Publications

2025

Hu, C-W., Chang, Y-J., Wang, Y-J., Chen, Y-R., Cooke, M., and Chao, M-R. 2025. Novel carbonylomics with stable isotope-coded derivatization for non-targeted analysis of reactive carbonyl species in cooking oils. Journal of Hazardous Materials. 494.

Keidel, A., Virzi, J., Deloso, L., Möller, C., Chaput, D., Evans-Nguyen, T., Chang, Y.-J., Chao, M.-R., Hu, C.-W., & Cooke, M. S. (2025). Development of an Optimized Two-Step Solid-Phase Extraction Method for Urinary Nucleic Acid Adductomics. Biomolecules, 15(4), 594.

Boysen, G., Alexandrov, L.B., Rahbari, R., Nookaew, I., Ussery, D., Chao, M-R., Hu, C-H., and Cooke, M. (2025). Investigating the origins of the mutational signatures in cancer. Nucleic Acids Research. 53: 1(13).

2024

Möller, C., Virzi, C., Chang, Y-J., Keidel, A., Chao, M-R., Hu, C-W., and Marcus S. Cooke. (2024). DNA modifications: Biomarkers for the exposome? Environmental Toxicology and Pharmacology. 108.

Chao, M-R., Change, Y-J., Cooke, M., and Hu, C-W. (2024). Multi-adductomics: Advancing mass spectrometry techniques for comprehensive exposome characterization. TrAC Trends in Analytical Chemistry. 180

Chung, MK., House, JS., Akhtari, FS., Makris, KC., Langston, MA., Islam, KT., Holmes, P., Chadeau-Hyam, M., Smirnov, AI., Du, X., Thessen, AE., Cui, Y., Zhang, K., Manrai, AK., Motsinger-Reif, M., Patel, CJ. Members of the Exposomics Consortium* (2024) Decoding the exposome: Data science methodologies and implications in Exposome-Wide association studies (ExWASs). Exposome.

* Cooke, MS. is a member of this consortium.

Hu, C-W., Chang, Y-J., Chang, W-H., Cooke, MS., Chen, Y-R. and Chao, M-R. (2024) A Novel Adductomics Workflow Incorporating “FeatureHunter” Software: Rapid Detection of Nucleic Acid Modifications for Studying the Exposome. Environmental Science & Technology. 58, 75-89.

Najeeb, HA., Sanusi, T., Saldanha, G., Brown, K., Cooke, MS.* and Jones, GDD. (2024) Redox modulation of oxidatively-induced DNA damage by ascorbate enhances both in vitro and ex-vivo DNA damage formation and cell death in melanoma cells. Free Radical Biology and Medicine. 213, 309-321. *Co-corresponding author.

Walmsley, SJ., Guo, J., Tarifa, A., DeCaprio, AP., Cooke, MS., Turesky, RJ. and Villalta, PW. (2024) A mass spectral library for DNA adductomics. Chemical Research in Toxicology.

2023 

Cooke, MS., Chang, Y-J., Chen, Y-R, Hu, C-W. and Chao, M-R. (2023) Nucleic acid adductomics – the next generation of adductomics assays towards assessing environmental health risks. Science of the Total Environment. 856, 159192-

Collins, A., Møller, P., Gajski, G., Vodenková, S., Abdulwahed, A., Anderson, D., Bankoglu, EE., Bonassi, S., Boutet-Robinet, E., Brunborg, G., Chao, C., Cooke, MS.,* Costa, C., Costa, S., Dhawan, A., de Lapuente, J., Del Bo', C., Dubus, J., Dusinska, M., Duthie, SJ., El Yamani, N., Engelward, B., Gaivão, I., Giovannelli, L. Godschalk, R., Guilherme, R., Gutzkow, KB., Habas, K., Hernández, A., Herrero, O., Isidori, M., Jha, AN., Knasmüller, S., Kooter, IM., Koppen, G., Kruszewski, M., Ladeira, C., Laffon, B., Larramendy, M., Le Hégarat, L., Lewies, A., Lewinska, A., Liwszyc, GE., López de Cerain, A., Manjanatha, M., Marcos, R., Milić, M., Moraes de Andrade, V., Moretti, M., Muruzabal, D., Novak, M., Oliveira, R., Olsen, A-K., Owiti, N., Pacheco, M., Pandey, AK., Pfuhler, S., Pourrut, B., Reisinger, K., Rojas, E., Rundén-Pran, E., Sanz-Serrano, J., Shaposhnikov, S., Sipinen, V., Smeets, K., Stopper, H., Teixeira, JP., Valdiglesias, V., Valverde, M., van Acker, F., van Schooten, F-J., Vasquez, M., Wentzel, JF., Wnuk, M., Wouters, A., Žegura, B., Zikmund, T., Langie, SAS. and Azqueta, A. (2023) Measuring DNA modifications with the comet assay: a compendium of protocols. Nature Protocols. 18, 929–989.

