URMC / Biochemistry & Biophysics / Research / Recent Publications

Recent Publications

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.
1. Klose AM
2. Katz JD
3. Boni R
4. Nelson D
5. Hassard B
6. Miller BL
Lambda Theta Reflectometry: A New Technique for Measuring Optical Film Thickness in Planar Protein Arrays.; ACS sensors. 2025 Jul 02.
1. Dai N
2. Zhou T
3. Tang WY
4. Mathews DH
5. Huang L
EnsembleDesign: messenger RNA design minimizing ensemble free energy via probabilistic lattice parsing.; Bioinformatics (Oxford, England); Vol 41(Supplement_1), pp. i391-i400. 2025 Jul 01.
1. McMahon M
2. Maquat LE
Corrigendum: Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay.; RNA (New York, N.Y.); Vol 31(7), pp. 1028. 2025 Jun 16.
1. Waild N
2. Ciesla J
3. Schafer X
4. Munger J
Cellular antibody affinity-based CRISPR Screening identifies JUNB as a broadly acting anti-viral factor.; bioRxiv : the preprint server for biology. 2025 Jun 13.
1. Das A
2. Ivanov AV
3. Wakabayashi H
4. Grove AK
5. Ermolenko DN
Observing intersubunit dynamics in single yeast ribosomes.; bioRxiv : the preprint server for biology. 2025 Jun 08.
1. Walunjkar N
2. Lai TY
3. Akhter N
4. Miller JH
5. Bettinger JQ
6. Marcus E
7. Phizicky EM
8. Ghaemmaghami S
9. Fay JC
Pervasive divergence in protein thermostability is mediated by both structural changes and cellular environments.; Molecular biology and evolution. 2025 Jun 06.
1. Hedaya OM
2. Jiang F
3. Baliga U
4. Ivanov A
5. Chen S
6. Schwartz JL
7. Kawakami Y
8. Yan C
9. Yao P
Upstream open reading frame inactivation augments GATA4 translation and cardiomyocyte hypertrophy in mice.; bioRxiv : the preprint server for biology. 2025 May 18.
1. Mathews DH
2. Casadio R
3. Sternberg MJE
Computational Resources for Molecular Biology 2025.; Journal of molecular biology. 2025 May 15.
1. Sharma S
2. Rodems BJ
3. Baker CD
4. Kaszuba CM
5. Franco EI
6. Smith BR
7. Ito T
8. Swovick K
9. Welle K
10. Zhang Y
11. Rock P
12. Chaves FA
13. Ghaemmaghami S
14. Calvi LM
15. Ganguly A
16. Burack WR
17. Becker MW
18. Liesveld JL
19. Brookes PS
20. Munger JC
21. Jordan CT
22. Ashton JM
23. Bajaj J
Taurine from tumour niche drives glycolysis to promote leukaemogenesis.; Nature. 2025 May 14.
1. Waldern JM
2. Taylor C
3. Giannetti CA
4. Irving PS
5. Allen SR
6. Zhu M
7. Backofen R
8. Mathews DH
9. Weeks KM
10. Laederach A
Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.; Nucleic acids research; Vol 53(9). 2025 May 10.
1. Dillingham CM
2. Cormaty H
3. Morgan EC
4. Tak AI
5. Esgdaille DE
6. Boutz PL
7. Sridharan R
KDM3A and KDM3B regulate alternative splicing in mouse pluripotent stem cells.; iScience; Vol 28(6), pp. 112612. 2025 May 08.
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.