URMC / Center for RNA Biology / Publications Publications Zhu MMathews DH Sequence Design Using RNAstructure.; Methods in molecular biology (Clifton, N.J.); Vol 2847, pp. 17-31. 2025. Maji DJenkins JLBoutz PLKielkopf CL Recurrent Neurodevelopmentally Associated Variants of the Pre-mRNA Splicing Factor U2AF2 Alter RNA Binding Affinities and Interactions.; Biochemistry. 2024 Oct 10. Oberstrass LTants JNLichtenthaeler CAli SEKoch LMathews DHSchlundt AWeigand J Comprehensive Profiling of Roquin Binding Preferences for RNA Stem-Loops.; Angewandte Chemie (International ed. in English). 2024 Sep 30. Casadio RMathews DHSternberg MJE Computational Resources for Molecular Biology 2024.; Journal of molecular biology. 2024 Aug 06. Thalalla Gamage SKhoogar RHowpay Manage SCrawford MCGeorgeson JPolevoda BVSanders CLee KANance KDIyer VKustanovich APerez MThu CTNance SRAmin RMiller CNHolewinski RJMeyer TKoparde VYang AJailwala PNguyen JTAndresson THunter KGu SMock BAEdmondson EFDifilippantonio SChari RSchwartz SO'Connell MRWu CCMeier JL Transfer RNA acetylation regulates in vivo mammalian stress signaling.; bioRxiv : the preprint server for biology. 2024 Jul 28. Franchini LPorter JJLueck JDOrlandi C Gz Enhanced Signal Transduction assaY (G Z ESTY) for GPCR deorphanization.; bioRxiv : the preprint server for biology. 2024 Jul 26. Lin MHJensen MKElrod NDChu HFHaseley MBeam ACHuang KLChiang WRussell WKWilliams KPröschel CWagner EJTong L Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.; Molecular cell. 2024 Jul 08. Malik AZhang LGautam MDai NLi SZhang HMathews DHHuang L LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments.; Journal of molecular biology. 2024 Jul 04. Morais PZhang RYu YT Therapeutic Nonsense Suppression Modalities: From Small Molecules to Nucleic Acid-Based Approaches.; Biomedicines; Vol 12(6). 2024 Jun 10. Gondil VSButman HSYoung MWalsh DJNarkhede YZeiler MJCrow AHCarpenter MEMardikar AMelander RJWiest ODunman PMMelander C Development of phenyl-urea-based small molecules that target penicillin-binding protein 4.; Chemical biology & drug design; Vol 103(6), pp. e14569. 2024 Jun. Porter JJLueck JD A cystic fibrosis gene editing approach that is on target.; Molecular therapy. Nucleic acids; Vol 35(2), pp. 102197. 2024 May 08. Pan YAdachi HHe XChen JLYu YTBoutz PL Updated Pseudo-seq Protocol for Transcriptome-Wide Detection of Pseudouridines.; Bio-protocol; Vol 14(9), pp. e4985. 2024 May 05. Rambout XMaquat LE Nuclear mRNA decay: regulatory networks that control gene expression.; Nature reviews. Genetics. 2024 Apr 18. Haugen RJBarnier CElrod NDLuo HJensen MKJi PSmibert CALipshitz HDWagner EJFreddolino PLGoldstrohm AC Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex.; RNA (New York, N.Y.). 2024 Apr 16. Gowtham LWozniak RAFDunman PMSheba EGarg PJoseph J Efficacy of a Novel Antibiotic Drug Combination Toward Multidrug-Resistant Ocular Pathogens.; Cornea. 2024 Mar 26. Mittal ATurner DHMathews DH NNDB: An expanded database of nearest neighbor parameters for predicting stability of nucleic acid secondary structures.; Journal of molecular biology. 2024 Mar 22. McGrath KEKoniski ADMurphy KGetman MAn HHSchulz VPKim ARZhang BSchofield TLPapoin JBlanc LKingsley PDWesthoff CMGallagher PGChou STSteiner LAPalis J BMI1 regulates human erythroid self-renewal through both gene repression and gene activation.; bioRxiv : the preprint server for biology. 2024 Feb 06. Jonnakuti VSWagner EJMaletić-Savatić MLiu ZYalamanchili HK PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.; Cell reports methods. 