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John Stephen Garavelli - Publications

Affiliations: 
University of Delaware, Center for Bioinformatics & Computational Biology 
Area:
Bioinformatics, Proteomics, Biological Information Theory
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26 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, ... ... Garavelli J, et al. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. Bioinformatics (Oxford, England). PMID 32399560 DOI: 10.1093/Bioinformatics/Btaa485  0.445
2019 Chen C, Wang Q, Huang H, Vinayaka CR, Garavelli JS, Arighi CN, Natale DA, Wu CH. PIRSitePredict for protein functional site prediction using position-specific rules. Database : the Journal of Biological Databases and Curation. 2019. PMID 30805646 DOI: 10.1093/Database/Baz026  0.415
2012 Apweiler R, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, Antunes R, Casanova EB, Bely B, Bingley M, Bower L, Bursteinas B, Chan WM, Chavali G, Da Silva A, Dimmer E, ... ... Garavelli J, et al. Reorganizing the protein space at the Universal Protein Resource (UniProt) Nucleic Acids Research. 40: D71-D75. PMID 22102590 DOI: 10.1093/nar/gkr981  0.391
2011 Apweiler R, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, Antunes R, Barrell D, Bely B, Bingley M, Binns D, Bower L, Browne P, Chan WM, Dimmer E, Eberhardt R, ... ... Garavelli J, et al. Ongoing and future developments at the Universal Protein Resource Nucleic Acids Research. 39: D214-D219. PMID 21051339 DOI: 10.1093/Nar/Gkq1020  0.466
2009 Furnham N, Garavelli JS, Apweiler R, Thornton JM. Missing in action: enzyme functional annotations in biological databases. Nature Chemical Biology. 5: 521-5. PMID 19620987 DOI: 10.1038/Nchembio0809-521  0.382
2008 Montecchi-Palazzi L, Beavis R, Binz PA, Chalkley RJ, Cottrell J, Creasy D, Shofstahl J, Seymour SL, Garavelli JS. The PSI-MOD community standard for representation of protein modification data. Nature Biotechnology. 26: 864-6. PMID 18688235 DOI: 10.1038/Nbt0808-864  0.343
2007 Asara JM, Garavelli JS, Slatter DA, Schweitzer MH, Freimark LM, Phillips M, Cantley LC. Interpreting sequences from mastodon and T. rex. Science (New York, N.Y.). 317: 1324-5. PMID 17823333 DOI: 10.1126/Science.317.5843.1324  0.307
2006 Taylor CF, Hermjakob H, Julian RK, Garavelli JS, Aebersold R, Apweiler R. The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). Omics : a Journal of Integrative Biology. 10: 145-51. PMID 16901219 DOI: 10.1089/Omi.2006.10.145  0.311
2006 Orchard S, Apweiler R, Barkovich R, Field D, Garavelli JS, Horn D, Jones A, Jones P, Julian R, McNally R, Nerothin J, Paton N, Pizarro A, Seymour S, Taylor C, et al. Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA. Proteomics. 6: 4439-43. PMID 16897683 DOI: 10.1002/Pmic.200600452  0.339
2006 Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R. Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics. 6: 738-41. PMID 16411267 DOI: 10.1002/Pmic.200500868  0.361
2004 LeDuc RD, Taylor GK, Kim YB, Januszyk TE, Bynum LH, Sola JV, Garavelli JS, Kelleher NL. ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Research. 32: W340-5. PMID 15215407 DOI: 10.1093/Nar/Gkh447  0.448
2004 Farriol-Mathis N, Garavelli JS, Boeckmann B, Duvaud S, Gasteiger E, Gateau A, Veuthey AL, Bairoch A. Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics. 4: 1537-50. PMID 15174124 DOI: 10.1002/Pmic.200300764  0.407
