URMC / Biochemistry & Biophysics / Research / Recent Publications Recent Publications Glasser EAgrawal AAJenkins JLKielkopf CL (2017 Sep 01). Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry. Novosjolova IKennedy SDRozners E (2017 Aug 31). 2-Methoxypyridine as Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability and NMR Structural Studies. Chembiochem : a European journal of chemical biology. Hayashi TJean MHuang HSimpson SSantoso NGZhu J (2017 Aug 22). Screening of an FDA-approved compound library identifies levosimendan as a novel anti-HIV-1 agent that inhibits viral transcription. Antiviral research. Mutisya DHardcastle TCheruiyot SKPallan PSKennedy SDEgli MKelley MLSmith AVBRozners E (2017 Aug 21). Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs. Nucleic acids research. Poole ARVicino IAdachi HYu YTHebert MD (2017 Aug 14). Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity. Biology open. Tan ZSharma GMathews DH (2017 Jul 20). Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data. Biophysical journal. Kauffmann ADKennedy SDZhao JTurner DH (2017 Jul 12). Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions. Biochemistry. Romo TDLewis AKBraun ARGrossfield ASachs JN (2017 Jul 05). Minimal nucleation state of alpha-Synuclein is stabilized by dynamic threonine-water networks. ACS chemical neuroscience. Nadtochiy SMWang YTZhang JNehrke KSchafer XWelle KGhaemmaghami SMunger JBrookes PS (2017 Jul 03). Potential mechanisms linking SIRT activity and hypoxic 2-hydroxyglutarate generation: no role for direct enzyme (de)acetylation. The Biochemical journal. Ward MDatta AWise MMathews DH (2017 Jun 06). Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. Nucleic acids research. Elbarbary RAMaquat LE (2017 Jun 06). Distinct mechanisms obviate the potentially toxic effects of inverted-repeat Alu elements on cellular RNA metabolism. Nature structural & molecular biology. Bednar JGarcia-Saez IBoopathi RCutter ARPapai GReymer ASyed SHLone INTonchev OCrucifix CMenoni HPapin CSkoufias DAKurumizaka HLavery RHamiche AHayes JJSchultz PAngelov DPetosa CDimitrov S (2017 Jun 01). Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. Molecular cell. Elbarbary RAMiyoshi KMyers JRDu PAshton JMTian BMaquat LE (2017 May 26). Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G1/S phase transition. Science (New York, N.Y.). Polevoda BJoseph RFriedman AEBennett RPGreiner RDe Zoysa TStewart RASmith HC (2017 May 26). DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315. The Journal of biological chemistry. Hilimire TAChamberlain JMAnokhina VBennett RPSwart OMyers JRAshton JMStewart RAFeatherston ALGates KHelms EDSmith HCDewhurst SMiller BL (2017 May 05). HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells. ACS chemical biology. Bednar JGarcia-Saez IBoopathi RCutter ARPapai GReymer ASyed SHLone INTonchev OCrucifix CMenoni HPapin CSkoufias DAKurumizaka HLavery RHamiche AHayes JJSchultz PAngelov DPetosa CDimitrov S (2017 May 04). Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. Molecular cell. East-Seletsky AO'Connell MRBurstein DKnott GJDoudna JA (2017 May 04). RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes. Molecular cell. Wedekind JEDutta DBelashov IAJenkins JL (2017 Apr 28). Metalloriboswitches: RNA-Based Inorganic Ion Sensors that Regulate Genes. The Journal of biological chemistry. Gamache ERDoh JHRitz JLaederach ABellaousov SMathews DHCurcio MJ (2017 Apr 26). Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA. Viruses. Jean MJPower DKong WHuang HSantoso NZhu J (2017 Apr 01). Identification of HIV-1 Tat-Associated Proteins Contributing to HIV-1 Transcription and Latency. Viruses. Vats KMarsh GHarding KZampetakis IWaugh REBenoit DS (2017 Apr). Nanoscale physicochemical properties of chain- and step-growth polymerized PEG hydrogels affect cell-material interactions. Journal of biomedical materials research. Part A. Cutter ARHayes JJ (2017 Apr). Linker histones: novel insights into structure-specific recognition of the nucleosome. Biochemistry and cell biology = Biochimie et biologie cellulaire. Jenkins JLKielkopf CL (2017 Mar 31). Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures. Trends in genetics : TIG. Baker JESriram RMiller BL (2017 Mar 30). Recognition-mediated particle detection under microfluidic flow with waveguide-coupled 2D photonic crystals: towards integrated photonic virus detectors. Lab on a chip. Zuber JSun HZhang XMcFadyen IMathews DH (2017 Mar 15). A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction. Nucleic acids research. Liu KXie FGao AZhang RZhang LXiao ZHu QHuang WHuang QLin BZhu JWang HQue JLan X (2017 Mar 14). SOX2 regulates multiple malignant processes of breast cancer development through the SOX2/miR-181a-5p, miR-30e-5p/TUSC3 axis. Molecular cancer. Brule CEGrayhack EJ (2017 Mar 11). Synonymous Codons: Choose Wisely for Expression. Trends in genetics : TIG. Murphy PSWang JBhagwat SPMunger JCJanssen WJWright TWElliott MR (2017 Mar). CD73 regulates anti-inflammatory signaling between apoptotic cells and endotoxin-conditioned tissue macrophages. Cell death and differentiation. Yang FZhang LWakabayashi HMyers JJiang YCao YJimenez-Ortigosa CPerlin DSRustchenko E (2017 Feb 21). Tolerance to caspofungin in Candida albicans is associated with at least three distinctive mechanisms that govern expression of FKS genes and cell wall remodeling. Antimicrobial agents and chemotherapy. Aytenfisu AHSpasic AGrossfield AStern HAMathews DH (2017 Feb 14). Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics. Journal of chemical theory and computation. Clark KMJenkins JLFedoriw NDumont ME (2017 Feb). Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors. Protein science : a publication of the Protein Society. Balliano AHao FNjeri CBalakrishnan LHayes JJ (2017 Jan 18). HMGB1 Stimulates Activity of Polymerase β on Nucleosome Substrates. Biochemistry. Patra BKon YYadav GSevold AWFrumkin JPVallabhajosyula RRHintze AØstman BSchossau JBhan AMarzolf BTamashiro JKKaur ABaliga NSGrayhack EJAdami CGalas DJRaval APhizicky EMRay A (2017 Jan 09). A genome wide dosage suppressor network reveals genomic robustness. Nucleic acids research. Hrabeta-Robinson EMarcus ECozen AEPhizicky EMLowe TM (2017). High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq). Methods in molecular biology (Clifton, N.J.). De Zoysa MDYu YT (2017). Posttranscriptional RNA Pseudouridylation. The Enzymes. Huang HLiu SJean MSimpson SHuang HMerkley MHayashi TKong WRodríguez-Sánchez IZhang XYosief HOMiao HQue JKobie JJBradner JSantoso NGZhang WZhu J (2017). A Novel Bromodomain Inhibitor Reverses HIV-1 Latency through Specific Binding with BRD4 to Promote Tat and P-TEFb Association. Frontiers in microbiology. Coudray NL Seyler SLasala RZhang ZClark KMDumont MERohou ABeckstein OStokes DL (2017 Jan). Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Protein science : a publication of the Protein Society. Han LMarcus ED'Silva SPhizicky EM (2016 Dec 21). S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates. RNA (New York, N.Y.). Chatrikhi RWang WGupta ALoerch SMaucuer AKielkopf CL (2016 Dec 20). SF1 Phosphorylation Enhances Specific Binding to U2AF(65) and Reduces Binding to 3'-Splice-Site RNA. Biophysical journal. Komisarof JMcCall MNewman LBshara WMohler JLMorrison CLand H (2016 Dec 09). A four gene signature predictive of recurrent prostate cancer. Oncotarget. Ling CErmolenko DN (2016 Dec 06). Caught on Camera: Intermediates of Ribosome Recycling. Structure (London, England : 1993). Loerch SKielkopf CL (2016 Dec). Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. RNA (New York, N.Y.). Suwunnakorn SWakabayashi HRustchenko E (2016 Dec). Chromosome 5 of Human Pathogen Candida albicans Carries Multiple Genes for Negative Control of Caspofungin and Anidulafungin Susceptibility. Antimicrobial agents and chemotherapy. Ikpeze TCSmith HCLee DJElfar JC (2016 Dec). Distal Radius Fracture Outcomes and Rehabilitation. Geriatric orthopaedic surgery & rehabilitation. Sloma MFMathews DH (2016 Dec). Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures. RNA (New York, N.Y.). Mathews DHTurner DHWatson RM (2016 Dec 01). RNA Secondary Structure Prediction. Current protocols in nucleic acid chemistry. Pei SMinhajuddin MD'Alessandro ANemkov TStevens BMAdane BKhan NHagen FKYadav VKDe SAshton JMHansen KCGutman JAPollyea DACrooks PASmith CJordan CT (2016 Nov 25). Rational design of a parthenolide-based drug regimen that selectively eradicates acute myelogenous leukemia stem cells. The Journal of biological chemistry. Smith HC (2016 Nov 21). RNA binding to APOBEC deaminases; Not simply a substrate for C to U editing. RNA biology. Dutt SBinney RJHeuer HWLuong PAttygalle SBhatt PMarx GAElofson JTartaglia MCLitvan IMcGinnis SMDickerson BCKornak JWaltzman DVoltarelli LSchuff NRabinovici GDKramer JHJack CRMiller BLRosen HJBoxer AL (2016 Nov 08). Progression of brain atrophy in PSP and CBS over 6 months and 1 year. Neurology. 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. Fang HWei SLee THHayes JJ (2016 Nov 02). Chromatin structure-dependent conformations of the H1 CTD. Nucleic acids research. Xu CIshikawa HIzumikawa KLi LHe HNobe YYamauchi YShahjee HMWu XHYu YTIsobe TTakahashi NMin J (2016 Nov 01). Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. Genes & development. Pei SMinhajuddin MD'Alessandro ANemkov TStevens BMAdane BKhan NHagen FKYadav VKDe SAshton JMHansen KCGutman JAPollyea DACrooks PASmith CJordan CT (2016 Oct 14). Rational Design of a Parthenolide-based Drug Regimen That Selectively Eradicates Acute Myelogenous Leukemia Stem Cells. The Journal of biological chemistry. East-Seletsky AO'Connell MRKnight SCBurstein DCate JHTjian RDoudna JA (2016 Oct 13). Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. Smith BSchafer XLAmbeskovic ASpencer CMLand HMunger J (2016 Oct 11). Addiction to Coupling of the Warburg Effect with Glutamine Catabolism in Cancer Cells. Cell reports. Mishra LNPepenella SRogge RHansen JCHayes JJ (2016 Oct 06). Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays. Scientific reports. 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. Sridharan RConnelly SMNaider FDumont ME (2016 Sep 19). Variable Dependence of Signaling Output on Agonist Occupancy of Ste2p, a G Protein Coupled Receptor in Yeast. The Journal of biological chemistry. Nadtochiy SMSchafer XFu DNehrke KMunger JBrookes PS (2016 Aug 10). Acidic pH is a Metabolic Switch for 2-Hydroxyglutarate Generation and Signaling. The Journal of biological chemistry. 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. Gamble CEBrule CEDean KMFields SGrayhack EJ (2016 Jun 29). Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast. Cell. Black PJMiller ASHayes JJ (2016 Jun 27). Radioresistance of GGG sequences to prompt strand break formation from direct-type radiation damage. Radiation and environmental biophysics. Gleghorn MLZhao JTurner DHMaquat LE (2016 Jun 10). Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation. Nucleic acids research. Wu GRadwan MKXiao MAdachi HFan JYu YT (2016 Jun 7). The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA. RNA (New York, N.Y.). Popp MWMaquat LE (2016 Jun 2). Leveraging Rules of Nonsense-Mediated mRNA Decay for Genome Engineering and Personalized Medicine. Cell. Svetina SKokot GKebe TŠŽekš BWaugh RE (2016 Jun). A novel strain energy relationship for red blood cell membrane skeleton based on spectrin stiffness and its application to micropipette deformation. Biomechanics and modeling in mechanobiology. Marsh GWaugh RE (2016 Jun). A simple approach for bioactive surface calibration using evanescent waves. Journal of microscopy. Coudray NLasala RZhang ZClark KMDumont MEStokes DL (2016 May 30). Deducing the Symmetry of Helical Assemblies: Applications to Membrane Proteins. Journal of structural biology. Salter JDBennett RPSmith HC (2016 May 30). The APOBEC Protein Family: United by Structure, Divergent in Function. Trends in biochemical sciences. Salsi EFarah EErmolenko DN (2016 May 22). EF-G Activation by Phosphate Analogs. Journal of molecular biology. 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. Xu SSchafer XMunger J (2016 May 1). Expression of Oncogenic Alleles Induces Multiple Blocks to Human Cytomegalovirus Infection. Journal of virology. Monaghan MWakabayashi HGriffiths AEFay PJ (2016 May). Stabilizing interactions between D666-S1787 and T657-Y1792 at the A2-A3 interface support factor VIIIa stability in the blood clotting pathway. Journal of thrombosis and haemostasis : JTH. Ling CErmolenko DN (2016 Apr 27). Structural insights into ribosome translocation. Wiley interdisciplinary reviews. RNA. Piekna-Przybylska DBambara RABalakrishnan L (2016 Apr 22). Acetylation regulates DNA repair mechanisms in human cells. Cell cycle (Georgetown, Tex.). Yue HFang HWei SHayes JJLee TH (2016 Apr 12). Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome. Biochemistry. Shaheen RHan LFaqeih EEwida NAlobeid EPhizicky EMAlkuraya FS (2016 Apr 7). A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. Human genetics. Nelles DAFang MYO'Connell MRXu JLMarkmiller SJDoudna JAYeo GW (2016 Apr 07). Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell. Maquat LE (2016 Apr). Eukaryotic antisense ahead of its time. Nature reviews. Molecular cell biology. DiChiacchio LSloma MFMathews DH (2016 Apr 1). AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. Bioinformatics (Oxford, England). Hollenbaugh JAMontero CSchinazi RFMunger JKim B (2016 Apr). Metabolic profiling during HIV-1 and HIV-2 infection of primary human monocyte-derived macrophages. Virology. Carter JATriplett EStriemer CCMiller BL (2016 Mar 15). A label-free, multiplex competitive assay for small molecule pollutants. Biosensors & bioelectronics. 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.). Bertozzi CZimmermann IEngeler SHilf RJDutzler R (2016 Mar). Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels. PLoS biology. 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. Vukomanovic DRahman MNMaines MDOzolinš TRSzarek WAJia ZNakatsu K (2016 Mar). Cysteine-independent activation/inhibition of heme oxygenase-2. Medical gas research. Nganou CKennedy SDMcCamant DW (2016 Feb 25). Disagreement Between the Structure of the dTpT Thymine Pair Determined by NMR and Molecular Dynamics Simulations Using Amber 14 Force Fields. The journal of physical chemistry. B. McAnany JDReichert JPMiller BL (2016 Feb 24). Probing the geometric constraints of RNA binding via dynamic covalent chemistry. Bioorganic & medicinal chemistry. 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.). 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. Huang CWu GYu YT (2016). Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles. Methods in molecular biology (Clifton, N.J.). Gibbs PEMiralem TLerner-Marmarosh NMaines MD (2016). Nanoparticle Delivered Human Biliverdin Reductase-Based Peptide Increases Glucose Uptake by Activating IRK/Akt/GSK3 Axis: The Peptide Is Effective in the Cell and Wild-Type and Diabetic Ob/Ob Mice. Journal of diabetes research. 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.). Kennedy SD (2016). NMR Methods for Characterization of RNA Secondary Structure. 