Recent Publications

• 1. Rodríguez-Sánchez I
  2. Munger J
  Meal for Two: Human Cytomegalovirus-Induced Activation of Cellular Metabolism.; Viruses; Vol 11(3). 2019 Mar 19.
• 1. Kennedy SD
  2. Bauer WJ
  3. Wang W
  4. Kielkopf CL
  Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites.; Biochemical and biophysical research communications. 2019 Feb 20.
• 1. Shaheen R
  2. Tasak M
  3. Maddirevula S
  4. Abdel-Salam GMH
  5. Sayed ISM
  6. Alazami AM
  7. Al-Sheddi T
  8. Alobeid E
  9. Phizicky EM
  10. Alkuraya FS
  PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly.; Human genetics. 2019 Feb 18.
• 1. Goodwin CM
  2. Munger J
  The IκB kinases restrict human cytomegalovirus infection.; Journal of virology. 2019 Feb 13.
• 1. Kotikam V
  2. Kennedy SD
  3. MacKay JA
  4. Rozners E
  Synthetic, Structural, and RNA Binding Studies on 2-Aminopyridine-Modified Triplex-Forming Peptide Nucleic Acids.; Chemistry (Weinheim an der Bergstrasse, Germany). 2019 Feb 11.
• 1. Berger KD
  2. Kennedy SD
  3. Turner DH
  Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.; Biochemistry. 2019 Jan 31.
• 1. King MW
  2. Munger J
  Editing the human cytomegalovirus genome with the CRISPR/Cas9 system.; Virology; Vol 529. 2019 Jan 26.
• 1. Rodríguez-Sánchez I
  2. Schafer XL
  3. Monaghan M
  4. Munger J
  The Human Cytomegalovirus UL38 protein drives mTOR-independent metabolic flux reprogramming by inhibiting TSC2.; PLoS pathogens; Vol 15(1). 2019 Jan 24.
• 1. Starr ML
  2. Sparks RP
  3. Arango AS
  4. Hurst LR
  5. Zhao Z
  6. Lihan M
  7. Jenkins JL
  8. Tajkhorshid E
  9. Fratti RA
  Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming.; The Journal of biological chemistry. 2019 Jan 07.
• 1. Sparks RP
  2. Jenkins JL
  3. Fratti R
  Use of Surface Plasmon Resonance (SPR) to Determine Binding Affinities and Kinetic Parameters Between Components Important in Fusion Machinery.; Methods in molecular biology (Clifton, N.J.); Vol 1860. 2019.
• 1. Adachi H
  2. DeZoysa MD
  3. Yu YT
  Detection and Quantification of Pseudouridine in RNA.; Methods in molecular biology (Clifton, N.J.); Vol 1870. 2019.
• 1. Kurosaki T
  2. Myers JA
  3. Maquat LE
  Defining nonsense-mediated mRNA decay intermediates in human cells.; Methods: Biochemical and next generation sequencing approaches to study RNA regulation.. 2019 Jan 01.
• 1. Elbarbary RA
  2. Maquat LE
  Evaluating the susceptibility of AGO2-loaded microRNAs to degradation by nucleases in vitro.; Methods: MicroRNA biogenesis, identification, function and decay.; Vol 152, pp. 18-22. 2019 Jan 01.
• 1. Ghoneim DH
  2. Zhang X
  3. Brule CE
  4. Mathews DH
  5. Grayhack EJ
  Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection.; Nucleic acids research. 2018 Dec 21.
• 1. Loerch S
  2. Leach JR
  3. Horner SW
  4. Maji D
  5. Jenkins JL
  6. Pulvino M
  7. Kielkopf CL
  The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface.; The Journal of biological chemistry. 2018 Dec 19.
• 1. Mishra LN
  2. Hayes JJ
  A nucleosome-free region locally abrogates histone H1-dependent restriction of linker DNA accessibility in chromatin.; The Journal of biological chemistry; Vol 293(50). 2018 Dec 14.
• 1. Wang J
  2. Zhou J
  3. Yang Q
  4. Grayhack EJ
  Multi-protein Bridging Factor 1(Mbf1), Rps3 and Asc1 prevent stalled ribosomes from frameshifting.; eLife; Vol 7. 2018 Nov 22.
• 1. Yamagami R
  2. Kayedkhordeh M
  3. Mathews DH
  4. Bevilacqua PC
  Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.; Nucleic acids research. 2018 Nov 20.
• 1. Adachi H
  2. De Zoysa MD
  3. Yu YT
  Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs.; Biochimica et biophysica acta. Gene regulatory mechanisms. 2018 Nov 08.
• 1. Kurosaki T
  2. Miyoshi K
  3. Myers JR
  4. Maquat LE
  Publisher Correction: NMD-degradome sequencing reveals ribosome-bound intermediates with 3'-end non-templated nucleotides.; Nature structural & molecular biology; Vol 25(11). 2018 Nov.
• 1. Smith LG
  2. Tan Z
  3. Spasic A
  4. Dutta D
  5. Salas-Estrada LA
  6. Grossfield A
  7. Mathews DH
  Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.; Journal of chemical theory and computation. 2018 Oct 30.
• 1. Lai WC
  2. Kayedkhordeh M
  3. Cornell EV
  4. Farah E
  5. Bellaousov S
  6. Rietmeijer R
  7. Salsi E
  8. Mathews DH
  9. Ermolenko DN
  mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.; Nature communications; Vol 9(1). 2018 Oct 18.
• 1. Warnasooriya C
  2. Ling C
  3. Belashov IA
  4. Salim M
  5. Wedekind JE
  6. Ermolenko DN
  Observation of preQ1-II riboswitch dynamics using single-molecule FRET.; RNA biology. 2018 Oct 17.
• 1. Braun J
  2. Fischer S
  3. Xu ZZ
  4. Sun H
  5. Ghoneim DH
  6. Gimbel AT
  7. Plessmann U
  8. Urlaub H
  9. Mathews DH
  10. Weigand JE
  Identification of new high affinity targets for Roquin based on structural conservation.; Nucleic acids research. 2018 Oct 08.
