2025
“Biochemical characterization of disease-associated variants of human ornithine transcarbamylase,” Emily Micheloni, Samantha S. Watson, Penny J. Beuning, Mary Jo Ondrechen, ACS Chemical Biology 20(5), 1059-1067 (2025).
“Distal residues contribute to enzymatic catalysis in human phosphoglucose isomerase through modulation of dynamics and electrostatics,” Masoud Keramati, Lydia A. Ruffner, Shanadeen C. Begay, Penny J. Beuning, Mary Jo Ondrechen*, Journal of Chemical Physics, 163, 015101, (2025).
“Cartilage targeting cationic peptide carriers display deep cartilage penetration and retention in a rabbit model of post-traumatic osteoarthritis,” Timothy L. Boyer, Olivia Chao, Bill Hakim, Luke Childress, Quentin A. Meslier, Suhasini M. Iyengar, Mary Jo Ondrechen, Ryan M. Porter, Ambika G. Bajpayee, Osteoarthritis and Cartilage 33, 721-734 (2025).
“The need to implement FAIR principles in biomolecular simulations,” Rommie E. Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C. Biggin, Massimiliano Bonomi, Gregory R. Bowman, Richard A. Bryce, Giovanni Bussi, Paolo Carloni, David A. Case, Andrea Cavalli, Chia-En A. Chang, Thomas E. Cheatham III, Margaret S. Cheung, Christophe Chipot, Lillian T. Chong, Preeti Choudhary, G. Andres Cisneros, Cecilia Clementi, Rosana Collepardo-Guevara, Peter Coveney, Roberto Covino, T. Daniel Crawford, Matteo Dal Peraro, Bert L. de Groot, Lucie Delemotte, Marco De Vivo, Jonathan W. Essex, Franca Fraternali, Jiali Gao, Josep Ll. Gelpí, Francesco L. Gervasio, Fernando D. González-Nilo, Helmut Grubmüller, Marina G. Guenza, Horacio V. Guzman, Sarah Harris, Teresa Head-Gordon, Rigoberto Hernandez, Adam Hospital, Niu Huang, Xuhui Huang, Gerhard Hummer, Javier Iglesias-Fernández, Jan H. Jensen, Shantenu Jha, Wanting Jiao, William L. Jorgensen, Shina C. L. Kamerlin, Syma Khalid, Charles Laughton, Michael Levitt, Vittorio Limongelli, Erik Lindahl, Kresten Lindorff-Larsen, Sharon Loverde, Magnus Lundborg, Yun L. Luo, F. Javier Luque, Charlotte I. Lynch, Alexander D. MacKerell Jr, Alessandra Magistrato, Siewert J. Marrink, Hugh Martin, J. Andrew McCammon, Kenneth Merz, Vicent Moliner, Adrian J. Mulholland, Sohail Murad, Athi N. Naganathan, Shikha Nangia, Frank Noe, Agnes Noy, Julianna Oláh, Megan L. O’Mara, Mary Jo Ondrechen, Jose N. Onuchic, Alexey Onufriev, Sílvia Osuna, Giulia Palermo, Anna R. Panchenko, Sergio Pantano, Carol Parish, Michele Parrinello, Alberto Perez, Tomas Perez-Acle, Juan R. Perilla, B. Montgomery Pettitt, Adriana Pietropaolo, Jean-Philip Piquemal, Adolfo B. Poma, Matej Praprotnik, Maria J. Ramos, Pengyu Ren, Nathalie Reuter, Adrian Roitberg, Edina Rosta, Carme Rovira, Benoit Roux, Ursula Rothlisberger, Karissa Y. Sanbonmatsu, Tamar Schlick, Alexey K. Shaytan, Carlos Simmerling, Jeremy C. Smith, Yuji Sugita, Katarzyna Świderek, Makoto Taiji, Peng Tao, D. Peter Tieleman, Irina G. Tikhonova, Julian Tirado-Rives, Iñaki Tuñón, Marc W. van der Kamp, David van der Spoel, Sameer Velankar, Gregory A. Voth, Rebecca Wade, Ariel Warshel, Valerie Vaissier Welborn, Stacey D. Wetmore, Travis J. Wheeler, Chung F. Wong, Lee-Wei Yang, Martin Zacharias & Modesto Orozco, Nature Methods 22, 641-645 (2025).
