9 1036-1048 (2024).

2023

Chemoproteomic identification of a dipeptidyl peptidase 4 (DPP4) homolog in Bacteroides thetaiotaomicron
LJ Keller, TH Nguyen, L Liu, B Hurysz, M Lakemeyer, M Guerra, D Gelsinger, R Chanin, N Ngo, KM Lum, F Faucher, P Ipock, MJ Niphakis, AS Bhatt, AJ O’Donoghue, KC Huang, M Bogyo,
Nature Chem Bio 19 1469-1479 (2023).

Physiological and regulatory convergence between osmotic and nutrient stress responses in microbes
A Brauer, H Shi, P Levin, KC Huang,
Current Opin Cell Biology 81 102170 (2023).

Modulation of antibiotic effects on microbial communities by resource competition
DP Newton, P-Y Ho, KC Huang,
Nature Communications 14 2398 (2023).

Human metabolome variation along the upper intestinal tract
J Folz, RN Culver, JM Morales, J Grembi, D Relman, KC Huang, D Shalon, O Fiehn,
Nature Metabolism 5 777-788 (2023).

Previously uncharacterized rectangular bacterial structures in the dolphin mouth
NK Dudek, JG Galaz-Montoya, H Shi, M Mayer, C Danita, A Celis, G-H Wu, B Behr, KC Huang, W Chiu, DA Relman,
Nature Communications 14 2098 (2023).

What is the key challenge in engineering microbiomes
O Venturelli, HH Wang, S Estrela, KC Huang, R Ledesma-Amaro, A Fedorec, CE Lawson, B Stecher, A Zarrinpar, C-J Guo, O Soyer,
Cell Systems 14 85-90 (2023).

A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota
R Dodge, E Jones, B Obadia, D Martinez, H Zhu, A Aranda-Díaz, M Voltolini, M Sepanski, KC Huang, J Carlson, A Spradling, W Ludington,
Nature Communications 14 1557 (2023).

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device
D Shalon, RN Culver, JA Grembi, J Folz, PV Treit, H Shi, FA Schober, L Dethlefsen, X Meng, E Yaffe, S Spencer, A Aranda-Díaz, AD Patterson, G Triadafilopoulos, SP Holmes, M Mann, O Fiehn, DA Relman, KC Huang,
Nature 617 581-591 (2023).

Short-term evolution of the gut microbiome
T Đapa, DPGH Wong, KS Vasquez, K Xavier, KC Huang, and BH Good,
Current Opin Microbiology 71 102258 (2023).

The impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro
AI Celis, DA Relman, KC Huang,
Cell Chemical Biology 30 110 (2023).

2022

Cellular memory of rapid growth is sensitive to nutrient depletion during starvation
S Cesar, J Sun, and KC Huang,
Frontiers in Microbiology 13 1016371 (2022).

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron
HA Arjes, J Sun, H Liu, T Nguyen, R Culver, AI Celis, SJ Walton, K Vasquez, FB Yu, K Xue, D Newton, R Zermeno, M Waglerz, A Deutschbauer, KC Huang, and A Shiver,
BMC Biology 20 1-17 (2022).

Multiple conserved states characterize the twisting landscape of the bacterial actin homolog MreB
BD Knapp, MD Ward, GR Bowman, H Shi, and KC Huang,
Comp Struct Biotech J 20 5838-5846 (2022).

Design, construction, and in vivo augmentation of a complex gut bacterial community
AG Cheng, P-Y Ho, A Aranda-Díaz, S Jain, F Yu, X Meng, M Wang, M Iakiviak, K Nakashima, A Zhao, P Murugkar, A Patil, K Atabakhsh, A Weakley, J Yan, A Brumbaugh, S Higginbottom, A Dimas, AL Shiver, A Deutschbauer, N Neff, JL Sonnenburg, KC Huang, and MA Fischbach,
Cell 185 3617-3636 (2022).

Feedback linking cell envelope stiffness, curvature, and synthesis enables robust rod-shaped bacterial growth
S al-Mosleh, A Gopinathan, C Santangelo, KC Huang, and ER Rojas,
PNAS 119 e2200728119 (2022).

Fatty acid synthesis knockdown promotes biofilm wrinkling and inhibits sporulation in Bacillus subtilis
HA Arjes, H Gui, R Porter, E Atolia, J Peters, C Gross, DB Kearns, and KC Huang,
mBio 13 e01388-22 (2022).

M-TUBE enables large-volume bacterial gene delivery using a high-throughput microfluidic electroporation platform
P-H Huang, S Chen, AL Shiver, RN Culver, KC Huang, and CR Buie,
PLoS Biology 20 e3001727 (2022).

Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas
P-Y Ho, B Good, and KC Huang
eLife 11 e75168 (2022).

The Tabula Sapiens: a multiple-organ, single-cell transcriptomic atlas of humans
The Tabula Sapiens Consortium,
Science 376(6594), p.eabl4896.

Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals
AI Celis, A Aranda-Díaz, R Culver, K Xue, D Relman, H Shi, and KC Huang
iScience 25 4 (2022).

The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut
EOY Wong, EJE Brownlie, KM Ng, S Kathirgamanathan, FB Yu, B Merrill, KC Huang, A Martin, C Tropini, and WW Navarre,
mBio 13 e02949-21 (2022).

