Publications - Center for RNA Biology: From Genome to Therapeutics

URMC / Center for RNA Biology / Publications

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. 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. 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. 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. 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. 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. 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
11. Kustanovich A
12. Perez M
13. Thu CT
14. Nance SR
15. Amin R
16. Miller CN
17. Holewinski RJ
18. Meyer T
19. Koparde V
20. Yang A
21. Jailwala P
22. Nguyen JT
23. Andresson T
24. Hunter K
25. Gu S
26. Mock BA
27. Edmondson EF
28. Difilippantonio S
29. Chari R
30. Schwartz S
31. O'Connell MR
32. Wu CC
33. Meier JL
Transfer RNA acetylation regulates in vivo mammalian stress signaling.; bioRxiv : the preprint server for biology. 2024 Jul 28.
1. Franchini L
2. Porter JJ
3. Lueck JD
4. Orlandi C
Gz Enhanced Signal Transduction assaY (G Z ESTY) for GPCR deorphanization.; bioRxiv : the preprint server for biology. 2024 Jul 26.
1. Lin MH
2. Jensen MK
3. Elrod ND
4. Chu HF
5. Haseley M
6. Beam AC
7. Huang KL
8. Chiang W
9. Russell WK
10. Williams K
11. Pröschel C
12. Wagner EJ
13. Tong L
Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.; Molecular cell. 2024 Jul 08.
1. Malik A
2. Zhang L
3. Gautam M
4. Dai N
5. Li S
6. Zhang H
7. Mathews DH
8. Huang L
LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments.; Journal of molecular biology. 2024 Jul 04.
1. Morais P
2. Zhang R
3. Yu YT
Therapeutic Nonsense Suppression Modalities: From Small Molecules to Nucleic Acid-Based Approaches.; Biomedicines; Vol 12(6). 2024 Jun 10.
1. Gondil VS
2. Butman HS
3. Young M
4. Walsh DJ
5. Narkhede Y
6. Zeiler MJ
7. Crow AH
8. Carpenter ME
9. Mardikar A
10. Melander RJ
11. Wiest O
12. Dunman PM
13. Melander C
Development of phenyl-urea-based small molecules that target penicillin-binding protein 4.; Chemical biology & drug design; Vol 103(6), pp. e14569. 2024 Jun.
1. Porter JJ
2. Lueck JD
A cystic fibrosis gene editing approach that is on target.; Molecular therapy. Nucleic acids; Vol 35(2), pp. 102197. 2024 May 08.
1. Pan Y
2. Adachi H
3. He X
4. Chen JL
5. Yu YT
6. Boutz PL
Updated Pseudo-seq Protocol for Transcriptome-Wide Detection of Pseudouridines.; Bio-protocol; Vol 14(9), pp. e4985. 2024 May 05.
1. Lynch CA
2. Acosta SA
3. Anderson DM
4. Rogers GE
5. Wilson-Rawls J
6. Rawls A
The Transcription Factor Mohawk Facilitates Skeletal Muscle Repair via Modulation of the Inflammatory Environment; Int J Mol Sci 25. 2024 Jan 01.
1. Rambout X
2. Maquat LE
Nuclear mRNA decay: regulatory networks that control gene expression.; Nature reviews. Genetics. 2024 Apr 18.
1. Haugen RJ
2. Barnier C
3. Elrod ND
4. Luo H
5. Jensen MK
6. Ji P
7. Smibert CA
8. Lipshitz HD
9. Wagner EJ
10. Freddolino PL
11. Goldstrohm AC
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex.; RNA (New York, N.Y.). 2024 Apr 16.
1. Gowtham L
2. Wozniak RAF
3. Dunman PM
4. Sheba E
5. Garg P
6. Joseph J
Efficacy of a Novel Antibiotic Drug Combination Toward Multidrug-Resistant Ocular Pathogens.; Cornea. 2024 Mar 26.
1. Mittal A
2. Turner DH
3. Mathews DH
NNDB: An expanded database of nearest neighbor parameters for predicting stability of nucleic acid secondary structures.; Journal of molecular biology. 2024 Mar 22.
1. McGrath KE
2. Koniski AD
3. Murphy K
4. Getman M
5. An HH
6. Schulz VP
7. Kim AR
8. Zhang B
9. Schofield TL
10. Papoin J
11. Blanc L
12. Kingsley PD
13. Westhoff CM
14. Gallagher PG
15. Chou ST
16. Steiner LA
17. Palis J
BMI1 regulates human erythroid self-renewal through both gene repression and gene activation.; bioRxiv : the preprint server for biology. 2024 Feb 06.
1. Jonnakuti VS
2. Wagner EJ
3. Maletić-Savatić M
4. Liu Z
5. Yalamanchili HK
PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.; Cell reports methods. 2024 Feb 03.
1. Alessandrini F
2. Wright M
3. Kurosaki T
4. Maquat LE
5. Kiskinis E
ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3'UTR Length.; bioRxiv : the preprint server for biology. 2024 Feb 02.
1. De Zoysa T
2. Hauke AC
3. Iyer NR
4. Marcus E
5. Ostrowski SM
6. Stegemann F
7. Ermolenko DN
8. Fay JC
9. Phizicky EM
A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; PLoS genetics; Vol 20(1), pp. e1011146. 2024 Jan 31.
1. Kurosaki T
2. Rambout X
3. Maquat LE
FMRP-mediated spatial regulation of physiologic NMD targets in neuronal cells.; Genome biology; Vol 25(1), pp. 31. 2024 Jan 23.
1. Tumenbayar BI
2. Tutino VM
3. Brazzo JA
4. Yao P
5. Bae Y
FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism.; bioRxiv : the preprint server for biology. 2024 Jan 16.
1. Chen JL
2. Leeder WM
3. Morais P
4. Adachi H
5. Yu YT
Pseudouridylation-mediated gene expression modulation.; The Biochemical journal; Vol 481(1), pp. 1-16. 2024 Jan 10.
1. Cisco LA
2. Sipple MT
3. Edwards KM
4. Thornton CA
5. Lueck JD
Verapamil mitigates chloride and calcium bi-channelopathy in a myotonic dystrophy mouse model.; The Journal of clinical investigation; Vol 134(1). 2024 Jan 02.
1. Zuber J
2. Mathews DH
Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.; Methods in molecular biology (Clifton, N.J.); Vol 2726, pp. 1-13. 2024.
1. Wu J
2. Hollinger J
3. Bonanno E
4. Jiang F
5. Yao P
Cardiomyocyte-Specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy.; Cells; Vol 13(1). 2023 Dec 22.