• 1. Martin SES
  2. Tan ZW
  3. Itkonen HM
  4. Duveau DY
  5. Paulo JA
  6. Janetzko J
  7. Boutz PL
  8. Törk L
  9. Moss FA
  10. Thomas CJ
  11. Gygi SP
  12. Lazarus MB
  13. Walker S
  Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors.; Journal of the American Chemical Society. 2018 Oct 04.
• 1. Kurosaki T
  2. Miyoshi K
  3. Myers JR
  4. Maquat LE
  NMD-degradome sequencing reveals ribosome-bound intermediates with 3'-end non-templated nucleotides.; Nature structural & molecular biology; Vol 25(10). 2018 Oct.
• 1. Walling LR
  2. Butler JS
  Toxins targeting transfer RNAs: Translation inhibition by bacterial toxin-antitoxin systems.; Wiley interdisciplinary reviews. RNA. 2018 Sep 16.
• 1. Yuan B
  2. Neira J
  3. Pehlivan D
  4. Santiago-Sim T
  5. Song X
  6. Rosenfeld J
  7. Posey JE
  8. Patel V
  9. Jin W
  10. Adam MP
  11. Baple EL
  12. Dean J
  13. Fong CT
  14. Hickey SE
  15. Hudgins L
  16. Leon E
  17. Madan-Khetarpal S
  18. Rawlins L
  19. Rustad CF
  20. Stray-Pedersen A
  21. Tveten K
  22. Wenger O
  23. Diaz J
  24. Jenkins L
  25. Martin L
  26. McGuire M
  27. Pietryga M
  28. Ramsdell L
  29. Slattery L
  30. Abid F
  31. Bertuch AA
  32. Grange D
  33. Immken L
  34. Schaaf CP
  35. Van Esch H
  36. Bi W
  37. Cheung SW
  38. Breman AM
  39. Smith JL
  40. Shaw C
  41. Crosby AH
  42. Eng C
  43. Yang Y
  44. Lupski JR
  45. Xiao R
  46. Liu P
  Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies.; Genetics in medicine : official journal of the American College of Medical Genetics. 2018 Aug 30.
• 1. Goodwin CM
  2. Ciesla JH
  3. Munger J
  Who's Driving? Human Cytomegalovirus, Interferon, and NFκB Signaling.; Viruses; Vol 10(9). 2018 Aug 21.
• 1. Zuber J
  2. Cabral BJ
  3. McFadyen I
  4. Mauger DM
  5. Mathews DH
  Analysis of RNA Nearest Neighbor Parameters Reveals Interdependencies and Quantifies the Uncertainty in RNA Secondary Structure Prediction.; RNA (New York, N.Y.). 2018 Aug 13.
• 1. Bellaousov S
  2. Kayedkhordeh M
  3. Peterson RJ
  4. Mathews DH
  Accelerated RNA Secondary Structure Design Using Pre-Selected Sequences for Helices and Loops.; RNA (New York, N.Y.). 2018 Aug 10.
• 1. Tambe A
  2. East-Seletsky A
  3. Knott GJ
  4. Doudna JA
  5. O'Connell MR
  RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a.; Cell reports; Vol 24(4). 2018 Jul 24.
• 1. Han L
  2. Phizicky EM
  A rationale for tRNA modification circuits in the anticodon loop.; RNA (New York, N.Y.). 2018 Jul 19.
• 1. Thompson JL
  2. Lai-Zhao Y
  3. Stathopulos PB
  4. Grossfield A
  5. Shuttleworth TJ
  Phosphorylation-mediated structural changes within the SOAR domain of stromal interaction molecule 1 enable specific activation of distinct Orai channels.; The Journal of biological chemistry; Vol 293(28). 2018 Jul 13.
• 1. Zimmerman SM
  2. Kon Y
  3. Hauke AC
  4. Ruiz BY
  5. Fields S
  6. Phizicky EM
  Conditional accumulation of toxic tRNAs to cause amino acid misincorporation.; Nucleic acids research. 2018 Jul 11.
• 1. Belashov IA
  2. Crawford DW
  3. Cavender CE
  4. Dai P
  5. Beardslee PC
  6. Mathews DH
  7. Pentelute BL
  8. McNaughton BR
  9. Wedekind JE
  Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.; Nucleic acids research. 2018 Jun 29.
• 1. Nadtochiy SM
  2. Wang YT
  3. Nehrke K
  4. Munger J
  5. Brookes PS
  Cardioprotection by nicotinamide mononucleotide (NMN): Involvement of glycolysis and acidic pH.; Journal of molecular and cellular cardiology. 2018 Jun 26.
• 1. O'Connell M
  Molecular Mechanisms of RNA-Targeting by Cas13-containing Type VI CRISPR-Cas Systems.; Journal of molecular biology. 2018 Jun 22.
• 1. Dutta D
  2. Belashov IA
  3. Wedekind JE
  Coupling GFP Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria.; Biochemistry. 2018 Jun 13.
• 1. De Zoysa MD
  2. Wu G
  3. Katz R
  4. Yu YT
  Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation.; RNA (New York, N.Y.). 2018 Jun 05.
• 1. Zhang J
  2. Wang YT
  3. Miller JH
  4. Day MM
  5. Munger JC
  6. Brookes PS
  Accumulation of Succinate in Cardiac Ischemia Primarily Occurs via Canonical Krebs Cycle Activity.; Cell reports; Vol 23(9). 2018 May 29.
• 1. Salter JD
  2. Smith HC
  Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands.; Trends in biochemical sciences. 2018 May 23.
• 1. Bucukovski J
  2. Carter JA
  3. Striemer CC
  4. Müllner S
  5. Schulte-Pelkum J
  6. Schulz-Knappe P
  7. Miller BL
  Label-free microarray-based detection of autoantibodies in human serum.; Journal of immunological methods. 2018 May 23.
• 1. Chen W
  2. Anokhina V
  3. Dieudonne G
  4. Abramowitz MK
  5. Kashyap R
  6. Yan C
  7. Wu TT
  8. de Mesy Bentley KL
  9. Miller BL
  10. Bushinsky DA
  Patients with advanced chronic kidney disease and vascular calcification have a large hydrodynamic radius of secondary calciprotein particles.; Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. 2018 May 16.