Molecular hallmarks of heterochronic parabiosis at single cell resolution
R Pálovics, A Keller, N Schaum, W Tan, T Fehlmann, M Borja, J Webber, A McGeever, L Bonanno, The Tabula Muris Consortium, AO Pisco, J Karkanias, NF Neff, S Darmanis, SR Quake, and T Wyss-Coray,
Nature 603 309-314 (2022).

The effects of temperature on cellular physiology
BD Knapp, and KC Huang,
Ann Rev Biophysics 51 499-526 (2022).

Bacterial respiration during stationary phase induces intracellular damage that leads to delayed regrowth
S Cesar, L Willis, and KC Huang,
iScience 25 103765 (2022).

Physical properties of the bacterial outer membrane
J Sun, ST Rutherford, TJ Silhavy, and KC Huang,
Nat Rev Microbiol 20 236-248 (2022).

Stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota response to antibiotics
A Aranda-Díaz, KM Ng, T Thomsen, I Real-Ramírez, D Dahan, S Dittmar, CG Gonzalez, T Chavez, KS Vasquez, TH Nguyen, FB Yu, SK Higginbottom, NF Neff, JE Elias, JL Sonnenburg, and KC Huang,
Cell Host & Microbe 30 260-272 (2022).

2021

Bacterial filamentation drives colony chirality.
A Aranda-Díaz, CA Rodrigues, J Sun, A Grote, C Schreck, O Hallatschek, A Souslov, KC Huang, Wolfram Möbius,
mBio 12 e01542-21 (2021).

Morphological and transcriptional responses to CRISPRi knockdown of essential genes in Escherichia coli.
M Silvis, Rajendram M, Shi H, H Osadnik, A Gray, Cesar S, J Peters, CC Hearne, P Kumar, H Todor, Huang KC, C Gross,
mBio 12 e02561-21 (2021).

Hyperosmotic shock transiently accelerates constriction rate in Escherichia coli.
J Sun, Shi H, and Huang KC.
Frontiers in Microbiology 12 718600 (2021).

Toward point-of-care detection of Mycobacterium tuberculosis: A brighter solvatochromic probe detects Mycobacteria within minutes.
M Kamariza, SGL Keyser, A Utz, Knapp BD, G Ahn, CJ Cambier, A Pezacki, Huang KC, and CR Bertozzi.
JACS Au 1 1368-1379 (2021).

Quantifying rapid bacterial evolution and transmission within the mouse intestine.
Vasquez KS, Willis L, N Cira, KM Ng, MF Pedro, Aranda-Díaz A, Ranjendram M, FB Yu, SK Higginbottom, N Neff, G Sherlock, KB Xavier, S Quake, J Sonnenburg, BH Good, and Huang KC.
Cell Host & Microbe 29 1454-1468 (2021).

Variations of intracellular density during the cell cycle arise from tip-growth regulation in fission yeast.
Odermatt PD, T Miettinen, J Lemière, JH Kang, E Bostan, S Manalis, Huang KC and, Fred Chang.
eLife 10 e64901 (2021).

Starvation induces shrinkage of the bacterial cytoplasm.
Shi H, C Westfall, J Kao, Cesar S, M Sievert, J Moore, Huang KC, P Levin.
PNAS 118 e2104686118 (2021).

Entropy-driven translocation of disordered proteins through the Gram-positive bacterial cell wall.
D Halladin, FE Ortega, KM Ng, MJ Footer, N Mitic, S Malkov, A Gopinathan, Huang KC, and J Theriot.
Nature Microbiology 6 1055-1065 (2021).

Effects of fixation on bacterial cellular dimensions and integrity.
Zhu L, Rajendram M, and Huang KC.
iScience 24 102348 (2021).

Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.
Shiver AL, H Osadnik, JM Peters, RA Mooney, PI Wu, KK Henry, H Braberg, NJ Krogan, JC Hu, R Landick, Huang KC, CA Gross.
Molecular Cell 81 2201-2215 (2021).

Precise regulation of the relative rates of surface area and volume synthesis in bacterial cells growing in dynamic environments.
Shi H, Y Hu, Odermatt PD, CG Gonzalez, L Zhang, JE Elias, F Chang, and Huang KC.
Nature Communications 12 1975 (2021).

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments.
H Liu, Shiver AL, MN Price, HK Carlson, Y Chen, J Ray, CJ Petzold, P Turnbaugh, Huang KC, AP Arkin, AM Deutschbauer.
Cell Reports 34 108789 (2021).

Three-dimensional biofilm growth supports a mutualism involving matrix and nutrient sharing.
Arjes HA, Willis L, H Gui, Y Xiao, J Peters, C Gross, and Huang KC.
eLife 10 e64145 (2021).

2020

Straightening up for life in a biofilm.
Arjes HA, and Huang KC.
PNAS 117 31573-31574 (2020).

Environmental and physiological factors affecting high-throughput measurements of bacterial growth.
Atolia E, Cesar S, Arjes HA, Rajendram M, Shi H, Knapp BD, S Khare, Aranda-Díaz A, RE Lenski, and Huang KC.
mBio 11 e01378-20 1-19 (2020).

The inner membrane protein YhdP modulates the rate of anterograde phospholipid flow in Escherichia coli.
J Grimm, Shi H, W Wang, AM Mitchell, NS Wingreen, Huang KC, and TJ Silhavy.
PNAS 117 26907-26914 (2020).

SiCTeC: an inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging.
Knapp BD, Zhu L, and Huang KC.
PLoS Biology 18 e3000786 (2020).

