URMC / Center for RNA Biology / Publications Publications 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. 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. 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. 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. 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. Boutz PL Putting a finger on histidine methylation.; Genes & development; Vol 37(15-16), pp. 675-677. 2023 Sep 06. 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. 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. Vargas AMMOsborn RSinha SArantes PRPatel ADewhurst SPalermo GO'Connell MR New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity.; bioRxiv : the preprint server for biology. 2023 Jul 28. Sinha SMolina Vargas AMArantes PRPatel AO'Connell MRPalermo G RNA-mediated Allosteric Activation in CRISPR-Cas13a.; bioRxiv : the preprint server for biology. 2023 Jul 27. 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. 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. 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. 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 ; Muscle & nerve. 2022 Jul 01. Galardi JWBela VNJeffery NHe XGlasser ELoerch SJenkins JLPulvino MJBoutz PLKielkopf CL ; The Journal of biological chemistry. 2022 Jun 30. Szikszai MWise MDatta AWard MMathews DH ; Bioinformatics (Oxford, England). 2022 Jun 24. Ko WPorter JJSipple MTEdwards KMLueck JD ; Molecular therapy. Nucleic acids; Vol 28. 2022 Jun 14. Kumar JLackey LWaldern JMDey AMustoe AMWeeks KMathews DHLaederach A ; eLife; Vol 11. 2022 Jun 13. Subbaiah KCVWu JTang WHWYao P ; 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 ; 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 ; The Journal of clinical investigation; Vol 132(10). 2022 May 16. Szabat MProchota MKierzek RKierzek EMathews DH ; Journal of molecular biology. 2022 May 16. Casadio RMathews DHSternberg MJE ; Journal of molecular biology. 2022 May 12. Maquat LJohnson RValadkhan SCarninci P ; Mammalian genome : official journal of the International Mammalian Genome Society. 2022 May 09. Glasser EMaji DBiancon GPuthenpeedikakkal AMKCavender CETebaldi TJenkins JLMathews DHHalene SKielkopf CL ; Nucleic acids research. 2022 May 07. Zuber JSchroeder SJSun HTurner DHMathews DH ; Nucleic acids research. 2022 May 07. Mei JAJohnson WKinn BLaskey ENolin LBhamare PStalker CDunman PMWozniak RAF ; Translational vision science & technology; Vol 11(5). 2022 May 02. Funk HMDiVita DJSizemore HEWehrle KMiller CLWFraley MEMullins AKGuy ARPhizicky EMGuy MP ; ACS omega; Vol 7(16). 2022 Apr 26. Hamel JCreigh PDDekdebrun JEichinger KThornton CA ; Muscle & nerve. 2022 Apr 15. Walker EJBettinger JQWelle KAHryhorenko JRMolina Vargas AMO'Connell MRGhaemmaghami S ; The Journal of biological chemistry. 2022 Mar 25. Kierzek EZhang XWatson RMKennedy SDSzabat MKierzek RMathews DH ; Nature communications; Vol 13(1). 2022 Mar 11. Szutkowska BWieczorek KKierzek RZmora PPeterson JMMoss WNMathews DHKierzek E ; 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 ; Nature communications; Vol 13(1). 2022 Feb 21. Deutsch GKHagerman KASampson JDent GDekdebrun JParker DMThornton CAHeatwole CRSubramony SHMankodi AKAshizawa TStatland JMArnold WDMoxley RTDay JW ; 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 ; American journal of human genetics. 2022 Feb 11. LaForce GRFarr JSLiu JAkesson CGumus EPinkard OMiranda HCJohnson KSweet TJJi PLin AColler JPhilippidou PWagner EJSchaffer AE ; 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. 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 ; 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 ; 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 ; 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 ; Annals of the New York Academy of Sciences. 2021 Nov 17. Kurosaki TSakano HPröschel CWheeler JHewko AMaquat LE ; Genome biology; Vol 22(1). 2021 Nov 16. Chavali SSMali SMBonn RSaseendran ABennett RPSmith HCFasan RWedekind JE ; 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 ; Cell reports; Vol 37(5). 