URMC / Biochemistry & Biophysics / Research / Recent Publications Recent Publications Poruthoor AJSharma AGrossfield A Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics.; Biophysical journal. 2023 Sep 22. Pham TMMiffin TSun HSharp KKWang XZhu MHoshika SPeterson RJBenner SAKahn JDMathews DH DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.; ACS synthetic biology. 2023 Sep 06. Kosoy GMiller BL Two Decades of Arrayed Imaging Reflectometry for Sensitive, High-Throughput Biosensing.; Biosensors; Vol 13(9). 2023 Sep 05. Schroeder GMKiliushik DJenkins JLWedekind JE Structure and function analysis of a type III preQ1-I riboswitch from E. coli reveals direct metabolite-sensing by the Shine-Dalgarno sequence.; The Journal of biological chemistry. 2023 Sep 01. Zhang HLi SDai NZhang LMathews DHHuang L LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.; Nucleic acids research. 2023 Aug 31. Haugen RJBarnier CElrod NDLuo HJensen MKJi PSmibert CALipshitz HDWagner EJFreddolino PLGoldstrohm AC Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase.; bioRxiv : the preprint server for biology. 2023 Aug 30. Moran MCKlose AYoshida TDe Benedetto ASchneider LCOng PYSimpson ELLeung DYMMiller BLSeplaki CLBeck LA History of S. aureus Skin Infection Significantly Associates with History of Eczema Herpeticum in Patients with Atopic Dermatitis.; Dermatology and therapy. 2023 Aug 24. Kanti Das SKumar AHao FCutter DiPiazza ARFang HLee THHayes JJ Histone H3 tail modifications alter structure and dynamics of the H1 C-terminal domain within nucleosomes.; Journal of molecular biology. 2023 Aug 22. Wu JSubbaiah KCVHedaya OChen SMunger JTang WHWYan CYao P FAM210A regulates mitochondrial translation and maintains cardiac mitochondrial homeostasis.; Cardiovascular research. 2023 Jul 31. Liu LXu ZMolina Vargas AMDollery SJSchrlau MGCormier DO'Connell MRTobin GJDu K Aerosol Jet Printing-Enabled Dual-Function Electrochemical and Colorimetric Biosensor for SARS-CoV-2 Detection.; Analytical chemistry. 2023 Jul 28. Vargas AMMOsborn RSinha SArantes PRPatel ADewhurst SPalermo GO'Connell MR New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity.; bioRxiv : the preprint server for biology. 2023 Jul 28. Dehghani-Ghahnaviyeh SSmith MXia YDousis AGrossfield ASur S Ionizable Amino Lipids Distribution and Effects on DSPC/Cholesterol Membranes: Implications for Lipid Nanoparticle Structure.; The journal of physical chemistry. B. 2023 Jul 27. Sinha SMolina Vargas AMArantes PRPatel AO'Connell MRPalermo G RNA-mediated Allosteric Activation in CRISPR-Cas13a.; bioRxiv : the preprint server for biology. 2023 Jul 27. Dunn DMPack LJMunger JC Raf1 promotes successful Human Cytomegalovirus replication and is regulated by AMPK-mediated phosphorylation during infection.; bioRxiv : the preprint server for biology. 2023 Jul 26. Zuber JSah SKMathews DHRustchenko E Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants.; Microorganisms; Vol 11(8). 2023 Jul 25. Zhang KEldin PCiesla JHBriant LLentini JMRamos JCobb JMunger JFu D Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease.; bioRxiv : the preprint server for biology. 2023 Jul 20. Kretsch RCAndersen ESBujnicki JMChiu WDas RLuo BMasquida BMcRae EKSSchroeder GMSu ZWedekind JEXu LZhang KZheludev INMoult JKryshtafovych A RNA target highlights in CASP15: Evaluation of predicted models by structure providers.; Proteins. 2023 Jul 19. Ali SEMittal AMathews DH RNA Secondary Structure Analysis Using RNAstructure.; Current protocols; Vol 3(7), pp. e846. 2023 Jul. Jonnakuti VSJi PGao YLin AChu YElrod NHuang KLLi WYalamanchili HKWagner EJ NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.; Journal of neuro-oncology. 2023 Jun 30. Zhou TDai NLi SWard MMathews DHHuang L RNA design via structure-aware multifrontier ensemble optimization.; Bioinformatics (Oxford, England); Vol 39(39 Suppl 1), pp. i563-i571. 2023 Jun 30.