publications (updated May 2023)

Fielding-Miller, R., S. Karthikeyan, T. Gaines, R. S. Garfein, R. Salido, V. Cantu, L. Kohn, N. K. Martin, C. Wijaya, M. Flores, V. Omaleki, A. Majnoonian, P. Gonzalez-Zuniga, M. Nguyen, A. V. Vo, T. Le, D. Duong, A. Hassani, A. Dahl, S. Tweeten, K. Jepsen, B. Henson, A. Hakim, A. Birmingham, A. M. Mark, C. A. Nasamran, S. B. Rosenthal, N. Moshiri, K. M. Fisch, G. Humphrey, S. Farmer, H. M. Tubb, T. Valles, J. Morris, J. Kang, B. Khaleghi, C. Young, A. D. Akel, S. Eilert, J. Eno, K. Curewitz, L. C. Laurent, T. Rosing, Search and R. Knight (2021). "Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project." The Lancet RHA (2023)

Karthikeyan, S.#, Levy, J.I.#, De Hoff, P. et al. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature (2022). https://doi.org/10.1038/s41586-022-05049-6

Usyk M., Peters BA., Karthikeyan S., Daniel McDonald, Christopher C. Sollecito, Yoshiki Vazquez-Baeza, Justin P. Shaffer, Rob Knight, Qibin Qi, Robert Kaplan, Robert D. Burk (2022). “Comprehensive Evaluation of Shotgun Metagenomics and 16S rRNA gene and ITS1 Amplicon Sequencing for Epidemiological Studies Using a Multicenter Large Cohort”. Cell Reports Methods

Levy JI., Andersen KG., Knight R., Karthikeyan S., Wastewater surveillance for Public Health, Science, 10.1126/science.ade2503

Shaffer, J. P., L.-F. Nothias, L. R. Thompson, J. G. Sanders, R. A. Salido, S. P. Couvillion, A. D. Brejnrod, S. Huang, F. Lejzerowicz, H. L. Lutz, Q. Zhu, C. Martino, J. T. Morton, S. Karthikeyan, M. Nothias- Esposito, K. Dührkop, S. Böcker, H. W. Kim, A. A. Aksenov, W. Bittremieux, J. J. Minich, C. Marotz, M. M. Bryant, K. Sanders, T. Schwartz, G. Humphrey, Y. Vásquez-Baeza, A. Tripathi, L. Parida, A. P. Carrieri, N. Haiminen, K. L. Beck, P. Das, A. González, D. McDonald, S. M. Karst, M. Albertsen, G. Ackermann, J. DeReus, T. Thomas, D. Petras, A. Shade, J. Stegen, S. J. Song, T. O. Metz, A. D. Swafford, P. C. Dorrestein, J. K. Jansson, J. A. Gilbert, R. Knight and C. the Earth Microbiome Project (2022) “Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity” Nature Microbiology, volume 7, pages 2128–2150 (2022)

Karthikeyan, S., A. Nguyen, D. McDonald, Y. Zong, N. Ronquillo, J. Ren, J. Zou, S. Farmer, G. Humphrey and D. Henderson (2021). "Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus." Msystems 6(4): e00793-00721

Karthikeyan S., N. Ronquillo, P. Belda-Ferre, D. Alvarado, T. Javidi, C. A. Longhurst and R. Knight (2021). "High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County." Msystems 6(2): e00045-00021

Karthikeyan S., L. H. Orellana, E. R. Johnston, J. K. Hatt, F. E. Löffler, H. L. Ayala-del-Río, G. González and K. T. Konstantinidis (2021). "Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling." Applied and Environmental Microbiology 87(12): e00546-00521

Karthikeyan S, M. Kim, P. Heritier-Robbins, J. K. Hatt, J. C. Spain, W. A. Overholt, M. Huettel, J. E. Kostka and K. T. Konstantinidis (2020). "Integrated omics elucidate the mechanisms driving the rapid biodegradation of deepwater horizon oil in intertidal sediments undergoing oxic–anoxic cycles." Environmental Science & Technology 54(16): 10088-10099.

Karthikeyan S., L. M. Rodriguez-R, P. Heritier-Robbins, J. K. Hatt, M. Huettel, J. E. Kostka and K. T. Konstantinidis (2020). "Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes." Environmental Microbiology 22(6): 2094-2106. http://microbial-genomes.org/projects/GROS

Karthikeyan, S., L. M. Rodriguez-R, P. Heritier-Robbins, M. Kim, W. A. Overholt, J. C. Gaby, J. K. Hatt, J. C. Spain, R. Rosselló-Móra and M. Huettel (2019). "“Candidatus Macondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments." The ISME journal 13(8): 2129-2134.

Karthikeyan S., Z. Kurt, G. Pandey and J. C. Spain (2016). "Immobilized biocatalyst for detection and destruction of the insensitive explosive, 2, 4-Dinitroanisole (DNAN)." Environmental science & technology 50(20): 11193-11199.

Karthikeyan S.; Spain JC. (2016), "Biodegradation of 2, 4-dinitroanisole (DNAN) by Nocardioides sp. JS1661 in water, soil and bioreactors." Journal of hazardous materials 312: 37-44.

Karthikeyan S., J. K. Hatt, M. Kim, J. C. Spain, M. Huettel, J. E. Kostka and K. T. Konstantinidis (2021). "A novel, divergent alkane monooxygenase (alkB) clade involved in crude oil biodegradation." Environmental Microbiology Reports 13(6): 830-840.

Knyazev, S., K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P. I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T. I. Vasylyeva, J. O. Wertheim, B. T. Tierney, C. Y. Chiu, R. Sun, A. Wu, M. S. Abedalthagafi, V. M. Pak, S. H. Nagaraj, A. L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C. E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T. T.-Y. Lam, N. C. Wu, A. Zelikovsky, R. Knight, K. A. Crandall and S. Mangul (2022)., “Unlocking capacities of genomics for the COVID-19 response and future pandemics.” Nature Methods 19, 374–380 (2022). https://doi.org/10.1038/s41592-022-01444-z

Heritier-Robbins P., S. Karthikeyan, J. K. Hatt, M. Kim, M. Huettel, J. E. Kostka, K. T. Konstantinidis and L. M. Rodriguez-R (2021). "Beach sand oil spills select for generalist microbial populations." The ISME Journal: 1-5

Harris-Lovett S et al., (2021) Wastewater surveillance for SARS-CoV-2 on college campuses: Initial efforts, lessons learned and research needs. Int. J. Environ. Res. Public Health, 18(9), 4455; https://doi.org/10.3390/ijerph18094455

Matsuura N., Y. Masakke, S. Karthikeyan, S. Kanazawa, R. Honda, R. Yamamoto-Ikemoto and K. T. Konstantinidis (2021). "Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal." Applied Microbiology and Biotechnology 105(5): 2181-2193.

Ana S. Ramírez, Orestes M. Vega-Orellana, Tomeu Viver, José B. Poveda, Rubén S. Rosales, Carlos G. Poveda, Joachim Spergser, Michael P. Szostak, M José Caballero, Lorenzo Ressel, Janet M. Bradbury, M Mar Tavío, Smruthi Karthikeyan, Rudolf Amann, Konstantinos T. Konstantinidis and Ramon Rossello-Mora (2019), "First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov." Systematic and applied microbiology 42(4): 457-467.

Patent

Spain JC., Fida TT., Karthikeyan S., Palamuru S., Pandey, G., Bacterium and enzymes therefrom for bioremediation Patent: WO2016023074A1 [2016]