2021 Nov 02. Elahi AEmerson JRudlong JKeillor JWSalois GVisca AGirardi PJohnson GVWPröschel C ; Cells; Vol 10(11). 2021 Oct 29. Bao CErmolenko DN ; Biochemistry. Biokhimiia; Vol 86(8). 2021 Aug. Moon EJMello SSLi CGChi JTThakkar KKirkland JGLagory ELLee IJDiep ANMiao YRafat MVilalta MCastellini LKrieg AJGraves EEAttardi LDGiaccia AJ The HIF target MAFF promotes tumor invasion and metastasis through IL11 and STAT3 signaling.; Nature communications; Vol 12(1), pp. 4308. 2021 Jul 14. Li LHuang KLGao YCui YWang GElrod NDLi YChen YEJi PPeng FRussell WKWagner EJLi W ; Nature genetics; Vol 53(7). 2021 Jul. Murphy ZMurphy KMyers JAGetman MRCouch TSchulz VLezon-Geyda KPalumbo CYan HNarla MGallagher PGSteiner LA ; Blood. 2021 Jun 01. Adachi HHengesbach MYu YTMorais P ; Biomedicines; Vol 9(5). 2021 May 14. Yang HKundra SChojnacki MLiu KFuse MAAbouelhassan YKallifidas DZhang PHuang GJin SDing YLuesch HRohde KHDunman PMLemos JAHuigens RW ; Journal of medicinal chemistry. 2021 Apr 21. Suigo LChojnacki MZanotto CSebastián-Pérez VMorghen CGCasiraghi ADunman PMValoti EStraniero V ; Antibiotics (Basel, Switzerland); Vol 10(4). 2021 Apr 14. Enwerem IIIElrod NDChang CTLin AJi PBohn JALevdansky YWagner EJValkov EGoldstrohm AC ; RNA (New York, N.Y.); Vol 27(4). 2021 Apr. Chojnacki MCao XFlaherty DPDunman PM ; Antibiotics (Basel, Switzerland); Vol 10(4). 2021 Mar 31. Chojnacki MDobrotka COsborn RJohnson WYoung MMeyer BLaskey EWozniak RAFDewhurst SDunman PM ; mSphere; Vol 6(2). 2021 Mar 03. Srivastava YBonn-Breach RChavali SSLippa GMJenkins JLWedekind JE ; Crystals; Vol 11(3). 2021 Mar. Chatrikhi RFeeney CFPulvino MJAlachouzos GMacRae AJFalls ZRai SBrennessel WWJenkins JLWalter MJGraubert TASamudrala RJurica MSFrontier AJKielkopf CL ; Cell chemical biology. 2021 Feb 26. Porter JJHeil CSLueck JD ; Wiley interdisciplinary reviews. RNA. 2021 Feb 10. Li SZhang HZhang LLiu KLiu BMathews DHHuang L ; Proceedings of the National Academy of Sciences of the United States of America; Vol 118(52). 2021 Jan 28. Tanner MKTang ZThornton CA ; Nucleic acids research. 2021 Jan 27. Otero BAPoukalov KHildebrandt RPThornton CAJinnai KFujimura HKimura THagerman KASampson JBDay JWWang ET ; Cell reports; Vol 34(3). 2021 Jan 19. Chambers MRees ACronin JGNair MJones NThornton CA Macrophage Plasticity in Reproduction and Environmental Influences on Their Function.; Frontiers in immunology; Vol 11, pp. 607328. 2021 Jan 14. Scherzi TD'Ambrosio EADaher SSGrimes CLDunman PMAndrade RB ; 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. Han LMarcus EPhizicky EM ; Methods in enzymology; Vol 658. 2021. Morais PAdachi HYu YT ; Frontiers in cell and developmental biology; Vol 9. 2021. Yuan FHankey WWagner EJLi WWang Q ; Genes & diseases; Vol 8(1). 2021 Jan. Jensen MKElrod NDYalamanchili HKJi PLin ALiu ZWagner EJ ; Methods in enzymology; Vol 655. 2021. Yalamanchili HKElrod NDJensen MKJi PLin AWagner EJLiu Z ; 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 ; Nature cell biology; Vol 23(1). 2021 Jan. Morais PAdachi HYu YT ; Frontiers in genetics; Vol 12. 2021. Johnson WLSohn MBTaffner SChatterjee PDunman PMPecora NWozniak RAF ; PloS one; Vol 16(5). 2021. Kayedkhordeh MYamagami RBevilacqua PCMathews DH ; Methods in molecular biology (Clifton, N.J.); Vol 2167. 2021. Zhang HZhang LLi SMathews DHHuang L ; bioRxiv : the preprint server for biology. 2020 Dec 29. Wu JVenkata Subbaiah KCJiang FHedaya OMohan AYang TWelle KGhaemmaghami STang WHWSmall EYan CYao P ; EMBO molecular medicine. 2020 Dec 28. Lyu QRYao PMiano JM ; Journal of biomedical research; Vol 35(2). 2020 Dec 25. Maji DGlasser EHenderson SGalardi JPulvino MJJenkins JLKielkopf CL ; The Journal of biological chemistry; Vol 295(50). 2020 Dec 11. Chavali SSMali SMJenkins JLFasan RWedekind JE ; The Journal of biological chemistry; Vol 295(49). 2020 Dec 04. Chavali SSCavender CEMathews DHWedekind JE ; Journal of the American Chemical Society. 2020 Nov 10. Sparks RPArango ASJenkins JLGuida WCTajkhorshid ESparks CESparks JDFratti RA ; 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 ; Molecular cell; Vol 80(3). 