URMC / Center for RNA Biology / Publications Publications Mathews DHCasadio RSternberg MJE Computational Resources for Molecular Biology 2023.; Journal of molecular biology. 2023 May 25. Das ABao CErmolenko DN Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes.; bioRxiv : the preprint server for biology. 2023 May 09. Zhang HZhang LLin AXu CLi ZLiu KLiu BMa XZhao FJiang HChen CShen HLi HMathews DHZhang YHuang L Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity.; Nature. 2023 May 02. Mirska BWoźniak TLorent DRuszkowska APeterson JMMoss WNMathews DHKierzek RKierzek E In vivo secondary structural analysis of Influenza A virus genomic RNA.; Cellular and molecular life sciences : CMLS; Vol 80(5), pp. 136. 2023 May 02. VanderWal ARPark JUPolevoda BNicosia JKMolina Vargas AMKellogg EHO'Connell MR Csx28 is a membrane pore that enhances CRISPR-Cas13b-dependent antiphage defense.; Science (New York, N.Y.); Vol 380(6643), pp. 410-415. 2023 Apr 27. Zhou TGilliam NJLi SSpandau SOsborn RMConnor SAnderson CSMariani TJThakar JDewhurst SMathews DHHuang LSun Y Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection.; mBio. 2023 Apr 19. Phizicky EMHopper AK The Life and Times of a tRNA.; RNA (New York, N.Y.). 2023 Apr 13. Das AAdiletta NErmolenko DN Interplay between Inter-Subunit Rotation of the Ribosome and Binding of Translational GTPases.; International journal of molecular sciences; Vol 24(8). 2023 Apr 07. Wedekind JE RNA in the loop: Probing T-loop/T-loop receptor interactions as mediators of long-range RNA contacts that influence gene regulation.; Journal of molecular biology. 2023 Apr 06. Tepe BMacke ELNiceta MWeisz Hubshman MKanca OSchultz-Rogers LZarate YASchaefer GBGranadillo De Luque JLWegner DJCogne BGilbert-Dussardier BLe Guillou XWagner EJPais LSNeil JEMochida GHWalsh CAMagal NDrasinover VShohat MSchwab TSchmitz CClark KFine ALanpher BGavrilova RBlanc PBurglen LAfenjar ASteel DKurian MAPrabhakar PGößwein SDi Donato NBertini ESWangler MFYamamoto STartaglia MKlee EWBellen HJ Bi-allelic variants in INTS11 are associated with a complex neurological disorder.; American journal of human genetics. 2023 Apr 04. Thornton CAMoxley RTEichinger KHeatwole CMignon LArnold WDAshizawa TDay JWDent GTanner MKDuong TGreene EPHerbelin LJohnson NEKing WKissel JTLeung DGLott DJNorris DAPucillo EMSchell WStatland JMStinson NSubramony SHXia SBishop KMBennett CF Antisense oligonucleotide targeting DMPK in patients with myotonic dystrophy type 1: a multicentre, randomised, dose-escalation, placebo-controlled, phase 1/2a trial.; The Lancet. Neurology; Vol 22(3), pp. 218-228. 2023 Mar. Mello SSFlowers BMMazur PKLee JJMüller FDenny SKFerreira SHanson KKim SKGreenleaf WJWood LDAttardi LD Multifaceted role for p53 in pancreatic cancer suppression.; Proceedings of the National Academy of Sciences of the United States of America; Vol 120(10), pp. e2211937120. 2023 Feb 27. de Prisco NFord CElrod NDLee WTang LCHuang KLLin AJi PJonnakuti VSBoyle LCabaj MBotta SÕunap KReinson KWojcik MHRosenfeld JABi WTveten KPrescott TGerstner TSchroeder AFong CTGeorge-Abraham JKBuchanan CAHanson-Khan ABernstein JANella AAChung WKBrandt VJovanovic MTargoff KLYalamanchili HKWagner EJGennarino VA Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites.; Science advances; Vol 9(7), pp. eade4814. 2023 Feb 17. Schroeder GMAkinyemi OMalik JFocht CMPritchett EMBaker CDMcSally JPJenkins JLMathews DHWedekind JE A riboswitch separated from its ribosome-binding site still regulates translation.; Nucleic acids research. 