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John Lute Markley

TitleProfessor Adjoint
InstitutionUniversity of Colorado Denver - Denver Campus
DepartmentCLAS-Chemistry

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Shao H, Boulton S, Olivieri C, Mohamed H, Akimoto M, Subrahmanian MV, Veglia G, Markley JL, Melacini G, Lee W. CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. Bioinformatics. 2021 05 23; 37(8):1176-1177. PMID: 32926121.
      View in: PubMed
    2. Rahimi M, Lee Y, Markley JL, Lee W. iPick: Multiprocessing software for integrated NMR signal detection and validation. J Magn Reson. 2021 07; 328:106995. PMID: 34004411.
      View in: PubMed
    3. Weber DK, Wang S, Markley JL, Veglia G, Lee W. PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. Bioinformatics. 2020 05 01; 36(9):2915-2916. PMID: 31930377.
      View in: PubMed
    4. Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. Nat Commun. 2019 12 09; 10(1):5612. PMID: 31819058.
      View in: PubMed
    5. Lee W, Bahrami A, Dashti HT, Eghbalnia HR, Tonelli M, Westler WM, Markley JL. I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR. 2019 May; 73(5):213-222. PMID: 31165321.
      View in: PubMed
    6. Frederick RO, Haruta M, Tonelli M, Lee W, Cornilescu G, Cornilescu CC, Sussman MR, Markley JL. Function and solution structure of the Arabidopsis thaliana RALF8 peptide. Protein Sci. 2019 06; 28(6):1115-1126. PMID: 31004454.
      View in: PubMed
    7. Shrestha OK, Sharma R, Tomiczek B, Lee W, Tonelli M, Cornilescu G, Stolarska M, Nierzwicki L, Czub J, Markley JL, Marszalek J, Ciesielski SJ, Craig EA. Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70. PLoS One. 2019; 14(5):e0217098. PMID: 31091298.
      View in: PubMed
    8. Lee W, Tonelli M, Wu C, Aceti DJ, Amarasinghe GK, Markley JL. Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600-739 construct. Biomol NMR Assign. 2019 10; 13(2):315-319. PMID: 31076990.
      View in: PubMed
    9. Lee W, Markley JL. PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinformatics. 2018 05 01; 34(9):1586-1588. PMID: 29281006.
      View in: PubMed
    10. Schilke BA, Ciesielski SJ, Ziegelhoffer T, Kamiya E, Tonelli M, Lee W, Cornilescu G, Hines JK, Markley JL, Craig EA. Broadening the functionality of a J-protein/Hsp70 molecular chaperone system. PLoS Genet. 2017 Oct; 13(10):e1007084. PMID: 29084221.
      View in: PubMed
    11. Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR. 2016 06; 65(2):51-7. PMID: 27169728.
      View in: PubMed
    12. Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Henzler-Wildman KA, Markley JL. Integrative NMR for biomolecular research. J Biomol NMR. 2016 04; 64(4):307-32. PMID: 27023095.
      View in: PubMed
    13. Stark JL, Eghbalnia HR, Lee W, Westler WM, Markley JL. NMRmix: A Tool for the Optimization of Compound Mixtures in 1D (1)H NMR Ligand Affinity Screens. J Proteome Res. 2016 Apr 01; 15(4):1360-8. PMID: 26965640.
      View in: PubMed
    14. Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL. Probabilistic validation of protein NMR chemical shift assignments. J Biomol NMR. 2016 Jan; 64(1):17-25. PMID: 26724815.
      View in: PubMed
    15. Dashti H, Lee W, Tonelli M, Cornilescu CC, Cornilescu G, Assadi-Porter FM, Westler WM, Eghbalnia HR, Markley JL. NMRFAM-SDF: a protein structure determination framework. J Biomol NMR. 2015 Aug; 62(4):481-95. PMID: 25900069.
      View in: PubMed
    16. Lee W, Tonelli M, Markley JL. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics. 2015 Apr 15; 31(8):1325-7. PMID: 25505092.
      View in: PubMed
    17. Lee W, Stark JL, Markley JL. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. J Biomol NMR. 2014 Nov; 60(2-3):73-5. PMID: 25190042.
      View in: PubMed
    18. Lee W, Watters KE, Troupis AT, Reinen NM, Suchy FP, Moyer KL, Frederick RO, Tonelli M, Aceti DJ, Palmenberg AC, Markley JL. Solution structure of the 2A protease from a common cold agent, human rhinovirus C2, strain W12. PLoS One. 2014; 9(6):e97198. PMID: 24937088.
      View in: PubMed
    19. Tonelli M, Eller CH, Singarapu KK, Lee W, Bahrami A, Westler WM, Raines RT, Markley JL. Assignments of RNase A by ADAPT-NMR and enhancer. Biomol NMR Assign. 2015 Apr; 9(1):81-8. PMID: 24619609.
      View in: PubMed
    20. Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carlson S, Shi X, Balaz S, Markley JL, Glass KC. Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. J Mol Biol. 2014 Apr 17; 426(8):1661-76. PMID: 24333487.
      View in: PubMed
    21. Lee W, Hu K, Tonelli M, Bahrami A, Neuhardt E, Glass KC, Markley JL. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers. J Magn Reson. 2013 Nov; 236:83-8. PMID: 24091140.
      View in: PubMed
    22. Lee W, Bahrami A, Markley JL. ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. Bioinformatics. 2013 Feb 15; 29(4):515-7. PMID: 23220573.
      View in: PubMed
    23. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL. PACSY, a relational database management system for protein structure and chemical shift analysis. J Biomol NMR. 2012 Oct; 54(2):169-79. PMID: 22903636.
      View in: PubMed
    24. Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW. NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 2012 Jan; 40(Database issue):D519-24. PMID: 22139937.
      View in: PubMed
    25. Lee W, Kim JH, Westler WM, Markley JL. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. Bioinformatics. 2011 Jun 15; 27(12):1727-8. PMID: 21511715.
      View in: PubMed
    26. Takeda M, Hallenga K, Shigezane M, Waelchli M, Löhr F, Markley JL, Kainosho M. Construction and performance of an NMR tube with a sample cavity formed within magnetic susceptibility-matched glass. J Magn Reson. 2011 Apr; 209(2):167-73. PMID: 21316281.
      View in: PubMed
    27. Lee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JL. PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Bioinformatics. 2009 Aug 15; 25(16):2085-7. PMID: 19497931.
      View in: PubMed
    28. Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF, Westler WM, Eghbalnia HR, Sussman MR, Markley JL. Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol. 2008 Feb; 26(2):162-4. PMID: 18259166.
      View in: PubMed
    29. Wu WJ, Vidugiris G, Mooberry ES, Westler WM, Markley JL. Mixing apparatus for preparing NMR samples under pressure. J Magn Reson. 2003 Sep; 164(1):84-91. PMID: 12932460.
      View in: PubMed
    30. Dzakula Z, DeRider ML, Westler WM, Macura S, Markley JL. Analysis of error propagation from NMR-derived internuclear distances into molecular structure of cyclo-pro-gly. J Magn Reson. 1998 Dec; 135(2):454-65. PMID: 9878473.
      View in: PubMed
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