URMC / Center for RNA Biology / Publications Publications Spasic AKennedy SDNeedham LManoharan MKierzek RTurner DHMathews D (2018 Feb 06). 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.). Lucas BALavi EShiue LCho HKatzman SMiyoshi KSiomi MCCarmel LAres MMaquat LE (2018 Jan 16). Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay. Proceedings of the National Academy of Sciences of the United States of America. Hsieh WCBahal RThadke SBhatt KSobczak KThornton CALy DH (2018 Jan 15). Design of 'Mini' Nucleic Acid Probe for Cooperative Binding of RNA-Repeated Transcript Associated with Myotonic Dystrophy Type 1. Biochemistry. Heatwole CJohnson NDekdebrun JDilek NEichinger KHilbert JLuebbe EMartens WMcDermott MPThornton CMoxley R (2018 Jan 12). Myotonic Dystrophy Patient Preferences in Patient-Reported Outcome Measures. Muscle & nerve. Rodriguez LReedy SNogales AMurcia PRChambers TMMartinez-Sobrido L (2018 Jan 11). Development of a novel equine influenza virus live-attenuated vaccine. Virology. Payea MJSloma MFKon YYoung DLGuy MPZhang XDe Zoysa TFields SMathews DHPhizicky EM (2017 Dec 19). Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA. RNA (New York, N.Y.). Rambout XDequiedt FMaquat LE (2017 Dec 18). Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing. Chemical reviews. Duffney PFMcCarthy CENogales AThatcher THMartinez-Sobrido LPhipps RPSime PJ (2017 Dec 14). Cigarette Smoke Dampens Anti-viral Signaling in Small Airway Epithelial Cells by Disrupting TLR3 Cleavage. American journal of physiology. Lung cellular and molecular physiology. Chauché CNogales AZhu HGoldfarb DAhmad Shanizza AIGu QParrish CRMartínez-Sobrido LMarshall JFMurcia PR (2017 Dec 13). Mammalian adaptation of an avian influenza A virus involves stepwise changes in NS1. Journal of virology. Lai CWErmolenko DN (2017 Dec 13). Ensemble and single-molecule FRET studies of protein synthesis. Methods (San Diego, Calif.). Spasic AAssmann SMBevilacqua PCMathews DH (2017 Nov 21). Modeling RNA secondary structure folding ensembles using SHAPE mapping data. Nucleic acids research. Kielkopf CL (2017 Nov 09). Insights from structures of cancer-relevant pre-mRNA splicing factors. Current opinion in genetics & development. Guo BLyu QSlivano OJDirkx RChristie CKCzyzyk JHezel AFGharavi AGSmall EMMiano JM (2017 Nov 07). Serum Response Factor Is Essential for Maintenance of Podocyte Structure and Function. Journal of the American Society of Nephrology : JASN. Popp MWMaquat LE (2017 Nov 07). Nonsense-mediated mRNA Decay and Cancer. Current opinion in genetics & development. Sloma MFMathews DH (2017 Nov 06). Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS computational biology. Walling LRButler JS (2017 Nov 06). Homologous VapC toxins inhibit translation and cell growth by sequence specific cleavage of tRNA(fMet). Journal of bacteriology. Ge JKarijolich JZhai YZheng JYu YT (2017 Oct 31). 5-Fluorouracil Treatment Alters the Efficiency of Translational Recoding. Genes. Carrell STTang ZMohr SLambowitz AMThornton CA (2017 Oct 03). Detection of expanded RNA repeats using thermostable group II intron reverse transcriptase. Nucleic acids research. Musunuru KLagor WRMiano JM (2017 Oct). What Do We Really Think About Human Germline Genome Editing, and What Does It Mean for Medicine? Circulation. Cardiovascular genetics. Tan ZFu YSharma GMathews DH (2017 Sep 28). TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs. Nucleic acids research. DiPiazza ANogales APoulton NWilson PCMartínez-Sobrido LSant AJ (2017 Sep 07). Pandemic 2009 H1N1 Influenza Venus reporter virus reveals broad diversity of MHC class II-positive antigen-bearing cells following infection in vivo. Scientific reports. Rodriguez LNogales AMartínez-Sobrido L (2017 Sep 07). Influenza A Virus Studies in a Mouse Model of Infection. Journal of visualized experiments : JoVE. Glasser EAgrawal AAJenkins JLKielkopf CL (2017 Sep 01). Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry. Smith LGZhao JMathews DHTurner DH (2017 Sep). Physics-based all-atom modeling of RNA energetics and structure. Wiley interdisciplinary reviews. RNA. Hilbert JEBarohn RJClemens PRLuebbe EAMartens WBMcDermott MPParkhill ALTawil RThornton CAMoxley RT (2017 Aug 30). High frequency of gastrointestinal manifestations in myotonic dystrophy type 1 and type 2. Neurology. Nogales AChauché CDeDiego MLTopham DJParrish CRMurcia PRMartínez-Sobrido L (2017 Aug 23). Amino acid substitution K186E in the canine influenza virus H3N8 NS1 protein restores its ability to inhibit host gene expression. Journal of virology. Poole ARVicino IAdachi HYu YTHebert MD (2017 Aug 14). Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity. Biology open. Domm WYee MMisra RSGelein RNogales AMartinez Sobrido LO'Reilly MA (2017 Aug 10). Oxygen-dependent changes in lung development do not affect epithelial infection with influenza A virus. American journal of physiology. Lung cellular and molecular physiology. Tan ZSharma GMathews DH (2017 Jul 20). Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data. Biophysical journal. Elbarbary RAMiyoshi KHedaya OMyers JRMaquat LE (2017 Jul 15). UPF1 helicase promotes TSN-mediated miRNA decay. Genes & development. Rodriguez LNogales AMurcia PRParrish CRMartínez-Sobrido L (2017 Jul 11). A bivalent live-attenuated influenza vaccine for the control and prevention of H3N8 and H3N2 canine influenza viruses. Vaccine. Nogales ARodriguez LDeDiego MLTopham DJMartínez-Sobrido L (2017 Jun 21). Interplay of PA-X and NS1 proteins in replication and pathogenesis of a temperature-sensitive 2009 pandemic H1N1 influenza A virus. Journal of virology. Clark AMNogales AMartinez-Sobrido LTopham DJDeDiego ML (2017 Jun 21). Functional evolution of influenza NS1 protein in currently circulating human 2009 pandemic H1N1 viruses. Journal of virology. Jauvin DChrétien JPandey SKMartineau LRevillod LBassez GLachon AMcLeod ARGourdon GWheeler TMThornton CABennett CFPuymirat J (2017 Jun 16). Targeting DMPK with Antisense Oligonucleotide Improves Muscle Strength in Myotonic Dystrophy Type 1 Mice. Molecular therapy. Nucleic acids. Ward MDatta AWise MMathews DH (2017 Jun 06). Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. Nucleic acids research. Elbarbary RAMaquat LE (2017 Jun 06). Distinct mechanisms obviate the potentially toxic effects of inverted-repeat Alu elements on cellular RNA metabolism. Nature structural & molecular biology. Elbarbary RAMiyoshi KMyers JRDu PAshton JMTian BMaquat LE (2017 May 26). Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G1/S phase transition. Science (New York, N.Y.). Polevoda BJoseph RFriedman AEBennett RPGreiner RDe Zoysa TStewart RASmith 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. Yao PWu JLindner DFox PL (2017 May 17). Interplay between miR-574-3p and hnRNP L regulates VEGFA mRNA translation and tumorigenesis. Nucleic acids research. Hilimire TAChamberlain JMAnokhina VBennett RPSwart OMyers JRAshton JMStewart RAFeatherston ALGates KHelms EDSmith HCDewhurst SMiller 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. East-Seletsky AO'Connell MRBurstein DKnott GJDoudna JA (2017 May 04). RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes. Molecular cell. Wedekind JEDutta DBelashov IAJenkins JL (2017 Apr 28). Metalloriboswitches: RNA-Based Inorganic Ion Sensors that Regulate Genes. The Journal of biological chemistry. Gamache ERDoh JHRitz JLaederach ABellaousov SMathews DHCurcio MJ (2017 Apr 26). Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA. Viruses. Sun YHXie LHZhuo XChen QGhoneim DZhang BJagne JYang CLi XZ (2017 Apr 06). Domestic chickens activate a piRNA defense against avian leukosis virus. eLife. Rodriguez LNogales AReilly ECTopham DJMurcia PRParrish CRMartinez Sobrido L (2017 Apr). A live-attenuated influenza vaccine for H3N2 canine influenza virus. Virology. Thornton CAWang ECarrell EM (2017 Apr 01). Myotonic dystrophy: approach to therapy. Current opinion in genetics & development. Jenkins JLKielkopf CL (2017 Mar 31). Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures. Trends in genetics : TIG. Halim DWilson MPOliver DBrosens EVerheij JBHan YNanda VLyu QDoukas MStoop HBrouwer RWvan IJcken WFSlivano OJBurns AJChristie CKde Mesy Bentley KLBrooks ASTibboel DXu SJin ZGDjuwantono TYan WAlves MMHofstra RMMiano JM (2017 Mar 28). Loss of LMOD1 impairs smooth muscle cytocontractility and causes megacystis microcolon intestinal hypoperistalsis syndrome in humans and mice. Proceedings of the National Academy of Sciences of the United States of America. Zuber JSun HZhang XMcFadyen IMathews 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. Brule CEGrayhack EJ (2017 Mar 11). Synonymous Codons: Choose Wisely for Expression. Trends in genetics : TIG. de Campo DMCameron JLMiano JMLewis DAMirnics KFudge JL (2017 Mar). Maternal deprivation alters expression of neural maturation gene tbr1 in the amygdala paralaminar nucleus in infant female macaques. Developmental psychobiology. Nogales AMartinez-Sobrido LTopham DJDeDiego ML (2017 Mar 01). NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses. Journal of virology. Nogales ARodriguez LChauché CHuang KReilly ECTopham DJMurcia PRParrish CRMartínez-Sobrido L (2017 Feb 15). Temperature-Sensitive Live-Attenuated Canine Influenza Virus H3N8 Vaccine. Journal of virology. Aytenfisu AHSpasic AGrossfield AStern HAMathews DH (2017 Feb 14). Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics. Journal of chemical theory and computation. Zhu QMKo KATure SMastrangelo MAChen MHJohnson ADO'Donnell CJMorrell CNMiano JMLowenstein CJ (2017 Feb). Novel Thrombotic Function of a Human SNP in STXBP5 Revealed by CRISPR/Cas9 Gene Editing in Mice. Arteriosclerosis, thrombosis, and vascular biology. Clark KMJenkins JLFedoriw NDumont 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. Cheng BYNogales Ade la Torre JCMartínez-Sobrido L (2017 Jan 15). Development of live-attenuated arenavirus vaccines based on codon deoptimization of the viral glycoprotein. Virology. Patra BKon YYadav GSevold AWFrumkin JPVallabhajosyula RRHintze AØstman BSchossau JBhan AMarzolf BTamashiro JKKaur ABaliga NSGrayhack EJAdami CGalas DJRaval APhizicky EMRay A (2017 Jan 09). A genome wide dosage suppressor network reveals genomic robustness. Nucleic acids research. Santhakumar DRubbenstroth DMartinez-Sobrido LMunir M (2017). Avian Interferons and Their Antiviral Effectors. Frontiers in immunology. Martínez-Sobrido Lde la Torre JC (2017). Development of Recombinant Arenavirus-Based Vaccines. Methods in molecular biology (Clifton, N.J.). Freedman JEMiano JM (2017 Jan). Challenges and Opportunities in Linking Long Noncoding RNAs to Cardiovascular, Lung, and Blood Diseases. Arteriosclerosis, thrombosis, and vascular biology. Lee MYPark CHa SEPark PJBerent RMJorgensen BGCorrigan RDGrainger NBlair PJSlivano OJMiano JMWard SMSmith TKSanders KMRo S (2017). Serum response factor regulates smooth muscle contractility via myotonic dystrophy protein kinases and L-type calcium channels. PloS one. Hrabeta-Robinson EMarcus ECozen AEPhizicky EMLowe TM (2017). High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq). Methods in molecular biology (Clifton, N.J.). Martínez-Sobrido LPaessler Sde la Torre JC (2017). Lassa Virus Reverse Genetics. Methods in molecular biology (Clifton, N.J.). Nogales APerez DRSantos JFinch CMartínez-Sobrido L (2017). Reverse Genetics of Influenza B Viruses. Methods in molecular biology (Clifton, N.J.). Perez DRAngel MGonzalez-Reiche ASSantos JObadan AMartinez-Sobrido L (2017). Plasmid-Based Reverse Genetics of Influenza A Virus. Methods in molecular biology (Clifton, N.J.). De Zoysa MDYu YT (2017). Posttranscriptional RNA Pseudouridylation. The Enzymes. Clark AMDeDiego MLAnderson CSWang JYang HNogales AMartinez-Sobrido LZand MSSangster MYTopham DJ (2017). Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. PloS one. Nogales AMartínez-Sobrido L (2016 Dec 22). Reverse Genetics Approaches for the Development of Influenza Vaccines. International journal of molecular sciences. Han LMarcus ED'Silva SPhizicky 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.). Chatrikhi RWang WGupta ALoerch SMaucuer AKielkopf CL (2016 Dec 20). SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA. Biophysical journal. Ling CErmolenko DN (2016 Dec 06). Caught on Camera: Intermediates of Ribosome Recycling. Structure (London, England : 1993). Loerch SKielkopf CL (2016 Dec). Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. RNA (New York, N.Y.). Ikpeze TCSmith HCLee DJElfar JC (2016 Dec). Distal Radius Fracture Outcomes and Rehabilitation. Geriatric orthopaedic surgery & rehabilitation. Sloma MFMathews DH (2016 Dec). Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures. RNA (New York, N.Y.). Mathews DHTurner DHWatson RM (2016 Dec 01). RNA Secondary Structure Prediction. Current protocols in nucleic acid chemistry. Smith HC (2016 Nov 21). RNA binding to APOBEC deaminases; Not simply a substrate for C to U editing. RNA biology. Choby JEMike LAMashruwala AADutter BFDunman PMSulikowski GABoyd JMSkaar EP (2016 Nov 17). A Small-Molecule Inhibitor of Iron-Sulfur Cluster Assembly Uncovers a Link between Virulence Regulation and Metabolism in Staphylococcus aureus. Cell chemical biology. Leimgruber CQuintar AAPeinetti NScalerandi MVNicola JPMiano JMMaldonado CA (2016 Nov 09). Testosterone Rescues the De-Differentiation of Smooth Muscle Cells through Serum Response Factor/Myocardin. Journal of cellular physiology. Bennett RPStewart RAHogan PAPtak RGMankowski MKHartman TLBuckheit RWSnyder BASalter JDMorales GASmith 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. Xu CIshikawa HIzumikawa KLi LHe HNobe YYamauchi YShahjee HMWu XHYu YTIsobe TTakahashi NMin J (2016 Nov 01). Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. Genes & development. Nogales AHuang KChauché CDeDiego MLMurcia PRParrish CRMartínez-Sobrido L (2016 Oct 14). Canine influenza viruses with modified NS1 proteins for the development of live-attenuated vaccines. Virology. East-Seletsky AO'Connell MRKnight SCBurstein DCate JHTjian RDoudna JA (2016 Oct 13). Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. Fei DLMotowski HChatrikhi RPrasad SYu JGao SKielkopf CLBradley RKVarmus H (2016 Oct). Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival. PLoS genetics. Walling LRButler JS (2016 Sep 26). Structural determinants for antitoxin identity and insulation of cross talk between homologous toxin-antitoxin systems. Journal of bacteriology. Sparks RPJenkins JLMiner GEWang YGuida WCSparks CEFratti RASparks 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. Romero-Beltran LBaker SFPuerto-Solís MGonzález-Losa RConde-Ferraez LAlvarez-Sánchez LCMartínez-Sobrido LAyora-Talavera G (2016 Sep 2). Mutations at highly conserved residues in influenza A(H1N1)pdm09 virus affect neuraminidase activity. Virus research. Wagner SDStruck AJGupta RFarnsworth DRMahady AEEichinger KThornton CAWang ETBerglund JA (2016 Sep). Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy. PLoS genetics. Blanchard CBrooks LEbsworth-Mojica KDidione LWucher BDewhurst SKrysan DDunman PMWozniak RA (2016 Sep). Zinc Pyrithione Improves the Antibacterial Activity of Silver Sulfadiazine Ointment. mSphere. DeDiego MLNogales ALambert-Emo KMartinez-Sobrido LTopham DJ (2016 Aug 17). An NS1 protein mutation (I64T) affects interferon responses and virulence of circulating H3N2 human influenza A viruses. Journal of virology. Carrell STCarrell EMAuerbach DPandey SKBennett CFDirksen RTThornton CA (2016 Aug 13). Dmpk Gene Deletion or Antisense Knockdown Does Not Compromise Cardiac or Skeletal Muscle Function in Mice. Human molecular genetics. Chettimada SJoshi SRDhagia VAiezza ALincoln TMGupte RMiano JMGupte SA (2016 Aug 12). Vascular smooth muscle cell contractile protein expression is increased through PKG-dependent and -independent pathways by G6PD inhibition and deficiency. American journal of physiology. Heart and circulatory physiology. Sparks RPGuida WCSowden MPJenkins JLStarr MLFratti RASparks CESparks JD (2016 Aug 2). Sortilin facilitates VLDL-B100 secretion by insulin sensitive McArdle RH7777 cells. Biochemical and biophysical research communications. Lenartowicz ENogales AKierzek EKierzek RMartínez-Sobrido LTurner DH (2016 Jul 27). Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication. Nucleic acid therapeutics. Zhao JZhang WLin MWu WJiang PTou EXue MRichards AJourd'heuil DAsif AZheng DSinger HAMiano JMLong X (2016 Jul 21). MYOSLID Is a Novel Serum Response Factor-Dependent Long Noncoding RNA That Amplifies the Vascular Smooth Muscle Differentiation Program. Arteriosclerosis, thrombosis, and vascular biology. Gamble CEBrule CEDean KMFields SGrayhack EJ (2016 Jun 29). Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast. Cell. Gleghorn MLZhao JTurner DHMaquat 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. Wu GRadwan MKXiao MAdachi HFan JYu YT (2016 Jun 7). The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA. RNA (New York, N.Y.). Popp MWMaquat LE (2016 Jun 2). Leveraging Rules of Nonsense-Mediated mRNA Decay for Genome Engineering and Personalized Medicine. Cell. Miano JMZhu QMLowenstein CJ (2016 Jun). A CRISPR Path to Engineering New Genetic Mouse Models for Cardiovascular Research. Arteriosclerosis, thrombosis, and vascular biology. Salter JDBennett RPSmith HC (2016 May 30). The APOBEC Protein Family: United by Structure, Divergent in Function. Trends in biochemical sciences. Ballantyne MDPinel KDakin RVesey ATDiver LMackenzie RGarcia RWelsh PSattar NHamilton GJoshi NDweck MRMiano JMMcBride MWNewby DEMcDonald RABaker AH (2016 May 24). Smooth Muscle Enriched Long Noncoding RNA (SMILR) Regulates Cell Proliferation. Circulation. Salsi EFarah EErmolenko DN (2016 May 22). EF-G Activation by Phosphate Analogs. Journal of molecular biology. Martinez-Sobrido