2004 Garavelli JS. The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics. 4: 1527-33. PMID 15174122 DOI: 10.1002/Pmic.200300777  0.508
2003 Garavelli JS. The RESID Database of Protein Modifications: 2003 developments. Nucleic Acids Research. 31: 499-501. PMID 12520062 DOI: 10.1093/Nar/Gkg038  0.501
2002 Wolfe MT, Heo J, Garavelli JS, Ludden PW. Hydroxylamine reductase activity of the hybrid cluster protein from Escherichia coli. Journal of Bacteriology. 184: 5898-902. PMID 12374823 DOI: 10.1128/Jb.184.21.5898-5902.2002  0.352
2001 Garavelli JS, Hou Z, Pattabiraman N, Stephens RM. The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database. Nucleic Acids Research. 29: 199-201. PMID 11125090 DOI: 10.1093/Nar/29.1.199  0.473
2001 Barker WC, Garavelli JS, Hou Z, Huang H, Ledley RS, McGarvey PB, Mewes HW, Orcutt BC, Pfeiffer F, Tsugita A, Vinayaka CR, Xiao C, Yeh LS, Wu C. Protein Information Resource: a community resource for expert annotation of protein data. Nucleic Acids Research. 29: 29-32. PMID 11125041 DOI: 10.1093/Nar/29.1.29  0.507
2000 McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LS, Xiao C, Wu CH. PIR: a new resource for bioinformatics. Bioinformatics (Oxford, England). 16: 290-1. PMID 10869023 DOI: 10.1093/Bioinformatics/16.3.290  0.476
2000 Garavelli JS. The RESID database of protein structure modifications: 2000 update. Nucleic Acids Research. 28: 209-11. PMID 10592227 DOI: 10.1093/Nar/28.1.209  0.468
2000 Barker WC, Garavelli JS, Huang H, McGarvey PB, Orcutt BC, Srinivasarao GY, Xiao C, Yeh LS, Ledley RS, Janda JF, Pfeiffer F, Mewes HW, Tsugita A, Wu C. The protein information resource (PIR). Nucleic Acids Research. 28: 41-4. PMID 10592177 DOI: 10.1093/Nar/28.1.41  0.48
1999 Garavelli JS. The RESID Database of protein structure modifications. Nucleic Acids Research. 27: 198-9. PMID 9847179 DOI: 10.1093/Nar/27.1.198  0.459
1999 Barker WC, Garavelli JS, McGarvey PB, Marzec CR, Orcutt BC, Srinivasarao GY, Yeh LS, Ledley RS, Mewes HW, Pfeiffer F, Tsugita A, Wu C. The PIR-International Protein Sequence Database. Nucleic Acids Research. 27: 39-43. PMID 9847137 DOI: 10.1093/Nar/24.1.17  0.472
1998 Barker WC, Garavelli JS, Haft DH, Hunt LT, Marzec CR, Orcutt BC, Srinivasarao GY, Yeh LS, Ledley RS, Mewes HW, Pfeiffer F, Tsugita A. The PIR-International Protein Sequence Database. Nucleic Acids Research. 26: 27-32. PMID 9399794 DOI: 10.1093/nar/26.1.27  0.382
1997 George DG, Dodson RJ, Garavelli JS, Haft DH, Hunt LT, Marzec CR, Orcutt BC, Sidman KE, Srinivasarao GY, Yeh LS, Arminski LM, Ledley RS, Tsugita A, Barker WC. The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database. Nucleic Acids Research. 25: 24-8. PMID 9016497 DOI: 10.1093/Nar/25.1.24  0.468
1991 Barker WC, George DG, Hunt LT, Garavelli JS. The PIR protein sequence database. Nucleic Acids Research. 19: 2231-36. PMID 2041808 DOI: 10.1093/Nar/19.Suppl.2231  0.443
1974 Noyes BE, Glatthaar BE, Garavelli JS, Bradshaw RA. Structural and functional similarities between mitochondrial malate dehydrogenase and L-3-hydroxyacyl CoA dehydrogenase. Proceedings of the National Academy of Sciences of the United States of America. 71: 1334-8. PMID 4133851 DOI: 10.1073/Pnas.71.4.1334  0.454
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