Education / Graduate Education / PhD Programs / Biophysics, Structural & Computational Biology (BSCB) / Students / Publications Publications Murphy KJCutter ARFang HPostnikov YVBustin MHayes JJ (2017 Sep 29). HMGN1 and 2 remodel core and linker histone tail domains within chromatin. Nucleic acids research. Tan ZFu YSharma GMathews DH (2017 Sep 28). TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs. Nucleic acids research. Glasser EAgrawal AAJenkins JLKielkopf CL (2017 Sep 01). Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry. 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. Hansraj NHamdi AWise ESDiChiacchio LSarkar RToursavadkohi S (2017 May 04). Open and Endovascular Management of Inferior Mesenteric Artery Aneurysms: A Report of Two Cases. Annals of vascular surgery. Harris DGHuffner MECroal-Abrahams LDiChiacchio LFarivar BSAyers JDToursavadkohi SRabin JCrawford RS (2017 Apr 05). Thoracic Endovascular Repair of Blunt Thoracic Aortic Injury in the Setting of an Aberrant Right Subclavian Artery. Annals of vascular surgery. Kamen CGarland SNHeckler CEPeoples ARKleckner IRCole CLPerlis MLMorrow GRMustian KMRoscoe JA (2017 Jan 27). Social Support, Insomnia, and Adherence to Cognitive Behavioral Therapy for Insomnia After Cancer Treatment. Behavioral sleep medicine. Peoples ARGarland SNPerlis MLSavard JHeckler CEKamen CSRyan JLMustian KMJanelsins MCPeppone LJMorrow GRRoscoe JA (2017 Jan 19). Effects of cognitive behavioral therapy for insomnia and armodafinil on quality of life in cancer survivors: a randomized placebo-controlled trial. Journal of cancer survivorship : research and practice. 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. Peoples ARRoscoe JABlock RCHeckler CERyan JLMustian KMJanelsins MCPeppone LJMoore DFColes CHoelzer KLMorrow GRDozier AM (2016 Dec 20). Nausea and disturbed sleep as predictors of cancer-related fatigue in breast cancer patients: a multicenter NCORP study. Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer. 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.). Fang HWei SLee THHayes JJ (2016 Nov 02). Chromatin structure-dependent conformations of the H1 CTD. Nucleic acids research. Heckler CEGarland SNPeoples ARPerlis MLShayne MMorrow GRKamen CHoefler JRoscoe JA (2016 May). Cognitive behavioral therapy for insomnia, but not armodafinil, improves fatigue in cancer survivors with insomnia: a randomized placebo-controlled trial. Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer. Yue HFang HWei SHayes JJLee TH (2016 Apr 12). Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome. Biochemistry. DiChiacchio LSloma MFMathews DH (2016 Apr 1). AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. Bioinformatics (Oxford, England). Garland SNRoscoe JAHeckler CEBarilla HGehrman PFindley JCPeoples ARMorrow GRKamen CPerlis ML (2016 Apr). Effects of armodafinil and cognitive behavior therapy for insomnia on sleep continuity and daytime sleepiness in cancer survivors. Sleep medicine. Peoples ARBushunow PWGarland SNHeckler CERoscoe JAPeppone LLDudgeon DJKirshner JJBanerjee TKHopkins JODakhil SRFlannery MAMorrow GR (2016 Mar). Buspirone for management of dyspnea in cancer patients receiving chemotherapy: a randomized placebo-controlled URCC CCOP study. Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer. 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. 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. 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.). 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. Lin D (2015 Sep 21). Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors. The Journal of chemical physics. Lin DGrossfield A (2015 Aug 18). Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity. Biophysical journal. Roscoe JAGarland SNHeckler CEPerlis MLPeoples ARShayne MSavard JDaniels NPMorrow GR (2015 Jan 10). Randomized placebo-controlled trial of cognitive behavioral therapy and armodafinil for insomnia after cancer treatment. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 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. Fu YSharma GMathews DH (2014 Dec 16). Dynalign II: common secondary structure prediction for RNA homologs with domain insertions. Nucleic acids research. 