*Member of final writing/editorial team.

Muthukumaran, RB., Bhattacharjee, P., Bhowmick, P., Zote, L., Malsawmtluangi, M., Kumar, NS., Jahau, L., Cooke, MS., Wang, Y-J., Hu C-W. and Chao, M-R. (2023) Genetic and epigenetic instability induced by betel quid associated chemicals. Toxicology Reports, 10, 223-234.

Karbaschi, M., Ji, Y., Mujawar, MA., Mendoza, M., Marquez, JS., Sonawane, A., Shah, P., Ross, C., Bhansali, S. and Cooke, MS. (2023) Development of a novel, automated high-throughput device for performing the comet assay. International Journal of Molecular Sciences. 24, 7187-.

Scala, G., Ambrosio, S., Menna, M., Gorini, F., Caiazza, C., Cooke, MS., Majello, B. and Amente S. (2023) Accumulation of 8-oxodG within human mitochondrial genome positively associates with transcription. NAR Genomics and Bioinformatics. 5, 1-7.

Sumner, S., Rushing, B., Thessen, A., Soliman, G., Ramesh, A. and Members of The Exposomics Consortium*. (2023) The exposome and nutritional pharmacology and toxicology: a new application for metabolomics. Exposome. 3, osad008.

* Cooke, MS. is a member of this consortium.

Stingone, J., Geller, A., Hood, D., Makris, K., Mouton, C., States, J., Sumner, S., Wu, KL., Rajasekar, A. and Members of The Exposomics Consortium*. Community-level exposomics: A population-centered approach to address public health concerns. Exposome. 3, osad009.

* Cooke, MS. is a member of this consortium.

Schmitt, C., Stingone, J., Rajasekar, A., Cui, Y., Du, X., Duncan, C., Heacock, M., Hu, H., Gonzalez, J., Juarez, P., Smirnov, A. and Members of The Exposomics Consortium*. (2023) A roadmap to advance exposomics through federation of data. Exposome. 3, osad010,

* Cooke, MS. is a member of this consortium.

2022 

Møller, P, Azqueta, A., Boutet-Robinet, E., Koppen, G., Bonassi, S., Milić, M., Gajski, G., Costa, S., Teixeira, JP., Pereira, CC., Dusinska, M., Godschalk, R., Brunborg, G., Giovannelli, L., Cooke, MS., Richling, E., Laffon, B., Valdiglesias, V., Basaran, N., del Bo’, C., Zegura, B., Stopper, H., Vodicka, P., Vodenkova, S., de Andrade, VM., Sramkova, M., Gabelova, A., Collins, A. and Langie, S. Measuring DNA damage using the comet assay: a compendium of protocols. Nature Protocols. (In press.)

Lawrence, KP., Delinasios, G., Premi, S., Young, AR. and Cooke, MS. (2022) Perspectives on Cyclobutane Pyrimidine Dimers – Rise of the Dark Dimers. Photochemistry and Photobiology. 98, 609 - 616. (Invited article for special edition in honour of Jean Cadet.)

Ji., Y., Karbaschi, M., Abdulwahed, A., Quinente, NS., Evans, MD. and Cooke, MS. (2022) A High-Throughput Comet Assay Approach for Assessing Cellular DNA Damage. Journal of Visual Experiments. 183,

2021

Peña-Fernández, A., Evans, M. D., & Cooke, M. S. (Eds.). (2021) Toxicology for the Health and Pharmaceutical Sciences. CRC Press.

Amente, S., Scala, G., Majello, B. et al. (2021) Genome-wide mapping of genomic DNA damage: methods and implications. Cell. Mol. Life Sci. 78, 6745–6762. https://doi.org/10.1007/s00018-021-03923-6

Lawrence, K.P., Delinasios, G.J., Premi, S., Young, A.R. and Cooke, M.S. (2022) Perspectives on Cyclobutane Pyrimidine Dimers—Rise of the Dark Dimers†. Photochem Photobiol. https://doi.org/10.1111/php.13551

Chao, M., Evans, M., Hu, H., Ji, Y., Møller, P., Rossner, P., Cooke, M. (2021) Biomarkers of nucleic acid oxidation – A summary state-of-the-art. Redox Biology, 42. https://doi.org/10.1016/j.redox.2021.101872.