1. Lv X
2. Murphy K
3. Murphy Z
4. Getman MR
5. Rahman NF
6. Nakamura Y
7. Blanc L
8. Gallagher PG
9. Palis J
10. Mohandas N
11. Steiner LA
HEXIM1 is an Essential Transcription Regulator During Human Erythropoiesis.; Blood. 2023 Sep 22.
1. Wu J
2. Hollinger J
3. Bonanno E
4. Jiang F
5. Yao P
Cardiomyocyte-specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy.; bioRxiv : the preprint server for biology. 2023 Sep 22.
1. De Zoysa T
2. Hauke AC
3. Iyer NR
4. Marcus E
5. Ostrowski SM
6. Fay JC
7. Phizicky EM
A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; bioRxiv : the preprint server for biology. 2023 Sep 18.
1. Pham TM
2. Miffin T
3. Sun H
4. Sharp KK
5. Wang X
6. Zhu M
7. Hoshika S
8. Peterson RJ
9. Benner SA
10. Kahn JD
11. Mathews DH
DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.; ACS synthetic biology. 2023 Sep 06.
1. Boutz PL
Putting a finger on histidine methylation.; Genes & development; Vol 37(15-16), pp. 675-677. 2023 Sep 06.
1. Schroeder GM
2. Kiliushik D
3. Jenkins JL
4. Wedekind JE
Structure and function analysis of a type III preQ1-I riboswitch from E. coli reveals direct metabolite-sensing by the Shine-Dalgarno sequence.; The Journal of biological chemistry. 2023 Sep 01.
1. Zhang H
2. Li S
3. Dai N
4. Zhang L
5. Mathews DH
6. Huang L
LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.; Nucleic acids research. 2023 Aug 31.
1. Haugen RJ
2. Barnier C
3. Elrod ND
4. Luo H
5. Jensen MK
6. Ji P
7. Smibert CA
8. Lipshitz HD
9. Wagner EJ
10. Freddolino PL
11. Goldstrohm AC
Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase.; bioRxiv : the preprint server for biology. 2023 Aug 30.
1. Cazarin J
2. DeRollo RE
3. Shahidan SNABA
4. Burchett JB
5. Mwangi D
6. Krishnaiah S
7. Hsieh AL
8. Walton ZE
9. Brooks R
10. Mello SS
11. Weljie AM
12. Dang CV
13. Altman BJ
MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis.; PLoS genetics; Vol 19(8), pp. e1010904. 2023 Aug 28.
1. Wu J
2. Subbaiah KCV
3. Hedaya O
4. Chen S
5. Munger J
6. Tang WHW
7. Yan C
8. Yao P
FAM210A regulates mitochondrial translation and maintains cardiac mitochondrial homeostasis.; Cardiovascular research. 2023 Jul 31.
1. Liu L
2. Xu Z
3. Molina Vargas AM
4. Dollery SJ
5. Schrlau MG
6. Cormier D
7. O'Connell MR
8. Tobin GJ
9. Du K
Aerosol Jet Printing-Enabled Dual-Function Electrochemical and Colorimetric Biosensor for SARS-CoV-2 Detection.; Analytical chemistry. 2023 Jul 28.
1. Zuber J
2. Sah SK
3. Mathews DH
4. Rustchenko E
Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants.; Microorganisms; Vol 11(8). 2023 Jul 25.
1. Kretsch RC
2. Andersen ES
3. Bujnicki JM
4. Chiu W
5. Das R
6. Luo B
7. Masquida B
8. McRae EKS
9. Schroeder GM
10. Su Z
11. Wedekind JE
12. Xu L
13. Zhang K
14. Zheludev IN
15. Moult J
16. Kryshtafovych A
RNA target highlights in CASP15: Evaluation of predicted models by structure providers.; Proteins. 2023 Jul 19.
1. Piraino L
2. Chen CY
3. Mereness J
4. Dunman PM
5. Ovitt C
6. Benoit D
7. DeLouise L
Identifying novel radioprotective drugs via salivary gland tissue chip screening.; bioRxiv : the preprint server for biology. 2023 Jul 13.
1. Young M
2. Chojnacki M
3. Blanchard C
4. Cao X
5. Johnson WL
6. Flaherty D
7. Dunman PM
Genetic Determinants of Acinetobacter baumannii Serum-Associated Adaptive Efflux-Mediated Antibiotic Resistance.; Antibiotics (Basel, Switzerland); Vol 12(7). 2023 Jul 11.
1. Liu X
2. Burke RM
3. Lighthouse JK
4. Baker CD
5. Dirkx RA
6. Kang B
7. Chakraborty Y
8. Mickelsen DM
9. Twardowski J
10. Mello SS
11. Ashton JM
12. Small EM
P53 Regulates the Extent of Fibroblast Proliferation and Fibrosis in Left Ventricle Pressure Overload.; Circulation research. 2023 Jul 06.
1. Ali SE
2. Mittal A
3. Mathews DH
RNA Secondary Structure Analysis Using RNAstructure.; Current protocols; Vol 3(7), pp. e846. 2023 Jul.
1. Jonnakuti VS
2. Ji P
3. Gao Y
4. Lin A
5. Chu Y
6. Elrod N
7. Huang KL
8. Li W
9. Yalamanchili HK
10. Wagner EJ
NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.; Journal of neuro-oncology. 2023 Jun 30.
1. Zhou T
2. Dai N
3. Li S
4. Ward M
5. Mathews DH
6. Huang L
RNA design via structure-aware multifrontier ensemble optimization.; Bioinformatics (Oxford, England); Vol 39(39 Suppl 1), pp. i563-i571. 2023 Jun 30.
1. Das A
2. Bao C
3. Ermolenko DN
Comparing FRET Pairs that Report on Intersubunit Rotation in Bacterial Ribosomes.; Journal of molecular biology; Vol 435(15), pp. 168185. 2023 Jun 20.
1. Hollinger J
2. Wu J
3. Awayda KM
4. O'Connell MR
5. Yao P
Expression and purification of the mitochondrial transmembrane protein FAM210A in Escherichia coli.; Protein expression and purification; Vol 210, pp. 106322. 2023 Jun 15.
1. Hedaya OM
2. Subbaiah KCV
3. Jiang F
4. Xie LH
5. Wu J
6. Khor E
7. Zhu M
8. Mathews DH
9. Proschel C
10. Yao P
Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.; bioRxiv : the preprint server for biology. 2023 Jun 15.
1. Pham TM
2. Miffin T
3. Sun H
4. Sharp KK
5. Wang X
6. Zhu M
7. Hoshika S
8. Peterson RJ
9. Benner SA
10. Kahn JD
11. Mathews DH
DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.; bioRxiv : the preprint server for biology. 2023 Jun 08.
