CBI Scholar Publications

Dwyer, K., Agarwal, N., Pile, L., and Ansari, A., 2021, Gene Architecture Facilitates Intron-Mediated Enhancement of Transcription, Front Mol Biosci, 8, 669004.  

Dwyer, K., Agarwal, N., Gega, A., and Ansari, A., 2021, Proximity to the Promoter and Terminator Regions Regulates Transcription Enhancement Potential of an Intron. Front Mol Biosci, 8, 712639.  

Fidler, E., Dwyer, K., and Ansari, A., 2024, Ssu72: A Versatile Protein with Functions in Transcription and Beyond. Front Mol Biosci, 11, 1332878. 

Kelm, J.M., Samarbakhsh, A., Pillai, A., VanderVere-Carozza, P.S., Aruri, H., Pandey, D.S., Pawelczak, K.S., Turchi, J.J., and Gavande, N.S., 2022, Recent Advances in the Development of Non-PIKKs Targeting Small Molecule Inhibitors of DNA Double-Strand Break Repair. Front Oncol, 12, 850883. 

Kelm, J., Aruri, H., Nyalapatla, P., and Gavande, N., 2023, Benzene Fused Pyrimidine-based Derivatives and Their Biological Properties. In: Kumar, R, Vardanyan, R, eds. Heterocyclic Drug Discovery: Fused Pyrimidine-Based Drug Discovery. Elsevier, 165-191.   

Patel, N., Hasse, T., Malin, E., Kelm, J., Gavande, N., and Huang, Y., 2023, Identification of Novel Inhibitors Targeting KRAS-SOS1 Interactions by Structure-based Drug Design. Biophys J, 122(3), 184a.   

Kelm, J.M., Pandey, D.S., Malin, E., Kansou, H., Arora, S., Kumar, R., and Gavande, N.S., 2023, PROTAC'ing Oncoproteins: Targeted Protein Degradation for Cancer Therapy. Mol Cancer, 22(1), 62. 

Dorandish, S., Bhayekar, K., Singh, A., Kushwaha, N.D., Malin, E., Serafimovski, S., Kelm, J.M., Gavande, N.S., and Lakkaniga, N.R. (2025). Evolution of structure-guided drug design strategies targeting mutations in codon 12 of KRAS. RSC Medicinal Chem, 16(8), 3429-3455.

Debarba, L.K., Mulka, A., Lima, J.B.M., Didyuk, O., Fakhoury, P., Koshko, L., Awada, A.A., Zhang, K., Klueh, U., and Sadagurski, M., 2020, Acarbose Protects from Central and Peripheral Metabolic Imbalance Induced by Benzene Exposure, Brain Behav Immun. 89, 87-99.

Koshko, L., Debarba, L.K., Sacla, M., Lima, J.M.B., Didyuk, O., Fakhoury, P., and Sadagurski M., 2021, In Utero Maternal Benzene Exposure Predisposes to the Metabolic Imbalance in the Offspring. Toxicological Sciences, 180(2), 252-261.

Koshko, L., Scofield, S., Mor, G., and Sadagurski, M., 2022, Prenatal Pollutant Exposures and Hypothalamic Development: Early Life Disruption of Metabolic Programming, Front Endocrinol, 13, 93809.

Debarba, L.K., Koshko, L., Jayarathne, H., Yi, Z., Klueh, U., and Sadagurski. M., 2022, 1309-P: Central Mechanisms of Pollution-Induced Metabolic Disease, Diabetes, 1, 71.

Koshko, L., Scofield, S., Debarba, L., Stilgenbauer, L., Sacla, M., Fakhoury, P., Jayarathne, H., Perez-Mojica, J.E., Griggs, E., Lempradl, A., and Sadagurski M., 2023, Prenatal Benzene Exposure Alters Offspring Hypothalamic Development Predisposing to Metabolic Disease in Later Life, Chemosphere, 330, 138738.

Stilgenbauer, L., de Lima, J.B.M., Debarba, L.K., Khan, M., Koshko, L., Kopchick, J.J., Bartke, A., Schneider, A., and Sadagurski, M., 2023 Growth Hormone Receptor (GHR) in AgRP Neurons Regulates Thermogenesis in a Sex-specific Manner, Geroscience, 45(3), 1745-1759.

