URMC / Center for RNA Biology / Publications Publications 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. 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.). Smith HC (2016 Nov 21). RNA binding to APOBEC deaminases; Not simply a substrate for C to U editing. RNA biology. 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. 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. 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. 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. 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. 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. 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. Uppal NFoxe JJButler JSAcluche FMolholm S (2016 Jan 13). The neural dynamics of somatosensory processing and adaptation across childhood: A high-density electrical mapping study. Journal of neurophysiology. 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. 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.). Aroda VRChristophi CAEdelstein SLZhang PHerman WHBarrett-Connor EDelahanty LMMontez MGAckermann RTZhuo XKnowler WCRatner 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. 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. Lee MYPark CBerent RMPark PJFuchs RSyn HChin ATownsend JBenson CCRedelman DShen TWPark JKMiano JMSanders KMRo S (2015). Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes. PloS one. Krawczyk KKYao Mattisson IEkman MOskolkov NGrantinge RKotowska DOlde BHansson OAlbinsson SMiano JMRippe CSwärd K (2015). Myocardin Family Members Drive Formation of Caveolae. PloS one. Park CLee MYSlivano OJPark PJHa SBerent RMFuchs RCollins NCYu TJSyn HPark JKHoriguchi KMiano JMSanders KMRo S (2015). Loss of serum response factor induces microRNA-mediated apoptosis in intestinal smooth muscle cells. Cell death & disease. Guy MPPhizicky EM (2015 Jan). Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. RNA (New York, N.Y.). Shaheen RAbdel-Salam GMGuy MPAlomar RAbdel-Hamid MSAfifi HHIsmail SIEmam BAPhizicky EMAlkuraya FS (2015). Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome biology. Enwerem IIWu GYu YTHebert MD (2015). Cajal body proteins differentially affect the processing of box C/D scaRNPs. PloS one. Wu GHuang CYu YT (2015). Pseudouridine in mRNA: Incorporation, Detection, and Recoding. Methods in enzymology. Yao PEswarappa SMFox PL (2015 Jan 01). "Translational control mechanisms in angiogenesis and vascular biology." Current Atherosclerosis Reports. Fu YSharma GMathews DH (2014 Dec 16). Dynalign II: common secondary structure prediction for RNA homologs with domain insertions. Nucleic acids research. DeVito SROrtiz-Riaño EMartínez-Sobrido LMunger 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. Ramon SBaker SFSahler JMKim NFeldsott EASerhan CNMartínez-Sobrido LTopham DJPhipps RP (2014 Dec 15). The specialized proresolving mediator 17-HDHA enhances the antibody-mediated immune response against influenza virus: a new class of adjuvant? Journal of immunology (Baltimore, Md. : 1950). Yadava RSFoff EPYu QGladman JTKim YKBhatt KSThornton CAZheng TSMahadevan MS (2014 Dec 11). TWEAK/Fn14, a pathway and novel therapeutic target in myotonic dystrophy. Human molecular genetics. Agrawal AAMcLaughlin KJJenkins JLKielkopf 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. Mathers CSchafer XMartínez-Sobrido LMunger J (2014 Dec). The human cytomegalovirus UL26 protein antagonizes NF-κB activation. Journal of virology. Adachi HYu YT (2014 Nov 26). Insight into the mechanisms and functions of spliceosomal snRNA pseudouridylation. World journal of biological chemistry. Blanchard CBarnett PPerlmutter JDunman PM (2014 Nov). Identification of Acinetobacter baumannii serum-associated antibiotic efflux pump inhibitors. Antimicrobial agents and chemotherapy. Perlmutter