URMC / Biochemistry & Biophysics / Research / Recent Publications

Recent Publications

1. Tang WY
2. Dai N
3. Zhou T
4. Mathews DH
5. Huang L
SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo sampling.; Nature communications. 2026 Feb 20.
1. Rambout X
2. Maquat LE
Keeping cells fit.; Science (New York, N.Y.); Vol 391(6786), pp. 657-658. 2026 Feb 12.
1. Butt JN
2. Scott RL
3. Bryan MR
4. Steiner DJ
5. Bachmann R
6. Santonastaso B
7. Gatchell M
8. Refaai M
9. Miller BL
A multi-readout photonic sensor for rapid diagnosis of Von Willebrand disease.; Npj biosensing; Vol 3(1), pp. 7. 2026 Feb 02.
1. Zhou T
2. Malik A
3. Tang WY
4. Mathews DH
5. Huang L
Theory, Algorithms, and Applications for Identification of Undesignable RNA Secondary Structures and Motifs.; Journal of computational biology : a journal of computational molecular cell biology; Vol 33(1), pp. 134-167. 2026 Jan 30.
1. Shen Z
2. Siriboe MG
3. Ren X
4. Dayananda T
5. Jenkins JL
6. Khare SD
7. Fasan R
Computational design of generalist cyclopropanases with stereodivergent selectivity.; Nature communications. 2026 Jan 26.
1. Yuan B
2. Das SK
3. Wang W
4. Camacho G
5. Kumar A
6. Hayes JJ
7. Lee TH
Conformations of linker histone H1 bound to nucleosome arrays.; Journal of molecular biology. 2026 Jan 21.
1. Kirchhoff CL
2. Powell HR
3. Galardi JW
4. Loerch S
5. Pulvino MJ
6. Jenkins JL
7. Boutz PL
8. Kielkopf CL
SF3B1 Phosphorylation Prompts U2AF2 Dissociation for Widespread Control of pre-mRNA Splicing.; bioRxiv : the preprint server for biology. 2026 Jan 20.
1. Li S
2. Feng S
3. Liu Y
4. Qin C
5. Zhang J
6. Saito T
7. Xie X
8. Fu W
9. Wang R
10. Zheng Y
11. Shu Z
12. Yeh W
13. Sasaki S
14. Tjokro N
15. Chen L
16. Munger J
17. Jung J
18. Chen C
19. Feng P
Bacteria-herpesvirus interaction reveals a proviral role of ISGylation in promoting herpesvirus capsid assembly.; bioRxiv : the preprint server for biology. 2026 Jan 20.
1. Szikszai M
2. Wang TY
3. Krueger R
4. Mathews DH
5. Ward M
6. Aviran S
Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.; RNA (New York, N.Y.). 2026 Jan 09.
1. Evans AL
2. Sogn AK
3. Mora AC
4. Arthur MN
5. Leach JR
6. Bosch SI
7. Araselvan S
8. Beard JW
9. Dewhurst S
10. Mace CR
11. Miller BL
QuickDraw: detecting HIV in whole blood using an integrated paper-based consumable that enables direct amplification of purified RNA from paper.; Lab on a chip. 2026 Jan 05.
1. Luchsinger C
2. Dai AZ
3. Yalamanchili H
4. Balakrishnan A
5. Huang K-L
6. Bertelli C
7. Cui B
8. Lorenzo-Redondo R
9. Wagner EJ
10. Diaz-Griffero F
HIV-1 infection regulates gene expression by altering alternative polyadenylation correlated with CPSF6 and CPSF5 redistribution.; mBio. 2025 Dec 17.
1. Alessandrini F
2. Wright M
3. Kurosaki T
4. Perloff OS
5. Ngo M
6. Kofler JK
7. Donnelly CJ
8. Maquat LE
9. Kiskinis E
TDP-43 dysfunction compromises UPF1-dependent mRNA metabolism in ALS.; Neuron. 2025 Dec 12.
1. Soto CA
2. Lesch ML
3. Becker JL
4. Sharipol A
5. Khan A
6. Schafer XL
7. Li Z
8. Streeter AR
9. Becker MW
10. Munger JC
11. Frisch BJ
Elevated Lactate in AML Bone Marrow Contributes to Macrophage Polarization via GPR81 Signaling.; Blood advances. 2025 Dec 09.
1. Abshire ET
2. Maquat LE
Gene regulation through exon junction complex modularity.; Nature structural & molecular biology. 2025 Dec 03.
1. Akinyemi O
2. Kennedy SD
3. McSally JP
4. Mathews DH
NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent base pairs determine conformational preference.; Biophysical journal. 2025 Nov 18.
1. Land H
2. Land SA
3. Chen S
Fournier's gangrene in remote Northern Ontario, Canada: A rare but critical condition.; Canadian journal of rural medicine : the official journal of the Society of Rural Physicians of Canada = Journal canadien de la medecine rurale : le journal officiel de la Societe de medecine rurale du Canada; Vol 30(4), pp. 189-191. 2025 Nov 12.
1. Grove AK
2. Das A
3. Wakabayashi H
4. Ivanov AV
5. Ermolenko DN
An smFRET assay to probe the impact of antibiotics on intersubunit rotation in eukaryotic ribosomes.; Methods in enzymology; Vol 725, pp. 77-103. 2025 Nov 11.
1. Szikszai M
2. Wang TY
3. Krueger R
4. Mathews DH
5. Ward M
6. Aviran S
Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.; bioRxiv : the preprint server for biology. 2025 Nov 07.
1. Simpson LA
2. Dunn DM
3. Fales W
4. Moore ZJ
5. Ciesla JH
6. Waild N
7. Raymonda MH
8. Harris IS
9. Munger J
HCMV infection depends on EGLN1-mediated mitochondrial activation to increase dNTP pools for viral DNA replication.; bioRxiv : the preprint server for biology. 2025 Oct 31.
1. Park BJ
2. Hua S
3. Casler KD
4. Cefaloni E
5. Ayers MC
6. Lake RF
7. Murphy KE
8. Vertino PM
9. O'Connell MR
10. Murphy PJ
CUT&Tag overcomes biases of ChIP and establishes chromatin patterns for repetitive genomic loci.; iScience; Vol 28(11), pp. 113757. 2025 Oct 13.