Faculty

Hu, C-W., Chang, Y-J., Chang, W-H., Cooke, MS., Chen, Y-R. and Chao, M-R. (2023) A Novel Adductomics Workflow Incorporating “FeatureHunter” Software: Rapid Detection of Nucleic Acid Modifications for Studying the Exposome. Environmental Science & Technology. 

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

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. *Co-corresponding author. 

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

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.)

• Journal featured article.

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. https://www.jove.com/t/63559/a-high-throughput-comet-assay-approach-for-assessing-cellular-dna-damage

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, 129991

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.

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.

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).

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.

Chang, 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.

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.

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.

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.