1. Cisco LA
2. Sipple MT
3. Edwards KM
4. Thornton CA
5. Lueck JD
Combinatorial chloride and calcium channelopathy in myotonic dystrophy.; bioRxiv : the preprint server for biology. 2023 Jun 01.
1. Mathews DH
2. Casadio R
3. Sternberg MJE
Computational Resources for Molecular Biology 2023.; Journal of molecular biology. 2023 May 25.
1. Wu J
2. Subbaiah KCV
3. Hedaya O
4. Chen S
5. Munger J
6. Tang WHW
7. Yan C
8. Yao P
FAM210A Regulates Mitochondrial Translation and Maintains Cardiac Mitochondrial Homeostasis.; bioRxiv : the preprint server for biology. 2023 May 22.
1. Das A
2. Bao C
3. Ermolenko DN
Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes.; bioRxiv : the preprint server for biology. 2023 May 09.
1. Zhang H
2. Zhang L
3. Lin A
4. Xu C
5. Li Z
6. Liu K
7. Liu B
8. Ma X
9. Zhao F
10. Jiang H
11. Chen C
12. Shen H
13. Li H
14. Mathews DH
15. Zhang Y
16. Huang L
Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity.; Nature. 2023 May 02.
1. Mirska B
2. Woźniak T
3. Lorent D
4. Ruszkowska A
5. Peterson JM
6. Moss WN
7. Mathews DH
8. Kierzek R
9. Kierzek E
In vivo secondary structural analysis of Influenza A virus genomic RNA.; Cellular and molecular life sciences : CMLS; Vol 80(5), pp. 136. 2023 May 02.
1. Jiang F
2. Hedaya OM
3. Khor E
4. Wu J
5. Auguste M
6. Yao P
RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression.; Nucleic acids research. 2023 May 01.
1. VanderWal AR
2. Park JU
3. Polevoda B
4. Nicosia JK
5. Molina Vargas AM
6. Kellogg EH
7. O'Connell MR
Csx28 is a membrane pore that enhances CRISPR-Cas13b-dependent antiphage defense.; Science (New York, N.Y.); Vol 380(6643), pp. 410-415. 2023 Apr 27.
1. Insco ML
2. Abraham BJ
3. Dubbury SJ
4. Kaltheuner IH
5. Dust S
6. Wu C
7. Chen KY
8. Liu D
9. Bellaousov S
10. Cox AM
11. Martin BJE
12. Zhang T
13. Ludwig CG
14. Fabo T
15. Modhurima R
16. Esgdaille DE
17. Henriques T
18. Brown KM
19. Chanock SJ
20. Geyer M
21. Adelman K
22. Sharp PA
23. Young RA
24. Boutz PL
25. Zon LI
Oncogenic CDK13 mutations impede nuclear RNA surveillance.; Science (New York, N.Y.); Vol 380(6642), pp. eabn7625. 2023 Apr 21.
1. Zhou T
2. Gilliam NJ
3. Li S
4. Spandau S
5. Osborn RM
6. Connor S
7. Anderson CS
8. Mariani TJ
9. Thakar J
10. Dewhurst S
11. Mathews DH
12. Huang L
13. Sun Y
Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection.; mBio. 2023 Apr 19.
1. Phizicky EM
2. Hopper AK
The Life and Times of a tRNA.; RNA (New York, N.Y.). 2023 Apr 13.
1. Das A
2. Adiletta N
3. Ermolenko DN
Interplay between Inter-Subunit Rotation of the Ribosome and Binding of Translational GTPases.; International journal of molecular sciences; Vol 24(8). 2023 Apr 07.
1. Wedekind JE
RNA in the loop: Probing T-loop/T-loop receptor interactions as mediators of long-range RNA contacts that influence gene regulation.; Journal of molecular biology. 2023 Apr 06.
1. Tepe B
2. Macke EL
3. Niceta M
4. Weisz Hubshman M
5. Kanca O
6. Schultz-Rogers L
7. Zarate YA
8. Schaefer GB
9. Granadillo De Luque JL
10. Wegner DJ
11. Cogne B
12. Gilbert-Dussardier B
13. Le Guillou X
14. Wagner EJ
15. Pais LS
16. Neil JE
17. Mochida GH
18. Walsh CA
19. Magal N
20. Drasinover V
21. Shohat M
22. Schwab T
23. Schmitz C
24. Clark K
25. Fine A
26. Lanpher B
27. Gavrilova R
28. Blanc P
29. Burglen L
30. Afenjar A
31. Steel D
32. Kurian MA
33. Prabhakar P
34. Gößwein S
35. Di Donato N
36. Bertini ES
37. Wangler MF
38. Yamamoto S
39. Tartaglia M
40. Klee EW
41. Bellen HJ
Bi-allelic variants in INTS11 are associated with a complex neurological disorder.; American journal of human genetics. 2023 Apr 04.
1. Thornton CA
2. Moxley RT
3. Eichinger K
4. Heatwole C
5. Mignon L
6. Arnold WD
7. Ashizawa T
8. Day JW
9. Dent G
10. Tanner MK
11. Duong T
12. Greene EP
13. Herbelin L
14. Johnson NE
15. King W
16. Kissel JT
17. Leung DG
18. Lott DJ
19. Norris DA
20. Pucillo EM
21. Schell W
22. Statland JM
23. Stinson N
24. Subramony SH
25. Xia S
26. Bishop KM
27. Bennett CF
Antisense oligonucleotide targeting DMPK in patients with myotonic dystrophy type 1: a multicentre, randomised, dose-escalation, placebo-controlled, phase 1/2a trial.; The Lancet. Neurology; Vol 22(3), pp. 218-228. 2023 Mar.
1. Mello SS
2. Flowers BM
3. Mazur PK
4. Lee JJ
5. Müller F
6. Denny SK
7. Ferreira S
8. Hanson K
9. Kim SK
10. Greenleaf WJ
11. Wood LD
12. Attardi LD
Multifaceted role for p53 in pancreatic cancer suppression.; Proceedings of the National Academy of Sciences of the United States of America; Vol 120(10), pp. e2211937120. 2023 Feb 27.
1. de Prisco N
2. Ford C
3. Elrod ND
4. Lee W
5. Tang LC
6. Huang KL
7. Lin A
8. Ji P
9. Jonnakuti VS
10. Boyle L
11. Cabaj M
12. Botta S
13. Õunap K
14. Reinson K
15. Wojcik MH
16. Rosenfeld JA
17. Bi W
18. Tveten K
19. Prescott T
20. Gerstner T
21. Schroeder A
22. Fong CT
23. George-Abraham JK
24. Buchanan CA
25. Hanson-Khan A
26. Bernstein JA
27. Nella AA
28. Chung WK
29. Brandt V
30. Jovanovic M
31. Targoff KL
32. Yalamanchili HK
33. Wagner EJ
34. Gennarino VA
Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites.; Science advances; Vol 9(7), pp. eade4814. 2023 Feb 17.
