URochester Medicine / Biochemistry & Biophysics / Research / Recent Publications

Recent Publications

1. Jain A
2. Mayeen NF
3. Meadow ME
4. Kalandadze N
5. Swovick K
6. Welle KA
7. Hryhorenko JR
8. Ghaemmaghami S
Structural proteomics reveals that misfolded nascent proteins expose buried lysines for ubiquitination and rapid proteasomal degradation.; Cell reports; Vol 45(7), pp. 117620. 2026 Jul 03.
1. Zhou T
2. Mathews DH
3. Huang L
Probabilistic RNA designability via interpretable ensemble approximation and dynamic decomposition.; Bioinformatics (Oxford, England); Vol 42(Supplement_1). 2026 Jul 01.
1. Ossevoort T
2. Chernaya O
3. Browning A
4. Mathews DH
5. Ermolenko DN
40S ribosomal subunits move along the 5' UTR through an eIF4A-independent mechanism in higher eukaryotes.; bioRxiv : the preprint server for biology. 2026 Jun 24.
1. Bruno BS
2. Platten EM
3. Houston L
4. Brule CE
5. Grayhack EJ
The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair in Saccharomyces cerevisiae.; RNA (New York, N.Y.). 2026 Jun 16.
1. Das A
2. Grove AK
3. Ivanov AV
4. Wakabayashi H
5. Ermolenko DN
Observing intersubunit dynamics in single yeast ribosomes.; Nucleic acids research; Vol 54(11). 2026 Jun 08.
1. Casadio R
2. Lu ZJ
3. Mathews DH
4. Sternberg MJE
Computational Resources for Molecular Biology 2026.; Journal of molecular biology. 2026 Jun 08.
1. Price JDW
2. Vizeacoumar FS
3. Abuhussein O
4. Maranda V
5. Zhang Y
6. Adachi H
7. Nguyen K
8. Kyrylenko L
9. Rangel-Pozzo A
10. Dong H
11. Gong L
12. Materi A
13. Walke P
14. Ganapathysamy A
15. Denomy C
16. Freywald T
17. Dahiya R
18. Elhasasna H
19. Saxena A
20. Vizeacoumar JP
21. Patel H
22. Rajamanickam K
23. de Oliveira DM
24. Lazell-Wright M
25. Morales AM
26. Aggarwal A
27. Xu JL
28. Alli N
29. Munhoz EP
30. Gao P
31. Salsman J
32. Dahiya DK
33. Kola NS
34. Gonzalez-Lopez C
35. Thibault P
36. Levin M
37. Dellaire G
38. Jette N
39. Groot G
40. Köbel M
41. Lee CH
42. Hopkins L
43. Krishnan A
44. Ahmed S
45. Eskiw C
46. Barakat KH
47. Thakur A
48. Wu Y
49. DePinho RA
50. Mai S
51. Yu YT
52. Wong JMY
53. Freywald A
54. Vizeacoumar FJ
Epigenetic control of telomeric RNA maintains heterochromatin in telomerase-driven cancers.; Signal transduction and targeted therapy; Vol 11(1). 2026 Jun 04.
1. Boopathi R
2. Garcia-Saez I
3. Turunç S
4. Lone IN
5. Kumar A
6. Abu Alhaija AA
7. Hayes JJ
8. Bednar J
9. Diril MK
10. Iliev D
11. Gospodinov A
12. Le Roy A
13. Skoufias D
14. Angelov D
15. Hamiche A
16. Kale S
17. Dimitrov S
18. Petosa C
A Rahman Syndrome mutation in histone H1.4 disrupts chromatin compaction and phase separation.; Nature communications. 2026 May 22.
1. Puthenpeedikakkal AMK
2. Cavender CE
3. Smith LG
4. Grossfield A
5. Mathews DH
Reparameterization of the Amber RNA Force Field Non-Bonded Terms.; bioRxiv : the preprint server for biology. 2026 May 19.
1. Shabangu TS
2. Kierzek E
3. Arteaga S
4. Orf GS
5. Stone J
6. Hiltke OM
7. Miaro M
8. Jolley EA
9. Soszyńska-Jóźwiak M
10. Szabat M
11. Aviran S
12. Bevilacqua PC
13. Znosko BM
14. Kierzek R
15. Mathews DH
Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.; bioRxiv : the preprint server for biology. 2026 May 17.
