Publications

Yadav, Aman; Birkby, Arlin; Armstrong, Noah; Arnob, Assame; Chou, Ming-Hsun; Fernandez, Alma; Verhoef, Aart; Yi, Zhenhuan; Gulati, Siddhant; Kotnis, Siddhi; Sun, Qing; Kao, Katy C.; Wu, Hung-Jen*. Evaluating Limits of Machine Learning-Assisted Raman Spectroscopy in Classification of Biological Samples. ACS Omega. July 30, 2026. doi.org/10.1021/acsomega.6c06456. 

Khoi-Nguyen Nguyen, Leena Sao, Kevin Kyllo, Danitza Hernandez#, Samantha Salomon#, Kalp Shah#, Dahyun Oh*, Katy C. Kao*. Anti-biofilm Activity of PDMS/TiO2 Against Candida glabrata Through Inhibited Hydrophobic Recovery. ACS Omega. 2024. doi:10.1021/acsomega.4c07869. 

Mohammed Saad Faizan Bangi, Katy Kao, Joseph Sang-Il Kwon*. Physics-informed neural networks for hybrid modeling of lab-scale batch fermentation for β-carotene production using Saccharomyces cerevisiae. Chemical Engineering Research and Design. 2022. doi:10.1016/j.cherd.2022.01.041.

Jibran Khan, Adam M. Guss, Katy C. Kao*. Enhancing transcription in Escherichia coli and Pseudomonas putida using bacteriophage lambda anti-terminator protein Q. Biotech Letters. 2021. https://doi.org/10.1007/s10529-021-03206-x. 

Pei-En Weng, Alexander Gooyandeh#, Muhammad Tariq, Tianyu Li, Avinash Godara, Jocelyn Valenzuela#, Steven Mancini, Samuel Ming Tuk Yeung, Ruth Sosa, David R. Wagner, Rohan Dhall, Nicole Adelstein, Katy Kao*, Dahyun Oh*. Microbe-Assisted Nanocomposite Anodes for Aqueous Li-Ion Batteries. ACS Applied Materials & Interfaces. 2021. https://doi.org/10.1021/acsami.1c07309. 

Avinash Godara and Katy C. Kao*. Adaptive laboratory evolution of β-caryophyllene producing Saccharomyces cerevisiae. Microbial Cell Factories, 2021. 20(1), 106–113. https://doi.org/10.1186/s12934-021-01598-z.

Man Li, Zhi-Hua Liu Liu, Naijia Hao, Michelle L. Olson, Qiang Li, Samarthya Bhagia, Katy Kao, Arthur Jonas Ragauskas, Shangxian Xie, Joshua S Yuan*. Synergistic Improvement of Carbohydrate and Lignin Processability by Biomimicking Biomass Processing. Frontiers in Energy Research. 2021. 8, 1318. https://doi.org/10.3389/fenrg.2020.00194. 

Avinash Godara and Katy C. Kao*. Adaptive laboratory evolution for growth coupled microbial production. World Journal of Microbiology and Biotechnology. 2020 Oct 21;36(11):447–10.

Mian Huang, Jibran Khan, Manpreet Kaur, Julian Daniel Torres Vanega#, Orlando Andres Aguilar Patiño#, Anand K. Ramasubramanian, Katy C. Kao*.  CgSTE11 mediates cross tolerance to multiple environmental stressors in Candida glabrata.  Scientific Reports.  2019. 9, 17036. doi:10.1038/s41598-019-53593-5.

Avinash Godara, Maria Alejandra Gomez Rodriguez#, Joshua D. Weatherston, George L. Peabody V, Hung-Jen Wu, Katy C. Kao*.  Beneficial mutations for carotenoids production identified from laboratory-evolved Saccharomyces cerevisiae.  J Industrial Microbiol Biotechnol. 2019 Oct 8. doi: 10.1007/s10295-019-02241-y.  

Guo Y, Xie S, Yuan JS, Kao KC*.  Improved Carotenoids Production with Seawater by Engineered Saccharomyces cerevisiae.  Fermentation.  2019.  