• 1. Elbarbary R
  2. Maquat LE
  Evaluating the susceptibility of AGO2-loaded microRNAs to degradation by nucleases in vitro.; Methods (San Diego, Calif.). 2018 May 16.
• 1. Spasic A
  2. Berger KD
  3. Chen JL
  4. Seetin MG
  5. Turner DH
  6. Mathews DH
  Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.; Nucleic acids research. 2018 May 01.
• 1. Bottaro S
  2. Bussi G
  3. Kennedy SD
  4. Turner DH
  5. Lindorff-Larsen K
  Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.; Science advances; Vol 4(5). 2018 May.
• 1. Walter NG
  2. Maquat LE
  Introduction-RNA: From Single Molecules to Medicine.; Chemical reviews; Vol 118(8). 2018 Apr 25.
• 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
  Correction for Yang et al., "Tolerance to Caspofungin in Candida albicans Is Associated with at Least Three Distinctive Mechanisms That Govern Expression ofFKSGenes and Cell Wall Remodeling".; Antimicrobial agents and chemotherapy; Vol 62(4). 2018 Apr.
• 1. Kurosaki T
  2. Maquat LE
  Molecular autopsy provides evidence for widespread ribosome-phased mRNA fragmentation.; Nature structural & molecular biology; Vol 25(4). 2018 Apr.
• 1. Cho H
  2. Rambout X
  3. Gleghorn ML
  4. Nguyen PQT
  5. Phipps CR
  6. Miyoshi K
  7. Myers JR
  8. Kataoka N
  9. Fasan R
  10. Maquat LE
  Transcriptional coactivator PGC-1α contains a novel CBP80-binding motif that orchestrates efficient target gene expression.; Genes & development; Vol 32(7-8). 2018 Apr 01.
• 1. Bennett RP
  2. Salter JD
  3. Smith HC
  A New Class of Antiretroviral Enabling Innate Immunity by Protecting APOBEC3 from HIV Vif-Dependent Degradation.; Trends in molecular medicine. 2018 Mar 30.
• 1. Han L
  2. Guy MP
  3. Kon Y
  4. Phizicky EM
  Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway.; PLoS genetics; Vol 14(3). 2018 Mar 29.
• 1. Berger KD
  2. Kennedy SD
  3. Schroeder SJ
  4. Znosko BM
  5. Sun H
  6. Mathews DH
  7. Turner DH
  Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.; Biochemistry. 2018 Mar 23.
• 1. Coller J
  2. Grayhack EJ
  The analysis of translational mechanisms that modulate gene expression.; Methods (San Diego, Calif.); Vol 137. 2018 Mar 15.
• 1. Spasic A
  2. Kennedy SD
  3. Needham L
  4. Manoharan M
  5. Kierzek R
  6. Turner DH
  7. Mathews D
  Molecular Dynamics Correctly Models the Unusual Major Conformation of the GAGU RNA Internal Loop and with NMR Reveals an Unusual Minor Conformation.; RNA (New York, N.Y.). 2018 Feb 06.
• 1. Sur S
  2. Romo TD
  3. Grossfield A
  Selectivity and Mechanism of Fengycin, an Antimicrobial Lipopeptide from Molecular Dynamics.; The journal of physical chemistry. B. 2018 Jan 27.
• 1. Tucker C
  2. Bhattacharya S
  3. Wakabayashi H
  4. Bellaousov S
  5. Kravets A
  6. Welle SL
  7. Myers J
  8. Hayes JJ
  9. Bulger M
  10. Rustchenko E
  Transcriptional Regulation on Aneuploid Chromosomes in Divers Candida albicans Mutants.; Scientific reports; Vol 8(1). 2018 Jan 26.
• 1. Salas-Estrada LA
  2. Leioatts N
  3. Romo TD
  4. Grossfield A
  Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions.; Biophysical journal; Vol 114(2). 2018 Jan 23.
• 1. Suwunnakorn S
  2. Wakabayashi H
  3. Kordalewska M
  4. Perlin DS
  5. Rustchenko E
  FKS2 and FKS3 genes of opportunistic human pathogen Candida albicans influence echinocandin susceptibility.; Antimicrobial agents and chemotherapy. 2018 Jan 22.
• 1. Lucas BA
  2. Lavi E
  3. Shiue L
  4. Cho H
  5. Katzman S
  6. Miyoshi K
  7. Siomi MC
  8. Carmel L
  9. Ares M
  10. Maquat LE
  Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay.; Proceedings of the National Academy of Sciences of the United States of America. 2018 Jan 16.
• 1. Thompson JL
  2. Zhao Y
  3. Stathopulos PB
  4. Grossfield A
  5. Shuttleworth TJ
  Phosphorylation-mediated structural changes within the SOAR domain of STIM1 enable specific activation of distinct Orai channels.; The Journal of biological chemistry. 2018 Jan 11.
• 1. Khire TS
  2. Nehilla BJ
  3. Getpreecharsawas J
  4. Gracheva ME
  5. Waugh RE
  6. McGrath JL
  Finite element modeling to analyze TEER values across silicon nanomembranes.; Biomedical microdevices; Vol 20(1). 2018 Jan 05.
• 1. Hardcastle T
  2. Novosjolova I
  3. Kotikam V
  4. Cheruiyot SK
  5. Mutisya D
  6. Kennedy SD
  7. Egli M
  8. Kelley ML
  9. Smith AVB
  10. Rozners E
  A Single Amide Linkage in the Passenger Strand Suppresses Its Activity and Enhances Guide Strand Targeting of siRNAs.; ACS chemical biology. 2018 Jan 03.
• 1. Murphy PA
  2. Butty VL
  3. Boutz PL
  4. Begum S
  5. Kimble AL
  6. Sharp PA
  7. Burge CB
  8. Hynes RO
  Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow.; eLife; Vol 7. 2018 Jan 02.
• 1. Zhao Y
  2. Dunker W
  3. Yu YT
  4. Karijolich J
  The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events.; Frontiers in bioengineering and biotechnology; Vol 6. 2018.
• 1. De Franco S
  2. O'Connell MR
  3. Vandevenne M
  Engineering RNA-Binding Proteins by Modular Assembly of RanBP2-Type Zinc Fingers.; Methods in molecular biology (Clifton, N.J.); Vol 1867. 2018.