JIForbes LTKrysan DJEbsworth-Mojica KColquhoun JMWang JLDunman PMFlaherty DP (2014 Oct 23). Repurposing the antihistamine terfenadine for antimicrobial activity against Staphylococcus aureus. Journal of medicinal chemistry. Salsi EFarah EDann JErmolenko 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. Olson METodd DASchaeffer CRPaharik AEVan Dyke MJBüttner HDunman PMRohde HCech NBFey PDHorswill AR (2014 Oct). Staphylococcus epidermidis agr quorum-sensing system: signal identification, cross talk, and importance in colonization. Journal of bacteriology. Guo HBaker SFMartínez-Sobrido LTopham DJ (2014 Oct). Induction of CD8 T cell heterologous protection by a single dose of single-cycle infectious influenza virus. Journal of virology. Batra RCharizanis KManchanda MMohan ALi MFinn DJGoodwin MZhang CSobczak KThornton CASwanson MS (2014 Sep 24). Loss of MBNL Leads to Disruption of Developmentally Regulated Alternative Polyadenylation in RNA-Mediated Disease. Molecular cell. Nogales ABaker SFOrtiz-Riaño EDewhurst STopham DJMartínez-Sobrido L (2014 Sep). Influenza A virus attenuation by codon deoptimization of the NS gene for vaccine development. Journal of virology. Kurosaki TLi WHoque MPopp MWErmolenko DNTian BMaquat LE (2014 Sep 1). A post-translational regulatory switch on UPF1 controls targeted mRNA degradation. Genes & development. Baker SFNogales AFinch CTuffy KMDomm WPerez DRTopham DJMartínez-Sobrido L (2014 Sep). Influenza A and B virus intertypic reassortment through compatible viral packaging signals. Journal of virology. Salter JDMorales GASmith HC (2014 Sep). Structural insights for HIV-1 therapeutic strategies targeting Vif. Trends in biochemical sciences. Zhang XWalker RCPhizicky EMMathews DH (2014 Aug 12). Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. Journal of chemical theory and computation. Guy MPYoung DLPayea MJZhang XKon YDean KMGrayhack EJMathews DHFields SPhizicky EM (2014 Aug 1). Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis. Genes & development. Karijolich JYu YT (2014 Aug). Therapeutic suppression of premature termination codons: mechanisms and clinical considerations (review). International journal of molecular medicine. Thornton CA (2014 Aug). Myotonic Dystrophy. Neurologic clinics. Takahashi MElbarbary RAWatanabe NGoto AKamiya DWatabe YUchiyama TNarita MTakahashi MTakahashi YIshihara NMiyazawa TYoshida TKawano MTamura MNashimoto M (2014 Jul). Screening of a heptamer-type sgRNA library for potential therapeutic agents against hematological malignancies. Leukemia research. Gleghorn MLMaquat LE (2014 Jul). 'Black sheep' that don't leave the double-stranded RNA-binding domain fold. Trends in biochemical sciences. Prohaska KMBennett RPSalter JDSmith HC (2014 Jul). The multifaceted roles of RNA binding in APOBEC cytidine deaminase functions. Wiley interdisciplinary reviews. RNA. Loerch SMaucuer AManceau VGreen MRKielkopf CL (2014 Jun 20). Cancer-relevant splicing factor CAPERα engages the essential splicing factor SF3b155 in a specific ternary complex. The Journal of biological chemistry. Heldenbrand HJanowski PAGiambaşu GGiese TJWedekind JEYork DM (2014 Jun 4). Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path. Journal of the American Chemical Society. Heatwole CBode RJohnson NDekdebrun JDilek NHeatwole MHilbert JELuebbe EMartens WMcdermott MPRothrock NThornton CVickrey BGVictorson DMoxley R (2014 Jun). Myotonic Dystrophy Health Index: initial evaluation of a disease-specific outcome measure. Muscle & nerve. Hoskins JWOfori LOChen CZKumar ASobczak KNakamori MSouthall NPatnaik SMarugan JJZheng WAustin CPDisney MDMiller BLThornton CA (2014 Jun 1). Lomofungin and dilomofungin: inhibitors of MBNL1-CUG RNA binding with distinct cellular effects. Nucleic acids research. Lindgren JKThomas VCOlson MEChaudhari SSNuxoll ASSchaeffer CRLindgren KEJones JZimmerman MCDunman PMBayles KWFey PD (2014 Jun). Arginine deiminase in Staphylococcus epidermidis functions to augment biofilm maturation through pH homeostasis. Journal of bacteriology. Bell RDLong XLin MBergmann JHNanda VCowan SLZhou QHan YSpector DLZheng DMiano JM (2014 Jun). Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. Arteriosclerosis, thrombosis, and vascular biology. Fisher EAMiano JM (2014 Apr 15). Don't judge books by their covers: vascular smooth muscle cells in arterial pathologies. Circulation. Eidem TMCoughlan ATowler MRDunman PMWren AW (2014 Apr). Drug-eluting cements for hard tissue repair: a comparative study using vancomycin and RNPA1000 to inhibit growth of Staphylococcus aureus. Journal of biomaterials applications. Moran YFredman DPraher DLi XZWee LMRentzsch FZamore PDTechnau USeitz H (2014 Apr). Cnidarian microRNAs frequently regulate targets by cleavage. Genome research. Popp MWMaquat LE (2014 Apr). Defective secretory-protein mRNAs take the RAPP. Trends in biochemical sciences. Ishiguro KKim JShibuya HHernández-Hernández ASuzuki AFukagawa TShioi GKiyonari HLi XCSchimenti JHöög CWatanabe Y (2014 Mar 15). Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes. Genes & development. Aytenfisu AHSpasic ASeetin MGSerafini JMathews DH (2014 Mar 11). Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA. Journal of chemical theory and computation. Domm WBrewer MBaker SFFeng CMartínez-Sobrido LTreanor JDewhurst S (2014 Mar). Use of bacteriophage particles displaying influenza virus hemagglutinin for the detection of hemagglutination-inhibition antibodies. Journal of virological methods. Ofori LOHilimire TABennett RPBrown NWSmith HCMiller BL (2014 Feb 13). High-affinity recognition of HIV-1 frameshift-stimulating RNA alters frameshifting in vitro and interferes with HIV-1 infectivity. Journal of medicinal chemistry. Marrero DPan QBarrett-Connor Ede Groot MZhang PPercy CFlorez HAckermann RMontez MRubin RR (2014 Feb). Impact of diagnosis of diabetes on health-related quality of life among high risk individuals: the Diabetes Prevention Program outcomes study. Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation. Pop CRouskin SIngolia NTHan LPhizicky EMWeissman JSKoller D (2014). Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Molecular systems biology. Hamilton BManzella ASchmidt KDiMarco VButler JS (2014). Analysis of non-typeable Haemophilous influenzae VapC1 mutations reveals structural features required for toxicity and flexibility in the active site. PloS one. Jacobs ACBlanchard CECatherman SCDunman PMMurata Y (2014). An ribonuclease T2 family protein modulates Acinetobacter baumannii abiotic surface colonization. PloS one. Hanses FRoux CDunman PMSalzberger BLee JC (2014). Staphylococcus aureus gene expression in a rat model of infective endocarditis. Genome medicine. Elbarbary RAMaquat LE (2014). Dodging two bullets with one dsRNA-binding protein. Cell cycle (Georgetown, Tex.). Popp MWMaquat LE (2014 Jan). The dharma of nonsense-mediated mRNA decay in mammalian cells. Molecules and cells. Belfort MMarraffini LMacfarlan TBoeke JSlotkin KMalik HMaquat L (2014). Mobile DNA: an evolving field. Mobile DNA. Ortiz-Riaño ENgo NDevito SEggink DMunger JShaw MLde la Torre JCMartínez-Sobrido L (2014 Jan). Inhibition of arenavirus by A3, a pyrimidine biosynthesis inhibitor. Journal of virology. Mathews DH (2014). Using the RNAstructure Software Package to Predict Conserved RNA Structures. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Mathews DH (2014). RNA Secondary Structure Analysis Using RNAstructure. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Shi FLong XHendershot AMiano JMSottile J (2014). Fibronectin matrix polymerization regulates smooth muscle cell phenotype through a Rac1 dependent mechanism. PloS one. Guy MPPhizicky EM (2014). Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification. RNA biology. Liberman JABogue JTJenkins JLSalim MWedekind JE (2014). ITC analysis of ligand binding to preQ₁ riboswitches. Methods in enzymology. Adachi HYu YT (2014). Purification of radiolabeled RNA products using denaturing gel electrophoresis. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]. Lim SJScott AXiong XPVahidpour SKarijolich JGuo DPei SYu YTZhou RLi WX (2014). Requirement for CRIF1 in RNA interference and Dicer-2 stability. RNA biology. Yu YTMeier UT (2014). RNA-guided isomerization of uridine to pseudouridine--pseudouridylation. RNA biology. Huang QZhou XHu QLei HFang ZYao PWang AE (2014 Jan 01). "A bridge between the aminoacylation and editing domains of leucyl-tRNA synthetase is crucial for its synthetic activity." RNA. Brilot AFKorostelev AAErmolenko DNGrigorieff N (2013 Dec 24). Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Proceedings of the National Academy of Sciences of the United States of America. Nakamori MSobczak KPuwanant AWelle SEichinger KPandya SDekdebrun JHeatwole CRMcDermott MPChen TCline MTawil ROsborne RJWheeler TMSwanson MSMoxley RTThornton CA (2013 Dec). Splicing biomarkers of disease severity in myotonic dystrophy. Annals of neurology. Axford MMWang YHNakamori MZannis-Hadjopoulos MThornton CAPearson CE (2013 Dec). Detection of slipped-DNAs at the trinucleotide repeats of the myotonic dystrophy type I disease locus in patient tissues. PLoS genetics. Scherr TDRoux CMHanke MLAngle ADunman PMKielian T (2013 Dec). Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells. Infection and immunity. Suddala KCRinaldi AJFeng JMustoe AMEichhorn CDLiberman JAWedekind JEAl-Hashimi HMBrooks CLWalter NG (2013 Dec). Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic acids research. Coonrod LANakamori MWang WCarrell SHilton CLBodner MJSiboni RBDocter AGHaley MMThornton CABerglund JA (2013 Nov 15). Reducing levels of toxic RNA with small molecules. ACS chemical biology. Bauman JDPatel DBaker SFVijayan RSXiang AParhi AKMartínez-Sobrido LLaVoie EJDas KArnold E (2013 Nov 15). Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors. ACS chemical biology. Azpurua JKe ZChen IXZhang QErmolenko DNZhang ZDGorbunova VSeluanov A (2013 Oct 22). Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage. Proceedings of the National Academy of Sciences of the United States of America. Rzuczek SGGao YTang ZZThornton CAKodadek TDisney MD (2013 Oct 18). Features of modularly assembled compounds that impart bioactivity against an RNA target. ACS chemical biology. Gong CTang YMaquat LE (2013 Oct). mRNA-mRNA duplexes that autoelicit Staufen1-mediated mRNA decay. Nature structural & molecular biology. Long XMiano JM (2013 Oct). Myocardin: new therapeutic agent in vascular disease? Arteriosclerosis, thrombosis, and vascular biology. Can MKrucinska JZoppellaro GAndersen NHWedekind JEHersleth HPAndersson KKBren KL (2013 Sep 23). Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure. Chembiochem : a European journal of chemical biology. Letzring DPWolf ASBrule CEGrayhack EJ (2013 Sep). Translation of CGA codon repeats in yeast involves quality control components and ribosomal protein L1. RNA (New York, N.Y.). Imamura MSugino YLong XSlivano OJNishikawa NYoshimura NMiano JM (2013 Sep). Myocardin and microRNA-1 modulate bladder activity through connexin 43 expression during post-natal development. Journal of cellular physiology. Baker SFGuo HAlbrecht RAGarcía-Sastre ATopham DJMartínez-Sobrido L (2013 Aug). Protection against lethal influenza with a viral mimic. Journal of virology. Fernández ISNg CLKelley ACWu GYu YTRamakrishnan V (2013 Aug 01). Unusual base pairing during the decoding of a stop codon by the ribosome. Nature.