2024 Feb 03. Alessandrini FWright MKurosaki TMaquat LEKiskinis E ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3'UTR Length.; bioRxiv : the preprint server for biology. 2024 Feb 02. De Zoysa THauke ACIyer NRMarcus EOstrowski SMStegemann FErmolenko DNFay JCPhizicky EM A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; PLoS genetics; Vol 20(1), pp. e1011146. 2024 Jan 31. Kurosaki TRambout XMaquat LE FMRP-mediated spatial regulation of physiologic NMD targets in neuronal cells.; Genome biology; Vol 25(1), pp. 31. 2024 Jan 23. Tumenbayar BITutino VMBrazzo JAYao PBae Y FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism.; bioRxiv : the preprint server for biology. 2024 Jan 16. Chen JLLeeder WMMorais PAdachi HYu YT Pseudouridylation-mediated gene expression modulation.; The Biochemical journal; Vol 481(1), pp. 1-16. 2024 Jan 10. Cisco LASipple MTEdwards KMThornton CALueck JD Verapamil mitigates chloride and calcium bi-channelopathy in a myotonic dystrophy mouse model.; The Journal of clinical investigation; Vol 134(1). 2024 Jan 02. Zuber JMathews DH Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.; Methods in molecular biology (Clifton, N.J.); Vol 2726, pp. 1-13. 2024. Wu JHollinger JBonanno EJiang FYao P Cardiomyocyte-Specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy.; Cells; Vol 13(1). 2023 Dec 22. Lv XMurphy KMurphy ZGetman MRRahman NFNakamura YBlanc LGallagher PGPalis JMohandas NSteiner LA HEXIM1 is an Essential Transcription Regulator During Human Erythropoiesis.; Blood. 2023 Sep 22. Wu JHollinger JBonanno EJiang FYao P Cardiomyocyte-specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy.; bioRxiv : the preprint server for biology. 2023 Sep 22. De Zoysa THauke ACIyer NRMarcus EOstrowski SMFay JCPhizicky EM A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; bioRxiv : the preprint server for biology. 2023 Sep 18. Pham TMMiffin TSun HSharp KKWang XZhu MHoshika SPeterson RJBenner SAKahn JDMathews DH DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.; ACS synthetic biology. 2023 Sep 06. Boutz PL Putting a finger on histidine methylation.; Genes & development; Vol 37(15-16), pp. 675-677. 2023 Sep 06. Schroeder GMKiliushik DJenkins JLWedekind JE Structure and function analysis of a type III preQ1-I riboswitch from E. coli reveals direct metabolite-sensing by the Shine-Dalgarno sequence.; The Journal of biological chemistry. 2023 Sep 01. Zhang HLi SDai NZhang LMathews DHHuang L LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.; Nucleic acids research. 2023 Aug 31. Haugen RJBarnier CElrod NDLuo HJensen MKJi PSmibert CALipshitz HDWagner EJFreddolino PLGoldstrohm AC Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase.; bioRxiv : the preprint server for biology. 2023 Aug 30. Cazarin JDeRollo REShahidan SNABABurchett JBMwangi DKrishnaiah SHsieh ALWalton ZEBrooks RMello SSWeljie AMDang CVAltman BJ MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis.; PLoS genetics; Vol 19(8), pp. e1010904. 2023 Aug 28. Wu JSubbaiah KCVHedaya OChen SMunger JTang WHWYan CYao P FAM210A regulates mitochondrial translation and maintains cardiac mitochondrial homeostasis.; Cardiovascular research. 2023 Jul 31. Liu LXu ZMolina Vargas AMDollery SJSchrlau MGCormier DO'Connell MRTobin GJDu K Aerosol Jet Printing-Enabled Dual-Function Electrochemical and Colorimetric Biosensor for SARS-CoV-2 Detection.; Analytical chemistry. 2023 Jul 28. Zuber JSah SKMathews DHRustchenko E Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants.; Microorganisms; Vol 11(8). 