Education / Graduate Education / PhD Programs / Biophysics, Structural & Computational Biology (BSCB) / Faculty & Students / Students / Publications

Publications

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. Burchett JB
2. Ambeskovic A
3. Ford M
4. Naccarato JC
5. Cazarin J
6. Hecht F
7. Hulver M
8. He X
9. Munger JC
10. Vertino PM
11. Harris IS
12. Mello SS
13. Altman BJ
MYC and Epithelial to Mesenchymal Transition (EMT) Independently Predict Circadian Rhythm Disruption in Lung Adenocarcinoma.; bioRxiv : the preprint server for biology. 2025 Aug 21.
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. Zhang K
2. Manning AC
3. Lentini JM
4. Howard J
5. Dalwigk F
6. Maroofian R
7. Efthymiou S
8. Chan P
9. Eliseev SI
10. Yang Z
11. Chang H
12. Karimiani EG
13. Bakhshoodeh B
14. Houlden H
15. Kaiser SM
16. Lowe TM
17. Fu D
Human TRMT1 and TRMT1L paralogs ensure the proper modification state, stability, and function of tRNAs.; Cell reports; Vol 44(1), pp. 115092. 2025 Jan 08.
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. 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. Poruthoor AJ
2. Stallone JJ
3. Miaro M
4. Sharma A
5. Grossfield A
System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers.; The Journal of chemical physics; Vol 161(14). 2024 Oct 14.
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. 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. Beard JW
2. Hunt SL
3. Evans A
4. Goenner C
5. Miller BL
Mimicking an in cellulo environment for enzyme-free paper-based nucleic acid tests at the point of care.; bioRxiv : the preprint server for biology. 2024 Feb 29.
1. Poruthoor AJ
2. Sharma A
3. Grossfield A
Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics.; Biophysical journal. 2023 Sep 22.
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. Poruthoor AJ
2. Grossfield A
Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics.; bioRxiv : the preprint server for biology. 2023 Feb 03.
1. Michel LV
2. Kaur R
3. Gleghorn ML
4. Holmquist M
5. Pryharski K
6. Perdue J
7. Jones SP
8. Jackson N
9. Pilo I
10. Kasper A
11. Labbe N
12. Pichichero M
Haemophilus influenzae Protein D antibody suppression in a multi-component vaccine formulation.; FEBS open bio; Vol 12(12), pp. 2191-2202. 2022 Oct 28.
1. Jones SP
2. Cook KH
3. Holmquist ML
4. Almekinder LJ
5. Delaney AM
6. Charles R
7. Labbe N
8. Perdue J
9. Jackson N
10. Pichichero ME
11. Kaur R
12. Michel LV
13. Gleghorn ML
Vaccine target and carrier molecule nontypeable Haemophilus influenzae protein D dimerizes like the close Escherichia coli GlpQ homolog but unlike other known homolog dimers.; Proteins; Vol 91(2), pp. 161-170. 2022 Sep 16.
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. Jones SP
2. Goossen C
3. Lewis SD
4. Delaney AM
5. Gleghorn ML
Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.; Journal of structural biology: X; Vol 6, pp. 100066. 2022 Mar 11.
1. Rook ML
2. Miaro M
3. Couch T
4. Kneisley DL
5. Musgaard M
6. MacLean DM
Mutation of a conserved glutamine residue does not abolish desensitization of acid-sensing ion channel 1.; The Journal of general physiology; Vol 153(8). 2021 Aug 02.
1. Beard JW
2. Murty S
3. Caulkins C
4. Strenk AR
5. Luta EP
6. Hunt SL
7. Yates MZ
8. Miller BL
Leveraging Arylboronic Acid - Cellulose Binding as a Versatile and Scalable Approach to Hydrophobic Patterning.; Advanced materials technologies; Vol 7(7). 2021 Jan 16.