2023 Feb 10. Adachi HPan YHe XChen JLKlein BPlatenburg GMorais PBoutz PYu YT Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes.; Molecular cell. 2023 Feb 03. Cui YArnold FJPeng FWang DLi JSMichels SWagner EJLa Spada ARLi W Alternative polyadenylation transcriptome-wide association study identifies APA-linked susceptibility genes in brain disorders.; Nature communications; Vol 14(1), pp. 583. 2023 Feb 03. Jonnakuti VSWagner EJMaletić-Savatić MLiu ZYalamanchili HK PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data.; bioRxiv : the preprint server for biology. 2023 Jan 24. Rambout XCho HBlanc RLyu QMiano JMChakkalakal JVNelson GMYalamanchili HKAdelman KMaquat LE PGC-1α senses the CBC of pre-mRNA to dictate the fate of promoter-proximally paused RNAPII.; Molecular cell; Vol 83(2), pp. 186-202.e11. 2023 Jan 19. Allaire NEGriesenbach UKerem BLueck JDStanleigh NOren YS Gene, RNA, and ASO-based therapeutic approaches in Cystic Fibrosis.; Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society. 2023 Jan 17. Liu SBaeg GHYang YGoh FGBao HWagner EJYang XCai Y The Integrator complex desensitizes cellular response to TGF-β/BMP signaling.; Cell reports; Vol 42(1), pp. 112007. 2023 Jan 14. Wagner EJTong LAdelman K Integrator is a global promoter-proximal termination complex.; Molecular cell. 2023 Jan 04. Cavender CESchroeder GMMathews DHWedekind JE Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model.; Methods in molecular biology (Clifton, N.J.); Vol 2568, pp. 53-73. 2023. Zhang HZhang LLiu KLi SMathews DHHuang L Linear-Time Algorithms for RNA Structure Prediction.; Methods in molecular biology (Clifton, N.J.); Vol 2586, pp. 15-34. 2023. Adachi HChen JLYin QMorais PYu YT In Vitro Reconstitution of Pseudouridylation Catalyzed by Human Box H/ACA Ribonucleoprotein Particles.; Methods in molecular biology (Clifton, N.J.); Vol 2666, pp. 177-191. 2023. Lin MHJensen MKElrod NDHuang KLWelle KAWagner EJTong L Inositol hexakisphosphate is required for Integrator function.; Nature communications; Vol 13(1), pp. 5742. 2022 Sep 30. Guo BFriedland SCAlexander WMyers JAWang WO'Dell MRGetman MWhitney-Miller CLAgostini-Vulaj DHuber ARMello SSVertino PMLand HKSteiner LAHezel AF Arid1a mutation suppresses TGF-β signaling and induces cholangiocarcinoma.; Cell reports; Vol 40(9), pp. 111253. 2022 Aug 30. Hogestyn JMSalois GXie LApa CYoungyunpipatkul JPröschel CMayer-Pröschel M Expression of the human herpesvirus 6A latency-associated transcript U94A impairs cytoskeletal functions in human neural cells.; Molecular and cellular neurosciences. 2022 Aug 30. Joseph Davis Burris BMoises Molina Vargas APark BJO'Connell MR Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13.; Methods (San Diego, Calif.). 2022 Aug 17. Tasak MPhizicky EM Initiator tRNA lacking 1-methyladenosine is targeted by the rapid tRNA decay path way in evolutionarily distant yeast species.; PLoS genetics; Vol 18(7), pp. e1010215. 2022 Jul 28. Hamel JIMcDermott MPHilbert JEMartens WBLuebbe ETawil RMoxley RTThornton CA Milestones of progression in myotonic dystrophy type 1 and type 2.; Muscle & nerve. 2022 Jul 01. Galardi JWBela VNJeffery NHe XGlasser ELoerch SJenkins JLPulvino MJBoutz PLKielkopf CL A UHM - ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing.; The Journal of biological chemistry. 2022 Jun 30. Szikszai MWise MDatta AWard MMathews DH Deep learning models for RNA secondary structure prediction (probably) do not generalise across families.; Bioinformatics (Oxford, England). 2022 Jun 24. Ko WPorter JJSipple MTEdwards KMLueck JD Efficient suppression of endogenous CFTR nonsense mutations using anticodon-engineered transfer RNAs.; Molecular therapy. Nucleic acids; Vol 28. 2022 Jun 14. Kumar JLackey LWaldern JMDey AMustoe AMWeeks KMathews DHLaederach A Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing.; eLife; Vol 11. 