URMC / Biochemistry & Biophysics / Research / Recent Publications

Recent Publications

1. Hao K
2. Nguyen T
3. Nakada Y
4. Walcott G
5. Wei Y
6. Wu Y
7. Garry DJ
8. Yao P
9. Zhang J
Newborn apical resection preserves the proliferative capacity of cardiomyocytes located throughout the left ventricle.; Stem cells (Dayton, Ohio). 2025 Apr 15.
1. Baluapuri A
2. Zhao NC
3. Marina RJ
4. Huang KL
5. Kuzkina A
6. Amodeo ME
7. Stein CB
8. Ahn LY
9. Farr JS
10. Schaffer AE
11. Khurana V
12. Wagner EJ
13. Adelman K
Integrator loss leads to dsRNA formation that triggers the integrated stress response.; Cell. 2025 Apr 10.
1. Meadow M
2. Boras S
3. Hoare M
4. Ahmed M
5. Alimohammadi F
6. Welle K
7. Swovick K
8. Hryhorenko J
9. Jain A
10. Martinez J
11. Seluanov A
12. Gorbunova V
13. Buchwalter A
14. Ghaemmaghami S
Proteome Birthdating: A Single-Sample Approach for Measuring Global Turnover Dynamics and "Protein Age"; Bio-protocol Journal. 2025 Jan 01.
1. Rodems B
2. Sharma S
3. Baker C
4. Kaszuba C
5. Ito T
6. Calvi L
7. Becker M
8. Jordan C
9. Ashton J
10. Franco E
11. Welle K
12. Swovick K
13. Ghaemmaghami S
14. Bajaj J
Taurine from tumour niche drives glycolysis to promote leukaemogenesis; Nature. 2025 Jan 01.
1. Klose AM
2. Katz JD
3. Boni R
4. Nelson D
5. Miller BL
Lambda Theta Reflectometry: a new technique to measure optical film thickness applied to planar protein arrays.; bioRxiv : the preprint server for biology. 2025 Mar 29.
1. Berger KD
2. Puthenpeedikakkal AMK
3. Mathews DH
4. Fu D
Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA.; Journal of molecular biology. 2025 Mar 29.
1. Thalalla Gamage S
2. Khoogar R
3. Howpay Manage S
4. DaRos JT
5. Crawford MC
6. Georgeson J
7. Polevoda BV
8. Sanders C
9. Lee KA
10. Nance KD
11. Iyer V
12. Kustanovich A
13. Perez M
14. Thu CT
15. Nance SR
16. Amin R
17. Miller CN
18. Holewinski RJ
19. Das S
20. Meyer TJ
21. Koparde V
22. Yang A
23. Jailwala P
24. Nguyen JT
25. Andresson T
26. Hunter K
27. Gu S
28. Mock BA
29. Edmondson EF
30. Difilippantonio S
31. Chari R
32. Schwartz S
33. O'Connell MR
34. Wu CC
35. Meier JL
Transfer RNA acetylation regulates in vivo mammalian stress signaling.; Science advances; Vol 11(12), pp. eads2923. 2025 Mar 19.
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 Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays.; bioRxiv : the preprint server for biology. 2025 Feb 05.
1. Dunn DM
2. Pack LJ
3. Munger JC
RAF1 promotes successful human cytomegalovirus replication and is regulated by AMPK-mediated phosphorylation during infection.; Journal of virology. 2025 Feb 04.
1. Bucukovski J
2. Miller BL
Everything's under Control: Maximizing Biosensor Performance through Negative Control Probe Selection.; Analytical chemistry. 2025 Feb 03.
1. Sah SK
2. Yadav A
3. Stahl T
4. Hayes JJ
5. Bulger M
6. Rustchenko E
Echinocandin Adaptation in Candida albicans Is Accompanied by Altered Chromatin Accessibility at Gene Promoters and by Cell Wall Remodeling.; Journal of fungi (Basel, Switzerland); Vol 11(2). 2025 Feb 01.
1. Linares I
2. Chen K
3. Saffren A
4. Mansouri M
5. Abhyankar VV
6. Miller BL
7. Begolo S
8. Awad HA
9. McGrath JL
Fluid flow impacts endothelial-monocyte interactions in a model of vascular inflammatory fibrosis.; Scientific reports; Vol 15(1), pp. 3227. 2025 Jan 25.
1. Ambeskovic A
2. McCall MN
3. Land H
Reply to Takefuji.; Gastroenterology. 2025 Jan 25.
1. Getsy PM
2. May WJ
3. Henderson F
4. Seckler JM
5. Grossfield A
6. Baby SM
7. Lewis SJ
Nitrosyl factors play a vital role in the ventilatory depressant effects of fentanyl in freely moving guinea pigs.; Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie; Vol 183, pp. 117847. 2025 Jan 24.
1. Stegemann F
2. Marcus E
3. Neupert S
4. Ostrowski S
5. Mathews DH
6. Phizicky EM
Schizosaccharomyces pombe pus1 mutants are temperature sensitive due to decay of tRNAIle(UAU) by the 5'-3' exonuclease Dhp1, primarily targeting the unspliced pre-tRNA.; RNA (New York, N.Y.). 2025 Jan 23.
1. Tanu T
2. Cox AM
3. Karlow J
4. Sharma P
5. He X
6. Wu C
7. Babu S
8. Brown J
9. Brown KM
10. Chanock SJ
11. Liu D
12. Zhang T
13. Burns KH
14. Boutz PL
15. Insco ML
Recurrent oncogenic ZC3H18 mutations stabilize endogenous retroviral RNA.; bioRxiv : the preprint server for biology. 2025 Jan 14.
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.; bioRxiv : the preprint server for biology. 2025 Jan 04.
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.