2025

• Liu J, Negi SS, Yang C, Zhou X, Schein CH, Braun W, Kim P. AllergenAI: a deep learning model predicting allergenicity based on protein sequence. BMC Bioinformatics. 2025 Nov 18;26(1):279. doi: 10.1186/s12859-025-06302-1.
• Bernstein JS, Canon N, Schein CH, Braun W, Negi SS, Tchekmedyian R, Pozzoli M, Kim EH, Kulis MD, Vu T, Liu W, Chen X, Dreskin SC. Fine resolution of the N-terminal IgE-binding epitope of Ara h 2: Discovery of variants with enhanced IgE binding. J Allergy Clin Immunol. 2025 Aug;156(2):385-393. doi: 10.1016/j.jaci.2025.03.032.
• Kolasangiani R, Farzanian K, Chen Y, Schwartz MA, Bidone TC. Conformational response of αIIbβ3 and αVβ3 integrins to force. Structure. 2025 Feb 6;33(2):289-299.e4. doi: 10.1016/j.str.2024.11.016.
• Torki ME, Liu F, Xu R, Chen Y, Fredberg J, Chen Z. Bridging the Gap in Cancer Cell Behavior Against Matrix Stiffening: Insights from a Trizonal Model. eLife, 2025, 14:RP102809. doi: 10.7554/eLife.102809.1
• Wu Y., Cao Z., Liu W., Cahoon J., Wang K., Wang P., Hu L., Chen Y., Moser M., Vella A. T., Ley K., Wen L., Fan Z., Nanoscopy reveals integrin clustering reliant on kindlin-3 but not talin-1. Cell Communication and Signaling. 2025, 23(1):12. doi: 10.1186/s12964-024-02024-8.
• Younis D. A., Marosvari M., Liu W., Pulikkot S., Cao Z., Zhou B., Vella A. T., McArdle S., Hu L., Chen Y., Gan W., Yu J., Bruscia E. M., Fan Z., CFTR dictates monocyte adhesion by facilitating integrin clustering but not activation. Proceedings of the National Academy of Sciences. 2025, 122 (3) e2412717122. doi: 10.1073/pnas.2412717122.
• Travin DY, Basu RS, Paranjpe MN, Klepacki D, Zhurakovskaya AI, Vázquez-Laslop N, Mankin AS, Polikanov YS, Gagnon MG. Sequence-specific trapping of EF-Tu/glycyl-tRNA complex on the ribosome by bottromycin. bioRxiv [Preprint]. 2025 Aug 20:2025.08.17.670399. doi: 10.1101/2025.08.17.670399.
• Aleksandrova EV, Syroegin EA, Basu RS, Vassilevski AA, Gagnon MG, Polikanov YS. Mechanism of release factor-mediated peptidyl-tRNA hydrolysis on the ribosome. Science. 2025 Jun 19;388(6753):eads9030. doi: 10.1126/science.ads9030.
• Wang X, Levy Y, Iwahara J. Competition between Nucleic Acids and Intrinsically Disordered Regions within Proteins. Acc Chem Res. 2025 Aug 5;58(15):2415-2424. doi: 10.1021/acs.accounts.5c00261.
• Iwahara J. Ion NMR for Biomolecular Systems. J Mol Biol. 2025 Dec 1;437(23):169285. doi: 10.1016/j.jmb.2025.169285.
• Wang T, Arcos D, Doty FD, Pettitt BM, Iwahara J. Strong field gradients enable NMR-based diffusion measurements for K+, Mg2+, Cl-, and SO42- ions in biomolecular solutions. J Magn Reson. 2025 Jul;376:107890. doi: 10.1016/j.jmr.2025.107890.
• Wang X, Yu B, Wang T, Iwahara J. Anisotropic Dynamics of Protein Side Chain NH2 Groups Revealed through Analysis of 2H and 15N NMR Relaxation Rates. J Phys Chem Lett. 2025 Feb 20:2175-2180. doi: 10.1021/acs.jpclett.4c03666.