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. Lin DGrossfield A (2014 Oct 21). Thermodynamics of antimicrobial lipopeptide binding to membranes: origins of affinity and selectivity. Biophysical journal. Zhang YXu ZShen XPan W (2014 Aug 1). Testing for association with multiple traits in generalized estimation equations, with application to neuroimaging data. NeuroImage. Wei CYu LCui CLin JWei CMathews NHuo FSritharan TXu Z (2014 Jul 25). Ultrathin MnO(2) nanoflakes as efficient catalysts for oxygen reduction reaction. Chemical communications (Cambridge, England). Loerch SMaucuer AManceau VGreen MRKielkopf CL (2014 Jun 20). Cancer-relevant splicing factor CAPERα engages the essential splicing factor SF3b155 in a specific ternary complex. The Journal of biological chemistry. Aytenfisu AHSpasic ASeetin MGSerafini JMathews DH (2014 Mar 11). Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA. Journal of chemical theory and computation. Ofori LOHilimire TABennett RPBrown NWSmith HCMiller BL (2014 Feb 13). High-affinity recognition of HIV-1 frameshift-stimulating RNA alters frameshifting in vitro and interferes with HIV-1 infectivity. Journal of medicinal chemistry. Kamen CTejani MAChandwani KJanelsins MPeoples ARRoscoe JAMorrow GR (2014 Jan 5). Anticipatory nausea and vomiting due to chemotherapy. European journal of pharmacology. Johnson DGKhire TSLyubarskaya YLSmith KJDesormeaux JPTaylor JGGaborski TRShestopalov AAStriemer CCMcGrath JL (2013 Nov). Ultrathin silicon membranes for wearable dialysis. Advances in chronic kidney disease. Letzring DPWolf ASBrule CEGrayhack EJ (2013 Sep). Translation of CGA codon repeats in yeast involves quality control components and ribosomal protein L1. RNA (New York, N.Y.). Bellaousov SReuter JSSeetin MGMathews DH (2013 Jul). RNAstructure: Web servers for RNA secondary structure prediction and analysis. Nucleic acids research. Jenkins JLAgrawal AAGupta AGreen MRKielkopf CL (2013 Apr 1). U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic acids research. Janelsins MCTejani MAKamen CPeoples ARMustian KMMorrow GR (2013 Apr). Current pharmacotherapy for chemotherapy-induced nausea and vomiting in cancer patients. Expert opinion on pharmacotherapy. Wang WMaucuer AGupta AManceau VThickman KRBauer WJKennedy SDWedekind JEGreen MRKielkopf CL (2013 Feb 5). Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex. Structure (London, England : 1993). Schmidt KXu ZMathews DHButler JS (2012 Oct). Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance. RNA (New York, N.Y.). Peoples ARLee JWeinfeld MMilligan JRBernhard WA (2012 Jul). Yields of damage to C4' deoxyribose and to pyrimidines in pUC18 by the direct effect of ionizing radiation. Nucleic acids research. Seetin MGMathews DH (2012 Mar 15). TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinformatics (Oxford, England). Horn JNSengillo JDLin DRomo TDGrossfield A (2012 Feb). Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics. Biochimica et biophysica acta. Fang HClark DJHayes JJ (2012 Feb). DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain. Nucleic acids research. Xu ZAlmudevar AMathews DH (2012 Feb). Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic acids research. Seetin MGMathews DH (2012). RNA structure prediction: an overview of methods. Methods in molecular biology (Clifton, N.J.). Seetin MGMathews DH (2011 Jul 30). Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. Journal of computational chemistry. Caterino TLFang HHayes JJ (2011 Jun). Nucleosome linker DNA contacts and induces specific folding of the intrinsically disordered H1 carboxyl-terminal domain. Molecular and cellular biology. Vockenhuber MPSharma CMStatt MGSchmidt DXu ZDietrich SLiesegang HMathews DHSuess B (2011 May). Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA biology. Gupta AKielkopf CL (2011 Apr 1). Purification, crystallization and preliminary X-ray crystallographic analysis of a central domain of human splicing factor 1. Acta crystallographica. Section F, Structural biology and crystallization communications. Xu ZMathews DH (2011 Mar 1). Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinformatics (Oxford, England). Gupta AJenkins JLKielkopf CL (2011 Feb 4). RNA induces conformational changes in the SF1/U2AF65 splicing factor complex. Journal of molecular biology. Letzring DPDean KMGrayhack EJ (2010 Dec). Control of translation efficiency in yeast by codon-anticodon interactions. RNA (New York, N.Y.). Peoples ARMercer KRBernhard WA (2010 Jul 22). What fraction of DNA double-strand breaks produced by the direct effect is accounted for by radical pairs? The journal of physical chemistry. B. Piekna-Przybylska DDiChiacchio LMathews DHBambara RA (2010 Jan). A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transfer. Nature structural & molecular biology.