Recent Publications

• 1. Poruthoor AJ
  2. Sharma A
  3. Grossfield A
  Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics.; Biophysical journal. 2023 Sep 22.
• 1. Pham TM
  2. Miffin T
  3. Sun H
  4. Sharp KK
  5. Wang X
  6. Zhu M
  7. Hoshika S
  8. Peterson RJ
  9. Benner SA
  10. Kahn JD
  11. Mathews 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.
• 1. Kosoy G
  2. Miller BL
  Two Decades of Arrayed Imaging Reflectometry for Sensitive, High-Throughput Biosensing.; Biosensors; Vol 13(9). 2023 Sep 05.
• 1. Schroeder GM
  2. Kiliushik D
  3. Jenkins JL
  4. Wedekind 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.
• 1. Zhang H
  2. Li S
  3. Dai N
  4. Zhang L
  5. Mathews DH
  6. Huang L
  LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.; Nucleic acids research. 2023 Aug 31.
• 1. Haugen RJ
  2. Barnier C
  3. Elrod ND
  4. Luo H
  5. Jensen MK
  6. Ji P
  7. Smibert CA
  8. Lipshitz HD
  9. Wagner EJ
  10. Freddolino PL
  11. Goldstrohm AC
  Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase.; bioRxiv : the preprint server for biology. 2023 Aug 30.
• 1. Moran MC
  2. Klose A
  3. Yoshida T
  4. De Benedetto A
  5. Schneider LC
  6. Ong PY
  7. Simpson EL
  8. Leung DYM
  9. Miller BL
  10. Seplaki CL
  11. Beck 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.
• 1. Kanti Das S
  2. Kumar A
  3. Hao F
  4. Cutter DiPiazza AR
  5. Fang H
  6. Lee TH
  7. Hayes JJ
  Histone H3 tail modifications alter structure and dynamics of the H1 C-terminal domain within nucleosomes.; Journal of molecular biology. 2023 Aug 22.
• 1. Wu J
  2. Subbaiah KCV
  3. Hedaya O
  4. Chen S
  5. Munger J
  6. Tang WHW
  7. Yan C
  8. Yao P
  FAM210A regulates mitochondrial translation and maintains cardiac mitochondrial homeostasis.; Cardiovascular research. 2023 Jul 31.
• 1. Liu L
  2. Xu Z
  3. Molina Vargas AM
  4. Dollery SJ
  5. Schrlau MG
  6. Cormier D
  7. O'Connell MR
  8. Tobin GJ
  9. Du K
  Aerosol Jet Printing-Enabled Dual-Function Electrochemical and Colorimetric Biosensor for SARS-CoV-2 Detection.; Analytical chemistry. 2023 Jul 28.
• 1. Vargas AMM
  2. Osborn R
  3. Sinha S
  4. Arantes PR
  5. Patel A
  6. Dewhurst S
  7. Palermo G
  8. O'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.
• 1. Dehghani-Ghahnaviyeh S
  2. Smith M
  3. Xia Y
  4. Dousis A
  5. Grossfield A
  6. Sur 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.
• 1. Sinha S
  2. Molina Vargas AM
  3. Arantes PR
  4. Patel A
  5. O'Connell MR
  6. Palermo G
  RNA-mediated Allosteric Activation in CRISPR-Cas13a.; bioRxiv : the preprint server for biology. 2023 Jul 27.
• 1. Dunn DM
  2. Pack LJ
  3. Munger 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.
• 1. Zuber J
  2. Sah SK
  3. Mathews DH
  4. Rustchenko E
  Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants.; Microorganisms; Vol 11(8). 2023 Jul 25.
• 1. Zhang K
  2. Eldin P
  3. Ciesla JH
  4. Briant L
  5. Lentini JM
  6. Ramos J
  7. Cobb J
  8. Munger J
  9. Fu 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.
• 1. Kretsch RC
  2. Andersen ES
  3. Bujnicki JM
  4. Chiu W
  5. Das R
  6. Luo B
  7. Masquida B
  8. McRae EKS
  9. Schroeder GM
  10. Su Z
  11. Wedekind JE
  12. Xu L
  13. Zhang K
  14. Zheludev IN
  15. Moult J
  16. Kryshtafovych A
  RNA target highlights in CASP15: Evaluation of predicted models by structure providers.; Proteins. 2023 Jul 19.
• 1. Ali SE
  2. Mittal A
  3. Mathews DH
  RNA Secondary Structure Analysis Using RNAstructure.; Current protocols; Vol 3(7), pp. e846. 2023 Jul.
• 1. Jonnakuti VS
  2. Ji P
  3. Gao Y
  4. Lin A
  5. Chu Y
  6. Elrod N
  7. Huang KL
  8. Li W
  9. Yalamanchili HK
  10. Wagner EJ
  NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.; Journal of neuro-oncology. 2023 Jun 30.
• 1. Zhou T
  2. Dai N
  3. Li S
  4. Ward M
  5. Mathews DH
  6. Huang L
  RNA design via structure-aware multifrontier ensemble optimization.; Bioinformatics (Oxford, England); Vol 39(39 Suppl 1), pp. i563-i571. 2023 Jun 30.