Education / Graduate Education / PhD Programs / Biophysics, Structural & Computational Biology (BSCB) / Faculty & Students / Students / Publications Publications Cornwell APalli RSingh MVBenoodt LTyrell AAbe JISchifitto GMaggirwar SBThakar J Molecular characterization of atherosclerosis in HIV positive persons.; Scientific reports; Vol 11(1). 2021 Feb 05. Alon RSportiello MKozlovski SKumar AReilly ECZarbock AGarbi NTopham DJ Leukocyte trafficking to the lungs and beyond: lessons from influenza for COVID-19.; Nature reviews. Immunology. 2020 Nov 19. Chavali SSCavender CEMathews DHWedekind JE Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove.; Journal of the American Chemical Society. 2020 Nov 10. Chavali SSMali SMJenkins JLFasan RWedekind JE Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.; The Journal of biological chemistry. 2020 Oct 13. Maji DGlasser EHenderson SGalardi JPulvino MJJenkins JLKielkopf CL Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.; The Journal of biological chemistry. 2020 Oct 05. Steiner DJCognetti JSLuta EPKlose AMBucukovski JBryan MRSchmuke JJNguyen-Contant PSangster MYTopham DJMiller BL Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients.; Biosensors & bioelectronics; Vol 169. 2020 Sep 21. Thakar JQian YBenoodt LRoumanes DQiu XLaniewski NChu CSlaunwhite CWang LMandava AChang IFalsey ARCaserta MTMariani TJScheuermann RHWalsh EETopham DJ Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein.; Vaccine: X; Vol 5. 2020 Aug 07. Schroeder GMDutta DCavender CEJenkins JLPritchett EMBaker CDAshton JMMathews DHWedekind JE Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.; Nucleic acids research. 2020 Jun 29. Hilchey SPPalshikar MGEmo JALi DGarigen JWang JMendelson ESCipolla VThakar JZand MS Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch.; BMC immunology; Vol 21(1). 2020 Mar 18. Benoodt LThakar J Network Analysis of Large-Scale Data and Its Application to Immunology.; Methods in molecular biology (Clifton, N.J.); Vol 2131. 2020. Maji DGrossfield AMKielkopf CL Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery.; Biochimica et biophysica acta. Gene regulatory mechanisms. 2019 Nov 07. Palli RPalshikar MGThakar J Executable pathway analysis using ensemble discrete-state modeling for large-scale data.; PLoS computational biology; Vol 15(9). 2019 Sep. Walsh EEMariani TJChu CGrier AGill SRQiu XWang LHolden-Wiltse JCorbett AThakar JBenoodt LMcCall MNTopham DJFalsey ARCaserta MT Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study.; JMIR research protocols; Vol 8(6). 2019 Jun 06. Chavali SSBonn-Breach RWedekind JE Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery.; The Journal of biological chemistry. 2019 May 12. Loerch SLeach JRHorner SWMaji DJenkins JLPulvino MKielkopf CL The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface.; The Journal of biological chemistry. 2018 Dec 19. Belashov IACrawford DWCavender CEDai PBeardslee PCMathews DHPentelute BLMcNaughton BRWedekind JE Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.; Nucleic acids research. 2018 Jun 29.