1. Klose AM
2. Beck CA
3. Kates SL
4. Muthukrishnan G
5. Schwarz EM
6. Miller BL
Dual-Scale StaphAIR: Predictive Modeling for the Diagnosis of S. aureus Infection via Simultaneous Detection and Quantification of Cytokines and Antibodies.; Analytical chemistry. 2026 May 16.
1. Simpson LA
2. Dunn DM
3. Fales W
4. Moore ZJ
5. Ciesla JH
6. Waild NC
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.; Cell reports; Vol 45(5), pp. 117329. 2026 Apr 29.
1. Gigas J
2. Meadow ME
3. Guo J
4. Lan C
5. Hillpot E
6. Martinez JC
7. Tombline G
8. Bellomio P
9. Almodovar VR
10. Welle KA
11. Swovick K
12. Hryhorenko JR
13. Ablaeva J
14. Ghaemmaghami S
15. Seluanov A
16. Gorbunova V
Long-lived mammals contain more phosphorylation sites in the SIRT6 C-terminus that enhance PARP1 interaction and resistance to oxidative stress.; bioRxiv : the preprint server for biology. 2026 Apr 24.
1. Ebrahim SAM
2. Talross GJS
3. Dweck HKM
4. Shepard JJ
5. Carlson JR
A phytoscreen identifies a garlic compound as a deterrent of mating and egg laying in Drosophila and mosquitoes.; Cell. 2026 Apr 17.
1. Kierzek E
2. Shabangu TS
3. Hiltke OM
4. Miaro M
5. Arteaga S
6. Znosko BM
7. Jolley EA
8. Bevilacqua PC
9. SantaLucia J
10. SantaLucia HA
11. Lin H
12. Metkar M
13. Aviran S
14. Soszyńska-Jóźwiak M
15. Kierzek R
16. Mathews DH
RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine.; bioRxiv : the preprint server for biology. 2026 Apr 11.
1. Hsieh KL
2. Panagoda NT
3. Jenkins JL
4. Sampson NS
Kinetic Insights into Cholera Toxin B-Biomimetic Glycan Interactions.; Biomacromolecules. 2026 Apr 07.
1. Linares I
2. Creveling A
3. Osman A
4. Grandwetter N
5. Miller BL
6. McGrath JL
7. Awad HA
A human synovial tendon-on-a-chip models key features of peritendinous adhesions and offers a new approach methodology for testing anti-fibrotic drugs.; bioRxiv : the preprint server for biology. 2026 Apr 07.
1. Waild NC
2. Ciesla JH
3. Schafer XL
4. Munger J
Cellular antibody affinity-based CRISPR screening identifies JUNB as a broadly acting antiviral factor.; Proceedings of the National Academy of Sciences of the United States of America; Vol 123(14), pp. e2534154123. 2026 Mar 30.
1. Malik A
2. Zhou T
3. Tang WY
4. Mathews DH
5. Huang L
Motif Server: Web Server for Undesignable RNA Motifs and Structures.; Journal of molecular biology. 2026 Mar 25.
1. Hecht F
2. Zocchi M
3. Tuttle ET
4. Ward NP
5. Alimohammadi F
6. Khan AA
7. Gomes VC
8. Smith B
9. Twardowski JJ
10. Mills BN
11. Welle KA
12. Ghaemmaghami S
13. Zhou Z
14. Gan Y
15. Kang YP
16. Cazarin J
17. Soares ZG
18. Ozgurses ME
19. Zhao H
20. Sheehan C
21. Cognet G
22. Munger LD
23. Trivedi D
24. Asantewaa G
25. Blick-Nitko SK
26. Zoeller JJ
27. Chen Y
28. Vasiliou V
29. Turner BM
30. Mello SS
31. Altman BJ
32. Muir A
33. Coloff JL
34. Munger J
35. DeNicola GM
36. Harris IS
Catabolism of extracellular glutathione supplies cysteine to support tumours.; Nature. 2026 Mar 18.