Limits and Constraints on Mechanisms of Cell-Cycle Regulation Imposed by Cell Size-Homeostasis Measurements.
Willis L, Jonsson H, and Huang KC.
Cell Reports 32 (2020)

Ageing hallmarks exhibit organ-specific temporal signatures.
Schaum N, Lehallier B, Hahn O, Palovics R, Hosseinzadeh S, Lee SE, Sit R, Lee DP, Losada PM, Zardeneta ME, Fehlmann T, Webber J, McGeever A, Calcuttawala K, Zhang H, Berdnik D, Mathur V, Tan W, Zee A, Tan M, The Tabula Muris Consortium, Pisco A, Kerkanias J, Neff NF, Keller A, Darmanis S, Quake SR, Wyss-Coray T.
Nature 583 596-602 (2020)

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse.
The Tabula Muris Consortium.
Nature 583 590-595 (2020)

Bacterial evolution in high osmolarity environments.
Cesar S*, Anjur-Dietrich M*, Yu FB, Li E, Rojas E, Neff N, Cooper TF, and Huang KC.
mBio 11 e01191-20 (2020)
*Co-first authors

Colons or semi-colons: punctuating the regional variation of intestinal microbial–immune interactions.
Culver R, Spencer S, and Huang KC.
Nat Rev Gastroenterol Hepatol 17, 319-320 (2020)

Pictures of Tongues Sticking Out
Shi H, and Huang KC.
Trends in Endocrinology & Metabolism, 1519, (2020)

AimB is a small protein regulator of cell size and MreB assembly
Werner J, Shi H, Hsin J, Huang KC, Gitai Z, and Klein EA.
Biophysical Journal, 119 593-604 (2020)

Chiral twisting in a bacterial cytoskeletal polymer affects filament size and orientation
Shi H, Quint D, Grason G, Gopinathan A, and Huang KC.
Nature Communications, 11:1408, (2020)

Biosurfactant-mediated membrane depolarization maintains viability during oxygen depletion in Bacillus subtilis
Arjes H, Vo L, Dunn C, Willis L, DeRosa C, Fraser C, Kearns D, and Huang KC.
Current Biology, 30:6, (2020)

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance
Aranda-Diaz A, Obadia B, Dodge R, Thomsen T , Hallberg Z, Guvener Z, Ludington W, and Huang KC.
eLife, (2020)

Bellymount enables longitudinal, intravital imaging of abdominal organs and the gut microbiota in adult Drosophila
Koyama L, Aranda-Diaz A, Su T, Balachandra S, Martin J, Ludington W, Huang KC, and O’Brien L.
PLOS Biology, (2020)

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition
Olicera R, Ng K, Correia M, Cabral V, Shi H, Sonnenburg J, Huang KC, and Xavier K.
Nature Microbiology, 5, 630-641, (2020)

2019

The meal plan that hinders the gut’s recovery from antibiotics
Nature research highlights Cell Host and Microbe publication.

Making room in a crowd
Shi H and Huang KC.
Current Biology, 29, R630-632 (2019)

FtsZ-independent mechanism of division inhibition by the small molecule PC190723 in Escherichia coli
Khare S*, Hsin J*, Sorto N, Nepomuceno G, Shaw J, Shi H†, KC Huang†.
Adv Biosys, 1900021, (2019).
*Co-first authors †Co-corresponding authors

tRNA methylation is a global determinant of bacterial multi-drug resistance
Masuda I, Matsubara R, Christian T, Rojas ER, SS Yadavalli, M Goulian, KC Huang, Y-M Hou.
Cell Systems, 8, 302-314, (2019).

Differential modes of crosslinking establish spatially distinct regions of peptidoglycan in Caulobacter crescentus
Stankeviciute G, Miguel AV, Radkov A, Chou S, Huang KC, Eric A Klein.
Molecular Microbiology, 111, 995-1008, (2019).

Conservation of conformational dynamics across prokaryotic actins
Ng N, Shi H, Colavin A, Huang KC.
PLoS Comp Biol, 15, e1006683, (2019).

Cell geometry and leaflet bilayer asymmetry regulate domain formation in plasma membranes
Ali MZ, Huang KC, Wingreen NS, Mukhopadhyay R.
Physics Rev E, 99, 012401, (2019).

2018

When a Physicist Wanders Into Biology… : an interview with KC Huang
Huang KC.
BMC Biology, 16, 130, (2018).

Who’s Your DadA? d-Alanine Levels Regulate Bacterial Stiffness
Odermatt PD*, Arjes HA*, Chang F, Huang KC.
mBio, 9(5), e02127-18, (2018).
*Co-first authors

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris
The Tabula Muris Consortium.
Nature, 562, 367-372, (2018).

Translating the Physical Code of Life.
Knapp BD and Huang KC.
Cell, 174(2), 253-255. (2018).

A gut commensal-produced metabolite mediates colonization resistance to Salmonella infection
Jacobson A, Lam L, Rajendram M, Tamburini F, Honeycutt J, Pham T, Van Treuren W, Pruss K, Stabler SR, Lugo K, Bouley DM, Vilches-Moure JG, Smith M, Sonnenburg JL, Bhatt AS, Huang KC, Monack D.
Cell Host and Microbe, 24(2), 296-307, (2018).

Cutting the Gordian knot of the microbiota
Vasquez KS, Shiver AL, KC Huang.
Molecular Cell, 70, 765-767, (2018).