1. Knott GJ
2. Lapinaite A
3. O'Connell MR
Methods special issue: RNA-targeting technologies.; Methods (San Diego, Calif.); Vol 212, pp. 10-11. 2023 Feb 13.
1. Schroeder GM
2. Akinyemi O
3. Malik J
4. Focht CM
5. Pritchett EM
6. Baker CD
7. McSally JP
8. Jenkins JL
9. Mathews DH
10. Wedekind JE
A riboswitch separated from its ribosome-binding site still regulates translation.; Nucleic acids research. 2023 Feb 10.
1. Adachi H
2. Pan Y
3. He X
4. Chen JL
5. Klein B
6. Platenburg G
7. Morais P
8. Boutz P
9. Yu YT
Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes.; Molecular cell. 2023 Feb 03.
1. Cui Y
2. Arnold FJ
3. Peng F
4. Wang D
5. Li JS
6. Michels S
7. Wagner EJ
8. La Spada AR
9. Li W
Alternative polyadenylation transcriptome-wide association study identifies APA-linked susceptibility genes in brain disorders.; Nature communications; Vol 14(1), pp. 583. 2023 Feb 03.
1. Molina Vargas AM
2. Sinha S
3. Osborn R
4. Arantes PR
5. Patel A
6. Dewhurst S
7. Hardy DJ
8. Cameron A
9. Palermo G
10. O'Connell MR
New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity.; Nucleic acids research. 2023 Jan 30.
1. Sinha S
2. Molina Vargas AM
3. Arantes PR
4. Patel A
5. O'Connell MR
6. Palermo G
Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a.; Nucleic acids research. 2023 Jan 30.
1. Subbaiah KCV
2. Wu J
3. Tang WHW
4. Yao P
Ciclopirox Inhibition of eIF5A Hypusination Attenuates Fibroblast Activation and Cardiac Fibrosis.; Journal of cardiovascular development and disease; Vol 10(2). 2023 Jan 29.
1. Jonnakuti VS
2. Wagner EJ
3. Maletić-Savatić M
4. Liu Z
5. Yalamanchili HK
PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data.; bioRxiv : the preprint server for biology. 2023 Jan 24.
1. Rambout X
2. Cho H
3. Blanc R
4. Lyu Q
5. Miano JM
6. Chakkalakal JV
7. Nelson GM
8. Yalamanchili HK
9. Adelman K
10. Maquat LE
PGC-1α senses the CBC of pre-mRNA to dictate the fate of promoter-proximally paused RNAPII.; Molecular cell; Vol 83(2), pp. 186-202.e11. 2023 Jan 19.
1. Fongang B
2. Wadop YN
3. Zhu Y
4. Wagner EJ
5. Kudlicki A
6. Rowicka M
Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits.; Computational and structural biotechnology journal; Vol 21, pp. 5686-5697. 2023 Jan 19.
1. Allaire NE
2. Griesenbach U
3. Kerem B
4. Lueck JD
5. Stanleigh N
6. Oren YS
Gene, RNA, and ASO-based therapeutic approaches in Cystic Fibrosis.; Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society. 2023 Jan 17.
1. Liu S
2. Baeg GH
3. Yang Y
4. Goh FG
5. Bao H
6. Wagner EJ
7. Yang X
8. Cai Y
The Integrator complex desensitizes cellular response to TGF-β/BMP signaling.; Cell reports; Vol 42(1), pp. 112007. 2023 Jan 14.
1. King KA
2. Benton AH
3. Caudill MT
4. Stoyanof ST
5. Kang L
6. Michalak P
7. Lahmers KK
8. Dunman PM
9. DeHart TG
10. Ahmad SS
11. Jutras BL
12. Poncin K
13. De Bolle X
14. Caswell CC
Post-transcriptional control of the essential enzyme MurF by a small regulatory RNA in Brucella abortus.; Molecular microbiology. 2023 Jan 11.
1. Srivastava Y
2. Blau ME
3. Jenkins JL
4. Wedekind JE
Full-Length NAD+-I Riboswitches Bind a Single Cofactor but Cannot Discriminate against Adenosine Triphosphate.; Biochemistry. 2023 Jan 10.
1. Rook ML
2. McCullock TW
3. Couch T
4. Lueck JD
5. MacLean DM
Photomodulation of the ASIC1a acidic pocket destabilizes the open state.; Protein science : a publication of the Protein Society. 2023 Jan 08.
1. Papoin J
2. Yan H
3. Leduc M
4. Le Gall M
5. Narla A
6. Palis J
7. Steiner LA
8. Gallagher PG
9. Hillyer CD
10. Gautier EF
11. Mohandas N
12. Blanc L
Phenotypic and proteomic characterization of the human erythroid progenitor continuum reveal dynamic changes in cell cycle and in metabolic pathways.; American journal of hematology. 2023 Jan 06.
1. Wagner EJ
2. Tong L
3. Adelman K
Integrator is a global promoter-proximal termination complex.; Molecular cell. 2023 Jan 04.
1. DeRollo RE
2. Cazarin J
3. Ahmad Shahidan SNAB
4. Burchett JB
5. Mwangi D
6. Krishnaiah S
7. Hsieh AL
8. Walton ZE
9. Brooks R
10. Mello SS
11. Weljie AM
12. Dang CV
13. Altman BJ
MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis.; bioRxiv : the preprint server for biology. 2023 Jan 04.
1. Hedaya OM
2. Venkata Subbaiah KC
3. Jiang F
4. Xie LH
5. Wu J
6. Khor ES
7. Zhu M
8. Mathews DH
9. Proschel C
10. Yao P
Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.; Nature communications; Vol 14(1), pp. 6166. 2023 Jan 03.
1. Zhang H
2. Zhang L
3. Liu K
4. Li S
5. Mathews DH
6. Huang L
Linear-Time Algorithms for RNA Structure Prediction.; Methods in molecular biology (Clifton, N.J.); Vol 2586, pp. 15-34. 2023.
1. Cavender CE
2. Schroeder GM
3. Mathews DH
4. Wedekind JE
Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model.; Methods in molecular biology (Clifton, N.J.); Vol 2568, pp. 53-73. 2023.
1. Adachi H
2. Chen JL
3. Yin Q
4. Morais P
5. Yu YT
In Vitro Reconstitution of Pseudouridylation Catalyzed by Human Box H/ACA Ribonucleoprotein Particles.; Methods in molecular biology (Clifton, N.J.); Vol 2666, pp. 177-191. 2023.
