URMC / Center for RNA Biology / Publications

Publications

1. Rambout X
2. Maquat LE
Keeping cells fit.; Science (New York, N.Y.); Vol 391(6786), pp. 657-658. 2026 Feb 12.
1. Porter JJ
2. Ko W
3. Sorensen EG
4. Cheung Z
5. Thrasher K
6. Couch T
7. Gabell JT
8. Shwe V
9. Hyatt J
10. Licata JB
11. Peterson LK
12. Dean DA
13. Lueck JD
Anticodon-edited transfer RNAs (ACE-tRNAs) encoded as therapeutic nonviral minimal DNA vectors.; Nucleic acids research; Vol 54(4). 2026 Feb 05.
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. 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. 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. Omachi K
2. Porter JJ
3. Lueck JD
4. Miner JH
Anticodon-edited tRNA enables translational readthrough of COL4A5 premature termination codons.; PloS one; Vol 20(12), pp. e0330804. 2025 Dec 19.
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. Mul K
2. Eichinger K
3. Hung M
4. Sansone VA
5. Gagnon C
6. Subramony S
7. Roxburgh RH
8. Hamel J
9. Statland JM
10. Elsheikh B
11. Turner C
12. Sampson J
13. Ragole T
14. Matthews E
15. Schoser B
16. Swenson A
17. Laverty C
18. Shieh P
19. Greene EP
20. Takahashi M
21. Wicklund M
22. Dekdebrun J
23. Raymond J
24. DeSpain E
25. Thornton CA
26. Johnson NE
Establishing biomarkers and clinical endpoints in myotonic dystrophy type 1 (END-DM1): Protocol of an international natural history study.; PloS one; Vol 20(12), pp. e0331163. 2025 Dec 11.
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. 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. 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. Piraino LR
2. Chen CY
3. Mereness JA
4. Dunman PM
5. Ovitt CE
6. Benoit DSW
7. DeLouise LA
Salivary gland tissue chip screening identifies candidate radioprotective drugs.; Communications medicine; Vol 5(1), pp. 420. 2025 Oct 09.
1. Gu N
2. Baliga UK
3. Porter JJ
4. Lueck JD
5. Dean DA
Subnuclear organization and mislocalization of plasmids reduce transgene expression.; Molecular therapy. Nucleic acids; Vol 36(4), pp. 102730. 2025 Oct 09.
1. Lin B
2. Woo S
3. Philbrick A
4. Bacsa J
5. Laskey E
6. Mehra N
7. Gondil VS
8. Mei JA
9. Jones G
10. Pavelka MS
11. Dziejman M
12. Shutter DA
13. Melander C
14. Perritt AM
15. Jakober R
16. Shen Y
17. Chang W-C
18. Quave CL
19. Dunman PM
20. Luedemann G
Testing the Luedemann hypothesis: the discovery of novel antimicrobials from slow-growing microbes from nutrient-limited environments.; mSphere. 2025 Sep 23.
1. Sipple MT
2. Hamazaki S
3. Todorow V
4. Cisco LA
5. Lupia KM
6. Heil CS
7. Meinke P
8. Thornton CA
9. Lueck JD
Elimination of myotonia improves myopathy in a muscleblind knockout model of myotonic dystrophy.; bioRxiv : the preprint server for biology. 2025 Sep 21.
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. Porter JJ
2. Ko W
3. Sorensen EG
4. Cheung Z
5. Couch T
6. Gabell JT
7. Shwe V
8. Hyatt J
9. Licata JB
10. Peterson LK
11. Dean DA
12. Lueck JD
Anticodon Edited Transfer RNAs (ACE-tRNAs) Encoded as Therapeutic Nonviral Minimal DNA Vectors.; bioRxiv : the preprint server for biology. 2025 Sep 06.
1. Heatwole CR
2. Luebbe E
3. Hamel J
4. Mongiovi PC
5. Ciafaloni E
6. Dilek N
7. Martens WB
8. Weber DR
9. Rashid H
10. Allen McKeown J
11. Smith CH
12. Howell S
13. Rosero SZ
14. Eichinger K
15. Baker LS
16. Dekdebrun JM
17. Hilbert JE
18. Varma A
19. Thornton CA
20. McDermott MP
21. Moxley RT
Study of Testosterone and Recombinant Human Growth Hormone in Facioscapulohumeral Muscular Dystrophy.; Neurology. Genetics; Vol 11(5), pp. e200292. 2025 Aug 27.
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. McGrath KE
2. Olsen JL
3. Koniski AD
4. Murphy KE
5. Getman M
6. An HH
7. Schulz VP
8. Kim AR
9. Zhang B
10. Carlson TL
11. Papoin J
12. Blanc L
13. Kingsley PD
14. Westhoff CM
15. Gallagher PG
16. Chou ST
17. Steiner LA
18. Palis J
BMI1 regulates human erythroid self-renewal through both gene repression and gene activation.; Nature communications; Vol 16(1), pp. 7619. 2025 Aug 15.
