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Biological Magnetic Resonance Data Bank.
Hoch, Jeffrey C; Baskaran, Kumaran; Burr, Harrison; Chin, John; Eghbalnia, Hamid R; Fujiwara, Toshimichi; Gryk, Michael R; Iwata, Takeshi; Kojima, Chojiro; Kurisu, Genji; Maziuk, Dmitri; Miyanoiri, Yohei; Wedell, Jonathan R; Wilburn, Colin; Yao, Hongyang; Yokochi, Masashi Nucleic acids research 2023 Jan;51(D1):D368-D376
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Merging NMR Data and Computation Facilitates Data-Centered Research
Baskaran Kumaran, Craft D. Levi, Eghbalnia Hamid R., Gryk Michael R., Hoch Jeffrey C., Maciejewski Mark W., Schuyler Adam D., Wedell Jonathan R., Wilburn Colin W. Frontiers in Molecular Biosciences 2022 Jan;8
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Merging NMR Data and Computation Facilitates Data-Centered Research.
Baskaran, Kumaran; Craft, D Levi; Eghbalnia, Hamid R; Gryk, Michael R; Hoch, Jeffrey C; Maciejewski, Mark W; Schuyler, Adam D; Wedell, Jonathan R; Wilburn, Colin W Frontiers in molecular biosciences 2021 Nov;8817175
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“Deconstructing the STAR File Format.” Presented at Balisage: The Markup Conference 2021, , August 2 - 6, 2021. In Proceedings of Balisage: The Markup Conference 2021. , vol. 26 (2021). https://doi.org/10.4242/BalisageVol26.Gryk01.
Gryk, Michael R. Balisage Series on Markup Technologies 2021 Aug;26
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Semantic Mediation to Improve Reproducibility for Biomolecular NMR Analysis.
Gryk, Michael R; Ludäscher, Bertram Transforming digital worlds : 13th International Conference, iConference 2018, Sheffield, UK, March 25-28, 2018, Proceedings. International Conference on Transforming Digital Worlds (13th : 2018 : Sheffield, England) 2018 Mar;10766620-625
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NMRbox: A Resource for Biomolecular NMR Computation.
Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C Biophysical journal 2017 Apr;112(8):1529-1534
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Workflows and Provenance: Toward Information Science Solutions for the Natural Sciences.
Gryk, M.R. & Ludäscher, B. Library Trends 2017 Apr;65555-562
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CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR-protein spectral assignment.
Fenwick, Matthew; Hoch, Jeffrey C; Ulrich, Eldon; Gryk, Michael R Journal of biomolecular NMR 2015 Aug;63(2):141-50
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CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.
Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R Journal of biomolecular NMR 2015 Jul;62(3):313-26
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A Pipeline Software Architecture for NMR Spectrum Data Translation.
Ellis, Heidi J C; Weatherby, Gerard; Nowling, Ronald J; Vyas, Jay; Fenwick, Matthew; Gryk, Michael R Computing in science & engineering 2013 Jan;15(1):76-83
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Parser Combinators: a Practical Application for Generating Parsers for NMR Data.
Fenwick, Matthew; Weatherby, Gerard; Ellis, Heidi Jc; Gryk, Michael R Proceedings of the ... International Conference on Information Technology: New Generations. International Conference on Information Technology: New Generations 2013 Jan;
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Achieving high accuracy prediction of minimotifs.
Mi, Tian; Rajasekaran, Sanguthevar; Merlin, Jerlin Camilus; Gryk, Michael; Schiller, Martin R PloS one 2012 Jan;7(9):e45589
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An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities.
Fenwick, Matthew; Sesanker, Colbert; Schiller, Martin R; Ellis, Heidi Jc; Hinman, M Lee; Vyas, Jay; Gryk, Michael R Proceedings of the ... International Conference on Information Technology: New Generations. International Conference on Information Technology: New Generations 2012 Jan;201289-94
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Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences.
Mi, Tian; Merlin, Jerlin Camilus; Deverasetty, Sandeep; Gryk, Michael R; Bill, Travis J; Brooks, Andrew W; Lee, Logan Y; Rathnayake, Viraj; Ross, Christian A; Sargeant, David P; Strong, Christy L; Watts, Paula; Rajasekaran, Sanguthevar; Schiller, Martin R Nucleic acids research 2012 Jan;40(Database issue):D252-60
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Secondary structure, a missing component of sequence-based minimotif definitions.
Sargeant, David P; Gryk, Michael R; Maciejewski, Mark W; Thapar, Vishal; Kundeti, Vamsi; Rajasekaran, Sanguthevar; Romero, Pedro; Dunker, Keith; Li, Shun-Cheng; Kaneko, Tomonori; Schiller, Martin R PloS one 2012 Jan;7(12):e49957
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CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.
Nowling, Ronald J; Vyas, Jay; Weatherby, Gerard; Fenwick, Matthew W; Ellis, Heidi J C; Gryk, Michael R Journal of biomolecular NMR 2011 May;50(1):83-9
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Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins.
Ellis, Heidi J C; Nowling, Ronald J; Vyas, Jay; Martyn, Timothy O; Gryk, Michael R Proceedings of the ... International Conference on Information Technology: New Generations. International Conference on Information Technology: New Generations 2011 Apr;1014-1020
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MimoSA: a system for minimotif annotation.