2022 Jun 13. Subbaiah KCVWu JTang WHWYao P FAM114A1 influences cardiac pathological remodeling by regulating angiotensin II signaling.; JCI insight. 2022 Jun 07. Tseng VCollum SDAllawzi ACrotty KYeligar STrammell ARyan Smith MKang BYSutliff RLIngram JLJyothula SSSKThandavarayan RAHuang HJNozik ESWagner EJMichael Hart CKarmouty-Quintana H 3'UTR shortening of HAS2 promotes hyaluronan hyper-synthesis and bioenergetic dysfunction in pulmonary hypertension.; Matrix biology : journal of the International Society for Matrix Biology; Vol 111, pp. 53-75. 2022 Jun 04. Cho HAbshire ETPopp MWPröschel CSchwartz JLYeo GWMaquat LE AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay.; Molecular cell. 2022 Jun 03. Wilson CMertens TCShivshankar PBi WCollum SDWareing NKo JWeng TNaikawadi RPWolters PJMaire PJyothula SSThandavarayan RARen DElrod NDWagner EJHuang HJDickey BFFord HLKarmouty-Quintana H Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis.; JCI insight; Vol 7(10). 2022 May 23. Szabat MProchota MKierzek RKierzek EMathews DH A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine.; Journal of molecular biology. 2022 May 16. Mackenzie SJHamel JThornton CA Benefits of aerobic exercise in myotonic dystrophy type 1.; The Journal of clinical investigation; Vol 132(10). 2022 May 16. Casadio RMathews DHSternberg MJE Computational Resources for Molecular Biology 2022.; Journal of molecular biology. 2022 May 12. Maquat LJohnson RValadkhan SCarninci P Lessons from the functional characterization of lncRNAs: introduction to mammalian genome special issue.; Mammalian genome : official journal of the International Mammalian Genome Society. 2022 May 09. Glasser EMaji DBiancon GPuthenpeedikakkal AMKCavender CETebaldi TJenkins JLMathews DHHalene SKielkopf CL Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.; Nucleic acids research. 2022 May 07. Zuber JSchroeder SJSun HTurner DHMathews DH Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.; Nucleic acids research. 2022 May 07. Mei JAJohnson WKinn BLaskey ENolin LBhamare PStalker CDunman PMWozniak RAF Antimicrobial Activity of a Triple Antibiotic Combination Toward Ocular Pseudomonas aeruginosa Clinical Isolates.; Translational vision science & technology; Vol 11(5). 2022 May 02. Funk HMDiVita DJSizemore HEWehrle KMiller CLWFraley MEMullins AKGuy ARPhizicky EMGuy MP Identification of a Trm732 Motif Required for 2'-O-methylation of the tRNA Anticodon Loop by Trm7.; ACS omega; Vol 7(16). 2022 Apr 26. Hamel JCreigh PDDekdebrun JEichinger KThornton CA Remote Assessment of Myotonic Dystrophy Type 1: A Feasibility Study.; Muscle & nerve. 2022 Apr 15. Walker EJBettinger JQWelle KAHryhorenko JRMolina Vargas AMO'Connell MRGhaemmaghami S Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues.; The Journal of biological chemistry. 2022 Mar 25. Kierzek EZhang XWatson RMKennedy SDSzabat MKierzek RMathews DH Secondary structure prediction for RNA sequences including N6-methyladenosine.; Nature communications; Vol 13(1). 2022 Mar 11. Szutkowska BWieczorek KKierzek RZmora PPeterson JMMoss WNMathews DHKierzek E Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment.; International journal of molecular sciences; Vol 23(5). 2022 Feb 23. Bao CZhu MNykonchuk IWakabayashi HMathews DHErmolenko DN Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.; Nature communications; Vol 13(1). 2022 Feb 21. Deutsch GKHagerman KASampson JDent GDekdebrun JParker DMThornton CAHeatwole CRSubramony SHMankodi AKAshizawa TStatland JMArnold WDMoxley RTDay JW Brief assessment of cognitive function in myotonic dystrophy: multicenter longitudinal study using computer-assisted evaluation.; Muscle & nerve. 