The outer membrane is an essential load-bearing element in Gram-negative bacteria
Rojas ER, Billings G, Odermatt P, Auer GK, Zhu L, Miguel A, Chang F, Weibel DB, Theriot JA, Huang KC.
Nature, 559, 617–621, (2018).

How to build a bacterial cell: MreB as a Foreman of E. coli Construction
Shi H*, Bratton B*, Gitai Z†, Huang KC†.
Cell, 172, 1294-1305, (2018).
*Co-first authors †Co-corresponding authors

Transient osmotic perturbation causes long-term alteration to the gut microbiota
Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM, Elias JE, Bhatt AS, Huang KC, Sonnenburg JL.
Cell, 173(7), 1742-1754, (2018).

Lateral interactions between protofilaments of the bacterial tubulin homolog FtsZ are essential for cell division
Guan F, Yu J, Yu J, Liu Y, Li Y, Feng X, Huang KC, Chang Z and Ye S.
Elife, 7, e35578. (2018).

Cutting the Gordian Knot of the microbiota
Vasquez K,Shiver AL, Huang KC.
Molecular Cell, 70(5), 765-767, (2018).

Regulation of bacterial growth by turgor pressure
Rojas ER, Huang KC.
Current Opinion in Microbiology, 42, 62-70, (2018).

RodZ modulates geometric localization of the bacterial actin MreB to regulate cell shape
Colavin A,Shi H Huang KC.
Nature Communications, 9(1), 1280, (2018).

The marine mammal microbiome yields a novel antibiotic with potent activity against Clostridium difficile
Ochoa JL, Sanchez L, Koo B-M, Doherty J, Rajendram M, Huang KC, Gross CA, Linington RG.
ACS Infectious Diseases, 4, 59-67, (2018).

2017

Plasmon actuated nano-assembled microshells: a multiscale system for optically controlled cargo encapsulation and release
Quint MT, Sarang S, Quint DA, Subramaniam AB, Huang KC, Gopinathan A, Hirst LS, Ghosh S.

Scientific Reports, 7, 17788, (2017).

Membrane tension and depolarization inhibit cell wall synthesis to ensure cell envelope homeostasis in Gram-positive bacteria
Rojas ER, Huang KC†, Theriot JA†.
Cell Systems, 5, 578-590 (2017).

Dash-and-recruit mechanism drives membrane curvature recognition by the small bacterial protein SpoVM
Kim EY, Tyndall ER, Huang KC, Tian F, Ramamurthi KS.
Cell Systems, (2017).

Marine Mammal Microbiota Yields Novel Antibiotic with Potent Activity Against Clostridium difficile
Ochoa JL, Sanchez LM, Koo BM, Doherty JS, Rajendram M, Huang KC, Gross CA, Linington RG.
ACS Infectious Diseases, (2017).

Deep Phenotypic Mapping of Bacterial Cytoskeletal Mutants Reveals Physiological Robustness to Cell Size
Shi H, Colavin A, Bigos M, Tropini C, Monds RD†, Huang KC†.
Current Biology, 27:1-1, (2017).
†Co-corresponding authors

Sizing up the bacterial cell cycle
Willis L, Huang KC.
Nature Reviews Microbiology 15(10):606-20, (2017).

Liquid Crystal Mediated Nano-assembled Gold Micro-shells
Quint M, Sarang S, Quint D, Huang KC, Gopinathan A, Hirst L, Ghosh S.
Bulletin of the American Physical Society, (2017).

Cell Size: Fat Makes Cells Fat
Willis L, & Huang KC.
Current Biology, 27(12), R592-R594, (2017).

The Gut Microbiome: Connecting Spatial Organization to Function
Tropini C*, Earle KA*, Huang KC, Sonnenburg JL.
Cell Host & Microbe, 21(4), 433-442, (2017).
*Co-first authors

Coupling between protein stability and catalytic activity determines pathogenicity of G6PD mutations
Cunningham AD, Colavin A, Huang KC, Mochly-Rosen Daria.
Cell Reports, 18, 2592-2599, (2017).

GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ directs septal cell-wall synthesis
Yang X, Lyu Z*, Miguel A*, McQuillen R, Huang KC†, Xiao J†.
Science, 355, 744-747, (2017).
*Equal Contributors †Co-corresponding authors

Emergent Phototactic Responses of Cyanobacteria under Complex Light Regimes
RMW Chau, D Bhaya†, Huang KC†.
mBio, 8 e02330-16, (2017).
†Co-corresponding authors

Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library
Ursell T*, Lee*, Shiomi D, Shi H, Tropini C, Monds RD, Colavin A, Billings G, Bhaya-Grossman I, Broxton M, Huang BE, Niki H, KC Huang.
BMC Biology 15 17 (2017).
*Co-first authors

Staying in touch while on the go
Huang KC
Cell, 168, 15-17, (2017).

Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing
Yu F, Willis L, Chau RM, Zambon A, Horowitz MA, Bhaya D†, Huang KC†, Quake SR†.
BMC Biology 15 11 (2017).
†Co-corresponding authors

Strain Library Imaging Protocol: high-throughput, automated single-cell microscopy for large bacterial collections arrayed on multiwell plates.
Shi H*, Colavin A*, Lee TK, Huang KC.
Nature Protocols 12 429-438 (2017).
*Co-first authors

Full color palette of fluorescent D-amino acids for in situ labeling of bacterial cell walls Authors
Hsu YP, Rittichier J, Kuru E, Yablonowski J, Pasciak E, Tekkam S, Hall E, Murphy B, Lee TK, Garner EC, Huang KC.
Chemical Science. 2017;8(9):6313-21.