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. Murphy K
2. Getman M
3. Lv X
4. Murphy Z
5. Abid D
6. Rahman N
7. Bulger M
8. Steiner L
Histone H4 lysine 20 methylation marks genes dynamically regulated during erythroid maturation.; Epigenetics & chromatin; Vol 18(1), pp. 48. 2025 Jul 26.
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. Ko W
2. Porter JJ
3. Spelier S
4. Sorensen EG
5. Bhatt P
6. Gabell JT
7. van der Windt I
8. Couch T
9. Coote K
10. Mense M
11. Beekman JM
12. Lueck JD
ACE-tRNAs are a platform technology for suppressing nonsense mutations that cause cystic fibrosis.; Nucleic acids research; Vol 53(13). 2025 Jul 08.
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. 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. Abid D
2. Murphy K
3. Murphy Z
4. Rahman N
5. Getman M
6. Steiner L
The Condensin II complex regulates essential gene expression programs during erythropoiesis.; Development (Cambridge, England); Vol 152(10). 2025 May 19.
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. Franchini L
2. Porter JJ
3. Lueck JD
4. Orlandi C
GzESTY as an optimized cell-based assay for initial steps in GPCR deorphanization.; Nature communications; Vol 16(1), pp. 4521. 2025 May 15.
1. Mathews DH
2. Casadio R
3. Sternberg MJE
Computational Resources for Molecular Biology 2025.; Journal of molecular biology. 2025 May 15.
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. Duarte LS
2. Blumberg N
3. Marvald J
4. Love T
5. Andolina JR
6. Noronha SA
7. Steiner LA
8. Henrichs K
9. Looney RJ
10. Refaai MA
11. Asante A
Differences in outcomes associated with ABO blood groups in recipients of IVIG.; Blood vessels, thrombosis & hemostasis; Vol 2(3), pp. 100075. 2025 May 09.
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. 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. Bhat SY
2. Bhattacharya A
3. Li H
4. Cui X
5. Lueck JD
6. Goldman YE
7. Cooperman BS
Mechanism-based approach in designing patient-specific combination therapies for nonsense mutation diseases.; Nucleic acids research; Vol 53(6). 2025 Mar 20.
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. Butman HS
2. Stefaniak MA
3. Walsh DJ
4. Gondil VS
5. Young M
6. Crow AH
7. Nemeth AM
8. Melander RJ
9. Dunman PM
10. Melander C
Phenyl urea based adjuvants for β-lactam antibiotics against methicillin resistant Staphylococcus aureus.; Bioorganic & medicinal chemistry letters. 2025 Mar 03.
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. Bucukovski J
2. Miller BL
Everything's under Control: Maximizing Biosensor Performance through Negative Control Probe Selection.; Analytical chemistry. 2025 Feb 03.
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. 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. Weeden T
2. Picariello T
3. Quinn B
4. Spring S
5. Shen PY
6. Qiu Q
7. Vieira BF
8. Schlaefke L
9. Russo RJ
10. Chang YA
11. Cui J
12. Yao M
13. Wen A
14. Hsia N
15. Evron T
16. Ovington K
17. Tsai PN
18. Yoder N
19. Lan B
20. Venkatesan R
21. Hall J
22. Desjardins CA
23. Qatanani M
24. Hilderbrand S
25. Najim J
26. Tang Z
27. Tanner MK
28. Subramanian R
29. Thornton CA
30. Ibraghimov-Beskrovnaya O
31. Zanotti S
FORCE platform overcomes barriers of oligonucleotide delivery to muscle and corrects myotonic dystrophy features in preclinical models.; Communications medicine; Vol 5(1), pp. 22. 2025 Jan 18.
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. Provenzano M
2. Ikegami K
3. Bates K
4. Gaynor A
5. Hartman JM
6. Jones AS
7. Butler A
8. Berggren KN
9. Dekdebrun J
10. Hung M
11. Lapato DM
12. Kiefer M
13. Thornton CA
14. Johnson NE
15. Hale MA
The Splice Index as a prognostic biomarker of strength and function in myotonic dystrophy type 1.; The Journal of clinical investigation. 2025 Jan 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.; 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. Pezzini S
2. Mustaccia A
3. Aboa P
4. Faustini G
5. Branchini A
6. Pinotti M
7. Frasca A
8. Porter JJ
9. Lueck JD
10. Landsberger N
Engineered tRNAs efficiently suppress CDKL5 premature termination codons.; Scientific reports; Vol 14(1), pp. 31791. 2024 Dec 30.
1. McMahon M
2. Maquat LE
Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay.; RNA (New York, N.Y.). 2024 Dec 12.
1. Tang WY
2. Dai N
3. Zhou T
4. Mathews DH
5. Huang L
Sampling-based Continuous Optimization with Coupled Variables for RNA Design.; ArXiv. 2024 Dec 11.
1. Porter JJ
2. Ko W
3. Sorensen EG
4. Lueck JD
Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations.; Nucleic acids research. 2024 Nov 30.
1. Reed CR
2. Kennedy SD
3. Horowitz RH
4. Keedakkatt Puthenpeedikakkal AM
5. Stern HA
6. Mathews DH
Modeling and NMR Data Elucidate the Structure of a G-Quadruplex-Ligand Interaction for a Pu22T-Cyclometalated Iridium(III) System.; The journal of physical chemistry. B. 2024 Nov 19.