2022 Feb 18. Broly MPolevoda BVAwayda KMTong NLentini JBesnard TDeb WO'Rourke DBaptista JEllard SAlmannai MHashem MAbdulwahab FShamseldin HAl-Tala SAlkuraya FSLeon Avan Loon RLEFerlini ASanchini MBigoni SCiorba Avan Bokhoven HIqbal ZAl-Maawali AAl-Murshedi FGanesh AAl-Mamari WLim SCPais LSBrown NRiazuddin SBézieau SFu DIsidor BCogné BO'Connell MR THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder.; American journal of human genetics. 2022 Feb 11. LaForce GRFarr JSLiu JAkesson CGumus EPinkard OMiranda HCJohnson KSweet TJJi PLin AColler JPhilippidou PWagner EJSchaffer AE Suppression of premature transcription termination leads to reduced mRNA isoform diversity and neurodegeneration.; Neuron. 2022 Feb 04. Stein CBField ARMimoso CAZhao CHuang KLWagner EJAdelman K Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci.; Molecular cell. 2022 Jan 28. Zhang HLi SZhang LMathews DHHuang L LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2.; Nucleic acids research. 2022 Jan 18. Dulmovits BMTang YPapoin JHe MLi JYang HAddorisio MEKennedy LKhan MBrindley ECAshley RJAckert-Bicknell CHale JKurita RKNakamura YDiamond BBarnes BJHermine OGallagher PGSteiner LALipton JMTaylor NMohandas NAndersson UAl-Abed YTracey KJBlanc L HMGB1-Mediated Restriction of EPO Signaling Contributes to Anemia of Inflammation.; Blood. 2022 Jan 18. Mascibroda LGShboul MElrod NDColleaux LHamamy HHuang KLPeart NSingh MKLee HMerriman BJodoin JNSitaram PLee LAFathalla RAl-Rawashdeh BAbabneh OEl-Khateeb MEscande-Beillard NNelson SFWu YTong LKenney LJRoy SRussell WKAmiel JReversade BWagner EJ INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex.; Nature communications; Vol 13(1), pp. 6054. 2022 Jan 13. Schroeder GMCavender CEBlau MEJenkins JLMathews DHWedekind JE A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.; Nature communications; Vol 13(1). 2022 Jan 11. Alkhunaizi EMartin NJelin ACRosner MBailey DJSteiner LALakhani SJi WKatzman PJForster KRJarinova OShannon PChitayat D Fetal akinesia deformation sequence syndrome associated with recessive TTN variants.; American journal of medical genetics. Part A. 2022 Jan 10. Lai WCZhu MBelinite MBallard GMathews DHErmolenko DN Intrinsically unstructured sequences in the mRNA 3' UTR reduce the ability of poly(A) tail to enhance translation.; Journal of molecular biology. 2022 Jan 08. Young MWalsh DJMasters EGondil VSLaskey EKlaczko MAwad HMcGrath JSchwarz EMMelander CDunman PM Identification of Staphylococcus aureus Penicillin Binding Protein 4 (PBP4) Inhibitors.; Antibiotics (Basel, Switzerland); Vol 11(10). 2022 Jan 04. Kurosaki TMitsutomi SHewko AAkimitsu NMaquat LE Integrative omics indicate FMRP sequesters mRNA from translation and deadenylation in human neuronal cells.; Molecular cell. 2022 Jan 01. Anderson KMAnderson DM LncRNAs at the heart of development and disease; . 2022 Jan 01. Houston LPlatten EMConnelly SMWang JGrayhack EJ Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by Integrated Stress Response regulators Gcn1 and Gcn20.; RNA (New York, N.Y.). 2021 Dec 16. Cable JHeard EHirose TPrasanth KVChen LLHenninger JEQuinodoz SASpector DLDiermeier SDPorman AMKumar DFeinberg MWShen XUnfried JPJohnson RChen CKWilusz JELempradl AMcGeary SEWahba LPyle AMHargrove AESimon MDMarcia MPrzanowska RKChang HYJaffrey SRContreras LMChen QShi JMendell JTHe LSong ERinn JLLalwani MKKalem MCChuong EBMaquat LELiu X Noncoding RNAs: biology and applications-a Keystone Symposia report.; Annals of the New York Academy of Sciences. 2021 Nov 17. Kurosaki TSakano HPröschel CWheeler JHewko AMaquat LE NMD abnormalities during brain development in the Fmr1-knockout mouse model of fragile X syndrome.; Genome biology; Vol 22(1). 