Maxwell, A., Adzibolosu, N., Hu, A., You, Y., Stemmer, P.M., Ruden, D.M., Petriello, M.C., Sadagurski, M., Debarba, L.K., Koshko, L., Ramadoss, J., Nguyen, A.T., Richards, D., Liao, A., Mor, G., and Ding, J., 2023, Intrinsic Sexual Dimorphism in the Placenta Determines the Differential Response to Benzene Exposure, iScience, 26(4), 106287.

Jayarathne, H.S.M., Sullivan, R., Stilgenbauer, L., Debarba, L.K., Kuchumov, A., Koshko, L., Scofield, S., Liu, W., Ginsburg, B.C., Miller, R.A., and Sadagurski, M., 2024, Hypothalamic Sex-Specific Metabolic Shift by Canagliflozin During Aging, Geroscience, 46(5), 4479-4493.

Debarba, L.K., Jayarathne, H.S.M., Stilgenbauer, L., Dos Santos, A.L.T., Koshko, L., Scofield, S., Sullivan, R., Mandal, A., Klueh, U., and Sadagurski M., 2024, Microglia Mediate Metabolic Dysfunction From Common Air Pollutants Through NF-κB Signaling, Diabetes, 73(12), 2065-2077.

Scofield, S.*, Koshko, L.*, Stilgenbauer, L., Booms, A., Berube, R., Kassotis, C., Lin, C.H., Jang, H., Kim, S., Stemmer, P., Lempradl, A., and Sadagurski, M., 2025, Integrative Multi-omics Analysis of Metabolic Dysregulation Induced by Occupational Benzene Exposure in Mice, Sci Total Environ, 971, 179060. (*co-First Authors)

Stilgenbauer, L., Chen, Q., Pungi, D., James, N., Jayarathne, H., Koshko, L., Scofield, S., Zhang, K., and Sadagurski, M., 2025, Microglial ER Stress Response via IRE1α Regulates Diet-induced Metabolic Imbalance and Obesity in Mice, Mol Metab, 95, 102128. 

Barraza, R., Jr., Sertage, A.G., Kajjam, A.B., Ward, C.L., Lutter, J.C., Schlegel, H.B., and Allen, M. J., 2022, Properties of Amine-Containing Ligands That Are Necessary for Visible-Light-Promoted Catalysis with Divalent Europium, Inorg Chem, 61, 19649-19657.

Lutter, J.C.; Batchev, A.L.; Ortiz, C.J.; Sertage, A.G.; Romero, J.; Subasinghe, S.A.A.S.; Pedersen, S.E.; Samee, M.A.H.; Pautler, R.G.; and Allen, M.J., 2023, Outersphere Approach to Increasing the Persistance of Oxygen-sensitive Europium(II)-containing Contrast Agents for Magnetic Resonance Imaging with Perfluorocarbon Nanoemulsions Toward Imaging of Hypoxia, Adv Healthc Mater, 12(19), e2203209.

Subasinghe, S.A.A.S., Ortiz, C.J., Romero, J., Ward, C.L., Sertage, A.G., Kurenbekova, L., Yustein, J.T., Pautler, R.G., and Allen, M.J., 2023, Toward Quantification of Hypoxia using fFuorinated Eu(II/III)-containing Ratiometric Probes, Proc Natl Acad Sci, USA, 120(15), e2220891120.

Sertage, A.G., Islam, M.S., and Allen, M.J., 2024, Targeted MRI Contrast Agents, Met Ions Life Sci, 99-117. 

Trimpin, S., Inutan, E.D., Pagnotti, V.S., Karki, S., Marshall, D.D., Hoang, K., Wang, B., Lietz, C.B., Richards, A.L., Yenchick, F.S., Lee, C., Lu, I.-C., Fenner, M., Madarshahian, S., Saylor, S., Chubatyu, N.D., Zimmerman, T., Moreno-Pedraza, A., Wang, T., Adeniji-Adele, A., Meher, A.K., Madagedara, H., Owczarzak, Z., Musavi, A., Hendrickson, T.L., Peacock, P.M., Tomsho, J.W., Larsen, B.S., Prokai, L., Shulaev, V., Pophristic, M., and McEwen, C.N., 2024, Direct Sub-atmospheric Pressure Ionization Mass Spectrometry: Evaporation/sublimation-driven Ionization is Amazing, Fundamentally, and Practically, J Mass Spectrom, 59(6), e5018.