2023 Jul 25. Kretsch RCAndersen ESBujnicki JMChiu WDas RLuo BMasquida BMcRae EKSSchroeder GMSu ZWedekind JEXu LZhang KZheludev INMoult JKryshtafovych A RNA target highlights in CASP15: Evaluation of predicted models by structure providers.; Proteins. 2023 Jul 19. Piraino LChen CYMereness JDunman PMOvitt CBenoit DDeLouise L Identifying novel radioprotective drugs via salivary gland tissue chip screening.; bioRxiv : the preprint server for biology. 2023 Jul 13. Young MChojnacki MBlanchard CCao XJohnson WLFlaherty DDunman PM Genetic Determinants of Acinetobacter baumannii Serum-Associated Adaptive Efflux-Mediated Antibiotic Resistance.; Antibiotics (Basel, Switzerland); Vol 12(7). 2023 Jul 11. Liu XBurke RMLighthouse JKBaker CDDirkx RAKang BChakraborty YMickelsen DMTwardowski JMello SSAshton JMSmall EM P53 Regulates the Extent of Fibroblast Proliferation and Fibrosis in Left Ventricle Pressure Overload.; Circulation research. 2023 Jul 06. Ali SEMittal AMathews DH RNA Secondary Structure Analysis Using RNAstructure.; Current protocols; Vol 3(7), pp. e846. 2023 Jul. Jonnakuti VSJi PGao YLin AChu YElrod NHuang KLLi WYalamanchili HKWagner EJ NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.; Journal of neuro-oncology. 2023 Jun 30. Zhou TDai NLi SWard MMathews DHHuang L RNA design via structure-aware multifrontier ensemble optimization.; Bioinformatics (Oxford, England); Vol 39(39 Suppl 1), pp. i563-i571. 2023 Jun 30. Das ABao CErmolenko DN Comparing FRET Pairs that Report on Intersubunit Rotation in Bacterial Ribosomes.; Journal of molecular biology; Vol 435(15), pp. 168185. 2023 Jun 20. Hollinger JWu JAwayda KMO'Connell MRYao P Expression and purification of the mitochondrial transmembrane protein FAM210A in Escherichia coli.; Protein expression and purification; Vol 210, pp. 106322. 2023 Jun 15. Hedaya OMSubbaiah KCVJiang FXie LHWu JKhor EZhu MMathews DHProschel CYao P Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.; bioRxiv : the preprint server for biology. 2023 Jun 15. Pham TMMiffin TSun HSharp KKWang XZhu MHoshika SPeterson RJBenner SAKahn JDMathews DH DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.; bioRxiv : the preprint server for biology. 2023 Jun 08. Cisco LASipple MTEdwards KMThornton CALueck JD Combinatorial chloride and calcium channelopathy in myotonic dystrophy.; bioRxiv : the preprint server for biology. 2023 Jun 01. Mathews DHCasadio RSternberg MJE Computational Resources for Molecular Biology 2023.; Journal of molecular biology. 2023 May 25. Wu JSubbaiah KCVHedaya OChen SMunger JTang WHWYan CYao P FAM210A Regulates Mitochondrial Translation and Maintains Cardiac Mitochondrial Homeostasis.; bioRxiv : the preprint server for biology. 2023 May 22. 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. Jiang FHedaya OMKhor EWu JAuguste MYao P RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression.; Nucleic acids research. 2023 May 01. 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. Insco MLAbraham BJDubbury SJKaltheuner IHDust SWu CChen KYLiu DBellaousov SCox AMMartin BJEZhang TLudwig CGFabo TModhurima REsgdaille DEHenriques TBrown KMChanock SJGeyer MAdelman KSharp PAYoung RABoutz PLZon LI Oncogenic CDK13 mutations impede nuclear RNA surveillance.; Science (New York, N.Y.); Vol 380(6642), pp. eabn7625. 2023 Apr 21. 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. Knott GJLapinaite AO'Connell MR Methods special issue: RNA-targeting technologies.; Methods (San Diego, Calif.); Vol 212, pp. 10-11. 2023 Feb 13. 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. Molina Vargas AMSinha SOsborn RArantes PRPatel ADewhurst SHardy DJCameron APalermo GO'Connell MR New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity.; Nucleic acids research. 