Recent Publications

• 1. Jiang M
  2. Li H
  3. Zhang Y
  4. Yang Y
  5. Lu R
  6. Liu K
  7. Lin S
  8. Lan X
  9. Wang H
  10. Wu H
  11. Zhu J
  12. Zhou Z
  13. Xu J
  14. Lee DK
  15. Zhang L
  16. Lee YC
  17. Yuan J
  18. Abrams JA
  19. Wang TC
  20. Sepulveda AR
  21. Wu Q
  22. Chen H
  23. Sun X
  24. She J
  25. Chen X
  26. Que J
  (2017 Oct 11). Transitional basal cells at the squamous-columnar junction generate Barrett's oesophagus. Nature.
• 1. Tencer AH
  2. Cox KL
  3. Di L
  4. Bridgers JB
  5. Lyu J
  6. Wang X
  7. Sims JK
  8. Weaver TM
  9. Allen HF
  10. Zhang Y
  11. Gatchalian J
  12. Darcy MA
  13. Gibson MD
  14. Ikebe J
  15. Li W
  16. Wade PA
  17. Hayes JJ
  18. Strahl BD
  19. Kono H
  20. Poirier MG
  21. Musselman CA
  22. Kutateladze TG
  (2017 Oct 10). Covalent Modifications of Histone H3K9 Promote Binding of CHD3. Cell reports.
• 1. Murphy KJ
  2. Cutter AR
  3. Fang H
  4. Postnikov YV
  5. Bustin M
  6. Hayes JJ
  (2017 Sep 29). HMGN1 and 2 remodel core and linker histone tail domains within chromatin. Nucleic acids research.
• 1. Glasser E
  2. Agrawal AA
  3. Jenkins JL
  4. Kielkopf CL
  (2017 Sep 01). Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry.
• 1. Novosjolova I
  2. Kennedy SD
  3. Rozners E
  (2017 Aug 31). 2-Methoxypyridine as Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability and NMR Structural Studies. Chembiochem : a European journal of chemical biology.
• 1. Hayashi T
  2. Jean M
  3. Huang H
  4. Simpson S
  5. Santoso NG
  6. Zhu J
  (2017 Aug 22). Screening of an FDA-approved compound library identifies levosimendan as a novel anti-HIV-1 agent that inhibits viral transcription. Antiviral research.
• 1. Mutisya D
  2. Hardcastle T
  3. Cheruiyot SK
  4. Pallan PS
  5. Kennedy SD
  6. Egli M
  7. Kelley ML
  8. Smith AVB
  9. Rozners E
  (2017 Aug 21). Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs. Nucleic acids research.
• 1. Poole AR
  2. Vicino I
  3. Adachi H
  4. Yu YT
  5. Hebert MD
  (2017 Aug 14). Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity. Biology open.
• 1. Tan Z
  2. Sharma G
  3. Mathews DH
  (2017 Jul 20). Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data. Biophysical journal.
• 1. Kauffmann AD
  2. Kennedy SD
  3. Zhao J
  4. Turner DH
  (2017 Jul 12). Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions. Biochemistry.
• 1. Romo TD
  2. Lewis AK
  3. Braun AR
  4. Grossfield A
  5. Sachs JN
  (2017 Jul 05). Minimal nucleation state of alpha-Synuclein is stabilized by dynamic threonine-water networks. ACS chemical neuroscience.
• 1. Nadtochiy SM
  2. Wang YT
  3. Zhang J
  4. Nehrke K
  5. Schafer X
  6. Welle K
  7. Ghaemmaghami S
  8. Munger J
  9. Brookes PS
  (2017 Jul 03). Potential mechanisms linking SIRT activity and hypoxic 2-hydroxyglutarate generation: no role for direct enzyme (de)acetylation. The Biochemical journal.
• 1. Ward M
  2. Datta A
  3. Wise M
  4. Mathews DH
  (2017 Jun 06). Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. Nucleic acids research.
• 1. Elbarbary RA
  2. Maquat LE
  (2017 Jun 06). Distinct mechanisms obviate the potentially toxic effects of inverted-repeat Alu elements on cellular RNA metabolism. Nature structural & molecular biology.
• 1. Bednar J
  2. Garcia-Saez I
  3. Boopathi R
  4. Cutter AR
  5. Papai G
  6. Reymer A
  7. Syed SH
  8. Lone IN
  9. Tonchev O
  10. Crucifix C
  11. Menoni H
  12. Papin C
  13. Skoufias DA
  14. Kurumizaka H
  15. Lavery R
  16. Hamiche A
  17. Hayes JJ
  18. Schultz P
  19. Angelov D
  20. Petosa C
  21. Dimitrov S
  (2017 Jun 01). Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. Molecular cell.
• 1. Elbarbary RA
  2. Miyoshi K
  3. Myers JR
  4. Du P
  5. Ashton JM
  6. Tian B
  7. Maquat LE
  (2017 May 26). Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G1/S phase transition. Science (New York, N.Y.).
• 1. Polevoda B
  2. Joseph R
  3. Friedman AE
  4. Bennett RP
  5. Greiner R
  6. De Zoysa T
  7. Stewart RA
  8. Smith HC
  (2017 May 26). DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315. The Journal of biological chemistry.
• 1. Hilimire TA
  2. Chamberlain JM
  3. Anokhina V
  4. Bennett RP
  5. Swart O
  6. Myers JR
  7. Ashton JM
  8. Stewart RA
  9. Featherston AL
  10. Gates K
  11. Helms ED
  12. Smith HC
  13. Dewhurst S
  14. Miller BL
  (2017 May 05). HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells. ACS chemical biology.
• 1. Bednar J
  2. Garcia-Saez I
  3. Boopathi R
  4. Cutter AR
  5. Papai G
  6. Reymer A
  7. Syed SH
  8. Lone IN
  9. Tonchev O
  10. Crucifix C
  11. Menoni H
  12. Papin C
  13. Skoufias DA
  14. Kurumizaka H
  15. Lavery R
  16. Hamiche A
  17. Hayes JJ
  18. Schultz P
  19. Angelov D
  20. Petosa C
  21. Dimitrov S
  (2017 May 04). Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. Molecular cell.
• 1. East-Seletsky A
  2. O'Connell MR
  3. Burstein D
  4. Knott GJ
  5. Doudna JA
  (2017 May 04). RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes. Molecular cell.
• 1. Wedekind JE
  2. Dutta D
  3. Belashov IA
  4. Jenkins JL
  (2017 Apr 28). Metalloriboswitches: RNA-Based Inorganic Ion Sensors that Regulate Genes. The Journal of biological chemistry.