• Mon KKZ, Kenney LJ. Evaluation of tumor-colonizing Salmonella strains using the chick chorioallantoic membrane model. mBio. 2025 Jan 28:e0359024. doi: 10.1128/mbio.03590-24.
• Mattenberger Y, Knyazhanskaya ES, Shneider MM, Buth SA, Nazarov S, Robins WP, Leiman PG, Belin D. The spike tip protein of bacteriophage T4. bioRxiv [Preprint]. 2025 Aug 28:2025.08.28.672839. doi: 10.1101/2025.08.28.672839.
• Jain K, Kishan K, Minhaj RF, Kanchanawong P, Sheetz MP, Changede R. Immobile Integrin Signaling Transit and Relay Nodes Organize Mechanosignaling through Force-Dependent Phosphorylation in Focal Adhesions. ACS Nano. 2025 Jan 21;19(2):2070-2088. doi: 10.1021/acsnano.4c03214.
• Chowdhury B, Zhu K, Li C, Alsing J, Luebeck J, Stefanova ME, Chapman OS, Kraft K, Zhang S, Lim JYS, Xie Y, Kim YJ, Wu S, Chavez L, Nir G, Henssen AG, Mischel PS, Chang HY, Bafna V. Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D. Nat Commun. 2025 Dec 20;17(1):894. doi: 10.1038/s41467-025-67614-7.
• Chen C, Yu B, Wang X, Iwahara J, Pettitt BM. Effects of Probe-Related Correlations on Local Electrostatic Potentials Around DNA. J Comput Chem. 2025 May 15;46(13):e70125. doi: 10.1002/jcc.70125.
• Jassal C, Strawn J, Rajarathnam K, Rajagopal S. CXCR1 and CXCR2 display receptor bias for shared chemokine agonists. bioRxiv [Preprint]. 2025 Oct 2:2025.09.30.679682. doi: 10.1101/2025.09.30.679682.
• Tarek S, ElMaghloob Y, Smith H, Smith TJ, ElRakaiby MT, Habib MH. A Scavenger Hunt for a DyP-Peroxidase from a Metagenome: Curated Peroxidase Database-Assisted Primer Design and Protein Structure Elucidation. ACS Chem Biol. 2025 Jul 18;20(7):1783-1791. doi: 10.1021/acschembio.5c00323.
• Sherman MB, Smith HQ, Cox F, Wobus CE, Lynch GC, Pettitt BM, Smith TJ. Murine norovirus allosteric escape mutants mimic gut activation. bioRxiv [Preprint]. 2025 Feb 4:2025.02.04.636510. doi: 10.1101/2025.02.04.636510.
• Sherman MB, Smith TJ. Cryogenic Electron Microscopy of Rift Valley Fever Virus. Methods Mol Biol. 2025;2893:57-72. doi: 10.1007/978-1-0716-4338-9_6.
• Sowers ML, Baljinnyam T, Herring JL, Chang-Gu B, Hackfeld LC, Tang H, Hatch S, Valdes P, Zhang K, Sowers LC. Temozolomide-Derived AIC Is Incorporated into Purine Synthesis in Glioblastoma. Chem Res Toxicol. 2025 Oct 20;38(10):1698-1707. doi: 10.1021/acs.chemrestox.5c00196.
• Herring JL, Sowers ML, Conrad JW, Hackfeld LC, Chang-Gu B, Dilawari R, Sowers LC. Incorporation and Repair of Epigenetic Intermediates as Potential Chemotherapy Agents. Molecules. 2025 Aug 1;30(15):3239. doi: 10.3390/molecules30153239.
• Singh K, Patten JJ, Dimet-Wiley A, Davey RA, Watowich SJ, Chandra A, Leverett J. Unlocking the potential of phytochemicals in inhibiting SARS-CoV-2 MPro protein - an in silico and cell-based approach. Sci Rep. 2025 Jul 2;15(1):22840. doi: 10.1038/s41598-025-05907-z.