• 1. Dubbury SJ
  2. Boutz PL
  3. Sharp PA
  CDK12 regulates DNA repair genes by suppressing intronic polyadenylation.; Nature; Vol 564(7734). 2018 Jan.
• 1. Grossfield A
  2. Patrone PN
  3. Roe DR
  4. Schultz AJ
  5. Siderius DW
  6. Zuckerman DM
  Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].; Living journal of computational molecular science; Vol 1(1). 2018.
• 1. Kurosaki T
  2. Hoque M
  3. Maquat LE
  Identifying Cellular Nonsense-Mediated mRNA Decay (NMD) Targets: Immunoprecipitation of Phosphorylated UPF1 Followed by RNA Sequencing (p-UPF1 RIP-Seq).; Methods in molecular biology (Clifton, N.J.); Vol 1720. 2018.
• 1. Payea MJ
  2. Sloma MF
  3. Kon Y
  4. Young DL
  5. Guy MP
  6. Zhang X
  7. De Zoysa T
  8. Fields S
  9. Mathews DH
  10. Phizicky EM
  Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA.; RNA (New York, N.Y.). 2017 Dec 19.
• 1. Rambout X
  2. Dequiedt F
  3. Maquat LE
  Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing.; Chemical reviews. 2017 Dec 18.
• 1. Lai CW
  2. Ermolenko DN
  Ensemble and single-molecule FRET studies of protein synthesis.; Methods (San Diego, Calif.). 2017 Dec 13.
• 1. Spasic A
  2. Assmann SM
  3. Bevilacqua PC
  4. Mathews DH
  Modeling RNA secondary structure folding ensembles using SHAPE mapping data.; Nucleic acids research. 2017 Nov 21.
• 1. Lee BH
  2. Reijnders MRF
  3. Abubakare O
  4. Tuttle E
  5. Lape B
  6. Minks KQ
  7. Stodgell C
  8. Bennetto L
  9. Kwon J
  10. Fong CT
  11. Gripp KW
  12. Marsh ED
  13. Smith WE
  14. Huq AM
  15. Coury SA
  16. Tan WH
  17. Solis O
  18. Mehta RI
  19. Leventer RJ
  20. Baralle D
  21. Hunt D
  22. Paciorkowski AR
  Expanding the neurodevelopmental phenotype of PURA syndrome.; American journal of medical genetics. Part A. 2017 Nov 17.
• 1. Gatchalian J
  2. Wang X
  3. Ikebe J
  4. Cox KL
  5. Tencer AH
  6. Zhang Y
  7. Burge NL
  8. Di L
  9. Gibson MD
  10. Musselman CA
  11. Poirier MG
  12. Kono H
  13. Hayes JJ
  14. Kutateladze TG
  Accessibility of the histone H3 tail in the nucleosome for binding of paired readers.; Nature communications; Vol 8(1). 2017 Nov 14.
• 1. Kielkopf CL
  Insights from structures of cancer-relevant pre-mRNA splicing factors.; Current opinion in genetics & development; Vol 48. 2017 Nov 09.
• 1. Wakabayashi H
  2. Tucker C
  3. Bethlendy G
  4. Kravets A
  5. Welle SL
  6. Bulger M
  7. Hayes JJ
  8. Rustchenko E
  Correction to: NuA4 histone acetyltransferase activity is required for H4 acetylation on a dosage-compensated monosomic chromosome that confers resistance to fungal toxins.; Epigenetics & chromatin; Vol 10(1). 2017 Nov 07.
• 1. Popp MW
  2. Maquat LE
  Nonsense-mediated mRNA Decay and Cancer.; Current opinion in genetics & development; Vol 48. 2017 Nov 07.
• 1. Sloma MF
  2. Mathews DH
  Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.; PLoS computational biology; Vol 13(11). 2017 Nov 06.
• 1. Walling LR
  2. Butler JS
  Homologous VapC toxins inhibit translation and cell growth by sequence specific cleavage of tRNA(fMet).; Journal of bacteriology. 2017 Nov 06.
• 1. Ge J
  2. Karijolich J
  3. Zhai Y
  4. Zheng J
  5. Yu YT
  5-Fluorouracil Treatment Alters the Efficiency of Translational Recoding.; Genes; Vol 8(11). 2017 Oct 31.
• 1. Wakabayashi H
  2. Tucker C
  3. Bethlendy G
  4. Kravets A
  5. Welle SL
  6. Bulger M
  7. Hayes J
  8. Rustchenko E
  NuA4 histone acetyltransferase activity is required for H4 acetylation on a dosage-compensated monosomic chromosome that confers resistance to fungal toxins.; Epigenetics & chromatin; Vol 10(1). 2017 Oct 23.
• 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
  Covalent Modifications of Histone H3K9 Promote Binding of CHD3.; Cell reports; Vol 21(2). 2017 Oct 10.
• 1. Knott GJ
  2. East-Seletsky A
  3. Cofsky JC
  4. Holton JM
  5. Charles E
  6. O'Connell MR
  7. Doudna JA
  Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.; Nature structural & molecular biology; Vol 24(10). 2017 Oct.
• 1. Murphy KJ
  2. Cutter AR
  3. Fang H
  4. Postnikov YV
  5. Bustin M
  6. Hayes JJ
  HMGN1 and 2 remodel core and linker histone tail domains within chromatin.; Nucleic acids research; Vol 45(17). 2017 Sep 29.
• 1. Tan Z
  2. Fu Y
  3. Sharma G
  4. Mathews DH
  TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.; Nucleic acids research. 2017 Sep 28.
• 1. Glasser E
  2. Agrawal AA
  3. Jenkins JL
  4. Kielkopf CL
  Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs.; Biochemistry. 2017 Sep 01.
• 1. Smith LG
  2. Zhao J
  3. Mathews DH
  4. Turner DH
  Physics-based all-atom modeling of RNA energetics and structure.; Wiley interdisciplinary reviews. RNA; Vol 8(5). 2017 Sep.
• 1. Novosjolova I
  2. Kennedy SD
  3. Rozners E
  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. 2017 Aug 31.
• 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
  Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs.; Nucleic acids research; Vol 45(14). 2017 Aug 21.