2024
“Revisiting the roles of catalytic residues in human ornithine transcarbamylase,” Samantha S. Watson, Emily Micheloni, Lisa Ngu, Kelly K. Barnsley, Lee Makowski, Penny J. Beuning, Mary Jo Ondrechen, Biochemistry 63, 1858-1875 (2024).
“Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS,” Md Amin Hossain, Richa Sarin, Daniel P. Donnelly, Brandon C. Miller, Alexandra Weiss, Luke McAlary, Svetlana V. Antonyuk, Joseph P. Salisbury, Jakal Amin, Jeremy B. Conway, Samantha S. Watson, Jenifer N. Winters, Yu Xu, Novera Alam, Rutali R. Brahme, Haneyeh Shahbazian, Durgalakshmi Sivasankar, Swathi Padmakumar, Aziza Sattarova, Aparna C. Ponmudiyan, Tanvi Gawde, David E. Verrill, Wensheng Yang, Sunanda Kannapadi, Leigh D. Plant, Jared R. Auclair, Lee Makowski, Gregory A. Petsko, Dagmar Ringe, Nathalie Y. R. Agar, David J. Greenblatt, Mary Jo Ondrechen, Yunqiu Chen, Justin J. Yerbury, Roman Manetsch, S. Samar Hasnain, Robert H. Brown Jr., Jeffrey N. Agar, PLoS Biology, https://doi.org/10.1371/journal.pbio.3002462 (2024).
“A community effort in SARS-CoV-2 drug discovery,” Schimunek, J., Seidl, P., Elez, K., Hempel, T., Le, T., Noé, F., Olsson, S., Raich, L., Winter, R., Gokcan, H., Gusev, F., Gutkin, E.M., Isayev, O., Kurnikova, M.G., Narangoda, C.H., Zubatyuk, R., Bosko, I.P., Furs, K.V., Karpenko, A.D., Kornoushenko, Y.V., Shuldau, M., Yushkevich, A., Benabderrahmane, M., Bousquet-Melou, P., Bureau, R., Charton, B., Cirou, B., Gil, G., Allen, W.J., Sirimulla, S., Watowich, S., Antonopoulos, N., Epitropakis, N., Krasoulis, A., Pitsikalis, V., Theodorakis, S., Kozlovskii, I., Maliutin, A., Medvedev, A., Popov, P., Zaretckii, M., Eghbal-zadeh, H., Halmich, C., Hochreiter, S., Mayr, A., Ruch, P., Widrich, M., Berenger, F., Kumar, A., Yamanishi, Y., Zhang, K., Bengio, E., Bengio, Y., Jain, M., Korablyov, M., Liu, C., Gilles, M., Glaab, E., Barnsley, K., Iyengar, S.M., Ondrechen, M.J., Haupt, V.J., Kaiser, F., Schroeder, M., Pugliese, L., Albani, S., Athanasiou, C., Beccari, A., Carloni, P., D’Arrigo, G., Gianquinto, E., Goßen, J., Hanke, A., Joseph, B.P., Kokh, D.B., Kovachka, S., Manelfi, C., Mukherjee, G., Muñiz-Chicharro, A., Musiani, F., Nunes-Alves, A., Paiardi, G., Rossetti, G., Sadiq, S.K., Spyrakis, F., Talarico, C., Tsengenes, A., Wade, R., Copeland, C., Gaiser, J., Olson, D.R., Roy, A., Venkatraman, V., Wheeler, T.J., Arthanari, H., Blaschitz, K., Cespugli, M., Durmaz, V., Fackeldey, K., Fischer, P.D., Gorgulla, C., Gruber, C., Gruber, K., Hetmann, M., Kinney, J.E., Das, K.M.P., Pandita, S., Singh, A., Steinkellner, G., Tesseyre, G., Wagner, G., Wang, Z., Yust, R.J., Druzhilovskiy, D.S., Filimonov, D., Pogodin, P.V., Poroikov, V., Rudik, A.V., Stolbov, L.A., Veselovsky, A.V., De Rosa, M., Simone, G.D., Gulotta, M.R., Lombino, J., Mekni, N., Perricone, U., Casini, A., Embree, A., Gordon, D.B., Lei, D., Pratt, K., Voigt, C.A., Chen, K., Jacob, Y., Krischuns, T., Lafaye, P., Zettor, A., Rodríguez, M.L., White, K.M., Fearon, D., von Delft, F., Walsh, M.A., Horvath, D., Brooks, C.L., Falsafi, B., Ford, B., García-Sastre, A., Lee, S.Y., Naffakh, N., Varnek, A., Klambauer, G. and Hermans, T.M., Molecular Informatics 43(1), e202300262 (2024).