Burke, S.L., Cobb, J., Agarwal, R. et al.  (2021) How Robust is the Evidence for a Role of Oxidative Stress in Autism Spectrum Disorders and Intellectual Disabilities?. J Autism Dev Disord 51, 1428–1445.  https://doi.org/10.1007/s10803-020-04611-3

Gorini, F., Scala, G., Cooke, MS., Majello, B. and Amente, S.  (2021)  Towards a comprehensive view of 8-oxo-7,8-dihydro-2’-deoxyguanosine: highlighting the intertwined roles of DNA damage and epigenetics in genomic instability.  DNA Repair, 97, 103027-.

Chang, Y-J., Cooke, MS., Chen, Y-R., Yang, S-F., Lia, P-S., Hu, C-W., and Chao, M-R.  (2021)  Is high resolution a strict requirement for mass spectrometry-based cellular DNA adductomics?  Chemosphere, 274.

Hu, C-W., Shih, Y-M., Chang, Y-J, Cooke, MS., Pan, C-H., Hu, C-H. and Chao, M-R.  (2021)  Alkylating and oxidative stresses in smoking and non-smoking patients with COPD: implications for lung carcinogenesis. Free Radical Biology and Medicine, 164, 99-106.

2020

Troccoli, CI., Samaranayake, GJ., Zhang, L., Huynh, M., Jayaraj, C., Ji, D., McPherson, L., Onishi, Y., Nguyen, DM., Robbins, DJ., Karbaschi, M., Cooke, MS., Barrientos, A., Kool, ET. and Rai, P. (2020) The existence of MTH1-independent 8-oxodGTPase activity in cancer cells as a compensatory mechanism against on-target effects of MTH1 inhibitors.  Molecular and Cellular Therapeutics, 19, 432-446. 

Guo, J., Turesky, RJ., Tarifa, A., DeCaprio, AP., Cooke, MS., Walmsley, SJ. and Villalta, PW. (2020) Development of a DNA Adductome Mass Spectral Database.  Chemical Research in Toxicology, 33, 4, 852-854.

Shih, BB., Farrar, M., Vail, A., Chao, M-R., Hu, C-W., Jones, GDD., Cooke, MS.* and Rhodes, LE.*  Influence of skin melanisation and ultraviolet radiation on biomarkers of systemic oxidative stress.  Free Radical Biology and Medicine 160, 40-46.

*Co-corresponding authors.

Burke, S.,* Cobb, J., Agarwal, R., Maddux, M. and Cooke, MS.*  (2020)  How Robust is the Evidence for a Role of Oxidative Stress in Autism Spectrum Disorders and Intellectual Disabilities?  Journal of Autism and Developmental Disorders.

*Co-corresponding authors.

Møller, P, Azqueta, A., Boutet-Robinet, E., Koppen, G., Bonassi, S., Milic, M., Gajski, G., Costa, S., Teixeira, JP., Pereira, CC., Dusinska, M., Godschalk, R., Brunborg, G., Giovannelli, L., Cooke, MS.,* Richling, E., Laffon, B., Valdiglesias, V., Basaran, N., del Bo’, C., Zegura, B., Stopper, H., Vodicka, P., Vodenkova, S., de Andrade, VM., Sramkova, M., Gabelova, A., Collins, A. and Langie, S.  (2020)  Minimum Information for reporting Comet Assay results (MIRCA) in cultured eukaryotic cells cultures, animals and non-mammalian species.  Nature Protocols. 15, (12) 3817–3826.

*Member of final writing/editorial team.

2019

Shih, Y-M., Cooke, MS., Pan, C-H., Chao, M-R. and Hu, C-W. (2019) Clinical relevance of guanine-derived urinary biomarkers of oxidative stress, determined by LC-MS/MS.  Redox Biology. 20, 556-565.

Tenenbaum, RB., Agarwal, R., Cooke, MS., Agarwal, M., Maddux, M. and Burke, SL. (2019) Utilisation of complementary and alternative therapies in youth with developmental disabilities. Evidence-Based Complementary and Alternative Medicine.

Ji, Y., Karbaschi, M. and Cooke, MS. (2019) Mycoplasma infection of cultured cells induces oxidative stress and attenuates cellular base excision repair activity.  Mutation Research - Genetic Toxicology and Environmental Mutagenesis. 845, 403054-.

Alhegaili, AS., Ji, Y., Karbaschi, M., Tempest, HG., Sylvius, N., Blades, MJ. Jones, GDD. and Cooke, MS. (2019) Genome-wide adductomics analysis reveals heterogeneity in the induction and loss of cyclobutane thymine dimers across the both nuclear and mitochondrial genomes.  International Journal of Molecular Sciences, 20, 5112-.