1. Lin MH
2. Jensen MK
3. Elrod ND
4. Huang KL
5. Welle KA
6. Wagner EJ
7. Tong L
Inositol hexakisphosphate is required for Integrator function.; Nature communications; Vol 13(1), pp. 5742. 2022 Sep 30.
1. Guo B
2. Friedland SC
3. Alexander W
4. Myers JA
5. Wang W
6. O'Dell MR
7. Getman M
8. Whitney-Miller CL
9. Agostini-Vulaj D
10. Huber AR
11. Mello SS
12. Vertino PM
13. Land HK
14. Steiner LA
15. Hezel AF
Arid1a mutation suppresses TGF-β signaling and induces cholangiocarcinoma.; Cell reports; Vol 40(9), pp. 111253. 2022 Aug 30.
1. Hogestyn JM
2. Salois G
3. Xie L
4. Apa C
5. Youngyunpipatkul J
6. Pröschel C
7. Mayer-Pröschel M
Expression of the human herpesvirus 6A latency-associated transcript U94A impairs cytoskeletal functions in human neural cells.; Molecular and cellular neurosciences. 2022 Aug 30.
1. Joseph Davis Burris B
2. Moises Molina Vargas A
3. Park BJ
4. O'Connell MR
Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13.; Methods (San Diego, Calif.). 2022 Aug 17.
1. Tasak M
2. Phizicky EM
Initiator tRNA lacking 1-methyladenosine is targeted by the rapid tRNA decay path way in evolutionarily distant yeast species.; PLoS genetics; Vol 18(7), pp. e1010215. 2022 Jul 28.
1. Hamel JI
2. McDermott MP
3. Hilbert JE
4. Martens WB
5. Luebbe E
6. Tawil R
7. Moxley RT
8. Thornton CA
Milestones of progression in myotonic dystrophy type 1 and type 2.; Muscle & nerve. 2022 Jul 01.
1. Galardi JW
2. Bela VN
3. Jeffery N
4. He X
5. Glasser E
6. Loerch S
7. Jenkins JL
8. Pulvino MJ
9. Boutz PL
10. Kielkopf CL
A UHM - ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing.; The Journal of biological chemistry. 2022 Jun 30.
1. Szikszai M
2. Wise M
3. Datta A
4. Ward M
5. Mathews DH
Deep learning models for RNA secondary structure prediction (probably) do not generalise across families.; Bioinformatics (Oxford, England). 2022 Jun 24.
1. Ko W
2. Porter JJ
3. Sipple MT
4. Edwards KM
5. Lueck JD
Efficient suppression of endogenous CFTR nonsense mutations using anticodon-engineered transfer RNAs.; Molecular therapy. Nucleic acids; Vol 28. 2022 Jun 14.
1. Kumar J
2. Lackey L
3. Waldern JM
4. Dey A
5. Mustoe AM
6. Weeks K
7. Mathews DH
8. Laederach A
Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing.; eLife; Vol 11. 2022 Jun 13.
1. Subbaiah KCV
2. Wu J
3. Tang WHW
4. Yao P
FAM114A1 influences cardiac pathological remodeling by regulating angiotensin II signaling.; JCI insight. 2022 Jun 07.
1. Tseng V
2. Collum SD
3. Allawzi A
4. Crotty K
5. Yeligar S
6. Trammell A
7. Ryan Smith M
8. Kang BY
9. Sutliff RL
10. Ingram JL
11. Jyothula SSSK
12. Thandavarayan RA
13. Huang HJ
14. Nozik ES
15. Wagner EJ
16. Michael Hart C
17. Karmouty-Quintana H
3'UTR shortening of HAS2 promotes hyaluronan hyper-synthesis and bioenergetic dysfunction in pulmonary hypertension.; Matrix biology : journal of the International Society for Matrix Biology; Vol 111, pp. 53-75. 2022 Jun 04.
1. Cho H
2. Abshire ET
3. Popp MW
4. Pröschel C
5. Schwartz JL
6. Yeo GW
7. Maquat LE
AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay.; Molecular cell. 2022 Jun 03.
1. Wilson C
2. Mertens TC
3. Shivshankar P
4. Bi W
5. Collum SD
6. Wareing N
7. Ko J
8. Weng T
9. Naikawadi RP
10. Wolters PJ
11. Maire P
12. Jyothula SS
13. Thandavarayan RA
14. Ren D
15. Elrod ND
16. Wagner EJ
17. Huang HJ
18. Dickey BF
19. Ford HL
20. Karmouty-Quintana H
Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis.; JCI insight; Vol 7(10). 2022 May 23.
1. Mackenzie SJ
2. Hamel J
3. Thornton CA
Benefits of aerobic exercise in myotonic dystrophy type 1.; The Journal of clinical investigation; Vol 132(10). 2022 May 16.
1. Szabat M
2. Prochota M
3. Kierzek R
4. Kierzek E
5. Mathews DH
A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine.; Journal of molecular biology. 2022 May 16.
1. Casadio R
2. Mathews DH
3. Sternberg MJE
Computational Resources for Molecular Biology 2022.; Journal of molecular biology. 2022 May 12.
1. Maquat L
2. Johnson R
3. Valadkhan S
4. Carninci P
Lessons from the functional characterization of lncRNAs: introduction to mammalian genome special issue.; Mammalian genome : official journal of the International Mammalian Genome Society. 2022 May 09.
1. Glasser E
2. Maji D
3. Biancon G
4. Puthenpeedikakkal AMK
5. Cavender CE
6. Tebaldi T
7. Jenkins JL
8. Mathews DH
9. Halene S
10. Kielkopf CL
Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.; Nucleic acids research. 2022 May 07.
1. Zuber J
2. Schroeder SJ
3. Sun H
4. Turner DH
5. Mathews DH
Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.; Nucleic acids research. 2022 May 07.
1. Mei JA
2. Johnson W
3. Kinn B
4. Laskey E
5. Nolin L
6. Bhamare P
7. Stalker C
8. Dunman PM
9. Wozniak RAF
Antimicrobial Activity of a Triple Antibiotic Combination Toward Ocular Pseudomonas aeruginosa Clinical Isolates.; Translational vision science & technology; Vol 11(5). 2022 May 02.
1. Funk HM
2. DiVita DJ
3. Sizemore HE
4. Wehrle K
5. Miller CLW
6. Fraley ME
7. Mullins AK
8. Guy AR
9. Phizicky EM
10. Guy MP
Identification of a Trm732 Motif Required for 2'-O-methylation of the tRNA Anticodon Loop by Trm7.; ACS omega; Vol 7(16). 2022 Apr 26.
1. Hamel J
2. Creigh PD
3. Dekdebrun J
4. Eichinger K
5. Thornton CA
Remote Assessment of Myotonic Dystrophy Type 1: A Feasibility Study.; Muscle & nerve. 2022 Apr 15.
