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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature. 2022 09; 609(7925):101-108.
Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. PMID: 35798029; PMCID: PMC9433318.
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Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv. 2022 Apr 04.
Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. PMID: 35411350; PMCID: PMC8996633.
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Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat Methods. 2022 04; 19(4):374-380.
Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. PMID: 35396471; PMCID: PMC9467803.
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HumansCellsPHPublic Health
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A novel, divergent alkane monooxygenase (alkB) clade involved in crude oil biodegradation. Environ Microbiol Rep. 2021 12; 13(6):830-840.
Karthikeyan S, Hatt JK, Kim M, Spain JC, Huettel M, Kostka JE, Konstantinidis KT. PMID: 34672103.
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CellsPHPublic Health
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Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus. mSystems. 2021 Aug 31; 6(4):e0079321.
Karthikeyan S, Nguyen A, McDonald D, Zong Y, Ronquillo N, Ren J, Zou J, Farmer S, Humphrey G, Henderson D, Javidi T, Messer K, Anderson C, Schooley R, Martin NK, Knight R. PMID: 34374562; PMCID: PMC8409724.
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Beach sand oil spills select for generalist microbial populations. ISME J. 2021 11; 15(11):3418-3422.
Heritier-Robbins P, Karthikeyan S, Hatt JK, Kim M, Huettel M, Kostka JE, Konstantinidis KT, Rodriguez-R LM. PMID: 34088976; PMCID: PMC8528907.
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PHPublic Health
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Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling. Appl Environ Microbiol. 2021 05 26; 87(12):e0054621.
Karthikeyan S, Orellana LH, Johnston ER, Hatt JK, Löffler FE, Ayala-Del-Río HL, González G, Konstantinidis KT. PMID: 33837013; PMCID: PMC8174771.
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Wastewater Surveillance for SARS-CoV-2 on College Campuses: Initial Efforts, Lessons Learned, and Research Needs. Int J Environ Res Public Health. 2021 04 22; 18(9).
Harris-Lovett S, Nelson KL, Beamer P, Bischel HN, Bivins A, Bruder A, Butler C, Camenisch TD, De Long SK, Karthikeyan S, Larsen DA, Meierdiercks K, Mouser PJ, Pagsuyoin S, Prasek SM, Radniecki TS, Ram JL, Roper DK, Safford H, Sherchan SP, Shuster W, Stalder T, Wheeler RT, Korfmacher KS. PMID: 33922263; PMCID: PMC8122720.
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HumansCellsPHPublic Health
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High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County. mSystems. 2021 Mar 02; 6(2).
Karthikeyan S, Ronquillo N, Belda-Ferre P, Alvarado D, Javidi T, Longhurst CA, Knight R. PMID: 33653938; PMCID: PMC8546963.
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Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal. Appl Microbiol Biotechnol. 2021 Mar; 105(5):2181-2193.
Matsuura N, Masakke Y, Karthikeyan S, Kanazawa S, Honda R, Yamamoto-Ikemoto R, Konstantinidis KT. PMID: 33555362.
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Cells
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Integrated Omics Elucidate the Mechanisms Driving the Rapid Biodegradation of Deepwater Horizon Oil in Intertidal Sediments Undergoing Oxic-Anoxic Cycles. Environ Sci Technol. 2020 08 18; 54(16):10088-10099.
Karthikeyan S, Kim M, Heritier-Robbins P, Hatt JK, Spain JC, Overholt WA, Huettel M, Kostka JE, Konstantinidis KT. PMID: 32667785.
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PHPublic Health
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Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes. Environ Microbiol. 2020 06; 22(6):2094-2106.
Karthikeyan S, Rodriguez-R LM, Heritier-Robbins P, Hatt JK, Huettel M, Kostka JE, Konstantinidis KT. PMID: 32114693.
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PHPublic Health
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Erratum to "First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarod is sp. nov" [Syst. Appl. Microbiol. 42 (2019) 457-467]. Syst Appl Microbiol. 2020 01; 43(1):126027.
Ramírez AS, Vega-Orellana OM, Viver T, Poveda JB, Rosales RS, Poveda CG, Spergser J, Szostak MP, Caballero MJ, Ressel L, Bradbury JM, Tavío MM, Karthikeyan S, Amann R, Konstantinidis KT, Rosselló-Móra R. PMID: 31699460.
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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. Syst Appl Microbiol. 2019 Jul; 42(4):457-467.
Ramírez AS, Vega-Orellana OM, Viver T, Poveda JB, Rosales RS, Poveda CG, Spergser J, Szostak MP, Caballero MJ, Ressel L, Bradbury JM, Mar Tavío M, Karthikeyan S, Amann R, Konstantinidis KT, Rossello-Mora R. PMID: 31072660.
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AnimalsCells
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"Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments. ISME J. 2019 08; 13(8):2129-2134.
Karthikeyan S, Rodriguez-R LM, Heritier-Robbins P, Kim M, Overholt WA, Gaby JC, Hatt JK, Spain JC, Rosselló-Móra R, Huettel M, Kostka JE, Konstantinidis KT. PMID: 30952995; PMCID: PMC6776044.
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CellsPHPublic Health
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Immobilized Biocatalyst for Detection and Destruction of the Insensitive Explosive, 2,4-Dinitroanisole (DNAN). Environ Sci Technol. 2016 10 18; 50(20):11193-11199.
Karthikeyan S, Kurt Z, Pandey G, Spain JC. PMID: 27617621.
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Cells
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Biodegradation of 2,4-dinitroanisole (DNAN) by Nocardioides sp. JS1661 in water, soil and bioreactors. J Hazard Mater. 2016 07 15; 312:37-44.
Karthikeyan S, Spain JC. PMID: 27015377.
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CellsPHPublic Health