2023
“Hydration sphere structure of architectural molecules: poly-ethylene glycol and poly-oxymethylene oligomers,” Ahmed M. Rozza, Danny E. P. Vanpoucke, Eva-Maria Krammer, Julie Bouckaert, Ralf Blossey, Mark F. Lensink, Mary Jo Ondrechen, Imre Bakó, Julianna Oláh, Goedele Roos, Journal of Molecular Liquids 384, 122172 https://doi.org/10.1016/j.molliq.2023.122172 (2023).
“Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences,” Riley A. Hess, Olivia A. Erickson, Rebecca B. Cole, Jared M. Isaacs, Silvia Alvarez-Clare, Jonathan Arnold, Allison Augustus-Wallace, Joseph C. Ayoob, Alan Berkowitz, Janet Branchaw, Kevin R. Burgio, Charles H. Cannon, Ruben Michael Ceballos, C. Sarah Cohen, Hilary Coller, Jane Disney, Van A. Doze, Margaret J. Eggers, Edwin L. Ferguson, Jeffrey J. Gray, Jean T. Greenberg, Alexander Hoffmann, Danielle Jensen-Ryan, Robert M. Kao, Alex C. Keene, Johanna E. Kowalko, Steven A. Lopez, Camille Mathis, Mona Minkara, Courtney J. Murren, Mary Jo Ondrechen, Patricia Ordoñez, Anne Osano, Elizabeth Padilla-Crespo, Soubantika Palchoudhury, Hong Qin, Juan Ramírez-Lugo, Jennifer Reithel, Colin A. Shaw, Amber Smith, Rosemary J. Smith, Fern Tsien, Erin L. Dolan, CBE Life Sciences Education, Jun 22(2):ar25. doi: 10.1187/cbe.22-01-0001 (2023).
“Functional annotation of haloacid dehalogenase superfamily structural genomics proteins,” Lakindu S. Pathira Kankanamge, Lydia A. Ruffner, Mong Mary Touch, Manuel Pina, Penny J. Beuning and Mary Jo Ondrechen, Biochemical Journal 480, 1553-1569 (2023).
“Biochemical activity of seventeen cancer associated variants of DNA polymerase kappa predicted by electrostatic properties,” Lakindu S. Pathira Kankanamge, Alexandra Mora, Mary Jo Ondrechen, Penny J. Beuning, Chemical Research in Toxicology, 36, 1789-1803 (2023).
2022
“Best Practices to Diversify Chemistry Faculty,” Marie Little Fawn Agan, Reni Joseph, Armando Rivera-Figueroa, Benny C Chan, Abby R O’Connor, Mary Jo Ondrechen, Wayne E Jones Jr, Peter K Dorhout, Ann C Kimble-Hill, Journal of Chemical Education 99, 435-443 (2022).
“Functional Characterization of Structural Genomics Proteins in the Crotonase Superfamily,” Caitlyn L. Mills, Pengcheng Yin, Becky Leifer, Lori Ferrins, George A. O’Doherty, Penny J. Beuning*, Mary Jo Ondrechen*, (ACS) Chemical Biology 17, 395-403 (2022).
“How do we do this at a distance?!” A descriptive study of remote undergraduate research programs during COVID-19.” Olivia A. Erickson, Rebecca B. Cole, Jared M. Isaacs, Silvia Alvarez-Clare, Jonathan Arnold, Allison Augustus-Wallace, Joseph C. Ayoob, Alan Berkowitz, Janet Branchaw, Kevin R. Burgio, Charles H. Cannon, Ruben Michael Ceballos, C. Sarah Cohen, Hilary Coller, Jane Disney, Van A. Doze, Margaret J. Eggers, Stacy Farina, Edwin L. Ferguson, Jeffrey J. Gray, Jean T. Greenberg, Alexander Hoffman, Danielle Jensen-Ryan, Robert M. Kao, Alex C. Keene, Johanna E. Kowalko, Steven A. Lopez, Camille Mathis, Mona Minkara, Courtney J. Murren, Mary Jo Ondrechen, Patricia Ordoñez, Anne Osano, Elizabeth Padilla-Crespo, Soubantika Palchoudhury, Hong Qin, Juan Ramírez-Lugo, Jennifer Reithel, Colin A. Shaw, Amber Smith, Rosemary Smith, Adam P. Summers, Fern Tsien, Erin L. Dolan, CBE – Life Sciences Education 21(1): ar1 (2022).