2023 Jan 30. Sinha SMolina Vargas AMArantes PRPatel AO'Connell MRPalermo G Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a.; Nucleic acids research. 2023 Jan 30. Subbaiah KCVWu JTang WHWYao P Ciclopirox Inhibition of eIF5A Hypusination Attenuates Fibroblast Activation and Cardiac Fibrosis.; Journal of cardiovascular development and disease; Vol 10(2). 2023 Jan 29. 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. Fongang BWadop YNZhu YWagner EJKudlicki ARowicka M Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits.; Computational and structural biotechnology journal; Vol 21, pp. 5686-5697. 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. King KABenton AHCaudill MTStoyanof STKang LMichalak PLahmers KKDunman PMDeHart TGAhmad SSJutras BLPoncin KDe Bolle XCaswell CC Post-transcriptional control of the essential enzyme MurF by a small regulatory RNA in Brucella abortus.; Molecular microbiology. 2023 Jan 11. Srivastava YBlau MEJenkins JLWedekind JE Full-Length NAD+-I Riboswitches Bind a Single Cofactor but Cannot Discriminate against Adenosine Triphosphate.; Biochemistry. 2023 Jan 10. Rook MLMcCullock TWCouch TLueck JDMacLean DM Photomodulation of the ASIC1a acidic pocket destabilizes the open state.; Protein science : a publication of the Protein Society. 2023 Jan 08. Papoin JYan HLeduc MLe Gall MNarla APalis JSteiner LAGallagher PGHillyer CDGautier EFMohandas NBlanc L Phenotypic and proteomic characterization of the human erythroid progenitor continuum reveal dynamic changes in cell cycle and in metabolic pathways.; American journal of hematology. 2023 Jan 06. Wagner EJTong LAdelman K Integrator is a global promoter-proximal termination complex.; Molecular cell. 2023 Jan 04. DeRollo RECazarin JAhmad Shahidan SNABBurchett JBMwangi DKrishnaiah SHsieh ALWalton ZEBrooks RMello SSWeljie AMDang CVAltman BJ MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis.; bioRxiv : the preprint server for biology. 2023 Jan 04. Hedaya OMVenkata Subbaiah KCJiang FXie LHWu JKhor ESZhu MMathews DHProschel CYao P Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.; Nature communications; Vol 14(1), pp. 6166. 2023 Jan 03. 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. 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. 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. Mackenzie SJHamel JThornton CA Benefits of aerobic exercise in myotonic dystrophy type 1.; The Journal of clinical investigation; Vol 132(10). 2022 May 16. 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. 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. Michard FThiele RHSaugel BJoosten AFlick MKhanna AK Wireless wearables for postoperative surveillance on surgical wards: a survey of 1158 anaesthesiologists in Western Europe and the USA.; BJA open; Vol 1, pp. 100002. 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. Waitkus JChang YLiu LPuttaswamy SVChung TVargas AMMDollery SJO'Connell MRCai HTobin GJBhalla NDu K Gold Nanoparticle Enabled Localized Surface Plasmon Resonance on Unique Gold Nanomushroom Structures for On-Chip CRISPR-Cas13a Sensing.; Advanced materials interfaces; Vol 10(1). 2022 Jan 27. Liu LXu ZAwayda KDollery SJBao MFan JCormier DO'Connell MTobin GJDu K Gold Nanoparticle-Labeled CRISPR-Cas13a Assay for the Sensitive Solid-State Nanopore Molecular Counting.; Advanced materials technologies; Vol 7(3). 2022 Jan 22. 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. 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