• 1. Gamache ER
  2. Doh JH
  3. Ritz J
  4. Laederach A
  5. Bellaousov S
  6. Mathews DH
  7. Curcio MJ
  (2017 Apr 26). Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA. Viruses.
• 1. Jean MJ
  2. Power D
  3. Kong W
  4. Huang H
  5. Santoso N
  6. Zhu J
  (2017 Apr 01). Identification of HIV-1 Tat-Associated Proteins Contributing to HIV-1 Transcription and Latency. Viruses.
• 1. Vats K
  2. Marsh G
  3. Harding K
  4. Zampetakis I
  5. Waugh RE
  6. Benoit DS
  (2017 Apr). Nanoscale physicochemical properties of chain- and step-growth polymerized PEG hydrogels affect cell-material interactions. Journal of biomedical materials research. Part A.
• 1. Cutter AR
  2. Hayes JJ
  (2017 Apr). Linker histones: novel insights into structure-specific recognition of the nucleosome. Biochemistry and cell biology = Biochimie et biologie cellulaire.
• 1. Jenkins JL
  2. Kielkopf CL
  (2017 Mar 31). Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures. Trends in genetics : TIG.
• 1. Baker JE
  2. Sriram R
  3. Miller BL
  (2017 Mar 30). Recognition-mediated particle detection under microfluidic flow with waveguide-coupled 2D photonic crystals: towards integrated photonic virus detectors. Lab on a chip.
• 1. Zuber J
  2. Sun H
  3. Zhang X
  4. McFadyen I
  5. Mathews DH
  (2017 Mar 15). A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction. Nucleic acids research.
• 1. Liu K
  2. Xie F
  3. Gao A
  4. Zhang R
  5. Zhang L
  6. Xiao Z
  7. Hu Q
  8. Huang W
  9. Huang Q
  10. Lin B
  11. Zhu J
  12. Wang H
  13. Que J
  14. Lan X
  (2017 Mar 14). SOX2 regulates multiple malignant processes of breast cancer development through the SOX2/miR-181a-5p, miR-30e-5p/TUSC3 axis. Molecular cancer.
• 1. Brule CE
  2. Grayhack EJ
  (2017 Mar 11). Synonymous Codons: Choose Wisely for Expression. Trends in genetics : TIG.
• 1. Murphy PS
  2. Wang J
  3. Bhagwat SP
  4. Munger JC
  5. Janssen WJ
  6. Wright TW
  7. Elliott MR
  (2017 Mar). CD73 regulates anti-inflammatory signaling between apoptotic cells and endotoxin-conditioned tissue macrophages. Cell death and differentiation.
• 1. Yang F
  2. Zhang L
  3. Wakabayashi H
  4. Myers J
  5. Jiang Y
  6. Cao Y
  7. Jimenez-Ortigosa C
  8. Perlin DS
  9. Rustchenko E
  (2017 Feb 21). Tolerance to caspofungin in Candida albicans is associated with at least three distinctive mechanisms that govern expression of FKS genes and cell wall remodeling. Antimicrobial agents and chemotherapy.
• 1. Aytenfisu AH
  2. Spasic A
  3. Grossfield A
  4. Stern HA
  5. Mathews DH
  (2017 Feb 14). Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics. Journal of chemical theory and computation.
• 1. Clark KM
  2. Jenkins JL
  3. Fedoriw N
  4. Dumont ME
  (2017 Feb). Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors. Protein science : a publication of the Protein Society.
• 1. Balliano A
  2. Hao F
  3. Njeri C
  4. Balakrishnan L
  5. Hayes JJ
  (2017 Jan 18). HMGB1 Stimulates Activity of Polymerase β on Nucleosome Substrates. Biochemistry.
• 1. Patra B
  2. Kon Y
  3. Yadav G
  4. Sevold AW
  5. Frumkin JP
  6. Vallabhajosyula RR
  7. Hintze A
  8. Østman B
  9. Schossau J
  10. Bhan A
  11. Marzolf B
  12. Tamashiro JK
  13. Kaur A
  14. Baliga NS
  15. Grayhack EJ
  16. Adami C
  17. Galas DJ
  18. Raval A
  19. Phizicky EM
  20. Ray A
  (2017 Jan 09). A genome wide dosage suppressor network reveals genomic robustness. Nucleic acids research.
• 1. Hrabeta-Robinson E
  2. Marcus E
  3. Cozen AE
  4. Phizicky EM
  5. Lowe TM
  (2017). High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq). Methods in molecular biology (Clifton, N.J.).
• 1. De Zoysa MD
  2. Yu YT
  (2017). Posttranscriptional RNA Pseudouridylation. The Enzymes.
• 1. Huang H
  2. Liu S
  3. Jean M
  4. Simpson S
  5. Huang H
  6. Merkley M
  7. Hayashi T
  8. Kong W
  9. Rodríguez-Sánchez I
  10. Zhang X
  11. Yosief HO
  12. Miao H
  13. Que J
  14. Kobie JJ
  15. Bradner J
  16. Santoso NG
  17. Zhang W
  18. Zhu J
  (2017). A Novel Bromodomain Inhibitor Reverses HIV-1 Latency through Specific Binding with BRD4 to Promote Tat and P-TEFb Association. Frontiers in microbiology.
• 1. Coudray N
  2. L Seyler S
  3. Lasala R
  4. Zhang Z
  5. Clark KM
  6. Dumont ME
  7. Rohou A
  8. Beckstein O
  9. Stokes DL
  (2017 Jan). Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Protein science : a publication of the Protein Society.
• 1. Han L
  2. Marcus E
  3. D'Silva S
  4. Phizicky EM
  (2016 Dec 21). S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates. RNA (New York, N.Y.).
• 1. Chatrikhi R
  2. Wang W
  3. Gupta A
  4. Loerch S
  5. Maucuer A
  6. Kielkopf CL
  (2016 Dec 20). SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA. Biophysical journal.
• 1. Komisarof J
  2. McCall M
  3. Newman L
  4. Bshara W
  5. Mohler JL
  6. Morrison C
  7. Land H
  (2016 Dec 09). A four gene signature predictive of recurrent prostate cancer. Oncotarget.
• 1. Ling C
  2. Ermolenko DN
  (2016 Dec 06). Caught on Camera: Intermediates of Ribosome Recycling. Structure (London, England : 1993).
• 1. Loerch S
  2. Kielkopf CL
  (2016 Dec). Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. RNA (New York, N.Y.).
• 1. Suwunnakorn S
  2. Wakabayashi H
  3. Rustchenko E
  (2016 Dec). Chromosome 5 of Human Pathogen Candida albicans Carries Multiple Genes for Negative Control of Caspofungin and Anidulafungin Susceptibility. Antimicrobial agents and chemotherapy.