A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis
Bartlett TM, Bratton BP, Duvshani A, Miguel A, Sheng Y, Martin NR, Nguyen JP, Persat A, Desmarais SM, VanNieuwenhze MS, Huang KC, Zhu J, Shaevitz JW, Gitai Z.
Cell doi: 10.1016/j.cell.2016.12.019 168(1):172-85. Epub 2017 Jan 12.

2016

Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche
Willis L, Refahia Y, Wightmana R, Landreina B, Telesa J, Huang KC, Meyerowitz EM, Jönssona H.
Proceedings of the National Academy of Sciences 113.51 doi: 10.1073/pnas.1616768113 Epub 2016 Nov 3.

Single-molecule imaging reveals modulation of cell wall synthesis dynamics in live bacterial cells.
Lee TK, Meng K, Shi H, Huang KC.
Nature Communications 2016 Sep 8. doi: 10.1038/ncomms13170. Epub 2016 Oct 24.

FtsZ-Dependent Elongation of a Coccoid Bacterium.
Pereira AR, Hsin J, Król E, Tavares AC, Flores P, Hoiczyk E, Ng N, Dajkovic A, Brun YV, VanNieuwenhze MS, Roemer T, Carballido-Lopez R, Scheffers D, Huang KC, Pinho, MG.
MBio 2016 Sep 6;7(5). doi: 10.1128/mBio.00908-16.

Mechanical Genomics Identifies Diverse Modulators of Bacterial Cell Stiffness.
Auer GK, Lee TK, Rajendram M, Cesar S, Miguel A, Huang KC†, Weibel DB†.
Cell Syst. 2(6):402-11. doi: 10.1016/j.cels.2016.05.006. Epub 2016 Jun 16.
†Co-corresponding authors

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria.
Peters JM*, Colavin A*, Shi H*, Czarny TL, Larson MH, Wong S, Hawkins JS , Lu CHS, Koo B-M , Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS†, Huang KC†, Gross CA†.
Cell. 2016 165 1-14 (2016).
*Co-first authors †Co-corresponding authors

Disruption of lipid homeostasis in the Gram-negative cell envelope activates a novel cell death pathway.
Sutterlin HA*, Shi H*, May KL, Miguel A, Khare S, Huang KC†, Silhavy TJ†.
Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):E1565-74. doi: 10.1073/pnas.1601375113. Epub 2016 Feb 29.
*Co-first authors †Co-corresponding authors

2015

The effect of microbial colonization on the host proteome varies by gastrointestinal location.
Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL†, Huang KC†, Elias JE†.
ISME J. 2016 May;10(5):1170-81. doi: 10.1038/ismej.2015.187. Epub 2015 Nov 17.
†Co-corresponding authors

Cytoskeletal Network Morphology Regulates Intracellular Transport Dynamics.
Ando D, Korabel N, Huang KC†, Gopinathan A†.
Biophys J. 2015 Oct 20;109(8):1574-82. doi: 10.1016/j.bpj.2015.08.034.
†Co-corresponding authors

Physics of Intracellular Organization in Bacteria.
Wingreen NS, Huang KC.
Annu Rev Microbiol. 2015;69:361-79. doi: 10.1146/annurev-micro-091014-104313. Review.

High-throughput, Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography.
Desmarais SM, Tropini C, Miguel A, Cava F, Monds RD, de Pedro MA, Huang KC.
J Biol Chem. 2015 Dec 25;290(52):31090-100. doi: 10.1074/jbc.M115.661660. Epub 2015 Oct 14.

Quantitative Imaging of Gut Microbiota Spatial Organization.
Earle KA*, Billings G*, Sigal M, Lichtman JS, Hansson GC, Elias JE, Amieva MR, Huang KC, Sonnenburg JL.
Cell Host Microbe. 2015 Oct 14;18(4):478-88. doi: 10.1016/j.chom.2015.09.002. Epub 2015 Oct 1.
*Co-first authors

Applications of imaging for bacterial systems biology.
Huang KC.
Curr Opin Microbiol. 2015 Oct;27:114-20. doi: 10.1016/j.mib.2015.08.003. Epub 2015 Sep 8. Review.

Nanoengineering: Super symmetry in cell division.
Huang KC.
Nat Nanotechnol. 2015 Aug;10(8):655-6. doi: 10.1038/nnano.2015.148.

How Does the Xenopus laevis Embryonic Cell Cycle Avoid Spatial Chaos?
Gelens L, Huang KC, Ferrell JE Jr.
Cell Rep. 2015 Aug 4;12(5):892-900. doi: 10.1016/j.celrep.2015.06.070. Epub 2015 Jul 23.

The bacterial tubulin FtsZ requires its intrinsically disordered linker to direct robust cell wall construction.
Sundararajan K, Miguel A, Desmarais SM, Meier EL, Huang KC, Goley ED.
Nat Commun. 2015 Jun 23;6:7281. doi: 10.1038/ncomms8281.

Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division.
Gray AN, Egan AJ, Van’t Veer IL, Verheul J, Colavin A, Koumoutsi A, Biboy J, Altelaar AF, Damen MJ, Huang KC, Simorre JP, Breukink E, den Blaauwen T, Typas A, Gross CA, Vollmer W.
Elife. 2015 May 7;4. doi: 10.7554/eLife.07118.