Liu, Zhi-Hua; Hao, Naijia; Shinde, Somnath; Olson, Michelle; Bhagia, Samarthya ; Dunlap, John; Kao, Katy; Kang, Xiaofeng; Ragauskas, Arthur; Yuan*, Joshua.  Co-design of Combinatorial Organosolv Pretreatment (COP) and Lignin Nanoparticles (LNPs) in Biorefineries.  ACS Sustainable Chemistry and Engineering.  2019, 7, 2, 2634-2647.

Huang M, Kao KC*.  Identifying novel genetic determinants for oxidative stress tolerance in Candida glabrata via adaptive laboratory evolution.  Yeast.  August 2018. 

Olson ML, Jayaraman A*, Kao KC*.  Relative abundance of Candida albicans and Candida glabrata in in vitro co-culture biofilms impacts biofilm structure and formation.  Appl Environ Microbiol.  April, 2018.    

Peabody GL V, Li H, Kao KC*. Sexual recombination and increased mutation rate expedite evolution of Escherichia coli in varied fitness landscapes. Nature Communications. 2017;8(1):1255. doi:10.1038/s41467-017-02323-4.

Liu Z-H, Olson ML, Shinde S, et al. Synergistic maximization of the carbohydrate output and lignin processability by combinatorial pretreatment. Green Chem. 2017;19(20):4939-4955. doi:10.1039/C7GC02057K.

Guo Y, Winkler J, Kao KC*. Insights on Osmotic Tolerance Mechanisms in Escherichia coli Gained from an rpoC Mutation. Bioengineering. 2017;4(3):61–19. doi:10.3390/bioengineering4030061.

Peabody G, Winkler J, Fountain W#, Castro DA#, Leiva-Aravena E#, Kao KC*. Experimental demonstration of the benefit of a recombination-proficient Escherichia coli system for Adaptive Laboratory Evolution. Appl Environ Microbiol. 2016;82(22):AEM.01850–16–6747. doi:10.1128/AEM.01850-16.

M. Carolina Ordonez, Jonathan P. Raftery, Tejasvi Jaladi, Xinhe Chen#, Katy Kao, M. Nazmul Karim*. Modelling of batch kinetics of aerobic carotenoid production using Saccharomyces cerevisiae.  Biochemical Eng Journal.  2016.  226–236.

Huang M, Peabody G, Kao KC*. Tolerance of Microbial Biocatalysts to Feedstocks, Products, and Environmental Conditions. In: Metabolic Engineering for Bioprocess Commercialization. Cham: Springer; 2016:73-100. doi:10.1007/978-3-319-41966-4_5.

Olson ML, Johnson J#, Carswell WF, Reyes LH, Senger RS, Kao KC*. Characterization of an evolved carotenoids hyper-producer of Saccharomyces cerevisiae through bioreactor parameter optimization and Raman spectroscopy. J Ind Microbiol Biotechnol. July 2016. doi:10.1007/s10295-016-1808-9. 

Peabody G, Kao KC*.  “Recent progress in bio-butanol tolerance in microbial systems with an emphasis on Clostridium.”  FEMS Microbiology Letters.  2016.  

Cheng C, Almario MP, Kao KC*.  “Generation of recombinant yeasts for tolerance to inhibitors present in lignocellulosic hydrolysates.”  Biotechnology Letters.  2015.

Shangxian Xie, Xing Qin, Yanbing Cheng, Dhrubojyoti Laskar, Weichuan Qiao, Su Sun, Luis H. Reyes, Xin Wang, Susie Y. Dai, Scott E. Sattler,, Katy Kao, Bin Yang, Xiaoyu Zhang, and Joshua S. Yuan*.  “Simultaneous Conversion of All Cell Wall Components by Oleaginous Fungus without Chemi-physical Pretreatment.”  Green Chemistry.  2015. doi:10.1039/C4GC01529K   

Cheng C, & Kao* KC. “How to survive being hot and inebriated.” Science 346, 35–36 (2014).

Winkler, JD & Kao* KC. “Recent Advances in the Evolutionary Engineering of Industrial Biocatalysts.” Genomics. (2014). doi:10.1016/j.ygeno.2014.09.006

Peabody GL V, Winkler J & Kao* KC. “Tools for developing tolerance to toxic chemicals in microbial systems and perspectives on moving the field forward and into the industrial setting.” Current Opinion in Chemical Engineering 6, 9–17 (2014).