2021 Nov 16. Chavali SSMali SMBonn RSaseendran ABennett RPSmith HCFasan RWedekind JE Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells.; The Journal of biological chemistry. 2021 Nov 09. Cao JVerma SKJaworski EMohan SNagasawa CKRayavara KSooter AMiller SNHolcomb RJPowell MJJi PElrod NDYildirim EWagner EJPopov VGarg NJRouth ALKuyumcu-Martinez MN RBFOX2 is critical for maintaining alternative polyadenylation patterns and mitochondrial health in rat myoblasts.; Cell reports; Vol 37(5). 2021 Nov 02. Elahi AEmerson JRudlong JKeillor JWSalois GVisca AGirardi PJohnson GVWPröschel C Deletion or Inhibition of Astrocytic Transglutaminase 2 Promotes Functional Recovery after Spinal Cord Injury.; Cells; Vol 10(11). 2021 Oct 29. Bao CErmolenko DN Ribosome as a Translocase and Helicase.; Biochemistry. Biokhimiia; Vol 86(8). 2021 Aug. Li LHuang KLGao YCui YWang GElrod NDLi YChen YEJi PPeng FRussell WKWagner EJLi W An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability.; Nature genetics; Vol 53(7). 2021 Jul. Murphy ZMurphy KMyers JAGetman MRCouch TSchulz VLezon-Geyda KPalumbo CYan HNarla MGallagher PGSteiner LA Regulation of RNA Polymerase II Activity is Essential for Terminal Erythroid Maturation.; Blood. 2021 Jun 01. Adachi HHengesbach MYu YTMorais P From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies.; Biomedicines; Vol 9(5). 2021 May 14. Yang HKundra SChojnacki MLiu KFuse MAAbouelhassan YKallifidas DZhang PHuang GJin SDing YLuesch HRohde KHDunman PMLemos JAHuigens RW A Modular Synthetic Route Involving N-Aryl-2-nitrosoaniline Intermediates Leads to a New Series of 3-Substituted Halogenated Phenazine Antibacterial Agents.; Journal of medicinal chemistry. 2021 Apr 21. Suigo LChojnacki MZanotto CSebastián-Pérez VMorghen CGCasiraghi ADunman PMValoti EStraniero V Staphylococcus aureus RnpA Inhibitors: Computational-Guided Design, Synthesis and Initial Biological Evaluation.; Antibiotics (Basel, Switzerland); Vol 10(4). 2021 Apr 14. Enwerem IIIElrod NDChang CTLin AJi PBohn JALevdansky YWagner EJValkov EGoldstrohm AC Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome.; RNA (New York, N.Y.); Vol 27(4). 2021 Apr. Chojnacki MCao XFlaherty DPDunman PM Optimization of 2-Acylaminocycloalkylthiophene Derivatives for Activity against Staphylococcus aureus RnpA.; Antibiotics (Basel, Switzerland); Vol 10(4). 2021 Mar 31. Chojnacki MDobrotka COsborn RJohnson WYoung MMeyer BLaskey EWozniak RAFDewhurst SDunman PM Evaluating the Antimicrobial Properties of Commercial Hand Sanitizers.; mSphere; Vol 6(2). 2021 Mar 03. Srivastava YBonn-Breach RChavali SSLippa GMJenkins JLWedekind JE Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.; Crystals; Vol 11(3). 2021 Mar. Chatrikhi RFeeney CFPulvino MJAlachouzos GMacRae AJFalls ZRai SBrennessel WWJenkins JLWalter MJGraubert TASamudrala RJurica MSFrontier AJKielkopf CL A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex.; Cell chemical biology. 2021 Feb 26. Porter JJHeil CSLueck JD Therapeutic promise of engineered nonsense suppressor tRNAs.; Wiley interdisciplinary reviews. RNA. 2021 Feb 10. Li SZhang HZhang LLiu KLiu BMathews DHHuang L LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2.; Proceedings of the National Academy of Sciences of the United States of America; Vol 118(52). 2021 Jan 28. Tanner MKTang ZThornton CA Targeted splice sequencing reveals RNA toxicity and therapeutic response in myotonic dystrophy.; Nucleic acids research. 2021 Jan 27. Otero BAPoukalov KHildebrandt RPThornton CAJinnai KFujimura HKimura THagerman KASampson JBDay JWWang ET Transcriptome alterations in myotonic dystrophy frontal cortex.; Cell reports; Vol 34(3). 2021 Jan 19. Scherzi TD'Ambrosio EADaher SSGrimes CLDunman PMAndrade RB Staphylococcus aureus resistance to albocycline can be achieved by mutations that alter cellular NAD/PH pools.; Bioorganic & medicinal chemistry; Vol 32. 