Vyas, Jay; Nowling, Ronald J; Meusburger, Thomas; Sargeant, David; Kadaveru, Krishna; Gryk, Michael R; Kundeti, Vamsi; Rajasekaran, Sanguthevar; Schiller, Martin R BMC bioinformatics 2010 Jan;11328
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VENN, a tool for titrating sequence conservation onto protein structures.
Vyas, Jay; Gryk, Michael R; Schiller, Martin R Nucleic acids research 2009 Oct;37(18):e124
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A proposed syntax for Minimotif Semantics, version 1.
Vyas, Jay; Nowling, Ronald J; Maciejewski, Mark W; Rajasekaran, Sanguthevar; Gryk, Michael R; Schiller, Martin R BMC genomics 2009 Jan;10360
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Minimotif miner 2nd release: a database and web system for motif search.
Rajasekaran, Sanguthevar; Balla, Sudha; Gradie, Patrick; Gryk, Michael R; Kadaveru, Krishna; Kundeti, Vamsi; Maciejewski, Mark W; Mi, Tian; Rubino, Nicholas; Vyas, Jay; Schiller, Martin R Nucleic acids research 2009 Jan;37(Database issue):D185-90
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Automatic maximum entropy spectral reconstruction in NMR.
Mobli, Mehdi; Maciejewski, Mark W; Gryk, Michael R; Hoch, Jeffrey C Journal of biomolecular NMR 2007 Oct;39(2):133-9
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Conceptual-level workflow modeling of scientific experiments using NMR as a case study.
Verdi, Kacy K; Ellis, Heidi Jc; Gryk, Michael R BMC bioinformatics 2007 Jan;831
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Minimotif Miner: a tool for investigating protein function.
Balla, Sudha; Thapar, Vishal; Verma, Snigdha; Luong, Thaibinh; Faghri, Tanaz; Huang, Chun-Hsi; Rajasekaran, Sanguthevar; del Campo, Jacob J; Shinn, Jessica H; Mohler, William A; Maciejewski, Mark W; Gryk, Michael R; Piccirillo, Bryan; Schiller, Stanley R; Schiller, Martin R Nature methods 2006 Mar;3(3):175-7
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High-performance exact algorithms for motif search.
Rajasekaran, Sanguthevar; Balla, Sudha; Huang, Chun-Hsi; Thapar, Vishal; Gryk, Michael; Maciejewski, Mark; Schiller, Martin Journal of clinical monitoring and computing 2005 Oct;19(4-5):319-28
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Identification of small molecule synthetic inhibitors of DNA polymerase beta by NMR chemical shift mapping.
Hu, Hong-Yu; Horton, Julie K; Gryk, Michael R; Prasad, Rajendra; Naron, Jana M; Sun, Di-An; Hecht, Sidney M; Wilson, Samuel H; Mullen, Gregory P The Journal of biological chemistry 2004 Sep;279(38):39736-44
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Delineation and analysis of the conceptual data model implied by the "IUPAC Recommendations for Biochemical Nomenclature".
Fox-Erlich, Susan; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R Protein science : a publication of the Protein Society 2004 Sep;13(9):2559-63
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Mapping of the interaction interface of DNA polymerase beta with XRCC1.
Gryk, Michael R; Marintchev, Assen; Maciejewski, Mark W; Robertson, Anthony; Wilson, Samuel H; Mullen, Gregory P Structure (London, England : 1993) 2002 Dec;10(12):1709-20
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Solution structure of a viral DNA repair polymerase.
Maciejewski, M W; Shin, R; Pan, B; Marintchev, A; Denninger, A; Mullen, M A; Chen, K; Gryk, M R; Mullen, G P Nature structural biology 2001 Nov;8(11):936-41
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Solution structure of the single-strand break repair protein XRCC1 N-terminal domain.
Marintchev, A; Mullen, M A; Maciejewski, M W; Pan, B; Gryk, M R; Mullen, G P Nature structural biology 1999 Sep;6(9):884-93
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Heteronuclear relaxation study of the PH domain of beta-spectrin: restriction of loop motions upon binding inositol trisphosphate.
Gryk, M R; Abseher, R; Simon, B; Nilges, M; Oschkinat, H Journal of molecular biology 1998 Jul;280(5):879-96
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Flexibility of DNA binding domain of trp repressor required for recognition of different operator sequences.
Gryk, M R; Jardetzky, O; Klig, L S; Yanofsky, C Protein science : a publication of the Protein Society 1996 Jun;5(6):1195-7
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AV77 hinge mutation stabilizes the helix-turn-helix domain of trp repressor.
Gryk, M R; Jardetzky, O Journal of molecular biology 1996 Jan;255(1):204-14
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Investigation of protein amide-proton exchange by 1H longitudinal spin relaxation.
Zheng, Z; Gryk, M R; Finucane, M D; Jardetzky, O Journal of magnetic resonance. Series B 1995 Sep;108(3):220-34
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Solution dynamics of the trp repressor: a study of amide proton exchange by T1 relaxation.
Gryk, M R; Finucane, M D; Zheng, Z; Jardetzky, O Journal of molecular biology 1995 Mar;246(5):618-27
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Embedding Analytics within the Curation of Scientifc Workfows.
Weatherby, G. & Gryk, M.R. International Journal of Digital Curation 15