“Synthesis and Characterization of 5-(2-Fluoro-4-[11C]methoxyphenyl)-2,2-dimethyl-3,4-dihydro-2H-pyrano[2,3-b]pyridine-7-carboxamide as a PET Imaging Ligand for Metabotropic Glutamate Receptor 2,” G. Yuan, M. Dhaynaut, Y. Lan, N.J. Guehl, D. Huynh, S.M. Iyengar, S. Afshar, M.K. Jain, J.E. Pickett, H.J. Kang, H. Wang, S.-H. Moon, M.J. Ondrechen, C. Wang, T.M. Shoup, G. El Fakhri, M.D. Normandin, and A.-L. Brownell,. Journal of Medicinal Chemistry 65(3), 2593-2609 (2022).
“Stereoselective Synthesis of β-Glycinamide Ribonucleotide,” Lisa Ngu, Debarpita Ray, Samantha S. Watson, Penny J. Beuning, Mary Jo Ondrechen, George A. O’Doherty, Molecules 27(8), 2528 https://doi.org/10.3390/molecules27082528 (2022).
“Electrostatic fingerprints of catalytically active amino acids in enzymes,” Suhasini M. Iyengar, Kelly K. Barnsley, Rholee Xu, Aleksandr Prystupa, Mary Jo Ondrechen. Protein Science 31(5), e4291 (2022).
“Enzyme active sites: Identification and prediction of function using computational chemistry,” Kelly K. Barnsley and Mary Jo Ondrechen, Current Opinion in Structural Biology 74: (2022).
“Design, Synthesis, and Characterization of [18F]mG2P026 as a High-Contrast PET Imaging Ligand for Metabotropic Glutamate Receptor 2,” Gengyang Yuan, Maeva Dhaynaut, Nicolas J. Guehl, Sepideh Afshar, Dalena Huynh, Sung-Hyun Moon, Suhasini M. Iyengar, Manish Kumar Jain, Julie E. Pickett, Hye Jin Kang, Mary Jo Ondrechen, Georges El Fakhri, Marc D. Normandin, and Anna-Liisa Brownell, Journal of Medicinal Chemistry 65(14) 9939-9954 (2022).
“Identification and characterization of alternative sites and molecular probes for SARS-CoV-2 target proteins,” Suhasini M. Iyengar, Kelly K. Barnsley, Hoang Yen Vu, Ian Jef A. Bongalonta, Alyssa S. Herrod, Jasmine A. Scott, Mary Jo Ondrechen, Frontiers in Chemistry 10, https://doi.org/10.3389/fchem.2022.1017394 (2022).
2021
“Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase,” Timothy A. Coulther, Moritz Pott, Cathleen Zeymer, Donald Hilvert, Mary Jo Ondrechen, Protein Science, 30(8), 1617-1627 (2021).
“Amino acid interactions that facilitate enzyme catalysis,” Timothy A. Coulther, Jaeju Ko, and Mary Jo Ondrechen, Chem. Phys. 154, 195101; https://doi.org/10.1063/5.0041156 (2021).
“Adapting Undergraduate Research to Remote Work to Increase Engagement,” Susan E. Cohen, Sara M. Hashmi, Andrew D. Jones, III, Vasiliki Lykourinou, Mary Jo Ondrechen, Srinivas Sridhar, Anne L. van de Ven, Lauren S. Waters, and Penny J. Beuning, The Biophysicist, 2(2), 28-32 (2021).
“Reintegrating Biology Through the Nexus of Energy, Information, and Matter,” Kim L. Hoke, Sara L. Zimmer, Adam B. Roddy, Mary Jo Ondrechen, Craig E. Williamson, Nicole R. Buan, Integrative and Comparative Biology, https://doi.org/10.1093/icb/icab174 (2021).