Lde la Torre JC (2016 May 13). Novel strategies for development of hemorrhagic fever arenavirus live-attenuated vaccines. Expert review of vaccines. Miralem TLerner-Marmarosh NGibbs PEJenkins JLHeimiller CMaines 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. Nogales ABaker SFDomm WMartínez-Sobrido L (2016 May 2). Development and applications of single-cycle infectious influenza A virus (sciIAV). Virus research. Boulberdaa MScott EBallantyne MGarcia RDescamps BAngelini GDBrittan MHunter AMcBride MMcClure JMiano JMEmanueli CMills NLMountford JCBaker AH (2016 May). A Role for the Long Noncoding RNA SENCR in Commitment and Function of Endothelial Cells. Molecular therapy : the journal of the American Society of Gene Therapy. Ling CErmolenko DN (2016 Apr 27). Structural insights into ribosome translocation. Wiley interdisciplinary reviews. RNA. Nogales ADeDiego MLTopham DJMartínez-Sobrido L (2016 Apr 27). Rearrangement of influenza virus spliced segments for the development of live attenuated vaccines. Journal of virology. Shaheen RHan LFaqeih EEwida NAlobeid EPhizicky EMAlkuraya FS (2016 Apr 7). A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. Human genetics. Nelles DAFang MYO'Connell MRXu JLMarkmiller SJDoudna JAYeo GW (2016 Apr 07). Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell. Maquat LE (2016 Apr). Eukaryotic antisense ahead of its time. Nature reviews. Molecular cell biology. DiChiacchio LSloma MFMathews DH (2016 Apr 1). AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. Bioinformatics (Oxford, England). Wu GAdachi HGe JStephenson DQuery CCYu YT (2016 Mar 15). Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly. The EMBO journal. Polevoda BMcDougall WMBennett RPSalter JDSmith HC (2016 Mar 14). Structural and functional assessment of APOBEC3G macromolecular complexes. Methods (San Diego, Calif.). Elbarbary RAMaquat 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. Elbarbary RALucas BAMaquat LE (2016 Feb 12). Retrotransposons as regulators of gene expression. Science (New York, N.Y.). Huang CKarijolich JYu YT (2016 Feb 4). Detection and quantification of RNA 2'-O-methylation and pseudouridylation. Methods (San Diego, Calif.). Nogales ARodríguez-Sánchez IMonte KLenschow DJPerez DRMartínez-Sobrido L (2016 Feb 2). Replication-competent fluorescent-expressing influenza B virus. Virus research. Blanchard CBrooks LBeckley AColquhoun JDewhurst SDunman PM (2016 Feb). Neomycin Sulfate Improves the Antimicrobial Activity of Mupirocin-Based Antibacterial Ointments. Antimicrobial agents and chemotherapy. Kurosaki TMaquat LE (2016 Feb 1). Nonsense-mediated mRNA decay in humans at a glance. Journal of cell science. Sharma UConine CCShea JMBoskovic ADerr AGBing XYBelleannee CKucukural ASerra RWSun FSong LCarone BRRicci EPLi XZFauquier LMoore MJSullivan RMello CCGarber MRando OJ (2016 Jan 22). Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science (New York, N.Y.). Hilimire TABennett RPStewart RAGarcia-Miranda PBlume ABecker JSherer NHelms EDButcher SESmith HCMiller 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. Agrawal AASalsi EChatrikhi RHenderson SJenkins JLGreen MRErmolenko DNKielkopf CL (2016). An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal. Nature communications. Brule CEDean KMGrayhack EJ (2016). RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences. Methods in enzymology. Yang HBaker SFGonzález METopham DJMartínez-Sobrido LZand MHolden-Wiltse JWu H (2016). An improved method for estimating antibody titers in microneutralization assay using green fluorescent protein. Journal of biopharmaceutical statistics. Breen MNogales ABaker SFPerez DRMartínez-Sobrido L (2016). Replication-Competent Influenza A and B Viruses Expressing a Fluorescent Dynamic Timer Protein for In Vitro and In Vivo Studies. PloS one. Martínez-Sobrido LCheng BYde la Torre JC (2016). Reverse Genetics Approaches to Control Arenavirus. Methods in molecular biology (Clifton, N.J.). Robinson JEHastie KMCross RWYenni REElliott DHRouelle JAKannadka CBSmira AAGarry CEBradley BTYu HShaffer JGBoisen MLHartnett JNZandonatti MARowland MMHeinrich MLMartínez-Sobrido LCheng Bde la Torre JCAndersen KGGoba AMomoh MFullah MGbakie MKanneh LKoroma VJFonnie RJalloh SCKargbo BVandi MAGbetuwa MIkponmwosa OAsogun DAOkokhere POFollarin OASchieffelin JSPitts KRGeisbert JBKulakoski PCWilson RBHappi CTSabeti PCGevao SMKhan SHGrant DSGeisbert TWSaphire EOBranco LMGarry RF (2016). Most neutralizing human monoclonal antibodies target novel epitopes requiring both Lassa virus glycoprotein subunits. Nature communications. Huang CWu GYu YT (2016). Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles. Methods in molecular biology (Clifton, N.J.). Jiang TNogales ABaker SFMartinez-Sobrido LTurner DH (2016). Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture. PloS one. Breen MNogales ABaker SFMartínez-Sobrido L (2016). Replication-Competent Influenza A Viruses Expressing Reporter Genes. Viruses. Martínez-Sobrido Lde la Torre JC (2016). Reporter-Expressing, Replicating-Competent Recombinant Arenaviruses. Viruses. DiChiacchio LMathews DH (2016). Predicting RNA-RNA Interactions Using RNAstructure. Methods in molecular biology (Clifton, N.J.). Xu ZZMathews DH (2016). Experiment-Assisted Secondary Structure Prediction with RNAstructure. Methods in molecular biology (Clifton, N.J.). Xu ZZMathews DH (2016). Prediction of Secondary Structures Conserved in Multiple RNA Sequences. Methods in molecular biology (Clifton, N.J.). Xu ZZMathews DH (2016). Secondary Structure Prediction of Single Sequences Using RNAstructure. Methods in molecular biology (Clifton, N.J.). Jenkins JLWedekind 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.). Leamy KAAssmann SMMathews DHBevilacqua PC (2016 Jan). Bridging the gap between in vitro and in vivo RNA folding. Quarterly reviews of biophysics. Ling CErmolenko 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. Burns TMSmith GAAllen JAAmato AAArnold WDBarohn RBenatar MBird SJBromberg MChahin NCiafaloni ECohen JACorse ACrum BADavid WSDimberg EDe Sousa EADonofrio PDDyck PJEngel AGEnsrud ERFerrante MFreimer MGable KLGibson SGilchrist JMGoldstein JMGooch CLGoodman BPGorelov DGospe SMGoyal NAGuidon ACGuptill JTGutmann LGutmann LGwathmey KHarati YHarper CMHehir MKHobson-Webb LDHoward JFJackson CEJohnson NJones SMJuel VCKaminski HJKaram CKennelly KDKhella SKhoury JKincaid JCKissel JTKolb NLacomis DLadha SLarriviere DLewis RALi YLitchy WJLogigian ELou JSMacGowen DJMaselli RMassey JMMauermann MLMathews KDMeriggioli MNMiller RGMoon JSMozaffar TNations SPNowak RJOstrow LWPascuzzi RMPeltier ARuzhansky KRichman DPRoss MARubin DIRussell JASachs GMSalajegheh MKSaperstein DSScelsa SSelcen DShaibani ASheih PBSilvestri NJSingleton JRSmith BESo YTSolorzano GSorenson EJSrinivasen JTavee JTawil RThaisetthawatkul PThornton CTrivedi JVernino SWang AKWebb TAWeiss MDWindebank AJWolfe GI (2015 Dec 10). Editorial by concerned physicians: Unintended effect of the Orphan Drug Act on the potential cost of 3,4-diaminopyridine. Muscle & nerve. Wilde ADSnyder DJPutnam NEValentino MDHammer NDLonergan ZRHinger SAAysanoa EEBlanchard CDunman PMWasserman GAChen JShopsin BGilmore MSSkaar EPCassat JE (2015 Dec). Bacterial Hypoxic Responses Revealed as Critical Determinants of the Host-Pathogen Outcome by TnSeq Analysis of Staphylococcus aureus Invasive Infection. PLoS pathogens. Quivey RGGrayhack EJFaustoferri RCHubbard CJBaldeck JDWolf ASMacGilvray MERosalen PLScott-Anne KSantiago BGopal SPayne JMarquis RE (2015 Dec). Functional profiling in Streptococcus mutans: construction and examination of a genomic collection of gene deletion mutants. Molecular oral microbiology. Guy MPShaw MWeiner CLHobson LStark ZRose KKalscheuer VMGecz JPhizicky 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. Heatwole CJohnson NBode RDekdebrun JDilek NHilbert JELuebbe EMartens WMcDermott MPQuinn CRothrock NThornton CVickrey BGVictorson DMoxley RT (2015 Nov 18). Patient-Reported Impact of Symptoms in Myotonic Dystrophy Type 2 (PRISM-2). Neurology. Chen JLBellaousov STubbs JDKennedy SDLopez MJMathews DHTurner DH (2015 Nov 17). Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. Biochemistry. Dutta DWedekind 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. Ma EHarrington LBO'Connell MRZhou KDoudna JA (2015 Nov 05). Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Molecular cell. Pandey SKWheeler TMJustice SLKim AYounis HSGattis DJauvin DPuymirat JSwayze EEFreier SMBennett CFThornton CAMacLeod AR (2015 Nov). Identification and Characterization of Modified Antisense Oligonucleotides Targeting DMPK in Mice and Nonhuman Primates for the Treatment of Myotonic Dystrophy Type 1. The Journal of pharmacology and experimental therapeutics. Aytenfisu AHLiberman JAWedekind JEMathews DH (2015 Nov). Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics. RNA (New York, N.Y.). Polevoda BMcDougall WMTun BNCheung MSalter JDFriedman AESmith HC (2015 Oct 30). RNA binding to APOBEC3G induces the disassembly of functional deaminase complexes by displacing single-stranded DNA substrates. Nucleic acids research. Halliley JLKhurana SKrammer FFitzgerald TCoyle EMChung KYBaker SFYang HMartínez-Sobrido LTreanor JJSubbarao KGolding HTopham DJSangster MY (2015 Oct 15). High-Affinity H7 Head and Stalk Domain-Specific Antibody Responses to an Inactivated Influenza H7N7 Vaccine After Priming With Live Attenuated Influenza Vaccine. The Journal of infectious diseases. Seward CHManzella AAlam AButler JSDziejman M (2015 Oct). Using S. cerevisiae as a Model System to Investigate V. cholerae VopX-Host Cell Protein Interactions and Phenotypes. Toxins. Sheehan LMBudnick JABlanchard CDunman PMCaswell CC (2015 Oct). A LysR-family transcriptional regulator required for virulence in Brucella abortus is highly conserved among the α-proteobacteria. Molecular microbiology. Tomaras APDunman PM (2015 Oct). In the midst of the antimicrobial discovery conundrum: an overview. Current opinion in microbiology. Dunman PMTomaras AP (2015 Oct). Translational deficiencies in antibacterial discovery and new screening paradigms. Current opinion in microbiology. Dunman PMTomaras AP (2015 Oct). Editorial overview: Antimicrobials. Current opinion in microbiology. Park CLee MYPark PJHa SEBerent RMFuchs RMiano JMBecker LSSanders KMRo S (2015 Oct 1). Serum Response Factor Is Essential for Prenatal Gastrointestinal Smooth Muscle Development and Maintenance of Differentiated Phenotype. Journal of neurogastroenterology and motility. Karijolich JYi CYu YT (2015 Oct). Transcriptome-wide dynamics of RNA pseudouridylation. Nature reviews. Molecular cell biology. Loerch SKielkopf CL (2015 Sep 25). Dividing and Conquering the Family of RNA Recognition Motifs: A Representative Case Based on hnRNP L. Journal of molecular biology. Wu YShi BDing XLiu THu XYip KYYang ZRMathews DHLu 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. Miano JMLong X (2015 Sep). The short and long of noncoding sequences in the control of vascular cell phenotypes. Cellular and molecular life sciences : CMLS. Cozen AEQuartley EHolmes ADHrabeta-Robinson EPhizicky EMLowe TM (2015 Sep). ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nature methods. Baker SFNogales ASantiago FWTopham DJMartínez-Sobrido L (2015 Jul 9). Competitive detection of influenza neutralizing antibodies using a novel bivalent fluorescence-based microneutralization assay (BiFMA). Vaccine. Liberman JASuddala KCAytenfisu AChan DBelashov IASalim MMathews DHSpitale RCWalter NGWedekind 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. Cheng BYOrtiz-Riaño Ede la Torre JCMartínez-Sobrido L (2015 Jul). Arenavirus Genome Rearrangement for the Development of Live Attenuated Vaccines. Journal of virology. Heatwole CBode RNicholas Johnson Dekdebrun JDilek NEichinger KHilbert JELogigian ELuebbe EMartens WMcDermott MPPandya SPuwanant ARothrock NThornton CVickrey BGVictorson DMoxley RT (2015 Jun 4). The myotonic dystrophy health index: Correlations with clinical tests and patient function. Muscle & nerve. Ling CErmolenko DN (2015 Jun 2). Ribosome subunit joining frozen in time. Structure (London, England : 1993). Pythoud CRothenberger SMartínez-Sobrido Lde la Torre JCKunz S (2015 Jun). Lymphocytic Choriomeningitis Virus Differentially Affects the Virus-Induced Type I Interferon Response and Mitochondrial Apoptosis Mediated by RIG-I/MAVS. Journal of virology. Baker SFNogales AMartínez-Sobrido L (2015 Jun). Downregulating viral gene expression: codon usage bias manipulation for the generation of novel influenza A virus vaccines. Future virology. Wolf ASGrayhack EJ (2015 May). Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats. RNA (New York, N.Y.). Jin GPavelka MSButler JS (2015 Apr). Structure-function analysis of VapB4 antitoxin identifies critical features of a minimal VapC4 toxin-binding module. Journal of bacteriology. Eidem TMLounsbury NEmery JFBulger JSmith AAbou-Gharbia MChilders WDunman PM (2015 Apr). Small-molecule inhibitors of Staphylococcus aureus RnpA-mediated RNA turnover and tRNA processing. Antimicrobial agents and chemotherapy. Mootz JMBenson MAHeim CECrosby HAKavanaugh JSDunman PMKielian TTorres VJHorswill AR (2015 Apr). Rot is a key regulator of Staphylococcus aureus biofilm formation. Molecular microbiology. Elbarbary RAMaquat LE (2015 Apr 1). CARMing down the SINEs of anarchy: two paths to freedom from paraspeckle detention. Genes & development. Okeyo-Owuor TWhite BSChatrikhi RMohan DRKim SGriffith MDing LKetkar-Kulkarni SHundal JLaird KMKielkopf CLLey TJWalter MJGraubert TA (2015 Apr). U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing. Leukemia. 