• 1. Ikpeze TC
  2. Smith HC
  3. Lee DJ
  4. Elfar JC
  (2016 Dec). Distal Radius Fracture Outcomes and Rehabilitation. Geriatric orthopaedic surgery & rehabilitation.
• 1. Sloma MF
  2. Mathews DH
  (2016 Dec). Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures. RNA (New York, N.Y.).
• 1. Mathews DH
  2. Turner DH
  3. Watson RM
  (2016 Dec 01). RNA Secondary Structure Prediction. Current protocols in nucleic acid chemistry.
• 1. Pei S
  2. Minhajuddin M
  3. D'Alessandro A
  4. Nemkov T
  5. Stevens BM
  6. Adane B
  7. Khan N
  8. Hagen FK
  9. Yadav VK
  10. De S
  11. Ashton JM
  12. Hansen KC
  13. Gutman JA
  14. Pollyea DA
  15. Crooks PA
  16. Smith C
  17. Jordan CT
  (2016 Nov 25). Rational design of a parthenolide-based drug regimen that selectively eradicates acute myelogenous leukemia stem cells. The Journal of biological chemistry.
• 1. Smith HC
  (2016 Nov 21). RNA binding to APOBEC deaminases; Not simply a substrate for C to U editing. RNA biology.
• 1. Dutt S
  2. Binney RJ
  3. Heuer HW
  4. Luong P
  5. Attygalle S
  6. Bhatt P
  7. Marx GA
  8. Elofson J
  9. Tartaglia MC
  10. Litvan I
  11. McGinnis SM
  12. Dickerson BC
  13. Kornak J
  14. Waltzman D
  15. Voltarelli L
  16. Schuff N
  17. Rabinovici GD
  18. Kramer JH
  19. Jack CR
  20. Miller BL
  21. Rosen HJ
  22. Boxer AL
  (2016 Nov 08). Progression of brain atrophy in PSP and CBS over 6 months and 1 year. Neurology.
• 1. Bennett RP
  2. Stewart RA
  3. Hogan PA
  4. Ptak RG
  5. Mankowski MK
  6. Hartman TL
  7. Buckheit RW
  8. Snyder BA
  9. Salter JD
  10. Morales GA
  11. Smith HC
  (2016 Nov 4). An analog of camptothecin inactive against Topoisomerase I is broadly neutralizing of HIV-1 through inhibition of Vif-dependent APOBEC3G degradation. Antiviral research.
• 1. Fang H
  2. Wei S
  3. Lee TH
  4. Hayes JJ
  (2016 Nov 02). Chromatin structure-dependent conformations of the H1 CTD. Nucleic acids research.
• 1. Xu C
  2. Ishikawa H
  3. Izumikawa K
  4. Li L
  5. He H
  6. Nobe Y
  7. Yamauchi Y
  8. Shahjee HM
  9. Wu XH
  10. Yu YT
  11. Isobe T
  12. Takahashi N
  13. Min J
  (2016 Nov 01). Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. Genes & development.
• 1. Pei S
  2. Minhajuddin M
  3. D'Alessandro A
  4. Nemkov T
  5. Stevens BM
  6. Adane B
  7. Khan N
  8. Hagen FK
  9. Yadav VK
  10. De S
  11. Ashton JM
  12. Hansen KC
  13. Gutman JA
  14. Pollyea DA
  15. Crooks PA
  16. Smith C
  17. Jordan CT
  (2016 Oct 14). Rational Design of a Parthenolide-based Drug Regimen That Selectively Eradicates Acute Myelogenous Leukemia Stem Cells. The Journal of biological chemistry.
• 1. East-Seletsky A
  2. O'Connell MR
  3. Knight SC
  4. Burstein D
  5. Cate JH
  6. Tjian R
  7. Doudna JA
  (2016 Oct 13). Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature.
• 1. Smith B
  2. Schafer XL
  3. Ambeskovic A
  4. Spencer CM
  5. Land H
  6. Munger J
  (2016 Oct 11). Addiction to Coupling of the Warburg Effect with Glutamine Catabolism in Cancer Cells. Cell reports.
• 1. Mishra LN
  2. Pepenella S
  3. Rogge R
  4. Hansen JC
  5. Hayes JJ
  (2016 Oct 06). Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays. Scientific reports.
• 1. Fei DL
  2. Motowski H
  3. Chatrikhi R
  4. Prasad S
  5. Yu J
  6. Gao S
  7. Kielkopf CL
  8. Bradley RK
  9. Varmus H
  (2016 Oct). Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival. PLoS genetics.
• 1. Walling LR
  2. Butler JS
  (2016 Sep 26). Structural determinants for antitoxin identity and insulation of cross talk between homologous toxin-antitoxin systems. Journal of bacteriology.
• 1. Sparks RP
  2. Jenkins JL
  3. Miner GE
  4. Wang Y
  5. Guida WC
  6. Sparks CE
  7. Fratti RA
  8. Sparks JD
  (2016 Sep 22). Phosphatidylinositol (3,4,5)-trisphosphate binds to sortilin and competes with neurotensin: Implications for very low density lipoprotein binding. Biochemical and biophysical research communications.
• 1. Sridharan R
  2. Connelly SM
  3. Naider F
  4. Dumont ME
  (2016 Sep 19). Variable Dependence of Signaling Output on Agonist Occupancy of Ste2p, a G Protein Coupled Receptor in Yeast. The Journal of biological chemistry.
• 1. Nadtochiy SM
  2. Schafer X
  3. Fu D
  4. Nehrke K
  5. Munger J
  6. Brookes PS
  (2016 Aug 10). Acidic pH is a Metabolic Switch for 2-Hydroxyglutarate Generation and Signaling. The Journal of biological chemistry.
• 1. Sparks RP
  2. Guida WC
  3. Sowden MP
  4. Jenkins JL
  5. Starr ML
  6. Fratti RA
  7. Sparks CE
  8. Sparks JD
  (2016 Aug 2). Sortilin facilitates VLDL-B100 secretion by insulin sensitive McArdle RH7777 cells. Biochemical and biophysical research communications.
• 1. Gamble CE
  2. Brule CE
  3. Dean KM
  4. Fields S
  5. Grayhack EJ
  (2016 Jun 29). Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast. Cell.
• 1. Black PJ
  2. Miller AS
  3. Hayes JJ
  (2016 Jun 27). Radioresistance of GGG sequences to prompt strand break formation from direct-type radiation damage. Radiation and environmental biophysics.
• 1. Gleghorn ML
  2. Zhao J
  3. Turner DH
  4. Maquat LE
  (2016 Jun 10). Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation. Nucleic acids research.