• 1. Poole AR
  2. Vicino I
  3. Adachi H
  4. Yu YT
  5. Hebert MD
  Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity.; Biology open. 2017 Aug 14.
• 1. Tan Z
  2. Sharma G
  3. Mathews DH
  Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.; Biophysical journal. 2017 Jul 20.
• 1. Elbarbary RA
  2. Miyoshi K
  3. Hedaya O
  4. Myers JR
  5. Maquat LE
  UPF1 helicase promotes TSN-mediated miRNA decay.; Genes & development; Vol 31(14). 2017 Jul 15.
• 1. Kauffmann AD
  2. Kennedy SD
  3. Zhao J
  4. Turner DH
  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. 2017 Jul 12.
• 1. Huang YS
  2. Delgadillo LF
  3. Cyr KH
  4. Kingsley PD
  5. An X
  6. McGrath KE
  7. Mohandas N
  8. Conboy JG
  9. Waugh RE
  10. Wan J
  11. Palis J
  Circulating primitive erythroblasts establish a functional, protein 4.1R-dependent cytoskeletal network prior to enucleating.; Scientific reports; Vol 7(1). 2017 Jul 12.
• 1. Romo TD
  2. Lewis AK
  3. Braun AR
  4. Grossfield A
  5. Sachs JN
  Minimal nucleation state of alpha-Synuclein is stabilized by dynamic threonine-water networks.; ACS chemical neuroscience. 2017 Jul 05.
• 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
  Potential mechanisms linking SIRT activity and hypoxic 2-hydroxyglutarate generation: no role for direct enzyme (de)acetylation.; The Biochemical journal. 2017 Jul 03.
• 1. Ward M
  2. Datta A
  3. Wise M
  4. Mathews DH
  Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best.; Nucleic acids research. 2017 Jun 06.
• 1. Elbarbary RA
  2. Maquat LE
  Distinct mechanisms obviate the potentially toxic effects of inverted-repeat Alu elements on cellular RNA metabolism.; Nature structural & molecular biology; Vol 24(6). 2017 Jun 06.
• 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
  Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.; Molecular cell; Vol 66(5). 2017 Jun 01.
• 1. Elbarbary RA
  2. Miyoshi K
  3. Myers JR
  4. Du P
  5. Ashton JM
  6. Tian B
  7. Maquat LE
  Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G1/S phase transition.; Science (New York, N.Y.); Vol 356(6340). 2017 May 26.
• 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
  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; Vol 292(21). 2017 May 26.
• 1. Yao P
  2. Wu J
  3. Lindner D
  4. Fox PL
  Interplay between miR-574-3p and hnRNP L regulates VEGFA mRNA translation and tumorigenesis.; Nucleic acids research. 2017 May 17.
• 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
  HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells.; ACS chemical biology. 2017 May 05.
• 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
  Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.; Molecular cell; Vol 66(3). 2017 May 04.
• 1. East-Seletsky A
  2. O'Connell MR
  3. Burstein D
  4. Knott GJ
  5. Doudna JA
  RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes.; Molecular cell; Vol 66(3). 2017 May 04.
• 1. Wedekind JE
  2. Dutta D
  3. Belashov IA
  4. Jenkins JL
  Metalloriboswitches: RNA-Based Inorganic Ion Sensors that Regulate Genes.; The Journal of biological chemistry. 2017 Apr 28.
• 1. Gamache ER
  2. Doh JH
  3. Ritz J
  4. Laederach A
  5. Bellaousov S
  6. Mathews DH
  7. Curcio MJ
  Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.; Viruses; Vol 9(5). 2017 Apr 26.
• 1. Sun YH
  2. Xie LH
  3. Zhuo X
  4. Chen Q
  5. Ghoneim D
  6. Zhang B
  7. Jagne J
  8. Yang C
  9. Li XZ
  Domestic chickens activate a piRNA defense against avian leukosis virus.; eLife; Vol 6. 2017 Apr 06.
• 1. Vats K
  2. Marsh G
  3. Harding K
  4. Zampetakis I
  5. Waugh RE
  6. Benoit DS
  Nanoscale physicochemical properties of chain- and step-growth polymerized PEG hydrogels affect cell-material interactions.; Journal of biomedical materials research. Part A; Vol 105(4). 2017 Apr.
• 1. Cutter AR
  2. Hayes JJ
  Linker histones: novel insights into structure-specific recognition of the nucleosome.; Biochemistry and cell biology = Biochimie et biologie cellulaire; Vol 95(2). 2017 Apr.
• 1. Jenkins JL
  2. Kielkopf CL
  Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures.; Trends in genetics : TIG. 2017 Mar 31.
• 1. Baker JE
  2. Sriram R
  3. Miller BL
  Recognition-mediated particle detection under microfluidic flow with waveguide-coupled 2D photonic crystals: towards integrated photonic virus detectors.; Lab on a chip. 2017 Mar 30.
• 1. Zuber J
  2. Sun H
  3. Zhang X
  4. McFadyen I
  5. Mathews DH
  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. 2017 Mar 15.
• 1. Brule CE
  2. Grayhack EJ
  Synonymous Codons: Choose Wisely for Expression.; Trends in genetics : TIG. 2017 Mar 11.
• 1. Murphy PS
  2. Wang J
  3. Bhagwat SP
  4. Munger JC
  5. Janssen WJ
  6. Wright TW
  7. Elliott MR
  CD73 regulates anti-inflammatory signaling between apoptotic cells and endotoxin-conditioned tissue macrophages.; Cell death and differentiation; Vol 24(3). 2017 Mar.
• 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
  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. 2017 Feb 21.
• 1. Aytenfisu AH
  2. Spasic A
  3. Grossfield A
  4. Stern HA
  5. Mathews DH
  Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.; Journal of chemical theory and computation; Vol 13(2). 2017 Feb 14.
• 1. Clark KM
  2. Jenkins JL
  3. Fedoriw N
  4. Dumont ME
  Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors.; Protein science : a publication of the Protein Society; Vol 26(2). 2017 Feb.
• 1. Balliano A
  2. Hao F
  3. Njeri C
  4. Balakrishnan L
  5. Hayes JJ
  HMGB1 Stimulates Activity of Polymerase β on Nucleosome Substrates.; Biochemistry. 2017 Jan 18.