Bacterial division. Mechanical crack propagation drives millisecond daughter cell separation in Staphylococcus aureus.
Zhou X*, Halladin DK*, Rojas ER*, Koslover EF, Lee TK, Huang KC, Theriot JA.
Science. 2015 May 1;348(6234):574-8. doi: 10.1126/science.aaa1511.
*Co-first authors

Maintenance of motility bias during cyanobacterial phototaxis.
Chau RM, Ursell T, Wang S, Huang KC†, Bhaya D†.
Biophys J. 2015 Apr 7;108(7):1623-32. doi: 10.1016/j.bpj.2015.01.042.
†Co-corresponding authors

Structural basis for the geometry-driven localization of a small protein.
Gill RL Jr*, Castaing JP*, Hsin J*, Tan IS, Wang X, Huang KC†, Tian F†, Ramamurthi KS†.
Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):E1908-15. doi: 10.1073/pnas.1423868112. Epub 2015 Mar 30.
*Co-first authors †Co-corresponding authors

Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species.
Miguel A, Hsin J, Liu T, Tang G, Altman RB, Huang KC.
PLoS Comput Biol. 2015 Mar;11(3):e1004117. doi: 10.1371/journal.pcbi.1004117.

2014

Systematic perturbation of cytoskeletal function reveals a linear scaling relationship between cell geometry and fitness.
Monds RD, Lee TK, Colavin A, Ursell T, Quan S, Cooper TF, Huang KC.
Cell Rep. 2014 Nov 20;9(4):1528-37. doi: 10.1016/j.celrep.2014.10.040. Epub 2014 Nov 13.

Principles of bacterial cell-size determination revealed by cell-wall synthesis perturbations.
Tropini C, Lee TK, Hsin J, Desmarais SM, Ursell T, Monds RD†, Huang KC†.
Cell Rep. 2014 Nov 20;9(4):1520-7. doi: 10.1016/j.celrep.2014.10.027. Epub 2014 Nov 6.
†Co-corresponding authors

The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokinesis.
Zhou Z, Munteanu EL, He J, Ursell T, Bathe M, Huang KC, Chang F.
Mol Biol Cell. 2015 Jan 1;26(1):78-90. doi: 10.1091/mbc.E14-10-1441. Epub 2014 Oct 29.

How and why cells grow as rods.
Chang F†, Huang KC†.
BMC Biol. 2014 Aug 2;12:54. doi: 10.1186/s12915-014-0054-8. Review.
†Co-corresponding authors

De novo morphogenesis in L-forms via geometric control of cell growth.
Billings G, Ouzounov N, Ursell T, Desmarais SM, Shaevitz J, Gitai Z†, Huang KC†.
Mol Microbiol. 2014 Sep;93(5):883-96. doi: 10.1111/mmi.12703. Epub 2014 Jul 23.
†Co-corresponding authors

Response of Escherichia coli growth rate to osmotic shock.
Rojas ER, Theriot JA†, Huang KC†.
Proc Natl Acad Sci U S A. 2014 May 27;111(21):7807-12. doi: 10.1073/pnas.1402591111. Epub 2014 May 12.
†Co-corresponding authors

Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.
Ursell TS, Nguyen J, Monds RD, Colavin A, Billings G, Ouzounov N, Gitai Z, Shaevitz JW, Huang KC.
Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):E1025-34. doi: 10.1073/pnas.1317174111. Epub 2014 Feb 18.

Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB.
Colavin A, Hsin J, Huang KC.
Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3585-90. doi: 10.1073/pnas.1317061111. Epub 2014 Feb 18.

A dynamically assembled cell wall synthesis machinery buffers cell growth.
Lee TK, Tropini C, Hsin J, Desmarais SM, Ursell TS, Gong E, Gitai Z, Monds RD†, Huang KC†.
Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4554-9. doi: 10.1073/pnas.1313826111. Epub 2014 Feb 18.
†Co-corresponding authors

Isolation and preparation of bacterial cell walls for compositional analysis by ultra performance liquid chromatography.
Desmarais SM, Cava F, de Pedro MA, Huang KC.
J Vis Exp. 2014 Jan 15;(83):e51183. doi: 10.3791/51183.

2013

Motility enhancement through surface modification is sufficient for cyanobacterial community organization during phototaxis.
Ursell T*, Chau RM*, Wisen S*, Bhaya D†, Huang KC†.
PLoS Comput Biol. 2013;9(9):e1003205. doi: 10.1371/journal.pcbi.1003205. Epub 2013 Sep 5.
*Co-first authors †Co-corresponding authors

The role of hydrolases in bacterial cell-wall growth.
Lee TK, Huang KC.
Curr Opin Microbiol. 2013 Dec;16(6):760-6. doi: 10.1016/j.mib.2013.08.005. Epub 2013 Sep 12. Review.

FtsZ protofilaments use a hinge-opening mechanism for constrictive force generation.
Li Y, Hsin J*, Zhao L*, Cheng Y*, Shang W, Huang KC, Wang HW, Ye S.
Science. 2013 Jul 26;341(6144):392-5. doi: 10.1126/science.1239248.
*Co-first authors

Optimal dynamics for quality control in spatially distributed mitochondrial networks.
Patel PK, Shirihai O, Huang KC.
PLoS Comput Biol. 2013;9(7):e1003108. doi: 10.1371/journal.pcbi.1003108. Epub 2013 Jul 11.