2021 Jan 07. Lin AJi PNiu XZhao XChen YLiu WLiu YFan WSun YMiao CZhang STan WLin DWagner EJWu C CstF64-Induced Shortening of the BID 3'UTR Promotes Esophageal Squamous Cell Carcinoma Progression by Disrupting ceRNA Cross-talk with ZFP36L2.; Cancer research; Vol 81(22), pp. 5638-5651. 2021 Jan 04. Morais PAdachi HYu YT The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines.; Frontiers in cell and developmental biology; Vol 9. 2021. Han LMarcus EPhizicky EM A semi-quantitative pull-down assay to study tRNA substrate specificity of modification enzymes.; Methods in enzymology; Vol 658. 2021. Yuan FHankey WWagner EJLi WWang Q Alternative polyadenylation of mRNA and its role in cancer.; Genes & diseases; Vol 8(1). 2021 Jan. Jensen MKElrod NDYalamanchili HKJi PLin ALiu ZWagner EJ Application and design considerations for 3'-end sequencing using click-chemistry.; Methods in enzymology; Vol 655. 2021. Yalamanchili HKElrod NDJensen MKJi PLin AWagner EJLiu Z A computational pipeline to infer alternative poly-adenylation from 3' sequencing data.; Methods in enzymology; Vol 655. 2021. Anderson DMAnderson KMNelson BRMcAnally JRBezprozvannaya SShelton JMBassel-Duby ROlson EN A myocardin-adjacent lncRNA balances SRF-dependent gene transcription in the heart.; Genes & Development; Vol 35, pp. 835-840. 2021 Jan 01. Kurosaki TImamachi NPröschel CMitsutomi SNagao RAkimitsu NMaquat LE Loss of the fragile X syndrome protein FMRP results in misregulation of nonsense-mediated mRNA decay.; Nature cell biology; Vol 23(1). 2021 Jan. Morais PAdachi HYu YT Spliceosomal snRNA Epitranscriptomics.; Frontiers in genetics; Vol 12. 2021. Johnson WLSohn MBTaffner SChatterjee PDunman PMPecora NWozniak RAF Genomics of Staphylococcus aureus ocular isolates.; PloS one; Vol 16(5). 2021. Kayedkhordeh MYamagami RBevilacqua PCMathews DH Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots.; Methods in molecular biology (Clifton, N.J.); Vol 2167. 2021. Zhang HZhang LLi SMathews DHHuang L LinearSampling: Linear-Time Stochastic Sampling of RNA Secondary Structure with Applications to SARS-CoV-2.; bioRxiv : the preprint server for biology. 2020 Dec 29. Wu JVenkata Subbaiah KCJiang FHedaya OMohan AYang TWelle KGhaemmaghami STang WHWSmall EYan CYao P MicroRNA-574 regulates FAM210A expression and influences pathological cardiac remodeling.; EMBO molecular medicine. 2020 Dec 28. Lyu QRYao PMiano JM Generating a CRISPR knockout mouse through a strong premature termination codon: a cautionary tale.; Journal of biomedical research; Vol 35(2). 2020 Dec 25. Maji DGlasser EHenderson SGalardi JPulvino MJJenkins JLKielkopf CL Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.; The Journal of biological chemistry; Vol 295(50). 2020 Dec 11. Chavali SSMali SMJenkins JLFasan RWedekind JE Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.; The Journal of biological chemistry; Vol 295(49). 2020 Dec 04. Chavali SSCavender CEMathews DHWedekind JE Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove.; Journal of the American Chemical Society. 2020 Nov 10. Sparks RPArango ASJenkins JLGuida WCTajkhorshid ESparks CESparks JDFratti RA An Allosteric Binding Site on Sortilin Regulates the Trafficking of VLDL, PCSK9, and LDLR in Hepatocytes.; Biochemistry. 2020 Nov 05. Bieging-Rolett KTKaiser AMMorgens DWBoutelle AMSeoane JAVan Nostrand ELZhu CHoulihan SLMello SSYee BAMcClendon JPierce SEWinters IPWang MConnolly AJLowe SWCurtis CYeo GWWinslow MMBassik MCAttardi LD Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.; Molecular cell; Vol 80(3). 