• 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
  A genome wide dosage suppressor network reveals genomic robustness.; Nucleic acids research; Vol 45(1). 2017 Jan 09.
• 1. Braun CJ
  2. Stanciu M
  3. Boutz PL
  4. Patterson JC
  5. Calligaris D
  6. Higuchi F
  7. Neupane R
  8. Fenoglio S
  9. Cahill DP
  10. Wakimoto H
  11. Agar NYR
  12. Yaffe MB
  13. Sharp PA
  14. Hemann MT
  15. Lees JA
  Coordinated Splicing of Regulatory Detained Introns within Oncogenic Transcripts Creates an Exploitable Vulnerability in Malignant Glioma.; Cancer cell; Vol 32(4). 2017 Jan 09.
• 1. Hrabeta-Robinson E
  2. Marcus E
  3. Cozen AE
  4. Phizicky EM
  5. Lowe TM
  High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq).; Methods in molecular biology (Clifton, N.J.); Vol 1562. 2017.
• 1. De Zoysa MD
  2. Yu YT
  Posttranscriptional RNA Pseudouridylation.; The Enzymes; Vol 41. 2017.
• 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
  Structure of the SLC4 transporter Bor1p in an inward-facing conformation.; Protein science : a publication of the Protein Society; Vol 26(1). 2017 Jan.
• 1. Han L
  2. Marcus E
  3. D'Silva S
  4. Phizicky EM
  S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates.; RNA (New York, N.Y.). 2016 Dec 21.
• 1. Chatrikhi R
  2. Wang W
  3. Gupta A
  4. Loerch S
  5. Maucuer A
  6. Kielkopf CL
  SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA.; Biophysical journal; Vol 111(12). 2016 Dec 20.
• 1. Komisarof J
  2. McCall M
  3. Newman L
  4. Bshara W
  5. Mohler JL
  6. Morrison C
  7. Land H
  A four gene signature predictive of recurrent prostate cancer.; Oncotarget. 2016 Dec 09.
• 1. Ling C
  2. Ermolenko DN
  Caught on Camera: Intermediates of Ribosome Recycling.; Structure (London, England : 1993); Vol 24(12). 2016 Dec 06.
• 1. Loerch S
  2. Kielkopf CL
  Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise.; RNA (New York, N.Y.); Vol 22(12). 2016 Dec.
• 1. Suwunnakorn S
  2. Wakabayashi H
  3. Rustchenko E
  Chromosome 5 of Human Pathogen Candida albicans Carries Multiple Genes for Negative Control of Caspofungin and Anidulafungin Susceptibility.; Antimicrobial agents and chemotherapy; Vol 60(12). 2016 Dec.
• 1. Ikpeze TC
  2. Smith HC
  3. Lee DJ
  4. Elfar JC
  Distal Radius Fracture Outcomes and Rehabilitation.; Geriatric orthopaedic surgery & rehabilitation; Vol 7(4). 2016 Dec.
• 1. Sloma MF
  2. Mathews DH
  Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.; RNA (New York, N.Y.); Vol 22(12). 2016 Dec.
• 1. Mathews DH
  2. Turner DH
  3. Watson RM
  RNA Secondary Structure Prediction.; Current protocols in nucleic acid chemistry; Vol 67. 2016 Dec 01.
• 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
  Rational design of a parthenolide-based drug regimen that selectively eradicates acute myelogenous leukemia stem cells.; The Journal of biological chemistry; Vol 291(48). 2016 Nov 25.
• 1. Smith HC
  RNA binding to APOBEC deaminases; Not simply a substrate for C to U editing.; RNA biology. 2016 Nov 21.
• 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
  Progression of brain atrophy in PSP and CBS over 6 months and 1 year.; Neurology; Vol 87(19). 2016 Nov 08.
• 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
  An analog of camptothecin inactive against Topoisomerase I is broadly neutralizing of HIV-1 through inhibition of Vif-dependent APOBEC3G degradation.; Antiviral research. 2016 Nov 4.
• 1. Fang H
  2. Wei S
  3. Lee TH
  4. Hayes JJ
  Chromatin structure-dependent conformations of the H1 CTD.; Nucleic acids research; Vol 44(19). 2016 Nov 02.
• 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
  Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly.; Genes & development; Vol 30(21). 2016 Nov 01.
• 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
  Rational Design of a Parthenolide-based Drug Regimen That Selectively Eradicates Acute Myelogenous Leukemia Stem Cells.; The Journal of biological chemistry; Vol 291(42). 2016 Oct 14.
• 1. East-Seletsky A
  2. O'Connell MR
  3. Knight SC
  4. Burstein D
  5. Cate JH
  6. Tjian R
  7. Doudna JA
  Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection.; Nature; Vol 538(7624). 2016 Oct 13.
• 1. Smith B
  2. Schafer XL
  3. Ambeskovic A
  4. Spencer CM
  5. Land H
  6. Munger J
  Addiction to Coupling of the Warburg Effect with Glutamine Catabolism in Cancer Cells.; Cell reports; Vol 17(3). 2016 Oct 11.
• 1. Mishra LN
  2. Pepenella S
  3. Rogge R
  4. Hansen JC
  5. Hayes JJ
  Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays.; Scientific reports; Vol 6. 2016 Oct 06.
• 1. Weiss K
  2. Terhal PA
  3. Cohen L
  4. Bruccoleri M
  5. Irving M
  6. Martinez AF
  7. Rosenfeld JA
  8. Machol K
  9. Yang Y
  10. Liu P
  11. Walkiewicz M
  12. Beuten J
  13. Gomez-Ospina N
  14. Haude K
  15. Fong CT
  16. Enns GM
  17. Bernstein JA
  18. Fan J
  19. Gotway G
  20. Ghorbani M
  21. van Gassen K
  22. Monroe GR
  23. van Haaften G
  24. Basel-Vanagaite L
  25. Yang XJ
  26. Campeau PM
  27. Muenke M
  De Novo Mutations in CHD4, an ATP-Dependent Chromatin Remodeler Gene, Cause an Intellectual Disability Syndrome with Distinctive Dysmorphisms.; American journal of human genetics; Vol 99(4). 2016 Oct 06.