Dimer dynamics and filament organization of the bacterial cell division protein FtsA.
Hsin J, Fu R, Huang KC.
J Mol Biol. 2013 Nov 15;425(22):4415-26. doi: 10.1016/j.jmb.2013.07.016. Epub 2013 Jul 17.

Design of High-Specificity Nanocarriers by Exploiting Non-Equilibrium Effects in Cancer Cell Targeting.
Tsekouras K, Goncharenko I, Colvin ME, Huang KC†, Gopinathan A†.
PLoS One. 2013 Jun 26;8(6):e65623. doi: 10.1371/journal.pone.0065623. Print 2013.
†Co-corresponding authors

Biological consequences and advantages of asymmetric bacterial growth.
Kysela DT, Brown PJ, Huang KC, Brun YV.
Annu Rev Microbiol. 2013;67:417-35. doi: 10.1146/annurev-micro-092412-155622. Epub 2013 Jun 26. Review.

Mechanical consequences of cell-wall turnover in the elongation of a Gram-positive bacterium.
Misra G, Rojas ER, Gopinathan A, Huang KC.
Biophys J. 2013 Jun 4;104(11):2342-52. doi: 10.1016/j.bpj.2013.04.047.

Peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly.
Desmarais SM, De Pedro MA, Cava F†, Huang KC†.
Mol Microbiol. 2013 Jul;89(1):1-13. doi: 10.1111/mmi.12266. Epub 2013 Jun 3. Review.
†Co-corresponding authors

2012

The molecular origins of chiral growth in walled cells.
Huang KC†, Ehrhardt DW, Shaevitz JW†.
Curr Opin Microbiol. 2012 Dec;15(6):707-14. doi: 10.1016/j.mib.2012.11.002. Epub 2012 Nov 26. Review.
†Co-corresponding authors

Analysis of surface protein expression reveals the growth pattern of the gram-negative outer membrane.
Ursell TS*, Trepagnier EH*, Huang KC†, Theriot JA†.
PLoS Comput Biol. 2012;8(9):e1002680. doi: 10.1371/journal.pcbi.1002680. Epub 2012 Sep 27.
*Co-first authors †Co-corresponding authors

Physical constraints on the establishment of intracellular spatial gradients in bacteria.
Tropini C, Rabbani N, Huang KC.
BMC Biophys. 2012 Aug 29;5:17. doi: 10.1186/2046-1682-5-17.

Interplay between the localization and kinetics of phosphorylation in flagellar pole development of the bacterium Caulobacter crescentus.
Tropini C, Huang KC.
PLoS Comput Biol. 2012;8(8):e1002602. doi: 10.1371/journal.pcbi.1002602. Epub 2012 Aug 2.

Posttranslational acetylation of a-tubulin constrains protofilament number in native microtubules.
Cueva JG, Hsin J, Huang KC, Goodman MB.
Curr Biol. 2012 Jun 19;22(12):1066-74. doi: 10.1016/j.cub.2012.05.012. Epub 2012 May 31.

Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations
Hsin J, Gopinathan A, Huang KC. Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9432-7. doi: 10.1073/pnas.1120761109. Epub 2012 May 30.

Measuring the stiffness of bacterial cells from growth rates in hydrogels of tunable elasticity.
Tuson HH*, Auer GK*, Renner LD, Hasebe M, Tropini C, Salick M, Crone WC, Gopinathan A, Huang KC†, Weibel DB†.
Mol Microbiol. 2012 Jun;84(5):874-91. doi: 10.1111/j.1365-2958.2012.08063.x. Epub 2012 May 2.
*Co-first authors †Co-corresponding authors

Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.
Wang S, Furchtgott L, Huang KC†, Shaevitz JW†.
Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):E595-604. doi: 10.1073/pnas.1117132109. Epub 2012 Feb 17.
†Co-corresponding authors

2011

Resolution limits of optical microscopy and the mind.
Ursell TS and Huang, KC.
Biomed Comp Rev 7 27 (2011).

The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.
van Teeffelen S, Wang S, Furchtgott L, Huang KC, Wingreen NS, Shaevitz JW, Gitai Z.
Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15822-7. doi: 10.1073/pnas.1108999108. Epub 2011 Sep 8.

Conformational changes, diffusion and collective behavior in monomeric kinesin-based motility.
Huang KC, Vega C, Gopinathan A.
J Phys Condens Matter. 2011 Sep 21;23(37):374106. doi: 10.1088/0953-8984/23/37/374106. Epub 2011 Aug 23.

Does the potential for chaos constrain the embryonic cell-cycle oscillator?
McIsaac RS*, Huang KC*, Sengupta A, Wingreen NS.
PLoS Comput Biol. 2011 Jul;7(7):e1002109. doi: 10.1371/journal.pcbi.1002109. Epub 2011 Jul 14.
*Co-first authors

Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria.
Daly KE, Huang KC, Wingreen NS, Mukhopadhyay R.
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Apr;83(4 Pt 1):041922. Epub 2011 Apr 25.

Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria.
Furchtgott L, Wingreen NS, Huang KC.
Mol Microbiol. 2011 Jul;81(2):340-53. doi: 10.1111/j.1365-2958.2011.07616.x. Epub 2011 Apr 18.