1. Walker EJ
2. Bettinger JQ
3. Welle KA
4. Hryhorenko JR
5. Molina Vargas AM
6. O'Connell MR
7. Ghaemmaghami S
Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues.; The Journal of biological chemistry. 2022 Mar 25.
1. Kierzek E
2. Zhang X
3. Watson RM
4. Kennedy SD
5. Szabat M
6. Kierzek R
7. Mathews DH
Secondary structure prediction for RNA sequences including N6-methyladenosine.; Nature communications; Vol 13(1). 2022 Mar 11.
1. Szutkowska B
2. Wieczorek K
3. Kierzek R
4. Zmora P
5. Peterson JM
6. Moss WN
7. Mathews DH
8. Kierzek E
Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment.; International journal of molecular sciences; Vol 23(5). 2022 Feb 23.
1. Michard F
2. Thiele RH
3. Saugel B
4. Joosten A
5. Flick M
6. Khanna AK
Wireless wearables for postoperative surveillance on surgical wards: a survey of 1158 anaesthesiologists in Western Europe and the USA.; BJA open; Vol 1, pp. 100002. 2022 Feb 23.
1. Bao C
2. Zhu M
3. Nykonchuk I
4. Wakabayashi H
5. Mathews DH
6. Ermolenko DN
Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.; Nature communications; Vol 13(1). 2022 Feb 21.
1. Deutsch GK
2. Hagerman KA
3. Sampson J
4. Dent G
5. Dekdebrun J
6. Parker DM
7. Thornton CA
8. Heatwole CR
9. Subramony SH
10. Mankodi AK
11. Ashizawa T
12. Statland JM
13. Arnold WD
14. Moxley RT
15. Day JW
Brief assessment of cognitive function in myotonic dystrophy: multicenter longitudinal study using computer-assisted evaluation.; Muscle & nerve. 2022 Feb 18.
1. Broly M
2. Polevoda BV
3. Awayda KM
4. Tong N
5. Lentini J
6. Besnard T
7. Deb W
8. O'Rourke D
9. Baptista J
10. Ellard S
11. Almannai M
12. Hashem M
13. Abdulwahab F
14. Shamseldin H
15. Al-Tala S
16. Alkuraya FS
17. Leon A
18. van Loon RLE
19. Ferlini A
20. Sanchini M
21. Bigoni S
22. Ciorba A
23. van Bokhoven H
24. Iqbal Z
25. Al-Maawali A
26. Al-Murshedi F
27. Ganesh A
28. Al-Mamari W
29. Lim SC
30. Pais LS
31. Brown N
32. Riazuddin S
33. Bézieau S
34. Fu D
35. Isidor B
36. Cogné B
37. O'Connell MR
THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder.; American journal of human genetics. 2022 Feb 11.
1. LaForce GR
2. Farr JS
3. Liu J
4. Akesson C
5. Gumus E
6. Pinkard O
7. Miranda HC
8. Johnson K
9. Sweet TJ
10. Ji P
11. Lin A
12. Coller J
13. Philippidou P
14. Wagner EJ
15. Schaffer AE
Suppression of premature transcription termination leads to reduced mRNA isoform diversity and neurodegeneration.; Neuron. 2022 Feb 04.
1. Stein CB
2. Field AR
3. Mimoso CA
4. Zhao C
5. Huang KL
6. Wagner EJ
7. Adelman K
Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci.; Molecular cell. 2022 Jan 28.
1. Waitkus J
2. Chang Y
3. Liu L
4. Puttaswamy SV
5. Chung T
6. Vargas AMM
7. Dollery SJ
8. O'Connell MR
9. Cai H
10. Tobin GJ
11. Bhalla N
12. Du K
Gold Nanoparticle Enabled Localized Surface Plasmon Resonance on Unique Gold Nanomushroom Structures for On-Chip CRISPR-Cas13a Sensing.; Advanced materials interfaces; Vol 10(1). 2022 Jan 27.
1. Liu L
2. Xu Z
3. Awayda K
4. Dollery SJ
5. Bao M
6. Fan J
7. Cormier D
8. O'Connell M
9. Tobin GJ
10. Du K
Gold Nanoparticle-Labeled CRISPR-Cas13a Assay for the Sensitive Solid-State Nanopore Molecular Counting.; Advanced materials technologies; Vol 7(3). 2022 Jan 22.
1. Zhang H
2. Li S
3. Zhang L
4. Mathews DH
5. Huang L
LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2.; Nucleic acids research. 2022 Jan 18.
1. Dulmovits BM
2. Tang Y
3. Papoin J
4. He M
5. Li J
6. Yang H
7. Addorisio ME
8. Kennedy L
9. Khan M
10. Brindley EC
11. Ashley RJ
12. Ackert-Bicknell C
13. Hale J
14. Kurita RK
15. Nakamura Y
16. Diamond B
17. Barnes BJ
18. Hermine O
19. Gallagher PG
20. Steiner LA
21. Lipton JM
22. Taylor N
23. Mohandas N
24. Andersson U
25. Al-Abed Y
26. Tracey KJ
27. Blanc L
HMGB1-Mediated Restriction of EPO Signaling Contributes to Anemia of Inflammation.; Blood. 2022 Jan 18.
1. Mascibroda LG
2. Shboul M
3. Elrod ND
4. Colleaux L
5. Hamamy H
6. Huang KL
7. Peart N
8. Singh MK
9. Lee H
10. Merriman B
11. Jodoin JN
12. Sitaram P
13. Lee LA
14. Fathalla R
15. Al-Rawashdeh B
16. Ababneh O
17. El-Khateeb M
18. Escande-Beillard N
19. Nelson SF
20. Wu Y
21. Tong L
22. Kenney LJ
23. Roy S
24. Russell WK
25. Amiel J
26. Reversade B
27. Wagner EJ
INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex.; Nature communications; Vol 13(1), pp. 6054. 2022 Jan 13.
1. Schroeder GM
2. Cavender CE
3. Blau ME
4. Jenkins JL
5. Mathews DH
6. Wedekind JE
A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.; Nature communications; Vol 13(1). 2022 Jan 11.
1. Alkhunaizi E
2. Martin N
3. Jelin AC
4. Rosner M
5. Bailey DJ
6. Steiner LA
7. Lakhani S
8. Ji W
9. Katzman PJ
10. Forster KR
11. Jarinova O
12. Shannon P
13. Chitayat D
Fetal akinesia deformation sequence syndrome associated with recessive TTN variants.; American journal of medical genetics. Part A. 2022 Jan 10.