• 1. Wu G
  2. Radwan MK
  3. Xiao M
  4. Adachi H
  5. Fan J
  6. Yu YT
  (2016 Jun 7). The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA. RNA (New York, N.Y.).
• 1. Popp MW
  2. Maquat LE
  (2016 Jun 2). Leveraging Rules of Nonsense-Mediated mRNA Decay for Genome Engineering and Personalized Medicine. Cell.
• 1. Svetina S
  2. Kokot G
  3. Kebe TŠ
  4. Žekš B
  5. Waugh RE
  (2016 Jun). A novel strain energy relationship for red blood cell membrane skeleton based on spectrin stiffness and its application to micropipette deformation. Biomechanics and modeling in mechanobiology.
• 1. Marsh G
  2. Waugh RE
  (2016 Jun). A simple approach for bioactive surface calibration using evanescent waves. Journal of microscopy.
• 1. Coudray N
  2. Lasala R
  3. Zhang Z
  4. Clark KM
  5. Dumont ME
  6. Stokes DL
  (2016 May 30). Deducing the Symmetry of Helical Assemblies: Applications to Membrane Proteins. Journal of structural biology.
• 1. Salter JD
  2. Bennett RP
  3. Smith HC
  (2016 May 30). The APOBEC Protein Family: United by Structure, Divergent in Function. Trends in biochemical sciences.
• 1. Salsi E
  2. Farah E
  3. Ermolenko DN
  (2016 May 22). EF-G Activation by Phosphate Analogs. Journal of molecular biology.
• 1. Miralem T
  2. Lerner-Marmarosh N
  3. Gibbs PE
  4. Jenkins JL
  5. Heimiller C
  6. Maines MD
  (2016 May 10). Interaction of human biliverdin reductase with Akt/protein kinase B and phosphatidylinositol-dependent kinase 1 regulates glycogen synthase kinase 3 activity: a novel mechanism of Akt activation. FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
• 1. Xu S
  2. Schafer X
  3. Munger J
  (2016 May 1). Expression of Oncogenic Alleles Induces Multiple Blocks to Human Cytomegalovirus Infection. Journal of virology.
• 1. Monaghan M
  2. Wakabayashi H
  3. Griffiths AE
  4. Fay PJ
  (2016 May). Stabilizing interactions between D666-S1787 and T657-Y1792 at the A2-A3 interface support factor VIIIa stability in the blood clotting pathway. Journal of thrombosis and haemostasis : JTH.
• 1. Ling C
  2. Ermolenko DN
  (2016 Apr 27). Structural insights into ribosome translocation. Wiley interdisciplinary reviews. RNA.
• 1. Piekna-Przybylska D
  2. Bambara RA
  3. Balakrishnan L
  (2016 Apr 22). Acetylation regulates DNA repair mechanisms in human cells. Cell cycle (Georgetown, Tex.).
• 1. Yue H
  2. Fang H
  3. Wei S
  4. Hayes JJ
  5. Lee TH
  (2016 Apr 12). Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome. Biochemistry.
• 1. Shaheen R
  2. Han L
  3. Faqeih E
  4. Ewida N
  5. Alobeid E
  6. Phizicky EM
  7. Alkuraya FS
  (2016 Apr 7). A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. Human genetics.
• 1. Nelles DA
  2. Fang MY
  3. O'Connell MR
  4. Xu JL
  5. Markmiller SJ
  6. Doudna JA
  7. Yeo GW
  (2016 Apr 07). Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell.
• 1. Maquat LE
  (2016 Apr). Eukaryotic antisense ahead of its time. Nature reviews. Molecular cell biology.
• 1. DiChiacchio L
  2. Sloma MF
  3. Mathews DH
  (2016 Apr 1). AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. Bioinformatics (Oxford, England).
• 1. Hollenbaugh JA
  2. Montero C
  3. Schinazi RF
  4. Munger J
  5. Kim B
  (2016 Apr). Metabolic profiling during HIV-1 and HIV-2 infection of primary human monocyte-derived macrophages. Virology.
• 1. Carter JA
  2. Triplett E
  3. Striemer CC
  4. Miller BL
  (2016 Mar 15). A label-free, multiplex competitive assay for small molecule pollutants. Biosensors & bioelectronics.
• 1. Wu G
  2. Adachi H
  3. Ge J
  4. Stephenson D
  5. Query CC
  6. Yu YT
  (2016 Mar 15). Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly. The EMBO journal.
• 1. Polevoda B
  2. McDougall WM
  3. Bennett RP
  4. Salter JD
  5. Smith HC
  (2016 Mar 14). Structural and functional assessment of APOBEC3G macromolecular complexes. Methods (San Diego, Calif.).
• 1. Bertozzi C
  2. Zimmermann I
  3. Engeler S
  4. Hilf RJ
  5. Dutzler R
  (2016 Mar). Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels. PLoS biology.
• 1. Elbarbary RA
  2. Maquat LE
  (2016 Mar 1). Coupling pre-mRNA splicing and 3' end formation to mRNA export: alternative ways to punch the nuclear export clock. Genes & development.
• 1. Vukomanovic D
  2. Rahman MN
  3. Maines MD
  4. Ozolinš TR
  5. Szarek WA
  6. Jia Z
  7. Nakatsu K
  (2016 Mar). Cysteine-independent activation/inhibition of heme oxygenase-2. Medical gas research.
• 1. Nganou C
  2. Kennedy SD
  3. McCamant DW
  (2016 Feb 25). Disagreement Between the Structure of the dTpT Thymine Pair Determined by NMR and Molecular Dynamics Simulations Using Amber 14 Force Fields. The journal of physical chemistry. B.
• 1. McAnany JD
  2. Reichert JP
  3. Miller BL
  (2016 Feb 24). Probing the geometric constraints of RNA binding via dynamic covalent chemistry. Bioorganic & medicinal chemistry.
• 1. Elbarbary RA
  2. Lucas BA
  3. Maquat LE
  (2016 Feb 12). Retrotransposons as regulators of gene expression. Science (New York, N.Y.).
• 1. Huang C
  2. Karijolich J
  3. Yu YT
  (2016 Feb 4). Detection and quantification of RNA 2'-O-methylation and pseudouridylation. Methods (San Diego, Calif.).
• 1. Kurosaki T
  2. Maquat LE
  (2016 Feb 1). Nonsense-mediated mRNA decay in humans at a glance. Journal of cell science.
• 1. Hilimire TA
  2. Bennett RP
  3. Stewart RA
  4. Garcia-Miranda P
  5. Blume A
  6. Becker J
  7. Sherer N
  8. Helms ED
  9. Butcher SE
  10. Smith HC
  11. Miller BL
  (2016 Jan 15). N-Methylation as a Strategy for Enhancing the Affinity and Selectivity of RNA-binding Peptides: Application to the HIV-1 Frameshift-Stimulating RNA. ACS chemical biology.