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. Xiao JMoon YLi LRustchenko EWakabayashi HZhao XFeng CGill SRMcLaren SMalmstrom HRen YQuivey RKoo HKopycka-Kedzierawski DT (2016). Candida albicans Carriage in Children with Severe Early Childhood Caries (S-ECC) and Maternal Relatedness. PloS one. 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. Hughes ADMarsh GWaugh REFoster DGKing MR (2015 Dec 22). Halloysite Nanotube Coatings Suppress Leukocyte Spreading. Langmuir : the ACS journal of surfaces and colloids. Zhu GKoszelak-Rosenblum MConnelly SMDumont MEMalkowski MG (2015 Dec 11). The Crystal Structure of an Integral Membrane Fatty Acid α-Hydroxylase. The Journal of biological chemistry. 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. Balliano AJHayes JJ (2015 Dec). Base excision repair in chromatin: Insights from reconstituted systems. DNA repair. Goodwin CMXu SMunger J (2015 Dec). Stealing the Keys to the Kitchen: Viral Manipulation of the Host Cell Metabolic Network. Trends in 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. 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. Huang HSantoso NPower DSimpson SDieringer MMiao HGurova KGiam CZElledge SJZhu J (2015 Nov 6). FACT Proteins, SUPT16H and SSRP1, Are Transcriptional Suppressors of HIV-1 and HTLV-1 That Facilitate Viral Latency. The Journal of biological chemistry. Ma EHarrington LBO'Connell MRZhou KDoudna JA (2015 Nov 05). Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Molecular cell. Nadtochiy SMUrciuoli WZhang JSchafer XMunger JBrookes PS (2015 Nov). Metabolomic profiling of the heart during acute ischemic preconditioning reveals a role for SIRT1 in rapid cardioprotective metabolic adaptation. Journal of molecular and cellular cardiology. 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. Campbell ABushman JMunger JNoble MPröschel CMayer-Pröschel M (2015 Oct 15). Mutation of ataxia-telangiectasia mutated is associated with dysfunctional glutathione homeostasis in cerebellar astroglia. Glia. Cutter ARHayes JJ (2015 Oct 7). A brief review of nucleosome structure. FEBS letters. 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. Yada KNogami KTakeyama MOgiwara KWakabayashi HShima M (2015 Oct). Mild hemophilia A patient with novel Pro1809Leu mutation develops an anti-C2 antibody inhibiting allogeneic but not autologous factor VIII activity. Journal of thrombosis and haemostasis : JTH. 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. Cinar EZhou SDeCourcey JWang YWaugh REWan J (2015 Sep 22). Piezo1 regulates mechanotransductive release of ATP from human RBCs. Proceedings of the National Academy of Sciences of the United States of America. 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. Beste MTLomakina EBHammer DAWaugh RE (2015 Sep). Immobilized IL-8 Triggers Phagocytosis and Dynamic Changes in Membrane Microtopology in Human Neutrophils. Annals of biomedical engineering. 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. Lin DGrossfield A (2015 Aug 18). Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity. Biophysical journal. Leioatts NRomo TDDanial SAGrossfield A (2015 Aug 4). Retinal Conformation Changes Rhodopsin's Dynamic Ensemble. Biophysical journal. Buescher JMAntoniewicz MRBoros LGBurgess SCBrunengraber HClish CBDeBerardinis RJFeron OFrezza CGhesquiere BGottlieb EHiller KJones RGKamphorst JJKibbey RGKimmelman ACLocasale JWLunt SYMaddocks ODMalloy CMetallo CMMeuillet EJMunger JNöh KRabinowitz JDRalser MSauer UStephanopoulos GSt-Pierre JTennant DAWittmann CVander Heiden MGVazquez AVousden KYoung JDZamboni NFendt SM (2015 Aug). A roadmap for interpreting (13)C metabolite labeling patterns from cells. Current opinion in biotechnology. 