Karbaschi, M., Ji, Y., Abdulwahed, AMS., Alohaly, A., Bedoya, JF., Burke, SL., Boulos, TM., Tempest, HG. and Cooke, MS. (2019) Evaluation of major steps in the conventional protocol for the comet assay.  International Journal of Molecular Sciences, 20, 6072,

Cooke, MS., Hu, C-W. and Chao, M-R. (2019) Editorial: Mass Spectrometry for Adductomic Analysis.  Frontiers Chemistry.  doi: 10.3389/fchem.2019.00794

Hu, C-W., Chang, Y-J., Cooke, MS. and Chao, M-R. (2019) DNA crosslinkomics: a tool for the comprehensive assessment of inter-strand crosslinks using high resolution mass spectrometry.  Analytical Chemistry. 91, 15193-15203. 

(an NIEHS Extramural Paper of the Month, Jan 2020).

2018

Olinski, R., Gackowski, D. and Cooke, MS. (2018) Endogenously generated DNA nucleobase modifications: source, and significance as possible biomarkers of malignant transformation risk, and role in anticancer therapy. BBA. Reviews on Cancer 1869, 29-41.

Delinassios, G., Karbaschi, M., Cooke, MS*. and Young, AR*. (2018) Vitamin E inhibits the UVAI induction of “light” and “dark” cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes. Scientific Reports 8, 423,

*Co-corresponding authors.

Kim, G., Karbaschi, M., Cooke, MS. and Gaitas, A. (2018) Evaluation of three light based whole blood pathogen inactivation methods enabled by a recirculating flow system.  Photochemistry and Photobiology.  94, 744-751.  DOI: 10.1111/php.12899

Cooke, MS.  (2018) Mycosporine-like amino acids: does Nature make a better sunscreen?  (Invited commentary.)  British Journal of Dermatology 178, 1239.

Hu, C-W., Cooke, MS., Chang, Y-J. and Chao, M-R. (2018) Direct-acting DNA ethylating agents in cigarette smoke primarily originate by transfer from the tobacco itself, not combustion.  Journal of Hazardous Materials. 358, 397-404.

g, Y-J., Cooke, MS., Hu, C-W. and Chao, M-R. (2018) Novel approach to integrated DNA adductomics for the assessment of in vitro and in vivo environmental exposures.  Archives of Toxicology. 92, 2665-2680.

Chao, M-R*., Cooke, MS*., Chang, Y-J., Pan, C-H, Liu, H-H. Yang, H-J., Chiang, Y-C. and Hu, C-W. (2018) Children are particularly vulnerable to environmental tobacco smoke exposure: evidence from biomarkers of tobacco-specific nitrosamines, and oxidative stress.  Environment International. 120, 238-245.

*Contributed equally.

Shih, BB., Farrar, MD., Cooke, MS., Osman, J., Langton, AK., Kift, R., Webb, AR., Berry, JL., Watson, REB., Vail, A., de Gruijl, FR. and Rhodes, LE. (2018) Sub-sunburn produces vitamin D and DNA damage equivalently but with absent to strong damage gradients in human skin types I-VI.  Journal of Investigative Dermatology. 138, 2244-2252.

Cooke, MS*., Chao, M-R., Chang, Y-J. and Hu, C-W*. (2018) Urinary DNA Adductomics – A Novel Approach for Exposomics.  Environment International. 121, 1033-1038. 

*Contributed equally.