2020 Nov 05. Angelbello AJBenhamou RIRzuczek SGChoudhary STang ZChen JLRoy MWang KWYildirim IJun ASThornton CADisney MD A Small Molecule that Binds an RNA Repeat Expansion Stimulates Its Decay via the Exosome Complex.; Cell chemical biology. 2020 Nov 05. Valente LJTarangelo ALi AMNaciri MRaj NBoutelle AMLi YMello SSBieging-Rolett KDeBerardinis RJYe JDixon SJAttardi LD p53 deficiency triggers dysregulation of diverse cellular processes in physiological oxygen.; The Journal of cell biology; Vol 219(11). 2020 Nov 02. Daher SSFranklin KPScherzi TDunman PMAndrade RB Synthesis and biological evaluation of semi-synthetic albocycline analogs.; Bioorganic & medicinal chemistry letters; Vol 30(21). 2020 Nov 01. Murphy ZCGetman MRMyers JAVillar KNBLeshen EKurita RNakamura YSteiner LA Codanin-1 Mutations Engineered in Human Erythroid Cells Demonstrate Role of CDAN1 in Terminal Erythroid Maturation.; Experimental hematology. 2020 Oct 16. Chavali SSMali SMJenkins JLFasan RWedekind JE Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.; The Journal of biological chemistry. 2020 Oct 13. Heatwole CLuebbe ERosero SEichinger KMartens WHilbert JDekdebrun JDilek NZizzi CJohnson NPuwanant ATawil RSchifitto GBeck CARicheson JFZareba WThornton CMcDermott MPMoxley R Mexiletine in myotonic dystrophy type-1: A randomized, double-blind, placebo-controlled trial.; Neurology. 2020 Oct 12. Maji DGlasser EHenderson SGalardi JPulvino MJJenkins JLKielkopf CL Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.; The Journal of biological chemistry. 2020 Oct 05. Rambout XMaquat LE NCBP3: A Multifaceted Adaptive Regulator of Gene Expression.; Trends in biochemical sciences. 2020 Oct 05. Huang JSachdeva MXu ERobinson TJLuo LMa YWilliams NTLopez OCervia LDYuan FQin XZhang DOwzar KGokgoz NSeto AOkada TSinger SAndrulis ILWunder JSLazar AJRubin BPPipho KMello SSGiudice JKirsch DG The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways.; Molecular cancer research : MCR; Vol 18(10). 2020 Oct. Chojnacki MCao XYoung MFritz RNDunman PMFlaherty DP Optimization of 4-Substituted Benzenesulfonamide Scaffold To Reverse Acinetobacter baumannii Serum-Adaptive Efflux Associated Antibiotic Tolerance.; ChemMedChem; Vol 15(18). 2020 Sep 16. Noble MPröschel C The many roles of C1q.; eLife; Vol 9. 2020 Sep 14. Chen CAStrouz KHuang KLShyu AB Tob2 phosphorylation regulates global mRNA turnover to reshape transcriptome and impact cell proliferation.; RNA (New York, N.Y.); Vol 26(9). 2020 Sep. Rambout XMaquat LE The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing.; Genes & development; Vol 34(17-18). 2020 Sep 01. De Zoysa TPhizicky EM Hypomodified tRNA in evolutionarily distant yeasts can trigger rapid tRNA decay to activate the general amino acid control response, but with different consequences.; PLoS genetics; Vol 16(8). 2020 Aug 25. Zheng DCho HWang WRambout XTian BMaquat LE 3'READS+RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association.; RNA (New York, N.Y.). 2020 Aug 12. Popp MWCho HMaquat LE Viral subversion of nonsense-mediated mRNA decay.; RNA (New York, N.Y.). 2020 Jul 22. Yalamanchili HKAlcott CEJi PWagner EJZoghbi HYLiu Z PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3'Seq data using vector projections and non-negative matrix factorization.; Nucleic acids research; Vol 48(12). 2020 Jul 09. Wu JSubbaiah KCVXie LHJiang FKhor ESMickelsen DMMyers JRTang WWYao P Glutamyl-Prolyl-tRNA Synthetase Regulates Proline-Rich Pro-fibrotic Protein Synthesis During Cardiac Fibrosis.; Circulation research. 2020 Jul 01. Zhang HZhang LMathews DHHuang L LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities.; Bioinformatics (Oxford, England); Vol 36(Supplement_1). 2020 Jul 01. 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