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. Miller BL (2015 Jul). mRNA regulation: A patch for a splice. Nature chemical biology. Power DSantoso NDieringer MYu JHuang HSimpson SSeth IMiao HZhu J (2015 Jul). IFI44 suppresses HIV-1 LTR promoter activity and facilitates its latency. Virology. Pulvino MChen LOleksyn DLi JCompitello GRossi RSpence SBalakrishnan VJordan CPoligone BCasulo CBurack RShapiro JLBernstein SFriedberg JWDeshaies RJLand HZhao J (2015 Jun 20). Inhibition of COP9-signalosome (CSN) deneddylating activity and tumor growth of diffuse large B-cell lymphomas by doxycycline. Oncotarget. Condon DEKennedy SDMort BCKierzek RYildirim ITurner DH (2015 Jun 9). Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics. Journal of chemical theory and computation. Kim AROlsen JLEngland SJHuang YSFegan KHDelgadillo LFMcGrath KEKingsley PDWaugh REPalis J (2015 Jun 9). Bmi-1 Regulates Extensive Erythroid Self-Renewal. Stem cell reports. Ling CErmolenko DN (2015 Jun 2). Ribosome subunit joining frozen in time. Structure (London, England : 1993). Chen JLKennedy SDTurner DH (2015 Jun 2). Structural features of a 3' splice site in influenza a. Biochemistry. Xu SSpencer CMMunger J (2015 Jun). Transformation with oncogenic Ras and the simian virus 40 T antigens induces caspase-dependent sensitivity to fatty acid biosynthetic inhibition. Journal of 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.). Xu FHuang YLi LGannon PLinster EHuber MKapos PBienvenut WPolevoda BMeinnel THell RGiglione CZhang YWirtz MChen SLi X (2015 May). Two N-terminal acetyltransferases antagonistically regulate the stability of a nod-like receptor in Arabidopsis. The Plant cell. 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. 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.). 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. Popp MWMaquat LE (2015 Mar 20). RNA. A TRICK'n way to see the pioneer round of translation. Science (New York, N.Y.). Zuber JDanial SAConnelly SMNaider FDumont ME (2015 Mar 10). Identification of destabilizing and stabilizing mutations of Ste2p, a G protein-coupled receptor in Saccharomyces cerevisiae. Biochemistry. Baker JESriram RMiller BL (2015 Feb 21). Two-dimensional photonic crystals for sensitive microscale chemical and biochemical sensing. Lab on a chip. 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.). Bulger MPalis J (2015 Feb). Environmentally-defined enhancer populations regulate diversity of tissue-resident macrophages. Trends in immunology. Kapogiannis DBoxer ASchwartz JBAbner ELBiragyn AMasharani UFrassetto LPetersen RCMiller BLGoetzl EJ (2015 Feb). Dysfunctionally phosphorylated type 1 insulin receptor substrate in neural-derived blood exosomes of preclinical Alzheimer's disease. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. Salsi EFarah ENetter ZDann JErmolenko DN (2015 Jan 30). Movement of elongation factor G between compact and extended conformations. Journal of molecular biology. Leong LSim DPatel CTran KLiu PHo EThompson TKretschmer PJWakabayashi HFay PJMurphy JE (2015 Jan 8). Noncovalent stabilization of the factor VIII A2 domain enhances efficacy in hemophilia A mouse vascular injury models. Blood. 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. Gibbs PEMiralem TMaines MD (2015). Biliverdin reductase: a target for cancer therapy? Frontiers in pharmacology. Aytenfisu AHSpasic AGrossfield AStern HMathews DH (2015). 99 Improving the amber RNA force field. Journal of biomolecular structure & dynamics. Mathew EDumont ME (2015). A Novel Screening Approach for Optimal and Functional Fusion of T4 Lysozyme in GPCRs. Methods in enzymology. 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. Sloma MFMathews DH (2015). Improving RNA secondary structure prediction with structure mapping data. Methods in enzymology. Bucukovski JLatorre-Margalef NStallknecht DEMiller BL (2015). A Multiplex Label-Free Approach to Avian Influenza Surveillance and Serology. PloS one. 