• Chambers TL, Dimet-Wiley A, Keeble AR, Haghani A, Lo WJ, Kang G, Brooke R, Horvath S, Fry CS, Watowich SJ, Wen Y, Murach KA. Methylome-proteome integration after late-life voluntary exercise training reveals regulation and target information for improved skeletal muscle health. J Physiol. 2025 Jan;603(1):211-237. doi: 10.1113/JP286681.
• Cansado-Utrilla C, Saldaña MA, Golovko G, Khanipov K, Watson RK, Wild AL, Brettell LE, Weaver SC, Heinz E, Hughes GL. Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti. Anim Microbiome. 2025 Nov 5;7(1):116. doi: 10.1186/s42523-025-00482-0.
• Bartlett ML, Miley K, Vermund SH, Weaver SC. Arthropod-borne disease challenges from planetary warming, urbanization, and migration. Virol J. 2025 Oct 10;22(1):325. doi: 10.1186/s12985-025-02950-0.
• Alcorn MDH, Sun C, Gilliland TC Jr, Lukash T, Crasto CM, Raju S, Diamond MS, Weaver SC, Klimstra WB. Three positively charged binding sites on the eastern equine encephalitis virus E2 glycoprotein coordinate heparan sulfate- and protein receptor-dependent infection. Nat Commun. 2025 Aug 5;16(1):7227. doi: 10.1038/s41467-025-62513-3.
• Rodriguez L, Adam A, Luo H, Osman SR, Plante K, Rossi SL, Weaver SC, Wang T. γδ T Cells Mediate Protective Immunity Following Vaccination with an Insect-Based Chikungunya Fever Vaccine in Mice. Pathogens. 2025 Aug 30;14(9):863. doi: 10.3390/pathogens14090863.
• Williams EP, Xue Y, Yang D, Lee J, Kim E, Ponce-Flores A, Zalduondo L, Cao X, Chung D, Golden JE, Meibohm B, Fitzpatrick EA, Weaver SC, Jonsson CB. Broad spectrum antiviral BDGR-164 provides protection against lethal neurotropic alphavirus infection in mice. Antiviral Res. 2025 Aug;240:106206. doi: 10.1016/j.antiviral.2025.106206.
• Carvalho DCM, Dunn T, Campos RK, Tierney JA, Onyoni F, Cavalcante-Silva LHA, Pena LJ, Rodrigues-Mascarenhas S, Wu P, Weaver SC. Antiviral and immunomodulatory effects of ouabain against congenital Zika syndrome model. Mol Ther. 2025 Feb 5;33(2):465-470. doi: 10.1016/j.ymthe.2024.12.021.
• Peel JE, Jardinella E, Qu Y, Plante JA, Mitchell BM, Walker JL, Garofalo RP, Weaver SC, Plante KS, Brasel T, Lawrence WS. Advanced photohydrolysis technology demonstrates rapid inactivation of aerosolized SARS-CoV-2 and efficacy against other respiratory viral pathogens. Am J Infect Control. 2025 Feb 17:S0196-6553(25)00062-8. doi: 10.1016/j.ajic.2025.02.008.
• Greenwald E, Galls D, Park J, Jain N, Montgomery SB, Roy B, Yin YW, Fire AZ. DragonRNA: Generality of DNA-primed RNA-extension activities by DNA-directed RNA polymerases. Nucleic Acids Res. 2025 Mar 20;53(6):gkaf236. doi: 10.1093/nar/gkaf236.
• Segev-Zarko L-a. mSphere of Influence: From pixels to parasite insight-cryo-EM is rewiring apicomplexan cell biology. mSphere. 2025 Sep 30;10(9):e0023125. doi: 10.1128/msphere.00231-25.
• Farmer SM, Solbach A, Xu S, Rios B, Ye X, Gao A, Covarrubias D, Yu Y, Ye L, Chuong V, Furr Stimming E, Zhao H, Zhang S. Structural-functional analyses of the huntingtin/HAP40 complex in Drosophila and humans. J Biomol Struct Dyn. 2025 Mar 17:1-16. doi: 10.1080/07391102.2025.2474683.