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.). Cheng BYOrtiz-Riaño ENogales Ade la Torre JCMartínez-Sobrido L (2015 Apr). Development of live-attenuated arenavirus vaccines based on codon deoptimization. Journal of virology. Ackers-Johnson MTalasila ASage APLong XBot IMorrell NWBennett MRMiano JMSinha S (2015 Apr). Myocardin regulates vascular smooth muscle cell inflammatory activation and disease. Arteriosclerosis, thrombosis, and vascular biology. Phizicky EMHopper AK (2015 Apr). tRNA processing, modification, and subcellular dynamics: past, present, and future. RNA (New York, N.Y.). Karijolich JYu YT (2015 Apr). The new era of RNA modification. RNA (New York, N.Y.). Yadava RSFoff EPYu QGladman JTKim YKBhatt KSThornton CAZheng TSMahadevan MS (2015 Apr 01). TWEAK/Fn14, a pathway and novel therapeutic target in myotonic dystrophy. Human molecular genetics. Wojtkowiak-Szlachcic ATaylor KStepniak-Konieczna ESznajder LJMykowska ASroka JThornton CASobczak K (2015 Mar 31). Short antisense-locked nucleic acids (all-LNAs) correct alternative splicing abnormalities in myotonic dystrophy. Nucleic acids research. Popp MWMaquat LE (2015 Mar 20). RNA. A TRICK'n way to see the pioneer round of translation. Science (New York, N.Y.). Cox ABaker SFNogales AMartínez-Sobrido LDewhurst S (2015 Mar). Development of a mouse-adapted live attenuated influenza virus that permits in vivo analysis of enhancements to the safety of live attenuated influenza virus vaccine. Journal of virology. Vengrenyuk YNishi HLong XOuimet MSavji NMartinez FOCassella CPMoore KJRamsey SAMiano JMFisher EA (2015 Mar). Cholesterol loading reprograms the microRNA-143/145-myocardin axis to convert aortic smooth muscle cells to a dysfunctional macrophage-like phenotype. Arteriosclerosis, thrombosis, and vascular biology. Han LKon YPhizicky 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.). Nogales ABaker SFMartínez-Sobrido L (2015 Feb). Replication-competent influenza A viruses expressing a red fluorescent protein. Virology. Han YSlivano OJChristie CKCheng AWMiano JM (2015 Feb). CRISPR-Cas9 genome editing of a single regulatory element nearly abolishes target gene expression in mice--brief report. Arteriosclerosis, thrombosis, and vascular biology. Salsi EFarah ENetter ZDann JErmolenko DN (2015 Jan 30). Movement of elongation factor G between compact and extended conformations. Journal of molecular biology. Fu YXu ZZLu ZJZhao SMathews DH (2015). Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PloS one. Payea MJGuy MPPhizicky EM (2015). Methodology for the High-Throughput Identification and Characterization of tRNA Variants That Are Substrates for a tRNA Decay Pathway. Methods in enzymology. Forbes LEbsworth-Mojica KDiDone LLi SGFreundlich JSConnell NDunman PMKrysan DJ (2015). A High Throughput Screening Assay for Anti-Mycobacterial Small Molecules Based on Adenylate Kinase Release as a Reporter of Cell Lysis. PloS one. Colquhoun JMWozniak RADunman PM (2015). Clinically Relevant Growth Conditions Alter Acinetobacter baumannii Antibiotic Susceptibility and Promote Identification of Novel Antibacterial Agents. PloS one. Gong CMaquat LE (2015). Affinity purification of long noncoding RNA-protein complexes from formaldehyde cross-linked mammalian cells. Methods in molecular biology (Clifton, N.J.). Jackson KLDayton RDOrchard EAJu SRinge DPetsko GAMaquat LEKlein RL (2015 Jan). Preservation of forelimb function by UPF1 gene therapy in a rat model of TDP-43-induced motor paralysis. Gene therapy. Popp MWMaquat LE (2015). Attenuation of nonsense-mediated mRNA decay facilitates the response to chemotherapeutics. Nature communications. Laguio-Vila MRThompson MGReynolds SSpencer SMGaglani MNaleway ABall SBozeman SBaker SMartínez-Sobrido LLevine MKatz JFry AMTreanor JJ (2015 Jan). Comparison of serum hemagglutinin and neuraminidase inhibition antibodies after 2010-2011 trivalent inactivated influenza vaccination in healthcare personnel. Open forum infectious diseases. Sloma MFMathews DH (2015). Improving RNA secondary structure prediction with structure mapping data. Methods in enzymology. Miano JM (2015 Jan). Myocardin in biology and disease. Journal of biomedical research.