• 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
  Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival.; PLoS genetics; Vol 12(10). 2016 Oct.
• 1. Walling LR
  2. Butler JS
  Structural determinants for antitoxin identity and insulation of cross talk between homologous toxin-antitoxin systems.; Journal of bacteriology. 2016 Sep 26.
• 1. Sparks RP
  2. Jenkins JL
  3. Miner GE
  4. Wang Y
  5. Guida WC
  6. Sparks CE
  7. Fratti RA
  8. Sparks JD
  Phosphatidylinositol (3,4,5)-trisphosphate binds to sortilin and competes with neurotensin: Implications for very low density lipoprotein binding.; Biochemical and biophysical research communications. 2016 Sep 22.
• 1. Sridharan R
  2. Connelly SM
  3. Naider F
  4. Dumont ME
  Variable Dependence of Signaling Output on Agonist Occupancy of Ste2p, a G Protein Coupled Receptor in Yeast.; The Journal of biological chemistry. 2016 Sep 19.
• 1. Nadtochiy SM
  2. Schafer X
  3. Fu D
  4. Nehrke K
  5. Munger J
  6. Brookes PS
  Acidic pH is a Metabolic Switch for 2-Hydroxyglutarate Generation and Signaling.; The Journal of biological chemistry. 2016 Aug 10.
• 1. Sparks RP
  2. Guida WC
  3. Sowden MP
  4. Jenkins JL
  5. Starr ML
  6. Fratti RA
  7. Sparks CE
  8. Sparks JD
  Sortilin facilitates VLDL-B100 secretion by insulin sensitive McArdle RH7777 cells.; Biochemical and biophysical research communications. 2016 Aug 2.
• 1. Gamble CE
  2. Brule CE
  3. Dean KM
  4. Fields S
  5. Grayhack EJ
  Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast.; Cell. 2016 Jun 29.
• 1. Black PJ
  2. Miller AS
  3. Hayes JJ
  Radioresistance of GGG sequences to prompt strand break formation from direct-type radiation damage.; Radiation and environmental biophysics. 2016 Jun 27.
• 1. Gleghorn ML
  2. Zhao J
  3. Turner DH
  4. Maquat LE
  Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation.; Nucleic acids research. 2016 Jun 10.
• 1. Wu G
  2. Radwan MK
  3. Xiao M
  4. Adachi H
  5. Fan J
  6. Yu YT
  The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA.; RNA (New York, N.Y.). 2016 Jun 7.
• 1. Popp MW
  2. Maquat LE
  Leveraging Rules of Nonsense-Mediated mRNA Decay for Genome Engineering and Personalized Medicine.; Cell; Vol 165(6). 2016 Jun 2.
• 1. Svetina S
  2. Kokot G
  3. Kebe TŠ
  4. Žekš B
  5. Waugh RE
  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; Vol 15(3). 2016 Jun.
• 1. Marsh G
  2. Waugh RE
  A simple approach for bioactive surface calibration using evanescent waves.; Journal of microscopy; Vol 262(3). 2016 Jun.
• 1. Jacob M
  2. Stewart P
  3. Medina-Walpole A
  4. Fong CT
  A culinary laboratory for nutrition education.; The clinical teacher; Vol 13(3). 2016 Jun.
• 1. Coudray N
  2. Lasala R
  3. Zhang Z
  4. Clark KM
  5. Dumont ME
  6. Stokes DL
  Deducing the Symmetry of Helical Assemblies: Applications to Membrane Proteins.; Journal of structural biology. 2016 May 30.
• 1. Salter JD
  2. Bennett RP
  3. Smith HC
  The APOBEC Protein Family: United by Structure, Divergent in Function.; Trends in biochemical sciences. 2016 May 30.
• 1. Salsi E
  2. Farah E
  3. Ermolenko DN
  EF-G Activation by Phosphate Analogs.; Journal of molecular biology; Vol 428(10 Pt B). 2016 May 22.
• 1. Miralem T
  2. Lerner-Marmarosh N
  3. Gibbs PE
  4. Jenkins JL
  5. Heimiller C
  6. Maines MD
  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. 2016 May 10.
• 1. Xu S
  2. Schafer X
  3. Munger J
  Expression of Oncogenic Alleles Induces Multiple Blocks to Human Cytomegalovirus Infection.; Journal of virology; Vol 90(9). 2016 May 1.
• 1. Monaghan M
  2. Wakabayashi H
  3. Griffiths AE
  4. Fay PJ
  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; Vol 14(5). 2016 May.
• 1. Ling C
  2. Ermolenko DN
  Structural insights into ribosome translocation.; Wiley interdisciplinary reviews. RNA. 2016 Apr 27.
• 1. Piekna-Przybylska D
  2. Bambara RA
  3. Balakrishnan L
  Acetylation regulates DNA repair mechanisms in human cells.; Cell cycle (Georgetown, Tex.). 2016 Apr 22.
• 1. Yue H
  2. Fang H
  3. Wei S
  4. Hayes JJ
  5. Lee TH
  Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome.; Biochemistry; Vol 55(14). 2016 Apr 12.
• 1. Shaheen R
  2. Han L
  3. Faqeih E
  4. Ewida N
  5. Alobeid E
  6. Phizicky EM
  7. Alkuraya FS
  A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition.; Human genetics. 2016 Apr 7.
• 1. Nelles DA
  2. Fang MY
  3. O'Connell MR
  4. Xu JL
  5. Markmiller SJ
  6. Doudna JA
  7. Yeo GW
  Programmable RNA Tracking in Live Cells with CRISPR/Cas9.; Cell; Vol 165(2). 2016 Apr 07.
• 1. Maquat LE
  Eukaryotic antisense ahead of its time.; Nature reviews. Molecular cell biology; Vol 17(4). 2016 Apr.
• 1. DiChiacchio L
  2. Sloma MF
  3. Mathews DH
  AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.; Bioinformatics (Oxford, England); Vol 32(7). 2016 Apr 1.
• 1. Hollenbaugh JA
  2. Montero C
  3. Schinazi RF
  4. Munger J
  5. Kim B
  Metabolic profiling during HIV-1 and HIV-2 infection of primary human monocyte-derived macrophages.; Virology; Vol 491. 2016 Apr.