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. 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. Romo TDLeioatts NGrossfield A (2014 Dec 15). Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations. Journal of computational chemistry. O'Connell MROakes BLSternberg SHEast-Seletsky AKaplan MDoudna JA (2014 Dec 11). Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature. 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. Zhu JDavoli TPerriera JMChin CRGaiha GDJohn SPSigiollot FDGao GXu QQu HPertel TSims JSSmith JABaker REMaranda LNg AElledge SJBrass AL (2014 Oct 23). Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents. Cell reports. Lin DGrossfield A (2014 Oct 21). Thermodynamics of antimicrobial lipopeptide binding to membranes: origins of affinity and selectivity. Biophysical journal. 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. Leioatts NSuresh PRomo TDGrossfield A (2014 Oct). Structure-based simulations reveal concerted dynamics of GPCR activation. Proteins. De CLiu DZheng BSingh USChavre SWhite CArnold RDHagen FKChu CKMoffat JF (2014 Oct). β-l-1-[5-(E-2-bromovinyl)-2-(hydroxymethyl)-1,3-(dioxolan-4-yl)] uracil (l-BHDU) prevents varicella-zoster virus replication in a SCID-Hu mouse model and does not interfere with 5-fluorouracil catabolism. Antiviral research. Le NTTakei YIzawa-Ishizawa YHeo KSLee HSmrcka AVMiller BLKo KATure SMorrell CFujiwara KAkaike MAbe J (2014 Oct 1). Identification of activators of ERK5 transcriptional activity by high-throughput screening and the role of endothelial ERK5 in vasoprotective effects induced by statins and antimalarial agents. Journal of immunology (Baltimore, Md. : 1950). Pepenella SMurphy KJHayes JJ (2014 Sep 26). A distinct switch in interactions of the histone H4 tail domain upon salt-dependent folding of nucleosome arrays. The Journal of biological chemistry. Lomakina EBMarsh GWaugh RE (2014 Sep 16). Cell surface topography is a regulator of molecular interactions during chemokine-induced neutrophil spreading. Biophysical journal. Tian LWang CHagen FKGormley MAddya SSoccio RCasimiro MCZhou JPowell MJXu PDeng HSauve AAPestell RG (2014 Sep 15). Acetylation-defective mutant of Pparγ is associated with decreased lipid synthesis in breast cancer cells. Oncotarget. Monaghan MWakabayashi HGriffiths AWintermute JFay PJ (2014 Sep 2). Enhanced factor VIIIa stability of A2 domain interface variants results from an increased apparent affinity for the A2 subunit. Results from an increased apparent affinity for the A2 subunit. Thrombosis and haemostasis. Kurosaki TLi WHoque MPopp MWErmolenko DNTian BMaquat LE (2014 Sep 1). A post-translational regulatory switch on UPF1 controls targeted mRNA degradation. Genes & development. Salter JDMorales GASmith HC (2014 Sep). Structural insights for HIV-1 therapeutic strategies targeting Vif. Trends in biochemical sciences. Kosloski MPShetty KAWakabayashi HFay PJBalu-Iyer SV (2014 Sep). Effects of replacement of factor VIII amino acids Asp519 and Glu665 with Val on plasma survival and efficacy in vivo. The AAPS journal. Jiang TKennedy SDMoss WNKierzek ETurner DH (2014 Aug 19). Secondary structure of a conserved domain in an intron of influenza A M1 mRNA. Biochemistry. McCall MNMcMurray HRLand HAlmudevar A (2014 Aug 15). On non-detects in qPCR data. Bioinformatics (Oxford, England). Fiandaca MSKapogiannis DMapstone MBoxer AEitan ESchwartz JBAbner ELPetersen RCFederoff HJMiller BLGoetzl EJ (2014 Aug 14). Identification of preclinical Alzheimer's disease by a profile of pathogenic proteins in neurally derived blood exosomes: A case-control study. Alzheimer's & dementia : the journal of the Alzheimer's Association.