1. Berger KD
2. Puthenpeedikakkal AMK
3. Mathews DH
4. Fu D
Structural impact of 3-methylcytosine modification on the anticodon stem of a neuronally-enriched arginine tRNA.; bioRxiv : the preprint server for biology. 2024 Nov 18.
1. Ajalik RE
2. Linares I
3. Alenchery RG
4. Zhang VZ
5. Wright TW
6. Miller BL
7. McGrath JL
8. Awad HA
Human Tendon-on-a-Chip for Modeling the Myofibroblast Microenvironment in Peritendinous Fibrosis.; Advanced healthcare materials. 2024 Nov 15.
1. Bhat S
2. Bhattacharya A
3. Li H
4. Lueck JD
5. Goldman YE
6. Cooperman BS
Mechanism-based approach in designing patient-specific combination therapies for nonsense mutation diseases.; bioRxiv : the preprint server for biology. 2024 Nov 14.
1. Connacher RP
2. Roden RT
3. Huang KL
4. Korte AJ
5. Yeruva S
6. Dittbenner N
7. DesMarais AJ
8. Weidmann CA
9. Randall TA
10. Williams J
11. Hall TMT
12. Wagner EJ
13. Goldstrohm AC
The TRIM-NHL RNA-binding protein Brain Tumor coordinately regulates expression of the glycolytic pathway and vacuolar ATPase complex.; Nucleic acids research; Vol 52(20), pp. 12669-12688. 2024 Nov 11.
1. Lindley S
2. Subbaiah K
3. Priyanka F
4. Poosala P
5. Ma Y
6. Jalinous L
7. West JA
8. Richardson W
9. Thomas TN
10. Anderson DM
Ribozyme-activated mRNA Trans-ligation Enables Large Gene Delivery to Treat Muscular Dystrophies; Science; Vol 386, pp. 762-767. 2024 Jan 01.
1. Mittal A
2. Ali SE
3. Mathews DH
Using the RNAstructure Software Package to Predict Conserved RNA Structures.; Current protocols; Vol 4(11), pp. e70054. 2024 Nov.
1. Kiliushik D
2. Goenner C
3. Law M
4. Schroeder GM
5. Srivastava Y
6. Jenkins JL
7. Wedekind JE
Knotty is nice: metabolite binding and RNA-mediated gene regulation by the preQ1 riboswitch family.; The Journal of biological chemistry. 2024 Oct 30.
1. Courtney E
2. Datta A
3. Mathews DH
4. Ward M
memerna: Sparse RNA Folding Including Coaxial Stacking.; Journal of molecular biology. 2024 Oct 18.
1. Iannuzzelli JA
2. Bonn R
3. Hong AS
4. Anitha AS
5. Jenkins JL
6. Wedekind JE
7. Fasan R
Cyclic peptides targeting the SARS-CoV-2 programmed ribosomal frameshifting RNA from a multiplexed phage display library.; Chemical science. 2024 Oct 17.
1. Srivastava Y
2. Akinyemi O
3. Rohe TC
4. Pritchett EM
5. Baker CD
6. Sharma A
7. Jenkins JL
8. Mathews DH
9. Wedekind JE
Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.; Nucleic acids research. 2024 Oct 16.
1. Zhu M
2. Zuber J
3. Tan Z
4. Sharma G
5. Mathews DH
DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.; bioRxiv : the preprint server for biology. 2024 Oct 15.
1. Maji D
2. Jenkins JL
3. Boutz PL
4. Kielkopf CL
Recurrent Neurodevelopmentally Associated Variants of the Pre-mRNA Splicing Factor U2AF2 Alter RNA Binding Affinities and Interactions.; Biochemistry. 2024 Oct 10.
1. Hassel GA
2. eflová J
3. Cho EE
4. Blair SN
5. Van Raamsdonk CD
6. Anderson DM
7. Robia SL
8. Makarewich CA
Another-regulin regulates cardiomyocyte calcium handling via integration of neuroendocrine signaling with SERCA2a activity; J Mol Cell Cardiol. 2024 Jan 01.
1. Beard JW
2. Hunt SL
3. Evans A
4. Goenner C
5. Miller BL
Mimicking a Cellular Crowding Environment for Enzyme-Free Paper-Based Nucleic Acid Tests at the Point of Care.; ACS sensors. 2024 Sep 30.
1. Oberstrass L
2. Tants JN
3. Lichtenthaeler C
4. Ali SE
5. Koch L
6. Mathews DH
7. Schlundt A
8. Weigand J
Comprehensive Profiling of Roquin Binding Preferences for RNA Stem-Loops.; Angewandte Chemie (International ed. in English). 2024 Sep 30.
1. Casadio R
2. Mathews DH
3. Sternberg MJE
Computational Resources for Molecular Biology 2024.; Journal of molecular biology. 2024 Aug 06.
1. Thalalla Gamage S
2. Khoogar R
3. Howpay Manage S
4. Crawford MC
5. Georgeson J
6. Polevoda BV
7. Sanders C
8. Lee KA
9. Nance KD
10. Iyer V
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