Wolak, T., Islam, R., Venneti, N.M., Stockdill, J.L., Nguyen, H.M., and Chow, C.S., 2025, Truncated and Disubstituted (P4K and L7R) Oncocin Peptides Target the Ribosome with Improved Antibacterial Activity, ACS Omega, 10(40), 47493-47503. 

Prasad, P., Hunt, L.A., Pall, A.E., Ranasinghe, M., Williams, A.E., Stemmler, T.L., Demeler, B., Hammer, N.I., and Chakraborty, S., 2023, Photocatalytic Hydrogen Evolution by a De Novo Designed Metalloprotein that Undergoes Ni-Mediated Oligomerization Shift, Chemistry, 29(14), e202202902.

Pall, A.E., Bond, S., Bailey, D.K., Stoj, C.S., Deschamps, I., Huggins, P., Parsons, J., Bradbury, M.J., Kosman, D.J., and Stemmler, T.L., 2024, ATH434, A Promising Iron-targeting Compound for Treating Iron Regulation Disorders, Metallomics, 16(10), mfae044.

Boyd, J.M., Ryan Kaler, K., Esquilín-Lebrón, K., Pall, A., Campbell, C.J., Foley, M.E., Rios-Delgado, G., Mustor, E.M., Stephens, T.G., Bovermann, H., Greco, T.M., Cristea, I.M., Carabetta, V.J., Beavers, W.N., Bhattacharya, D., Skaar, E.P., Shaw, L.N., and Stemmler, T.L., 2024, Fpa (YlaN) is An Iron(II) Binding Protein that Functions to Relieve Fur-mediated Repression of Gene Expression in Staphylococcus aureus, mBio, 15(11), e0231024. 

Armstrong, C., Luo, D., Gretzinger, A., Pande, D., Lipchik, A., Todi, S., and Dutta, A., 2024, Novel Piperazine Based Compounds Target Alzheimer’s disease relevant amyloid beta-42 and tau derived peptide AcPHF6, and the Lead Molecule Increases Viability in the Flies Expressing Human Tau Protein, ACS Chem Neurosci, 15(21), 3901-3914.

Torres, M., Lu, Y., Pederson, B., Wang, H., Gretzinger, A., Lin, L.L., Hwang, J., Chen, X., Rupp, A.C., Tomlinson, A.J., Soctt, A.J., Zhao, Z., Wahl, D.R., Myers, M.G., Lyssiotis, C.A., Qi, L., 2026, Neuronal SEL1L-HRD1 ER-Associated Degradation is Essential for Motor Function and Survival in Mice, J Clin Invest, 136(8), e196819. 

Ralph-Epps, T., Onu, C.J., Vo, L., Schmidtke, M.W., and Greenberg, M.L., 2021, Studying Lipid-related Pathophysiology Using the Yeast Model, Frontiers in Physiology, 12, 768411. 

Liang, Z., Ralph-Epps, T., Schmidtke, M.W., Lazcano, P., Denis, S.W., Balážová, M., Teixeira da Rosa, N., Jr, Chakkour, M., Hazime, S., Ren, M., Schlame, M., Houtkooper, R.H., and Greenberg, M.L., 2024, Upregulation of the AMPK-FOXO1-PDK4 Pathway is a Primary Mechanism of Pyruvate Dehydrogenase Activity Reduction in Tafazzin-deficient Cells, Sci Rep, 14(1), 14633.

Liang, Z., Ralph-Epps, T., Schmidtke, M.W., Kumar, V., and Greenberg, M.L., 2024, Decreased Pyruvate Dehydrogenase Activity in Tafazzin-deficient Cells is Caused by Dysregulation of Pyruvate Dehydrogenase Phosphatase 1 (PDP1), J Biol Chem, 300(3), 105697. 

Puscheck, E.E., Ruden, X., Singh, A., Abdulhasan, M., Ruden, D.M., Awonuga, A.O., and Rappolee, D.A., 2022, Using High Throughput Screen to Predict Miscarriages with Placental Stem Cells and Long-Term Stress Effects with Embryonic Stem Cells, Birth Defects Res, 114(16), 1014-1036.

Singh, A., Rappolee, D.A., and Ruden, D.M., 2023, Epigenetic Reprogramming in Mice and Humans: From Fertilization to Primordial Germ Cell Development, Cells, 12(14), 1874.