Winkler J, Garcia C#, Olson M, Callaway E#, Kao KC*.  "Evolved Escherichia coli osmotolerant mutants frequently exhibit defective n-acetylglucosamine catabolism and point mutations in the cell-shape regulating protein MreB."  Applied and Environmental Microbiology.  2014.  Doi: 10.1128/AEM.00499-14.  

Reyes LH, Gomez JM#, Kao KC*.  “Improving carotenoids production in yeast via adaptive laboratory evolution.”  Metabolic Engineering.  2014.  Jan:21:  26-33. 

            Highlighted in Evolutionary Applications March 2014.  Volume 7, Issue 3:  337-338. 

Reyes LH, Abdelaal AS, Kao KC*.  " Genetic Determinants For N-Butanol Tolerance In Evolved E. Coli Mutants.  Cross Adaptation And Antagonistic Pleiotropy Between N-Butanol And Other Stressors."  Applied and Environmental Microbiology.  2013.  Sept;79(17):5313-20.  

Almario MP, Reyes LH, Kao KC*.  "Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass."  Biotechnology and Bioengineering.  2013.  doi: 10.1002/bit.24938.

Winkler J, Kao KC*.  "Harnessing Recombination to Speed Adaptive Evolution in Escherichia coli."  Metabolic Engineering.  2012.  Sep;14(5):487-95.

Reyes LH, Almario MP#, Winkler J, Orozco MM#, Kao, KC*.  "Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli." Metabolic Engineering.  Metabolic Engineering.  2012.  Sep;14(5):487-95.

Reyes LH, Winkler J, Kao KC*.  "Visualizing evolution in real-time method for strain engineering."  Frontiers in Microbiotechnology, Ecotoxicology and Bioremediation.  2012.  3:198.

Huang M, Kao KC*.  "Population dynamics and the evolution of antifungal drug resistance in Candida albicans."  FEMS Microbiology Letters.  2012.  Aug;333(2):85-93.

Winkler J, Kao, KC*.  "Computational identification of adaptive mutants using the VERT system."  Journal of Biological Engineering.  2012.  6, 3.

Huang M, McClellan M, Berman J, Kao KC*.  "Evolutionary dynamics of Candida albicans during in vitro evolution." Eukaryotic Cell.  2011.  Sept 2.  PMID: 21890821.

Winkler J, Kao KC*.  “Transcriptional analysis of Lactobacillus brevis to n-butanol and ferulic acid responses.”  PLoS ONE.  2011.  6(8), e21438.

Reyes LH, Almario MP#, Kao KC*.  “Genomic Library Screens for Genes Involved in n-Butanol Tolerance in Escherichia coli.”  PLoS ONE.  2011: March 8;6(3):e17678. 

Kao KC, Sherlock G.  “A Genome-Wide Analysis Reveals No Nuclear Dobzhansky-Muller Pairs of Speciation Genes Between S. cerevisiae and S. paradoxus, but Suggests More Complex Incompatibilities.”  PLoS Genetics.  2010: Jul 29;6(7):e1001038.

Winkler J, Rehmann M#, Kao KC*, “Novel Escherichia coli hybrids with enhanced butanol tolerance.”  Biotech. Letters.  2010: 32(7): 915-20.

Kao, KC, Sherlock, G.  “Molecular Characterization of Clonal Interference during Adaptive Evolution in Asexual Populations of Saccharomyces cerevisiae.”  Nature Genetics.  2008 Dec 40 (12):  1499-504.

Kao, K.C, Tran, L.M., Liao, J.C.  “A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis.”  J. Biol. Chem. 2005 Oct: 280(43): 36079-36087.

Tran LM, Brynildsen MP, Kao KC, Suen JK, Liao JC. “gNCA:  A framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation.”  Metabolic Engineering.  2005 Mar;7(2):128-41.

Kao KC, Yang YL, Boscolo R, Sabatti C, Roychowdhury V, Liao JC. “Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis.”  Proc Natl Acad Sci U S A.  2004 Jan 13;101(2):641-6.

Hyduke DR, Rohlin L, Kao KC, Liao JC.  “A software package for cDNA microarray data normalization and assessing confidence intervals.”  OMICS.  2003 Fall;7(3):227-34.

Oh MK, Rohlin L, Kao KC, Liao JC.  “Global expression profiling of acetate-grown Escherichia coli.”  J Biol Chem.  2002 Apr 12;277(15):13175-83.