1. Lai WC
2. Zhu M
3. Belinite M
4. Ballard G
5. Mathews DH
6. Ermolenko DN
Intrinsically unstructured sequences in the mRNA 3' UTR reduce the ability of poly(A) tail to enhance translation.; Journal of molecular biology. 2022 Jan 08.
1. Young M
2. Walsh DJ
3. Masters E
4. Gondil VS
5. Laskey E
6. Klaczko M
7. Awad H
8. McGrath J
9. Schwarz EM
10. Melander C
11. Dunman PM
Identification of Staphylococcus aureus Penicillin Binding Protein 4 (PBP4) Inhibitors.; Antibiotics (Basel, Switzerland); Vol 11(10). 2022 Jan 04.
1. Kurosaki T
2. Mitsutomi S
3. Hewko A
4. Akimitsu N
5. Maquat LE
Integrative omics indicate FMRP sequesters mRNA from translation and deadenylation in human neuronal cells.; Molecular cell. 2022 Jan 01.
1. Anderson KM
2. Anderson DM
LncRNAs at the heart of development and disease; . 2022 Jan 01.
1. Houston L
2. Platten EM
3. Connelly SM
4. Wang J
5. Grayhack EJ
Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by Integrated Stress Response regulators Gcn1 and Gcn20.; RNA (New York, N.Y.). 2021 Dec 16.
1. Cable J
2. Heard E
3. Hirose T
4. Prasanth KV
5. Chen LL
6. Henninger JE
7. Quinodoz SA
8. Spector DL
9. Diermeier SD
10. Porman AM
11. Kumar D
12. Feinberg MW
13. Shen X
14. Unfried JP
15. Johnson R
16. Chen CK
17. Wilusz JE
18. Lempradl A
19. McGeary SE
20. Wahba L
21. Pyle AM
22. Hargrove AE
23. Simon MD
24. Marcia M
25. Przanowska RK
26. Chang HY
27. Jaffrey SR
28. Contreras LM
29. Chen Q
30. Shi J
31. Mendell JT
32. He L
33. Song E
34. Rinn JL
35. Lalwani MK
36. Kalem MC
37. Chuong EB
38. Maquat LE
39. Liu X
Noncoding RNAs: biology and applications-a Keystone Symposia report.; Annals of the New York Academy of Sciences. 2021 Nov 17.
1. Kurosaki T
2. Sakano H
3. Pröschel C
4. Wheeler J
5. Hewko A
6. Maquat LE
NMD abnormalities during brain development in the Fmr1-knockout mouse model of fragile X syndrome.; Genome biology; Vol 22(1). 2021 Nov 16.
1. Chavali SS
2. Mali SM
3. Bonn R
4. Saseendran A
5. Bennett RP
6. Smith HC
7. Fasan R
8. Wedekind JE
Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells.; The Journal of biological chemistry. 2021 Nov 09.
1. Cao J
2. Verma SK
3. Jaworski E
4. Mohan S
5. Nagasawa CK
6. Rayavara K
7. Sooter A
8. Miller SN
9. Holcomb RJ
10. Powell MJ
11. Ji P
12. Elrod ND
13. Yildirim E
14. Wagner EJ
15. Popov V
16. Garg NJ
17. Routh AL
18. Kuyumcu-Martinez MN
RBFOX2 is critical for maintaining alternative polyadenylation patterns and mitochondrial health in rat myoblasts.; Cell reports; Vol 37(5). 2021 Nov 02.
1. Elahi A
2. Emerson J
3. Rudlong J
4. Keillor JW
5. Salois G
6. Visca A
7. Girardi P
8. Johnson GVW
9. Pröschel C
Deletion or Inhibition of Astrocytic Transglutaminase 2 Promotes Functional Recovery after Spinal Cord Injury.; Cells; Vol 10(11). 2021 Oct 29.
1. Bao C
2. Ermolenko DN
Ribosome as a Translocase and Helicase.; Biochemistry. Biokhimiia; Vol 86(8). 2021 Aug.
1. Moon EJ
2. Mello SS
3. Li CG
4. Chi JT
5. Thakkar K
6. Kirkland JG
7. Lagory EL
8. Lee IJ
9. Diep AN
10. Miao Y
11. Rafat M
12. Vilalta M
13. Castellini L
14. Krieg AJ
15. Graves EE
16. Attardi LD
17. Giaccia AJ
The HIF target MAFF promotes tumor invasion and metastasis through IL11 and STAT3 signaling.; Nature communications; Vol 12(1), pp. 4308. 2021 Jul 14.
1. Li L
2. Huang KL
3. Gao Y
4. Cui Y
5. Wang G
6. Elrod ND
7. Li Y
8. Chen YE
9. Ji P
10. Peng F
11. Russell WK
12. Wagner EJ
13. Li W
An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability.; Nature genetics; Vol 53(7). 2021 Jul.
1. Murphy Z
2. Murphy K
3. Myers JA
4. Getman MR
5. Couch T
6. Schulz V
7. Lezon-Geyda K
8. Palumbo C
9. Yan H
10. Narla M
11. Gallagher PG
12. Steiner LA
Regulation of RNA Polymerase II Activity is Essential for Terminal Erythroid Maturation.; Blood. 2021 Jun 01.
1. Adachi H
2. Hengesbach M
3. Yu YT
4. Morais P
From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies.; Biomedicines; Vol 9(5). 2021 May 14.
1. Yang H
2. Kundra S
3. Chojnacki M
4. Liu K
5. Fuse MA
6. Abouelhassan Y
7. Kallifidas D
8. Zhang P
9. Huang G
10. Jin S
11. Ding Y
12. Luesch H
13. Rohde KH
14. Dunman PM
15. Lemos JA
16. Huigens RW
A Modular Synthetic Route Involving N-Aryl-2-nitrosoaniline Intermediates Leads to a New Series of 3-Substituted Halogenated Phenazine Antibacterial Agents.; Journal of medicinal chemistry. 2021 Apr 21.
1. Suigo L
2. Chojnacki M
3. Zanotto C
4. Sebastián-Pérez V
5. Morghen CG
6. Casiraghi A
7. Dunman PM
8. Valoti E
9. Straniero V
Staphylococcus aureus RnpA Inhibitors: Computational-Guided Design, Synthesis and Initial Biological Evaluation.; Antibiotics (Basel, Switzerland); Vol 10(4). 2021 Apr 14.
1. Enwerem III
2. Elrod ND
3. Chang CT
4. Lin A
5. Ji P
6. Bohn JA
7. Levdansky Y
8. Wagner EJ
9. Valkov E
10. Goldstrohm AC
Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome.; RNA (New York, N.Y.); Vol 27(4). 2021 Apr.