Bilayer-mediated clustering and functional interaction of MscL channels.
Grage SL, Keleshian AM, Turdzeladze T, Battle AR, Tay WC, May RP, Holt SA, Contera SA, Haertlein M, Moulin M, Pal P, Rohde PR, Forsyth VT, Watts A, Huang KC†, Ulrich AS,† Martinac B†.
Biophys J. 2011 Mar 2;100(5):1252-60. doi: 10.1016/j.bpj.2011.01.023.
†Co-corresponding authors

Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium
Chen YE*, Tropini C*, Huang KC†, Laub MT†.
Proc Nat Acad Sci USA108 1052-1057 (2011). Selected for Feb 1, 2011 issue of Virtual Journal of Biological Physics Research.
*Co-first authors †Co-corresponding authors

2010

Dynamic SpoIIIE assembly mediates septal membrane fission during Bacillus suptilis sporulation.
Fleming TC, Shin JY, Lee SH, Becker E, Huang KC, Bustamante C, Pogliano K.
Genes Dev. 2010 Jun 1;24(11):1160-72. doi: 10.1101/gad.1925210.

Macromolecules that prefer their membranes curvy.
Huang KC, Ramamurthi KS.
Mol Microbiol. 2010 May;76(4):822-32. doi: 10.1111/j.1365-2958.2010.07168.x. Epub 2010 Apr 25. Review.

2008

Cell shape and cell-wall organization in Gram-negative bacteria.
Huang KC, Mukhopadhyay R, Wen B, Gitai Z, Wingreen NS.
Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19282-7. doi: 10.1073/pnas.0805309105. Epub 2008 Dec 2.

Lipid localization in bacterial cells through curvature-mediated microphase separation.
Mukhopadhyay R*, Huang KC*, Wingreen NS.
Biophys J. 2008 Aug;95(3):1034-49. doi: 10.1529/biophysj.107.126920. Epub 2008 Apr 4.
*Co-first authors

The Min system as a general cell geometry detection mechanism: branch lengths in Y-shaped Escherichia coli cells affect Min oscillation patterns and division dynamics.
Varma A, Huang KC, Young KD.
J Bacteriol. 2008 Mar;190(6):2106-17. doi: 10.1128/JB.00720-07. Epub 2008 Jan 4.

2007

Cooperative gating and spatial organization of membrane proteins through elastic interactions.
Ursell T, Huang KC, Peterson E, Phillips R.
PLoS Comput Biol. 2007 May;3(5):e81.

Control of melting using nanoscale coatings
Huang KC, Wang T, and Joannopoulos JD.
Proceedings of The Minerals, Metals, and Materials Society (2007).

2006

A curvature-mediated mechanism for localization of lipids to bacterial poles.
Huang KC, Mukhopadhyay R, Wingreen NS.
PLoS Comput Biol. 2006 Nov 10;2(11):e151. Epub 2006 Oct 4.

2005

Nanoscale properties of melting at the surface of semiconductors
KC Huang, Wang T, and Joannopoulos JD.
Phys. Rev. B72 195314 (2005). Selected for November 21, 2005 issue of Virtual Journal of Nanoscale Science & Technology. 61.

Photonic Band-Gaps and Localization in the Thue-Morse Structures
X Jiang, Y Zhang, S Feng, KC Huang, Y Yi, and JD Joannopoulos.
Appl. Phys. Lett. 86 201110 (2005). Selected for May 23, 2005 issue of Virtual Journal of Nanoscale Science & Technology.

Superheating and induced melting at semiconductor interfaces.
Huang KC, Wang T, Joannopoulos JD.
Phys Rev Lett. 2005 May 6;94(17):175702. Epub 2005 May 3.

2004

Negative effective permeability in polaritonic photonic crystals
KC Huang, ML Povinelli, and JD Joannopoulos, Appl. Phys. Lett.85543 (2004). Selected for August 9, 2004 issue of Virtual Journal of Nanoscale Science & Technology

Min-protein oscillations in round bacteria.
Huang KC, Wingreen NS.
Phys Biol. 2004 Dec;1(3-4):229-35.

The nature of lossy Bloch states in polaritonic photonic crystals.
Huang KC, Lidorikis E, Jiang S, Joannopoulos JD, Nelson KA, Bienstman P, Fan S.
Phys Rev B. 2004 Jun 7; 69:195111. Epub 2004 Jun 7.

Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.
Kulkarni RV, Huang KC, Kloster M, Wingreen NS.
Phys Rev Lett. 2004 Nov 26;93(22):228103. Epub 2004 Nov 23.

2003

Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.
Huang KC, Meir Y, Wingreen NS.
Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12724-8. Epub 2003 Oct 20.

Phonon-polariton excitations in photonic crystals.
Huang KC, Bienstman P, Joannopoulos JD, Nelson KA, Fan S.
Phys Rev B. 2003 Sept 8; 68:1075209. Epub 2003 Sept 8.

Field expulsion and reconfiguration in polaritonic photonic crystals.
Huang KC, Bienstman P, Joannopoulos JD, Nelson KA, Fan S.
Phys Rev Lett. 2003 May 16;90(19):196402. Epub 2003 May 13. Erratum in: Phys Rev Lett. 2004 Apr 23;92(16):169901.

2000

Comment on “Quantum Monte Carlo study of the dipole moment of CO” - J. Chem. Phys. 110, 11700 (1999)
Huang KC, Needs RJ, Rajagopal G.
J. Chem. Phys. 112, 4419 (2000).