URMC / Biochemistry & Biophysics / Research / Recent Publications

Recent Publications

1. Zhu M
2. Mathews DH
Sequence Design Using RNAstructure.; Methods in molecular biology (Clifton, N.J.); Vol 2847, pp. 17-31. 2025.
1. Rasouli A
2. Pickard FC
3. Sur S
4. Grossfield A
5. Işık Bennett M
Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer.; Journal of chemical information and modeling. 2024 Dec 19.
1. Scales TQ
2. Smith B
3. Blanchard LM
4. Wixom N
5. Tuttle ET
6. Altman BJ
7. Peppone LJ
8. Munger J
9. Campbell TM
10. Campbell EK
11. Harris IS
A whole food, plant-based diet reduces amino acid levels in patients with metastatic breast cancer.; Cancer & metabolism; Vol 12(1), pp. 38. 2024 Dec 19.
1. McMahon M
2. Maquat LE
Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay.; RNA (New York, N.Y.). 2024 Dec 12.
1. Reed CR
2. Kennedy SD
3. Horowitz RH
4. Keedakkatt Puthenpeedikakkal AM
5. Stern HA
6. Mathews DH
Modeling and NMR Data Elucidate the Structure of a G-Quadruplex-Ligand Interaction for a Pu22T-Cyclometalated Iridium(III) System.; The journal of physical chemistry. B. 2024 Nov 19.
1. Berger KD
2. Puthenpeedikakkal AMK
3. Mathews DH
4. Fu D
Structural impact of 3-methylcytosine modification on the anticodon stem of a neuronally-enriched arginine tRNA.; bioRxiv : the preprint server for biology. 2024 Nov 18.
1. Ajalik RE
2. Linares I
3. Alenchery RG
4. Zhang VZ
5. Wright TW
6. Miller BL
7. McGrath JL
8. Awad HA
Human Tendon-on-a-Chip for Modeling the Myofibroblast Microenvironment in Peritendinous Fibrosis.; Advanced healthcare materials. 2024 Nov 15.
1. Mittal A
2. Ali SE
3. Mathews DH
Using the RNAstructure Software Package to Predict Conserved RNA Structures.; Current protocols; Vol 4(11), pp. e70054. 2024 Nov.
1. Kiliushik D
2. Goenner C
3. Law M
4. Schroeder GM
5. Srivastava Y
6. Jenkins JL
7. Wedekind JE
Knotty is nice: metabolite binding and RNA-mediated gene regulation by the preQ1 riboswitch family.; The Journal of biological chemistry. 2024 Oct 30.
1. Courtney E
2. Datta A
3. Mathews DH
4. Ward M
memerna: Sparse RNA Folding Including Coaxial Stacking.; Journal of molecular biology. 2024 Oct 18.
1. Iannuzzelli JA
2. Bonn R
3. Hong AS
4. Anitha AS
5. Jenkins JL
6. Wedekind JE
7. Fasan R
Cyclic peptides targeting the SARS-CoV-2 programmed ribosomal frameshifting RNA from a multiplexed phage display library.; Chemical science. 2024 Oct 17.
1. Srivastava Y
2. Akinyemi O
3. Rohe TC
4. Pritchett EM
5. Baker CD
6. Sharma A
7. Jenkins JL
8. Mathews DH
9. Wedekind JE
Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.; Nucleic acids research. 2024 Oct 16.
1. Zhu M
2. Zuber J
3. Tan Z
4. Sharma G
5. Mathews DH
DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.; bioRxiv : the preprint server for biology. 2024 Oct 15.
1. Poruthoor AJ
2. Stallone JJ
3. Miaro M
4. Sharma A
5. Grossfield A
System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers.; The Journal of chemical physics; Vol 161(14). 2024 Oct 14.
1. Hecht F
2. Zocchi M
3. Tuttle ET
4. Ward NP
5. Smith B
6. Kang YP
7. Cazarin J
8. Soares ZG
9. Ozgurses ME
10. Zhao H
11. Sheehan C
12. Alimohammadi F
13. Munger LD
14. Trivedi D
15. Asantewaa G
16. Blick-Nitko SK
17. Zoeller JJ
18. Chen Y
19. Vasiliou V
20. Turner BM
21. Muir A
22. Coloff JL
23. Munger J
24. DeNicola GM
25. Harris IS
Catabolism of extracellular glutathione supplies amino acids to support tumor growth.; bioRxiv : the preprint server for biology. 2024 Oct 11.
1. Maji D
2. Jenkins JL
3. Boutz PL
4. Kielkopf CL
Recurrent Neurodevelopmentally Associated Variants of the Pre-mRNA Splicing Factor U2AF2 Alter RNA Binding Affinities and Interactions.; Biochemistry. 2024 Oct 10.
1. Scales TQ
2. Smith B
3. Blanchard LM
4. Wixom N
5. Tuttle ET
6. Altman BJ
7. Peppone LJ
8. Munger J
9. Campbell TM
10. Campbell EK
11. Harris IS
A whole food, plant-based diet reduces amino acid levels in patients with metastatic breast cancer.; medRxiv : the preprint server for health sciences. 2024 Oct 09.
1. Beard JW
2. Hunt SL
3. Evans A
4. Goenner C
5. Miller BL
Mimicking a Cellular Crowding Environment for Enzyme-Free Paper-Based Nucleic Acid Tests at the Point of Care.; ACS sensors. 2024 Sep 30.
1. Oberstrass L
2. Tants JN
3. Lichtenthaeler C
4. Ali SE
5. Koch L
6. Mathews DH
7. Schlundt A
8. Weigand J
Comprehensive Profiling of Roquin Binding Preferences for RNA Stem-Loops.; Angewandte Chemie (International ed. in English). 2024 Sep 30.
1. Cosler LE
2. Midence L
3. Hayes JJ
4. Gondeck JT
5. Moy K
6. Chen MH
7. Hogan JD
The Influence of State Restrictions on Opioid Prescribing: 2006-2018.; Journal of public health management and practice : JPHMP. 2024 Sep 24.