1. Chojnacki M
2. Cao X
3. Flaherty DP
4. Dunman PM
Optimization of 2-Acylaminocycloalkylthiophene Derivatives for Activity against Staphylococcus aureus RnpA.; Antibiotics (Basel, Switzerland); Vol 10(4). 2021 Mar 31.
1. Chojnacki M
2. Dobrotka C
3. Osborn R
4. Johnson W
5. Young M
6. Meyer B
7. Laskey E
8. Wozniak RAF
9. Dewhurst S
10. Dunman PM
Evaluating the Antimicrobial Properties of Commercial Hand Sanitizers.; mSphere; Vol 6(2). 2021 Mar 03.
1. Srivastava Y
2. Bonn-Breach R
3. Chavali SS
4. Lippa GM
5. Jenkins JL
6. Wedekind JE
Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.; Crystals; Vol 11(3). 2021 Mar.
1. Chatrikhi R
2. Feeney CF
3. Pulvino MJ
4. Alachouzos G
5. MacRae AJ
6. Falls Z
7. Rai S
8. Brennessel WW
9. Jenkins JL
10. Walter MJ
11. Graubert TA
12. Samudrala R
13. Jurica MS
14. Frontier AJ
15. Kielkopf CL
A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex.; Cell chemical biology. 2021 Feb 26.
1. Porter JJ
2. Heil CS
3. Lueck JD
Therapeutic promise of engineered nonsense suppressor tRNAs.; Wiley interdisciplinary reviews. RNA. 2021 Feb 10.
1. Li S
2. Zhang H
3. Zhang L
4. Liu K
5. Liu B
6. Mathews DH
7. Huang L
LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2.; Proceedings of the National Academy of Sciences of the United States of America; Vol 118(52). 2021 Jan 28.
1. Tanner MK
2. Tang Z
3. Thornton CA
Targeted splice sequencing reveals RNA toxicity and therapeutic response in myotonic dystrophy.; Nucleic acids research. 2021 Jan 27.
1. Otero BA
2. Poukalov K
3. Hildebrandt RP
4. Thornton CA
5. Jinnai K
6. Fujimura H
7. Kimura T
8. Hagerman KA
9. Sampson JB
10. Day JW
11. Wang ET
Transcriptome alterations in myotonic dystrophy frontal cortex.; Cell reports; Vol 34(3). 2021 Jan 19.
1. Chambers M
2. Rees A
3. Cronin JG
4. Nair M
5. Jones N
6. Thornton CA
Macrophage Plasticity in Reproduction and Environmental Influences on Their Function.; Frontiers in immunology; Vol 11, pp. 607328. 2021 Jan 14.
1. Scherzi T
2. D'Ambrosio EA
3. Daher SS
4. Grimes CL
5. Dunman PM
6. Andrade RB
Staphylococcus aureus resistance to albocycline can be achieved by mutations that alter cellular NAD/PH pools.; Bioorganic & medicinal chemistry; Vol 32. 2021 Jan 07.
1. Lin A
2. Ji P
3. Niu X
4. Zhao X
5. Chen Y
6. Liu W
7. Liu Y
8. Fan W
9. Sun Y
10. Miao C
11. Zhang S
12. Tan W
13. Lin D
14. Wagner EJ
15. Wu C
CstF64-Induced Shortening of the BID 3'UTR Promotes Esophageal Squamous Cell Carcinoma Progression by Disrupting ceRNA Cross-talk with ZFP36L2.; Cancer research; Vol 81(22), pp. 5638-5651. 2021 Jan 04.
1. Han L
2. Marcus E
3. Phizicky EM
A semi-quantitative pull-down assay to study tRNA substrate specificity of modification enzymes.; Methods in enzymology; Vol 658. 2021.
1. Morais P
2. Adachi H
3. Yu YT
The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines.; Frontiers in cell and developmental biology; Vol 9. 2021.
1. Jensen MK
2. Elrod ND
3. Yalamanchili HK
4. Ji P
5. Lin A
6. Liu Z
7. Wagner EJ
Application and design considerations for 3'-end sequencing using click-chemistry.; Methods in enzymology; Vol 655. 2021.
1. Yalamanchili HK
2. Elrod ND
3. Jensen MK
4. Ji P
5. Lin A
6. Wagner EJ
7. Liu Z
A computational pipeline to infer alternative poly-adenylation from 3' sequencing data.; Methods in enzymology; Vol 655. 2021.
1. Anderson DM
2. Anderson KM
3. Nelson BR
4. McAnally JR
5. Bezprozvannaya S
6. Shelton JM
7. Bassel-Duby R
8. Olson EN
A myocardin-adjacent lncRNA balances SRF-dependent gene transcription in the heart.; Genes & Development; Vol 35, pp. 835-840. 2021 Jan 01.
1. Yuan F
2. Hankey W
3. Wagner EJ
4. Li W
5. Wang Q
Alternative polyadenylation of mRNA and its role in cancer.; Genes & diseases; Vol 8(1). 2021 Jan.
1. Kurosaki T
2. Imamachi N
3. Pröschel C
4. Mitsutomi S
5. Nagao R
6. Akimitsu N
7. Maquat LE
Loss of the fragile X syndrome protein FMRP results in misregulation of nonsense-mediated mRNA decay.; Nature cell biology; Vol 23(1). 2021 Jan.
1. Morais P
2. Adachi H
3. Yu YT
Spliceosomal snRNA Epitranscriptomics.; Frontiers in genetics; Vol 12. 2021.
1. Johnson WL
2. Sohn MB
3. Taffner S
4. Chatterjee P
5. Dunman PM
6. Pecora N
7. Wozniak RAF
Genomics of Staphylococcus aureus ocular isolates.; PloS one; Vol 16(5). 2021.
1. Kayedkhordeh M
2. Yamagami R
3. Bevilacqua PC
4. Mathews DH
Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots.; Methods in molecular biology (Clifton, N.J.); Vol 2167. 2021.
1. Zhang H
2. Zhang L
3. Li S
4. Mathews DH
5. Huang L
LinearSampling: Linear-Time Stochastic Sampling of RNA Secondary Structure with Applications to SARS-CoV-2.; bioRxiv : the preprint server for biology. 2020 Dec 29.
1. Wu J
2. Venkata Subbaiah KC
3. Jiang F
4. Hedaya O
5. Mohan A
6. Yang T
7. Welle K
8. Ghaemmaghami S
9. Tang WHW
10. Small E
11. Yan C
12. Yao P
MicroRNA-574 regulates FAM210A expression and influences pathological cardiac remodeling.; EMBO molecular medicine. 2020 Dec 28.
1. Lyu QR
2. Yao P
3. Miano JM
Generating a CRISPR knockout mouse through a strong premature termination codon: a cautionary tale.; Journal of biomedical research; Vol 35(2). 2020 Dec 25.