URMC / Biochemistry & Biophysics / Research / Recent Publications

Recent Publications

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.
1. Pan Y
2. Kierzek E
3. Kierzek R
4. Mathews DH
5. Yu YT
A Ψ-Ψ codon-anticodon pairing in nonsense suppression and translational recoding.; Nature chemical biology. 2025 Sep 12.
1. Land H
Beyond the exam room: skin health as a window into rural health equity.; Canadian medical education journal; Vol 16(4), pp. 77-78. 2025 Sep 10.
1. Burchett JB
2. Ambeskovic A
3. Ford M
4. Naccarato JC
5. Cazarin J
6. Hecht F
7. Hulver M
8. He X
9. Munger JC
10. Vertino PM
11. Harris IS
12. Mello SS
13. Altman BJ
MYC and Epithelial to Mesenchymal Transition (EMT) Independently Predict Circadian Rhythm Disruption in Lung Adenocarcinoma.; bioRxiv : the preprint server for biology. 2025 Aug 21.
1. Cognetti JS
2. Miller BL
Real-Time, Continuous Monitoring of Tissue Chips as an Emerging Opportunity for Biosensing.; Sensors (Basel, Switzerland); Vol 25(16). 2025 Aug 19.
1. Baliga UK
2. Yang L
3. Ivanov A
4. Schwartz JL
5. Jiang F
6. Khor ES
7. Das D
8. Wainwright L
9. Yao P
Translational Control in Cardiac Pathophysiology and Therapeutic Development: When mRNA Meets the Heart.; International journal of molecular sciences; Vol 26(16). 2025 Aug 14.
1. Luchsinger C
2. Dai AZ
3. Yalamanchili H
4. Balakrishnan A
5. Huang KL
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 Through CPSF6 and CPSF5 Delocalization.; bioRxiv : the preprint server for biology. 2025 Aug 07.
1. Wakabayashi H
2. Zhu M
3. Grayhack EJ
4. Mathews DH
5. Ermolenko DN
40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion.; RNA (New York, N.Y.). 2025 Jul 31.
1. Mittal A
2. Mathews DH
AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.; bioRxiv : the preprint server for biology. 2025 Jul 28.
1. Butt JN
2. Steiner DJ
3. Bryan MR
4. Mann KE
5. Miller BL
A Dual-Readout Photonic Sensor for Simultaneous Measurement of Enzyme Activity and Concentration.; ACS sensors. 2025 Jul 24.
1. Kurosaki T
2. Cho H
3. Abshire ET
4. Pröschel C
5. Mitsutomi S
6. Sato H
7. Simko EAJ
8. Fraser CS
9. Sakano H
10. Maquat LE
FMRP drives mRNP targets into translationally silenced complexes.; Molecular cell. 2025 Jul 08.