2017

Egea, J., Fabregat, I., Frapart, Y.M., Ghezzi, P., Görlach, A., Kietzmann, T., Kubaichuk, K., Knaus, U. G., Lopez, M.G., Olaso-Gonzalez, G., Petry, A., Schulz, R., Vina, J., Winyard, P., Abbas,K., Ademowo, S., Afonso, C.B., Andreadou, L., Antelmann, H.,Antunes, F., Aslan, M., Bachschmid, M.M., Barbosa, R. M., Belousov, V., Berndt, C., Bernlohr, D., Bertrán, E., Bindoli, A., Bottari, S.P., Brito, P.M., Carrara, G., Casas, A.I., Chatzi, A., Chondrogianni, N., Conrad, M., Cooke, M.S., Costa. J.G., 34, Cuadrado, A., Dang, P.M., Smet, B.D., Debelec–Butuner, B., Dia, I., Dunn, J.D., Edson, A.J, Assar, M.E., Benna, J.E., Ferdinandy, P., Fernandes, A.S., Fladmark, K.E., Förstermann, U., Giniatullin, R., Giricz, Z., Görbe, A., Griffiths, H., Hampl, V., Herget, J., Hernansanz-Agustín, P., Hillion, M., Huang, J., Ilikay, S., Jansen-Dürr, P., Jaquet, V., Joles, J.A., Kalyanaraman, B., Kaminskyy, D., Karbaschi, M., Kleanthous, M., Klotz, L.O., Korac, B.,Korkmaz, K.S., Koziel, R., Kracun, D., Krause, K.H., Kren, V., Krieg, T., Laranjinha, J., Lazou, A., Li, H., Martínez-Ruiz, A., Matsui, R., McBean, G.J., Meredith, S.P., Messens, J., Miguel, V., Mikhed, Y., Milisav, I., Milkovic, L., Miranda-Vizuete, A.,Mojovic, M., Monsalve, M., Mouthuy, P.A., Mulvey, J., Münzel, T., Muzykantov, V., Nguyen, I.T.N., Oliveira, N.G., Palmeira, C.M., Papaevgeniou, N., Pavicevic, A., Pedre, B., Peyrot, F., Phylactides, M., Pircalabioru, G.G., Pitt, A.R., Poulsen, H.E., Prieto, I., Rigobello, M.P., Robledinos-Antón, N., Rodríguez-Mañas, L., Rolo, A.P., Rousset, F., Ruskovska, T.,Saraiva, N., Sasson, S., Schröder, K., Semen, K., Seredenina, T., Shakirzyanova, A., Smith, G.L., Soldati, T., Sousa, B.C., Spickett, C.M., Stancic, A., Stasia, M.J., Steinbrenner, H., Stepanic, V., Steven, S., Tokatlidis, K., Tuncay, E., Turan, B., Ursini, F., Vacek, J., Vajnerova, O., Valentová, K., Varisli, L., Veal, E.A., Weber, A., Yalçin, A.S., Yelisyeyeva, O., Žarkovic, N., Zatloukalová, M., Zielonka, J., Touyz, R.M., Papapetropoulos, A., Grune, T., Lamas, S.,Schmidt, H.H., Lisa, F.D., and Daiber, A.  (2017)  Position paper by the EU-ROS consortium on RONS in health and disease: European Contribution to the study of ROS: A Summary of the Findings and Prospects for the Future from the COST Action BM1203 (EU-ROS). Redox Biology. 13, 94-162.

2016

Rossner, Jr., P., Orhan, H., Santella, RM., Sakai, K., Koppen, G., Ambroz, A., Rossnerova, A., Sram, RJ., Ciganek, M., Neca, J. and Cooke, MS.  (2016)  Urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine analysis by an improved ELISA: does assay standardization reduce inter-laboratory variability?  Free Radic. Biol. Med.  95, 169-179.

Felton, SJ., Cooke, MS., Kift, R., Berry, JL., Webb, AR., Lam, PMW., de Gruijl, FR., Vail, A. and Rhodes, LE.  (2016)  Concurrent beneficial (vitamin D production) and hazardous (cutaneous DNA damage) impact of low level summer sunlight exposures.  British Journal of Dermatology 175, 1320-1328.

Evans, MD., Misty, V., Singh, R., Gackowski, D., Rózalskic, R., Siomek-Goreckac, A., Phillips, DH., Zuod, J., Mullenders, L., Pines, A., Nakabeppu, Y., Sakumi, K., Sekiguchi, M., Tsuzuki, T., Bignami, M., Olinski, R. and Cooke, MS.  (2016)  Nucleotide excision repair of oxidised genomic DNA is not the primary source of urinary 8-oxo-7,8-dihydro-2’-deoxyguanosine. Free Radic. Biol. Med.  99, 385-391.

2015

Hu, C-W., Cooke, MS., Tsai, Y-H. and Chao, M-R.  (2015)  Comparison of 8-oxo-7,8-dihydroguanine and 8-oxo-7,8-dihydro-2'-deoxyguanosine concentrations in various human body fluids measured by isotope-dilution LC-MS/MS.  Arch. Toxicol. 89, 201-210.  DOI: 10.1007/s00204-014-1255-1

Karbaschi, M., Macip, S, Mistry, V., Abbas, HHK, Delinassios, GJ., Evans, MD., Young, AR. and Cooke, MS.  (2015)  Rescue of cells from apoptosis increases DNA repair in UVB exposed cells with implications for the DNA damage response.  Toxicol. Res. 4, 725-738. DOI: 10.1039/c4tx00197d.