• 1. Uppal N
  2. Foxe JJ
  3. Butler JS
  4. Acluche F
  5. Molholm S
  (2016 Jan 13). The neural dynamics of somatosensory processing and adaptation across childhood: A high-density electrical mapping study. Journal of neurophysiology.
• 1. Agrawal AA
  2. Salsi E
  3. Chatrikhi R
  4. Henderson S
  5. Jenkins JL
  6. Green MR
  7. Ermolenko DN
  8. Kielkopf CL
  (2016). An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal. Nature communications.
• 1. Brule CE
  2. Dean KM
  3. Grayhack EJ
  (2016). RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences. Methods in enzymology.
• 1. Huang C
  2. Wu G
  3. Yu YT
  (2016). Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles. Methods in molecular biology (Clifton, N.J.).
• 1. Gibbs PE
  2. Miralem T
  3. Lerner-Marmarosh N
  4. Maines MD
  (2016). Nanoparticle Delivered Human Biliverdin Reductase-Based Peptide Increases Glucose Uptake by Activating IRK/Akt/GSK3 Axis: The Peptide Is Effective in the Cell and Wild-Type and Diabetic Ob/Ob Mice. Journal of diabetes research.
• 1. DiChiacchio L
  2. Mathews DH
  (2016). Predicting RNA-RNA Interactions Using RNAstructure. Methods in molecular biology (Clifton, N.J.).
• 1. Xu ZZ
  2. Mathews DH
  (2016). Experiment-Assisted Secondary Structure Prediction with RNAstructure. Methods in molecular biology (Clifton, N.J.).
• 1. Xu ZZ
  2. Mathews DH
  (2016). Prediction of Secondary Structures Conserved in Multiple RNA Sequences. Methods in molecular biology (Clifton, N.J.).
• 1. Xu ZZ
  2. Mathews DH
  (2016). Secondary Structure Prediction of Single Sequences Using RNAstructure. Methods in molecular biology (Clifton, N.J.).
• 1. Jenkins JL
  2. Wedekind JE
  (2016). The Quick and the Dead: A Guide to Fast Phasing of Small Ribozyme and Riboswitch Crystal Structures. Methods in molecular biology (Clifton, N.J.).
• 1. Kennedy SD
  (2016). NMR Methods for Characterization of RNA Secondary Structure. Methods in molecular biology (Clifton, N.J.).
• 1. Leamy KA
  2. Assmann SM
  3. Mathews DH
  4. Bevilacqua PC
  (2016 Jan). Bridging the gap between in vitro and in vivo RNA folding. Quarterly reviews of biophysics.
• 1. Xiao J
  2. Moon Y
  3. Li L
  4. Rustchenko E
  5. Wakabayashi H
  6. Zhao X
  7. Feng C
  8. Gill SR
  9. McLaren S
  10. Malmstrom H
  11. Ren Y
  12. Quivey R
  13. Koo H
  14. Kopycka-Kedzierawski DT
  (2016). Candida albicans Carriage in Children with Severe Early Childhood Caries (S-ECC) and Maternal Relatedness. PloS one.
• 1. Ling C
  2. Ermolenko DN
  (2015 Dec 29). Initiation factor 2 stabilizes the ribosome in a semirotated conformation. Proceedings of the National Academy of Sciences of the United States of America.
• 1. Hughes AD
  2. Marsh G
  3. Waugh RE
  4. Foster DG
  5. King MR
  (2015 Dec 22). Halloysite Nanotube Coatings Suppress Leukocyte Spreading. Langmuir : the ACS journal of surfaces and colloids.
• 1. Zhu G
  2. Koszelak-Rosenblum M
  3. Connelly SM
  4. Dumont ME
  5. Malkowski MG
  (2015 Dec 11). The Crystal Structure of an Integral Membrane Fatty Acid α-Hydroxylase. The Journal of biological chemistry.
• 1. Quivey RG
  2. Grayhack EJ
  3. Faustoferri RC
  4. Hubbard CJ
  5. Baldeck JD
  6. Wolf AS
  7. MacGilvray ME
  8. Rosalen PL
  9. Scott-Anne K
  10. Santiago B
  11. Gopal S
  12. Payne J
  13. Marquis RE
  (2015 Dec). Functional profiling in Streptococcus mutans: construction and examination of a genomic collection of gene deletion mutants. Molecular oral microbiology.
• 1. Balliano AJ
  2. Hayes JJ
  (2015 Dec). Base excision repair in chromatin: Insights from reconstituted systems. DNA repair.
• 1. Goodwin CM
  2. Xu S
  3. Munger J
  (2015 Dec). Stealing the Keys to the Kitchen: Viral Manipulation of the Host Cell Metabolic Network. Trends in microbiology.
• 1. Guy MP
  2. Shaw M
  3. Weiner CL
  4. Hobson L
  5. Stark Z
  6. Rose K
  7. Kalscheuer VM
  8. Gecz J
  9. Phizicky EM
  (2015 Dec). Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1. Human mutation.
• 1. Chen JL
  2. Bellaousov S
  3. Tubbs JD
  4. Kennedy SD
  5. Lopez MJ
  6. Mathews DH
  7. Turner DH
  (2015 Nov 17). Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. Biochemistry.
• 1. Dutta D
  2. Wedekind JE
  (2015 Nov 6). Gene Regulation Gets in Tune: How Riboswitch Tertiary-Structure Networks Adapt to Meet the Needs of Their Transcription Units. Journal of molecular biology.
• 1. Huang H
  2. Santoso N
  3. Power D
  4. Simpson S
  5. Dieringer M
  6. Miao H
  7. Gurova K
  8. Giam CZ
  9. Elledge SJ
  10. Zhu J
  (2015 Nov 6). FACT Proteins, SUPT16H and SSRP1, Are Transcriptional Suppressors of HIV-1 and HTLV-1 That Facilitate Viral Latency. The Journal of biological chemistry.
• 1. Ma E
  2. Harrington LB
  3. O'Connell MR
  4. Zhou K
  5. Doudna JA
  (2015 Nov 05). Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Molecular cell.
• 1. Nadtochiy SM
  2. Urciuoli W
  3. Zhang J
  4. Schafer X
  5. Munger J
  6. Brookes PS
  (2015 Nov). Metabolomic profiling of the heart during acute ischemic preconditioning reveals a role for SIRT1 in rapid cardioprotective metabolic adaptation. Journal of molecular and cellular cardiology.
• 1. Aytenfisu AH
  2. Liberman JA
  3. Wedekind JE
  4. Mathews DH
  (2015 Nov). Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics. RNA (New York, N.Y.).