• 1. Carter JA
  2. Triplett E
  3. Striemer CC
  4. Miller BL
  A label-free, multiplex competitive assay for small molecule pollutants.; Biosensors & bioelectronics; Vol 77. 2016 Mar 15.
• 1. Wu G
  2. Adachi H
  3. Ge J
  4. Stephenson D
  5. Query CC
  6. Yu YT
  Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly.; The EMBO journal; Vol 35(6). 2016 Mar 15.
• 1. Polevoda B
  2. McDougall WM
  3. Bennett RP
  4. Salter JD
  5. Smith HC
  Structural and functional assessment of APOBEC3G macromolecular complexes.; Methods (San Diego, Calif.). 2016 Mar 14.
• 1. Bertozzi C
  2. Zimmermann I
  3. Engeler S
  4. Hilf RJ
  5. Dutzler R
  Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels.; PLoS biology; Vol 14(3). 2016 Mar.
• 1. Elbarbary RA
  2. Maquat LE
  Coupling pre-mRNA splicing and 3' end formation to mRNA export: alternative ways to punch the nuclear export clock.; Genes & development; Vol 30(5). 2016 Mar 1.
• 1. Vukomanovic D
  2. Rahman MN
  3. Maines MD
  4. Ozolinš TR
  5. Szarek WA
  6. Jia Z
  7. Nakatsu K
  Cysteine-independent activation/inhibition of heme oxygenase-2.; Medical gas research; Vol 6(1). 2016 Mar.
• 1. Nganou C
  2. Kennedy SD
  3. McCamant DW
  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; Vol 120(7). 2016 Feb 25.
• 1. McAnany JD
  2. Reichert JP
  3. Miller BL
  Probing the geometric constraints of RNA binding via dynamic covalent chemistry.; Bioorganic & medicinal chemistry. 2016 Feb 24.
• 1. Elbarbary RA
  2. Lucas BA
  3. Maquat LE
  Retrotransposons as regulators of gene expression.; Science (New York, N.Y.); Vol 351(6274). 2016 Feb 12.
• 1. Huang C
  2. Karijolich J
  3. Yu YT
  Detection and quantification of RNA 2'-O-methylation and pseudouridylation.; Methods (San Diego, Calif.). 2016 Feb 4.
• 1. Kurosaki T
  2. Maquat LE
  Nonsense-mediated mRNA decay in humans at a glance.; Journal of cell science; Vol 129(3). 2016 Feb 1.
• 1. Sharma U
  2. Conine CC
  3. Shea JM
  4. Boskovic A
  5. Derr AG
  6. Bing XY
  7. Belleannee C
  8. Kucukural A
  9. Serra RW
  10. Sun F
  11. Song L
  12. Carone BR
  13. Ricci EP
  14. Li XZ
  15. Fauquier L
  16. Moore MJ
  17. Sullivan R
  18. Mello CC
  19. Garber M
  20. Rando OJ
  Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals.; Science (New York, N.Y.); Vol 351(6271). 2016 Jan 22.
• 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
  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; Vol 11(1). 2016 Jan 15.
• 1. Agrawal AA
  2. Salsi E
  3. Chatrikhi R
  4. Henderson S
  5. Jenkins JL
  6. Green MR
  7. Ermolenko DN
  8. Kielkopf CL
  An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal.; Nature communications; Vol 7. 2016.
• 1. Brule CE
  2. Dean KM
  3. Grayhack EJ
  RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences.; Methods in enzymology; Vol 572. 2016.
• 1. Huang C
  2. Wu G
  3. Yu YT
  Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles.; Methods in molecular biology (Clifton, N.J.); Vol 1421. 2016.
• 1. Gibbs PE
  2. Miralem T
  3. Lerner-Marmarosh N
  4. Maines MD
  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; Vol 2016. 2016.
• 1. DiChiacchio L
  2. Mathews DH
  Predicting RNA-RNA Interactions Using RNAstructure.; Methods in molecular biology (Clifton, N.J.); Vol 1490. 2016.
• 1. Xu ZZ
  2. Mathews DH
  Experiment-Assisted Secondary Structure Prediction with RNAstructure.; Methods in molecular biology (Clifton, N.J.); Vol 1490. 2016.
• 1. Xu ZZ
  2. Mathews DH
  Prediction of Secondary Structures Conserved in Multiple RNA Sequences.; Methods in molecular biology (Clifton, N.J.); Vol 1490. 2016.
• 1. Xu ZZ
  2. Mathews DH
  Secondary Structure Prediction of Single Sequences Using RNAstructure.; Methods in molecular biology (Clifton, N.J.); Vol 1490. 2016.
• 1. Jenkins JL
  2. Wedekind JE
  The Quick and the Dead: A Guide to Fast Phasing of Small Ribozyme and Riboswitch Crystal Structures.; Methods in molecular biology (Clifton, N.J.); Vol 1490. 2016.
• 1. Kennedy SD
  NMR Methods for Characterization of RNA Secondary Structure.; Methods in molecular biology (Clifton, N.J.); Vol 1490. 2016.
• 1. Leamy KA
  2. Assmann SM
  3. Mathews DH
  4. Bevilacqua PC
  Bridging the gap between in vitro and in vivo RNA folding.; Quarterly reviews of biophysics; Vol 49. 2016 Jan.
• 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
  Candida albicans Carriage in Children with Severe Early Childhood Caries (S-ECC) and Maternal Relatedness.; PloS one; Vol 11(10). 2016.
• 1. Shang L
  2. Henderson LB
  3. Cho MT
  4. Petrey DS
  5. Fong CT
  6. Haude KM
  7. Shur N
  8. Lundberg J
  9. Hauser N
  10. Carmichael J
  11. Innis J
  12. Schuette J
  13. Wu YW
  14. Asaikar S
  15. Pearson M
  16. Folk L
  17. Retterer K
  18. Monaghan KG
  19. Chung WK
  De novo missense variants in PPP2R5D are associated with intellectual disability, macrocephaly, hypotonia, and autism.; Neurogenetics; Vol 17(1). 2016 Jan.