Ruden, D.M., Singh, A., and Rappolee, D.A., 2023, Pathological Epigenetic Events and Reversibility Review: The Intersection Between Hallmarks of Aging and Developmental Origin of Health and Disease, Epigenomics, 15(14), 741-754.

Kidder, B.L., Ruden, X., Singh, A., Marben, T.A., Rass, L., Chakravarty, A., Xie, Y., Puscheck, E.E., Awonuga, A.O., Harris, S., Ruden, D.M., and Rappolee, D.A., 2024, Novel High Throughput Screen Reports that Benzo(a)Pyrene Overrides Trophoblast Stem Cell Multipotency, Inducing SAPK Activity, HAND1 and Differentiated Trophoblast Giant Cells, Placenta, 152, 72-85.

Ruden, X.*, Singh, A.*, Marben, T., Tang, W., Awonuga, A., Ruden, D.M., Puscheck, E., Feng, H., Korzeniewski, S.J., and Rappolee, D., 2024, A Single Cell Transcriptomic Fingerprint of Stressed Premature, Imbalanced Differentiation of Embryonic Stem Cells, Birth Defects Res, 116(11), e2409. (*co-First Authors)   

Nandana, V., Rathnayaka-Mudiyanselage, I.W., Muthunayake, N.S., Hatami, A., Mousseau, C.B., Ortiz-Rodríguez, L.A., Vaishnav, J., Collins, M., Gega, A., Mallikaarachchi, K.S., Yassine, H., Ghosh, A., Biteen, J.S., Zhu, Y., Champion, M.M., Childers, W.S., and Schrader J.M., 2023, The BR-body Proteome Contains a Complex Network of Protein-protein and Protein-RNA Interactions, Cell Rep, 42(10), 113229

Yassine, H., and Schrader J.M., 2024, APEX2 Proximity Labeling of RNA in Bacteria. Cell Rep Methods, 5(11), 101206.

Ortiz-Rodríguez, L.A., Yassine, H., Nandana, V., Azaldegui, C.A., Cheng, J., Schrader, J.M., and Biteen J.S., 2025, Stress Changes the Bacterial Biomolecular Condensate Material State and Shifts Function from mRNA Decay to Storage, Nat Commun, 16(1), 10019.

Passos, C., Tomares, D., Yassine, H., Schnorr, W., Hunter, H., Wolfe-Feichter, H.K., Velier, J., Dzurik, K.G., Grillo, J., Gega, A., Saxena, S., Schrader, J., Childer, W.S., 2025, BR-Bodies Facilitate Adaptive Responses and Survival During Copper Stress in Caulobacter crescentus, J Biol Chem, 301(10) 110648. 

Bakkar, M., Khalil, S., Bhayekar, K., Kushwaha, N.D., Samarbakhsh, A., Dorandish, S., Edwards, H., Dou, Q.P., Ge, Y., and Gavande, N.S., 2025, Ubiquitin-Specific Protease Inhibitors for Cancer Therapy: Recent Advances and Future Prospects, Biomolecules, 15(2), 240.

Dorandish, S., Bhayekar, K., Singh, A., Kushwaha, N.D., Malin, E., Serafimovski, S., Kelm, J.M., Gavande N.S., and Lakkaniga, N.R., 2025, Evolution of Structure-guided Drug Design Strategies Targeting Mutations in Codon 12 of KRAS, RSC Med Chem, 16(8), 3429-3455. 

Hummel, K., Turro, C., and Kodanko, J.J., 2025, Recent Development of Ruthenium Complexes for Photochemotherapy (PCT) Applications. In RSC Photofunctional Materials, Scattergood, P. Eds. Royal Society of Chemistry, pp 68-107.

Hummel, K., Gupta, S., Marques Silva, M., Garcia, S.P., Odhiambo, D., Sygit, D., Ward, C. Kocarek, T., Sokolov, A.Y., Turro, C., and Kodanko, J.J., 2025, Cytochrome P450 Induction through the Efficient Photoinduced Release of a Pyridine-Substituted Agent from Ru(II). J Am Chem Soc, 147(39), 35198-35202.

