Publications

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Template-based RNA structure prediction advanced through a blind code competition.
Lee Y, He S, Oda T, Rao GJ, Kim Y, Kim R, Kim H, Heng CK, Kowerko D, Li H, et al. 2025. Template-based RNA structure prediction advanced through a blind code competition. bioRxiv : the preprint server for biology : . DOI: 10.64898/2025.12.30.696949
Metabolite Fraction Libraries for Quantitative NMR Metabolomics.
Esselman C, Garrison K, Ponce L, Borges RM, Delaglio F, Edison AS. 2025. Metabolite Fraction Libraries for Quantitative NMR Metabolomics. bioRxiv : the preprint server for biology : . DOI: 10.64898/2025.12.30.696914
Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.
Michel HM, Brown AM, MacKerell AD, Lemkul JA. 2025. Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design. bioRxiv : the preprint server for biology : . DOI: 10.64898/2025.12.20.695737
Multiplatform Benchtop NMR Interlaboratory Study of Model Liquid Dosage Forms of Pharmaceutical Products.
Briggs KT, Delaglio F, Taraban MB, Brinson RG, Arbogast L, Lichtenthal B, Pennestri M, Espina R, Robert H, Araneda JF, et al. 2026. Multiplatform Benchtop NMR Interlaboratory Study of Model Liquid Dosage Forms of Pharmaceutical Products. Analytical chemistry : . DOI: 10.1021/acs.analchem.5c05487
B cell transcriptomics reveals lasting dysregulation and rapid decline of protective memory after hepatitis C cure.
Chen F, Giang E, Natarajan P, Mondala TS, Head SR, Lau SC, Sundaresan A, Kulakova L, Lin X, Aneja J, et al. 2025. B cell transcriptomics reveals lasting dysregulation and rapid decline of protective memory after hepatitis C cure. bioRxiv : the preprint server for biology : . DOI: 10.1101/2025.10.24.664545
Rational design of flavivirus E protein vaccine optimizes immunogenicity and mitigates antibody dependent enhancement risk.
Wang Y, Galkin A, Shang X, Marin A, Jin S, Ye TJ, Bale S, Chiang CI, Chowdhury A, Chenine AL, et al. 2025. Rational design of flavivirus E protein vaccine optimizes immunogenicity and mitigates antibody dependent enhancement risk. Nature communications : . DOI: 10.1038/s41467-025-67447-4
Utilizing plant synthetic biology to accelerate plant-microbe interactions research.
Yang X, Tannous J, Rush TA, Del Valle I, Xiao S, Maharjan B, Liu Y, Weston DJ, De K, Tschaplinski TJ, et al. 2025. Utilizing plant synthetic biology to accelerate plant-microbe interactions research. Biodesign research 7(2): 100007. DOI: 10.1016/j.bidere.2025.100007
Top-Down Scoring of Spectral Fitness by Image Analysis for Protein Structure Validation.
Harding BD, DeZonia B, Garg R, Hu Z, Delaglio F, Grant T, Rienstra CM. 2025. Top-Down Scoring of Spectral Fitness by Image Analysis for Protein Structure Validation. Journal of chemical information and modeling : . DOI: 10.1021/acs.jcim.5c02159
Computational Modeling of PROTAC Ternary Complexes as Ensembles Using SILCS-xTAC.
Nordquist EB, Zhao M, Yu W, MacKerell AD. 2025. Computational Modeling of PROTAC Ternary Complexes as Ensembles Using SILCS-xTAC. Journal of chemical information and modeling : . DOI: 10.1021/acs.jcim.5c02045
Arrhythmia Risk Predictions from Molecular Simulations of Cardiac Ion Channel-Drug Interactions.
Rouen KC, Narang K, Han Y, Wang D, Jang E, Brunkow S, Yarov-Yarovoy V, MacKerell AD, Vorobyov I. 2025. Arrhythmia Risk Predictions from Molecular Simulations of Cardiac Ion Channel-Drug Interactions. Biophysical journal : . DOI: 10.1016/j.bpj.2025.12.015
Sleep health as a predictor of the course of depressed mood and loss of interest in individuals with depression.
Schmid SR, Schiel JE, Feige B, Holub F, Hertenstein E, Domschke K, Rutter MK, Spiegelhalder K. 2025. Sleep health as a predictor of the course of depressed mood and loss of interest in individuals with depression. International journal of clinical and health psychology : IJCHP 25(4): 100653. DOI: 10.1016/j.ijchp.2025.100653
Macromolecular dimensions of a synthetic polyelectrolyte as a factor in its interactions with protein and cells: desirability for longer chains.
Hlushko R, Marin A, Chowdhury A, Andrianov AK. 2025. Macromolecular dimensions of a synthetic polyelectrolyte as a factor in its interactions with protein and cells: desirability for longer chains. Journal of materials chemistry. B : . DOI: 10.1039/d5tb02163d
The use of multiple liquid chromatography methods augmented by phosphorus-31 nuclear magnetic resonance to characterize the diastereomer composition in synthetic oligonucleotides.
Ali M, Manghrani A, Szramowski M, Abdel-Megied AM, Liang L, Aberg NF, Yang K, Chen K, Wang Y, Zhang D, et al. 2025. The use of multiple liquid chromatography methods augmented by phosphorus-31 nuclear magnetic resonance to characterize the diastereomer composition in synthetic oligonucleotides. Journal of chromatography. A 1766: 466600. DOI: 10.1016/j.chroma.2025.466600
Structural insights into clonal restriction and diversity in T cell recognition of two immunodominant SARS-CoV-2 nucleocapsid epitopes.
Yuan P, Chen G, Li Y, Liu X, Saravanakumar S, Zhao J, Ji Q, Wang H, Lin YW, Elbahnasawy M, et al. 2025. Structural insights into clonal restriction and diversity in T cell recognition of two immunodominant SARS-CoV-2 nucleocapsid epitopes. Nature communications : . DOI: 10.1038/s41467-025-66322-6
Magnetodynamics of short nanoparticle chains.
Bui TQ, Oberdick SD, Abel FM, Donahue MJ, Quelhas KN, Dennis CL, Cleveland TE, Liu Y, Woods SI. 2025. Magnetodynamics of short nanoparticle chains. Scientific reports : . DOI: 10.1038/s41598-025-22864-9