• 1. Polevoda B
  2. McDougall WM
  3. Tun BN
  4. Cheung M
  5. Salter JD
  6. Friedman AE
  7. Smith HC
  (2015 Oct 30). RNA binding to APOBEC3G induces the disassembly of functional deaminase complexes by displacing single-stranded DNA substrates. Nucleic acids research.
• 1. Campbell A
  2. Bushman J
  3. Munger J
  4. Noble M
  5. Pröschel C
  6. Mayer-Pröschel M
  (2015 Oct 15). Mutation of ataxia-telangiectasia mutated is associated with dysfunctional glutathione homeostasis in cerebellar astroglia. Glia.
• 1. Cutter AR
  2. Hayes JJ
  (2015 Oct 7). A brief review of nucleosome structure. FEBS letters.
• 1. Seward CH
  2. Manzella A
  3. Alam A
  4. Butler JS
  5. Dziejman M
  (2015 Oct). Using S. cerevisiae as a Model System to Investigate V. cholerae VopX-Host Cell Protein Interactions and Phenotypes. Toxins.
• 1. Yada K
  2. Nogami K
  3. Takeyama M
  4. Ogiwara K
  5. Wakabayashi H
  6. Shima M
  (2015 Oct). Mild hemophilia A patient with novel Pro1809Leu mutation develops an anti-C2 antibody inhibiting allogeneic but not autologous factor VIII activity. Journal of thrombosis and haemostasis : JTH.
• 1. Karijolich J
  2. Yi C
  3. Yu YT
  (2015 Oct). Transcriptome-wide dynamics of RNA pseudouridylation. Nature reviews. Molecular cell biology.
• 1. Loerch S
  2. Kielkopf CL
  (2015 Sep 25). Dividing and Conquering the Family of RNA Recognition Motifs: A Representative Case Based on hnRNP L. Journal of molecular biology.
• 1. Cinar E
  2. Zhou S
  3. DeCourcey J
  4. Wang Y
  5. Waugh RE
  6. Wan J
  (2015 Sep 22). Piezo1 regulates mechanotransductive release of ATP from human RBCs. Proceedings of the National Academy of Sciences of the United States of America.
• 1. Wu Y
  2. Shi B
  3. Ding X
  4. Liu T
  5. Hu X
  6. Yip KY
  7. Yang ZR
  8. Mathews DH
  9. Lu ZJ
  (2015 Sep 3). Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data. Nucleic acids research.
• 1. Beste MT
  2. Lomakina EB
  3. Hammer DA
  4. Waugh RE
  (2015 Sep). Immobilized IL-8 Triggers Phagocytosis and Dynamic Changes in Membrane Microtopology in Human Neutrophils. Annals of biomedical engineering.
• 1. Cozen AE
  2. Quartley E
  3. Holmes AD
  4. Hrabeta-Robinson E
  5. Phizicky EM
  6. Lowe TM
  (2015 Sep). ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nature methods.
• 1. Lin D
  2. Grossfield A
  (2015 Aug 18). Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity. Biophysical journal.
• 1. Leioatts N
  2. Romo TD
  3. Danial SA
  4. Grossfield A
  (2015 Aug 4). Retinal Conformation Changes Rhodopsin's Dynamic Ensemble. Biophysical journal.
• 1. Buescher JM
  2. Antoniewicz MR
  3. Boros LG
  4. Burgess SC
  5. Brunengraber H
  6. Clish CB
  7. DeBerardinis RJ
  8. Feron O
  9. Frezza C
  10. Ghesquiere B
  11. Gottlieb E
  12. Hiller K
  13. Jones RG
  14. Kamphorst JJ
  15. Kibbey RG
  16. Kimmelman AC
  17. Locasale JW
  18. Lunt SY
  19. Maddocks OD
  20. Malloy C
  21. Metallo CM
  22. Meuillet EJ
  23. Munger J
  24. Nöh K
  25. Rabinowitz JD
  26. Ralser M
  27. Sauer U
  28. Stephanopoulos G
  29. St-Pierre J
  30. Tennant DA
  31. Wittmann C
  32. Vander Heiden MG
  33. Vazquez A
  34. Vousden K
  35. Young JD
  36. Zamboni N
  37. Fendt SM
  (2015 Aug). A roadmap for interpreting (13)C metabolite labeling patterns from cells. Current opinion in biotechnology.
• 1. Liberman JA
  2. Suddala KC
  3. Aytenfisu A
  4. Chan D
  5. Belashov IA
  6. Salim M
  7. Mathews DH
  8. Spitale RC
  9. Walter NG
  10. Wedekind JE
  (2015 Jul 7). Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proceedings of the National Academy of Sciences of the United States of America.
• 1. Miller BL
  (2015 Jul). mRNA regulation: A patch for a splice. Nature chemical biology.
• 1. Power D
  2. Santoso N
  3. Dieringer M
  4. Yu J
  5. Huang H
  6. Simpson S
  7. Seth I
  8. Miao H
  9. Zhu J
  (2015 Jul). IFI44 suppresses HIV-1 LTR promoter activity and facilitates its latency. Virology.
• 1. Pulvino M
  2. Chen L
  3. Oleksyn D
  4. Li J
  5. Compitello G
  6. Rossi R
  7. Spence S
  8. Balakrishnan V
  9. Jordan C
  10. Poligone B
  11. Casulo C
  12. Burack R
  13. Shapiro JL
  14. Bernstein S
  15. Friedberg JW
  16. Deshaies RJ
  17. Land H
  18. Zhao J
  (2015 Jun 20). Inhibition of COP9-signalosome (CSN) deneddylating activity and tumor growth of diffuse large B-cell lymphomas by doxycycline. Oncotarget.
• 1. Condon DE
  2. Kennedy SD
  3. Mort BC
  4. Kierzek R
  5. Yildirim I
  6. Turner DH
  (2015 Jun 9). Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics. Journal of chemical theory and computation.
• 1. Kim AR
  2. Olsen JL
  3. England SJ
  4. Huang YS
  5. Fegan KH
  6. Delgadillo LF
  7. McGrath KE
  8. Kingsley PD
  9. Waugh RE
  10. Palis J
  (2015 Jun 9). Bmi-1 Regulates Extensive Erythroid Self-Renewal. Stem cell reports.
• 1. Ling C
  2. Ermolenko DN
  (2015 Jun 2). Ribosome subunit joining frozen in time. Structure (London, England : 1993).
• 1. Chen JL
  2. Kennedy SD
  3. Turner DH
  (2015 Jun 2). Structural features of a 3' splice site in influenza a. Biochemistry.