2020 Nov 05. Angelbello AJBenhamou RIRzuczek SGChoudhary STang ZChen JLRoy MWang KWYildirim IJun ASThornton CADisney MD ; Cell chemical biology. 2020 Nov 05. Valente LJTarangelo ALi AMNaciri MRaj NBoutelle AMLi YMello SSBieging-Rolett KDeBerardinis RJYe JDixon SJAttardi LD ; The Journal of cell biology; Vol 219(11). 2020 Nov 02. Daher SSFranklin KPScherzi TDunman PMAndrade RB ; Bioorganic & medicinal chemistry letters; Vol 30(21). 2020 Nov 01. Murphy ZCGetman MRMyers JAVillar KNBLeshen EKurita RNakamura YSteiner LA ; Experimental hematology. 2020 Oct 16. Chavali SSMali SMJenkins JLFasan RWedekind JE ; 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 ; Neurology. 2020 Oct 12. Maji DGlasser EHenderson SGalardi JPulvino MJJenkins JLKielkopf CL ; The Journal of biological chemistry. 2020 Oct 05. Rambout XMaquat LE ; 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 ; Molecular cancer research : MCR; Vol 18(10). 2020 Oct. Chojnacki MCao XYoung MFritz RNDunman PMFlaherty DP ; 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 ; RNA (New York, N.Y.); Vol 26(9). 2020 Sep. Rambout XMaquat LE ; Genes & development; Vol 34(17-18). 2020 Sep 01. De Zoysa TPhizicky EM ; PLoS genetics; Vol 16(8). 2020 Aug 25. Zheng DCho HWang WRambout XTian BMaquat LE ; RNA (New York, N.Y.). 2020 Aug 12. Popp MWCho HMaquat LE ; RNA (New York, N.Y.). 2020 Jul 22. Yalamanchili HKAlcott CEJi PWagner EJZoghbi HYLiu Z ; Nucleic acids research; Vol 48(12). 2020 Jul 09. Wu JSubbaiah KCVXie LHJiang FKhor ESMickelsen DMMyers JRTang WWYao P ; Circulation research. 2020 Jul 01. Zhang HZhang LMathews DHHuang L ; Bioinformatics (Oxford, England); Vol 36(Supplement_1). 2020 Jul 01. Zhao SDejanovic DYao PBhilocha SSadler TSchirbel AWest GDoyon GLopez RMao RKurada SEl Ouali SGrassl GFox PLCruise MWorthley DLde la Motte CFiocchi CRieder F ; Mucosal immunology; Vol 13(4). 2020 Jul. Schroeder GMDutta DCavender CEJenkins JLPritchett EMBaker CDAshton JMMathews DHWedekind JE ; Nucleic acids research. 2020 Jun 29. Ermolenko DNMathews DH ; Wiley interdisciplinary reviews. RNA. 2020 Jun 29. Morais PAdachi HYu YT ; International journal of molecular sciences; Vol 21(12). 2020 Jun 20. Wakabayashi HWarnasooriya CErmolenko DN ; Journal of molecular biology. 2020 Jun 13. Warnasooriya CFeeney CFLaird KMErmolenko DNKielkopf CL ; Nucleic acids research; Vol 48(10). 2020 Jun 04. Tan ZWFei GPaulo JABellaousov SMartin SESDuveau DYThomas CJGygi SPBoutz PLWalker S O-GlcNAc regulates gene expression by controlling detained intron splicing.; Nucleic acids research; Vol 48(10), pp. 5656-5669. 2020 Jun 04. Adachi HYu YT ; RNA (New York, N.Y.). 2020 May 20. Bao CLoerch SLing CKorostelev AAGrigorieff NErmolenko DN ; eLife; Vol 9. 2020 May 19. Ketley AWojciechowska MGhidelli-Disse SBamborough PGhosh TKMorato MLSedehizadeh SMalik NATang ZPowalowska PTanner MBilleter-Clark RTrueman RCGeiszler PCAgostini AOthman OBösche MBantscheff MRüdiger MMossakowska DEDrewry DHZuercher WJThornton CADrewes GUings IHayes CJBrook JD ; Science translational medicine; Vol 12(541). 2020 Apr 29. Alcott CEYalamanchili HKJi Pvan der Heijden MESaltzman AElrod NLin ALeng MBhatt BHao SWang QSaliba ATang JMalovannaya AWagner EJLiu ZZoghbi HY ; eLife; Vol 9. 2020 Apr 22. Rambout XCho HMaquat LE ; Cold Spring Harbor symposia on quantitative biology. 2020 Apr 15. Maquat LE ; Philosophical transactions of the Royal Society of London. Series B, Biological sciences; Vol 375(1795). 2020 Mar 30. Myers JACouch TMurphy ZMalik JGetman MSteiner LA ; Epigenetics & chromatin; Vol 13(1). 2020 Mar 16. Rook MLWilliamson ALueck JDMusgaard MMaclean DM ; eLife; Vol 9. 2020 Feb 07. Tylock KMAuerbach DSTang ZZThornton CADirksen RT ; The Journal of general physiology; Vol 152(2). 2020 Feb 03. Weng THuang JWagner EJKo JWu MWareing NEXiang YChen NYJi PMolina JGVolcik KAHan LMayes MDBlackburn MRAssassi S Downregulation of CFIm25 amplifies dermal fibrosis through alternative polyadenylation.; The Journal of experimental medicine; Vol 217(2). 2020 Feb 03.