Hummel, K., Stringer, B., Thenuwara, S.I., Westrick, J.A., and Kodanko, J.J., 2026, Beyond IC50: Reframing Microcystin Potency against Protein Phosphatase 2A by Defining Two-step Irreversible Inhibition Kinetics. ACS Omega, ASAP DOI: 10.1021/acsomega.6c03076 

Lewandowski, E.C., Arban, C.B., Deal, M.P., Batchev, A.L., and Allen, M.J., 2024, Europium(II/III) Coordination Chemistry Toward Applications. Chem Commun, 60(77), 10655-10671.

Fidler, E. and Ansari, A., 2024, Sub2: A TFIIB Interacting Protein with Pleiotropic Roles in mRNA Synthesis, Processing and Transport. Int J Biochem Physiol, 9(1), 250.

Fidler, E., Dwyer, K. and Ansari, A., 2024, Ssu72: A Versatile Protein with Functions in Transcription and Beyond, Front Mol Biosci, 11, 1332878.

Fidler, E., Khan, Z., Awada, A., Dwyer, K, Pangeni, S., Sakamoto, T., and Ansari, A., 2025, Comprehensive Analysis of the Role of ASC1 and APE2 Introns on Cellular Fitness, Transcription, and Post‐transcriptional Dynamics, FEBS J, 293(4), 1238-1251. 

Martin, C.E., Murray, A.S., Mackinder, J.R., Sala-Hamrick, K.E., Flynn, M.G., Lundgren, J.G., Varela, F.A., and List, K., 2022, TMPRSS13 Zymogen Activation, Surface Localization, and Shedding is Regulated by Proteolytic Cleavage within the Non-catalytic Stem Region. Biol Chem, 403(10), 969-982.

Lundgren, J.G., Flynn, M.G., and List, K., 2025, GPI-Anchored Serine Proteases: Essential Roles in Development, Homeostasis, and Disease. Biol Chem, 406(1-2), 1-28.

Lundgren, J.G., Flynn, M.G., and List, K. 2025, The Cell-surface Serine Protease Prostasin is Lost During Cervical Squamous Cell Carcinogenesis, Human Cell, 38(5), 147.

Lundgren, J.G., Flynn, M.G., Winkler, A.R., Rivera, B.N., Tanabe, L.M., Stemmer, P.M., Chen, L.M., Chai, K.X., and List, K., 2026, Metastasis Suppressing Properties of the Cell-surface Anchored Serine Protease Prostasin: New Functional and Mechanistic Insights from Breast Cancer, Oncogenesis, 10.1038/s41389-026-00615-3. 

Hudock, J., and Kenney, J. W., 2024, Aging in Zebrafish is Associated with Reduced Locomotor Activity and Strain Dependent Changes in Bottom Dwelling and Thigmotaxis. PLoS One, 19(5), e0300227.

Fontana, B.D., Hudock, J., Rajput, N., Kanini, D., Luong, D., and Kenney, J.W., 2025, Individual Differences in Fear Memory Expression Engage Distinct Functional Brain Networks, bioRxiv,2025.05.12.653531.

Goldson, A.R., Hudock, J., and Kenney, J.W., 2026, Routine Metabolic Rate is not Associated with Boldness in Zebrafish. Biol Open, 15(3), bio062329. 

Adebayo, D., Obaseki, E., Vasudeva, K., Aboumourad, M., Sleiman, A., Bandyopadhyay, S., Kreinbring, L., and Hariri, H., 2025, Sphingolipid and Methionine Metabolism in Aging. J Cell Sci, 138(21), jcs264026, https://doi.org/10.1242/jcs.264026.

Adebayo, D., Obaseki, E., Miller, S., Aboumourad, M., Zaid Saadeh, Z., Pomicter, Z., Kreinbring, L., Rahal, M., Vasudeva, K., Frost, G., Smadi, R., and Hariri, H., 2026, Nvj3 Regulates Dga1-mediated Triacylglycerol Synthesis and Lipid Droplet Formation at ER Contact Sites. bioRxiv, doi: 10.64898/2026.01.05.695145. 

Hotor, M.,  Wakpal, J., Yost-Slinker, D., and Nguyen, H.M., 2026, Design, Synthesis, and Biological Evaluation of Heparan Sulfate-like Oligosaccharides for Their Interactions with Growth Factor Cytokines. J Med Chem, https://doi.org/10.1021/acs.jmedchem.6c00760.