• 1. Xu S
  2. Spencer CM
  3. Munger J
  (2015 Jun). Transformation with oncogenic Ras and the simian virus 40 T antigens induces caspase-dependent sensitivity to fatty acid biosynthetic inhibition. Journal of virology.
• 1. Wolf AS
  2. Grayhack EJ
  (2015 May). Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats. RNA (New York, N.Y.).
• 1. Xu F
  2. Huang Y
  3. Li L
  4. Gannon P
  5. Linster E
  6. Huber M
  7. Kapos P
  8. Bienvenut W
  9. Polevoda B
  10. Meinnel T
  11. Hell R
  12. Giglione C
  13. Zhang Y
  14. Wirtz M
  15. Chen S
  16. Li X
  (2015 May). Two N-terminal acetyltransferases antagonistically regulate the stability of a nod-like receptor in Arabidopsis. The Plant cell.
• 1. Jin G
  2. Pavelka MS
  3. Butler JS
  (2015 Apr). Structure-function analysis of VapB4 antitoxin identifies critical features of a minimal VapC4 toxin-binding module. Journal of bacteriology.
• 1. Elbarbary RA
  2. Maquat LE
  (2015 Apr 1). CARMing down the SINEs of anarchy: two paths to freedom from paraspeckle detention. Genes & development.
• 1. Okeyo-Owuor T
  2. White BS
  3. Chatrikhi R
  4. Mohan DR
  5. Kim S
  6. Griffith M
  7. Ding L
  8. Ketkar-Kulkarni S
  9. Hundal J
  10. Laird KM
  11. Kielkopf CL
  12. Ley TJ
  13. Walter MJ
  14. Graubert TA
  (2015 Apr). U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing. Leukemia.
• 1. Maquat LE
  (2015 Apr). The amazing web of post-transcriptional gene control: the sum of small changes can make for significant consequences. RNA (New York, N.Y.).
• 1. Phizicky EM
  2. Hopper AK
  (2015 Apr). tRNA processing, modification, and subcellular dynamics: past, present, and future. RNA (New York, N.Y.).
• 1. Karijolich J
  2. Yu YT
  (2015 Apr). The new era of RNA modification. RNA (New York, N.Y.).
• 1. Aroda VR
  2. Christophi CA
  3. Edelstein SL
  4. Zhang P
  5. Herman WH
  6. Barrett-Connor E
  7. Delahanty LM
  8. Montez MG
  9. Ackermann RT
  10. Zhuo X
  11. Knowler WC
  12. Ratner RE
  (2015 Apr). The effect of lifestyle intervention and metformin on preventing or delaying diabetes among women with and without gestational diabetes: the Diabetes Prevention Program outcomes study 10-year follow-up. The Journal of clinical endocrinology and metabolism.
• 1. Popp MW
  2. Maquat LE
  (2015 Mar 20). RNA. A TRICK'n way to see the pioneer round of translation. Science (New York, N.Y.).
• 1. Zuber J
  2. Danial SA
  3. Connelly SM
  4. Naider F
  5. Dumont ME
  (2015 Mar 10). Identification of destabilizing and stabilizing mutations of Ste2p, a G protein-coupled receptor in Saccharomyces cerevisiae. Biochemistry.
• 1. Baker JE
  2. Sriram R
  3. Miller BL
  (2015 Feb 21). Two-dimensional photonic crystals for sensitive microscale chemical and biochemical sensing. Lab on a chip.
• 1. Han L
  2. Kon Y
  3. Phizicky EM
  (2015 Feb). Functional importance of Ψ38 and Ψ39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast. RNA (New York, N.Y.).
• 1. Bulger M
  2. Palis J
  (2015 Feb). Environmentally-defined enhancer populations regulate diversity of tissue-resident macrophages. Trends in immunology.
• 1. Kapogiannis D
  2. Boxer A
  3. Schwartz JB
  4. Abner EL
  5. Biragyn A
  6. Masharani U
  7. Frassetto L
  8. Petersen RC
  9. Miller BL
  10. Goetzl EJ
  (2015 Feb). Dysfunctionally phosphorylated type 1 insulin receptor substrate in neural-derived blood exosomes of preclinical Alzheimer's disease. FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
• 1. Salsi E
  2. Farah E
  3. Netter Z
  4. Dann J
  5. Ermolenko DN
  (2015 Jan 30). Movement of elongation factor G between compact and extended conformations. Journal of molecular biology.
• 1. Leong L
  2. Sim D
  3. Patel C
  4. Tran K
  5. Liu P
  6. Ho E
  7. Thompson T
  8. Kretschmer PJ
  9. Wakabayashi H
  10. Fay PJ
  11. Murphy JE
  (2015 Jan 8). Noncovalent stabilization of the factor VIII A2 domain enhances efficacy in hemophilia A mouse vascular injury models. Blood.
• 1. Fu Y
  2. Xu ZZ
  3. Lu ZJ
  4. Zhao S
  5. Mathews DH
  (2015). Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PloS one.
• 1. Payea MJ
  2. Guy MP
  3. Phizicky EM
  (2015). Methodology for the High-Throughput Identification and Characterization of tRNA Variants That Are Substrates for a tRNA Decay Pathway. Methods in enzymology.
• 1. Gibbs PE
  2. Miralem T
  3. Maines MD
  (2015). Biliverdin reductase: a target for cancer therapy? Frontiers in pharmacology.
• 1. Aytenfisu AH
  2. Spasic A
  3. Grossfield A
  4. Stern H
  5. Mathews DH
  (2015). 99 Improving the amber RNA force field. Journal of biomolecular structure & dynamics.
• 1. Mathew E
  2. Dumont ME
  (2015). A Novel Screening Approach for Optimal and Functional Fusion of T4 Lysozyme in GPCRs. Methods in enzymology.
• 1. Gong C
  2. Maquat LE
  (2015). Affinity purification of long noncoding RNA-protein complexes from formaldehyde cross-linked mammalian cells. Methods in molecular biology (Clifton, N.J.).
• 1. Jackson KL
  2. Dayton RD
  3. Orchard EA
  4. Ju S
  5. Ringe D
  6. Petsko GA
  7. Maquat LE
  8. Klein RL
  (2015 Jan). Preservation of forelimb function by UPF1 gene therapy in a rat model of TDP-43-induced motor paralysis. Gene therapy.
• 1. Popp MW
  2. Maquat LE
  (2015). Attenuation of nonsense-mediated mRNA decay facilitates the response to chemotherapeutics. Nature communications.
• 1. Sloma MF
  2. Mathews DH
  (2015). Improving RNA secondary structure prediction with structure mapping data. Methods in enzymology.
• 1. Bucukovski J
  2. Latorre-Margalef N
  3. Stallknecht DE
  4. Miller BL
  (2015). A Multiplex Label-Free Approach to Avian Influenza Surveillance and Serology. PloS one.
• 1. Guy MP
  2. Phizicky EM
  (2015 Jan). Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. RNA (New York, N.Y.).
• 1. Shaheen R
  2. Abdel-Salam GM
  3. Guy MP
  4. Alomar R
  5. Abdel-Hamid MS
  6. Afifi HH
  7. Ismail SI
  8. Emam BA
  9. Phizicky EM
  10. Alkuraya FS
  (2015). Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome biology.
• 1. Enwerem II
  2. Wu G
  3. Yu YT
  4. Hebert MD
  (2015). Cajal body proteins differentially affect the processing of box C/D scaRNPs. PloS one.
• 1. Wu G
  2. Huang C
  3. Yu YT
  (2015). Pseudouridine in mRNA: Incorporation, Detection, and Recoding. Methods in enzymology.
• 1. Fu Y
  2. Sharma G
  3. Mathews DH
  (2014 Dec 16). Dynalign II: common secondary structure prediction for RNA homologs with domain insertions. Nucleic acids research.
• 1. DeVito SR
  2. Ortiz-Riaño E
  3. Martínez-Sobrido L
  4. Munger J
  (2014 Dec 16). Cytomegalovirus-mediated activation of pyrimidine biosynthesis drives UDP-sugar synthesis to support viral protein glycosylation. Proceedings of the National Academy of Sciences of the United States of America.
• 1. Romo TD
  2. Leioatts N
  3. Grossfield A
  (2014 Dec 15). Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations. Journal of computational chemistry.
• 1. O'Connell MR
  2. Oakes BL
  3. Sternberg SH
  4. East-Seletsky A
  5. Kaplan M
  6. Doudna JA
  (2014 Dec 11). Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature.
• 1. Agrawal AA
  2. McLaughlin KJ
  3. Jenkins JL
  4. Kielkopf CL
  (2014 Dec 9). Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA. Proceedings of the National Academy of Sciences of the United States of America.
• 1. Mathers C
  2. Schafer X
  3. Martínez-Sobrido L
  4. Munger J
  (2014 Dec). The human cytomegalovirus UL26 protein antagonizes NF-κB activation. Journal of virology.
• 1. Adachi H
  2. Yu YT
  (2014 Nov 26). Insight into the mechanisms and functions of spliceosomal snRNA pseudouridylation. World journal of biological chemistry.
• 1. Zhu J
  2. Davoli T
  3. Perriera JM
  4. Chin CR
  5. Gaiha GD
  6. John SP
  7. Sigiollot FD
  8. Gao G
  9. Xu Q
  10. Qu H
  11. Pertel T
  12. Sims JS
  13. Smith JA
  14. Baker RE
  15. Maranda L
  16. Ng A
  17. Elledge SJ
  18. Brass AL
  (2014 Oct 23). Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents. Cell reports.
• 1. Lin D
  2. Grossfield A
  (2014 Oct 21). Thermodynamics of antimicrobial lipopeptide binding to membranes: origins of affinity and selectivity. Biophysical journal.
• 1. Salsi E
  2. Farah E
  3. Dann J
  4. Ermolenko DN
  (2014 Oct 21). Following movement of domain IV of elongation factor G during ribosomal translocation. Proceedings of the National Academy of Sciences of the United States of America.
• 1. Leioatts N
  2. Suresh P
  3. Romo TD
  4. Grossfield A
  (2014 Oct). Structure-based simulations reveal concerted dynamics of GPCR activation. Proteins.
• 1. De C
  2. Liu D
  3. Zheng B
  4. Singh US
  5. Chavre S
  6. White C
  7. Arnold RD
  8. Hagen FK
  9. Chu CK
  10. Moffat JF
  (2014 Oct). β-l-1-[5-(E-2-bromovinyl)-2-(hydroxymethyl)-1,3-(dioxolan-4-yl)] uracil (l-BHDU) prevents varicella-zoster virus replication in a SCID-Hu mouse model and does not interfere with 5-fluorouracil catabolism. Antiviral research.
• 1. Le NT
  2. Takei Y
  3. Izawa-Ishizawa Y
  4. Heo KS
  5. Lee H
  6. Smrcka AV
  7. Miller BL
  8. Ko KA
  9. Ture S
  10. Morrell C
  11. Fujiwara K
  12. Akaike M
  13. Abe J
  (2014 Oct 1). Identification of activators of ERK5 transcriptional activity by high-throughput screening and the role of endothelial ERK5 in vasoprotective effects induced by statins and antimalarial agents. Journal of immunology (Baltimore, Md. : 1950).
• 1. Pepenella S
  2. Murphy KJ
  3. Hayes JJ
  (2014 Sep 26). A distinct switch in interactions of the histone H4 tail domain upon salt-dependent folding of nucleosome arrays. The Journal of biological chemistry.
• 1. Lomakina EB
  2. Marsh G
  3. Waugh RE
  (2014 Sep 16). Cell surface topography is a regulator of molecular interactions during chemokine-induced neutrophil spreading. Biophysical journal.
• 1. Tian L
  2. Wang C
  3. Hagen FK
  4. Gormley M
  5. Addya S
  6. Soccio R
  7. Casimiro MC
  8. Zhou J
  9. Powell MJ
  10. Xu P
  11. Deng H
  12. Sauve AA
  13. Pestell RG
  (2014 Sep 15). Acetylation-defective mutant of Pparγ is associated with decreased lipid synthesis in breast cancer cells. Oncotarget.
• 1. Monaghan M
  2. Wakabayashi H
  3. Griffiths A
  4. Wintermute J
  5. Fay PJ
  (2014 Sep 2). Enhanced factor VIIIa stability of A2 domain interface variants results from an increased apparent affinity for the A2 subunit. Results from an increased apparent affinity for the A2 subunit. Thrombosis and haemostasis.
• 1. Kurosaki T
  2. Li W
  3. Hoque M
  4. Popp MW
  5. Ermolenko DN
  6. Tian B
  7. Maquat LE
  (2014 Sep 1). A post-translational regulatory switch on UPF1 controls targeted mRNA degradation. Genes & development.
• 1. Salter JD
  2. Morales GA
  3. Smith HC
  (2014 Sep). Structural insights for HIV-1 therapeutic strategies targeting Vif. Trends in biochemical sciences.
• 1. Kosloski MP
  2. Shetty KA
  3. Wakabayashi H
  4. Fay PJ
  5. Balu-Iyer SV
  (2014 Sep). Effects of replacement of factor VIII amino acids Asp519 and Glu665 with Val on plasma survival and efficacy in vivo. The AAPS journal.