• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4643668)   Today's Articles (355)   Subscriber (50597)
For: Ross KE, Huang H, Ren J, Arighi CN, Li G, Tudor CO, Lv M, Lee JY, Chen SC, Vijay-Shanker K, Wu CH. iPTMnet: Integrative Bioinformatics for Studying PTM Networks. Methods Mol Biol 2017;1558:333-53. [PMID: 28150246 DOI: 10.1007/978-1-4939-6783-4_16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Number Cited by Other Article(s)
1
Arici MK, Tuncbag N. Unveiling hidden connections in omics data via pyPARAGON: an integrative hybrid approach for disease network construction. Brief Bioinform 2024;25:bbae399. [PMID: 39163205 PMCID: PMC11334722 DOI: 10.1093/bib/bbae399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/26/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024]  Open
2
Salcedo MV, Gravel N, Keshavarzi A, Huang LC, Kochut KJ, Kannan N. Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding. PeerJ 2023;11:e15815. [PMID: 37868056 PMCID: PMC10590106 DOI: 10.7717/peerj.15815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/10/2023] [Indexed: 10/24/2023]  Open
3
Kao DS, Du Y, DeMarco AG, Min S, Hall MC, Rochet JC, Tao WA. Identification of Novel Kinases of Tau Using Fluorescence Complementation Mass Spectrometry (FCMS). Mol Cell Proteomics 2022;21:100441. [PMID: 36379402 PMCID: PMC9755369 DOI: 10.1016/j.mcpro.2022.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]  Open
4
Gupta P, Venkadesan S, Mohanty D. Pf-Phospho: a machine learning-based phosphorylation sites prediction tool for Plasmodium proteins. Brief Bioinform 2022;23:6618232. [PMID: 35753700 DOI: 10.1093/bib/bbac249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/14/2022] [Accepted: 05/28/2022] [Indexed: 12/13/2022]  Open
5
OUP accepted manuscript. Hum Mol Genet 2022;31:2236-2261. [DOI: 10.1093/hmg/ddac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/12/2022]  Open
6
Liu Y, Yang H, Liu X, Gu H, Li Y, Sun C. Protein acetylation: a novel modus of obesity regulation. J Mol Med (Berl) 2021;99:1221-1235. [PMID: 34061242 DOI: 10.1007/s00109-021-02082-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/09/2021] [Accepted: 04/21/2021] [Indexed: 11/27/2022]
7
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. PATTERNS 2021;2:100257. [PMID: 34179843 PMCID: PMC8212145 DOI: 10.1016/j.patter.2021.100257] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/10/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
8
Caufield JH, Sigdel D, Fu J, Choi H, Guevara-Gonzalez V, Wang D, Ping P. Cardiovascular Informatics: building a bridge to data harmony. Cardiovasc Res 2021;118:732-745. [PMID: 33751044 DOI: 10.1093/cvr/cvab067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022]  Open
9
PhosPhAt 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions. Methods Mol Biol 2021;2358:189-202. [PMID: 34270056 DOI: 10.1007/978-1-0716-1625-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
10
Shi XX, Wu FX, Mei LC, Wang YL, Hao GF, Yang GF. Bioinformatics toolbox for exploring protein phosphorylation network. Brief Bioinform 2020;22:5871447. [PMID: 32666116 DOI: 10.1093/bib/bbaa134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/15/2020] [Accepted: 06/02/2020] [Indexed: 01/23/2023]  Open
11
Bensimon A, Koch JP, Francica P, Roth SM, Riedo R, Glück AA, Orlando E, Blaukat A, Aebersold DM, Zimmer Y, Aebersold R, Medová M. Deciphering MET-dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics. Mol Oncol 2020;14:1185-1206. [PMID: 32336009 PMCID: PMC7266272 DOI: 10.1002/1878-0261.12696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]  Open
12
Cunningham DL, Sarhan AR, Creese AJ, Larkins KPB, Zhao H, Ferguson HR, Brookes K, Marusiak AA, Cooper HJ, Heath JK. Differential responses to kinase inhibition in FGFR2-addicted triple negative breast cancer cells: a quantitative phosphoproteomics study. Sci Rep 2020;10:7950. [PMID: 32409632 PMCID: PMC7224374 DOI: 10.1038/s41598-020-64534-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/25/2020] [Indexed: 12/12/2022]  Open
13
Lin S, Wang C, Zhou J, Shi Y, Ruan C, Tu Y, Yao L, Peng D, Xue Y. EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Brief Bioinform 2020;22:298-307. [PMID: 32008039 DOI: 10.1093/bib/bbz169] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022]  Open
14
Gavali S, Cowart J, Chen C, Ross KE, Arighi C, Wu CH. RESTful API for iPTMnet: a resource for protein post-translational modification network discovery. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020;2020:5829784. [PMID: 32395768 PMCID: PMC7216315 DOI: 10.1093/database/baz157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/09/2019] [Accepted: 12/23/2019] [Indexed: 11/12/2022]
15
Fert-Bober J, Murray CI, Parker SJ, Van Eyk JE. Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. Circ Res 2019;122:1221-1237. [PMID: 29700069 DOI: 10.1161/circresaha.118.310966] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
16
Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH. iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Res 2019;46:D542-D550. [PMID: 29145615 PMCID: PMC5753337 DOI: 10.1093/nar/gkx1104] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/24/2017] [Indexed: 12/19/2022]  Open
17
Sandall CF, MacDonald JA. Effects of phosphorylation on the NLRP3 inflammasome. Arch Biochem Biophys 2019;670:43-57. [PMID: 30844378 DOI: 10.1016/j.abb.2019.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 01/04/2023]
18
Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018;142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
19
Liu B, Sureda-Gómez M, Zhen Y, Amador V, Reverter D. A quaternary tetramer assembly inhibits the deubiquitinating activity of USP25. Nat Commun 2018;9:4973. [PMID: 30478318 PMCID: PMC6255862 DOI: 10.1038/s41467-018-07510-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 11/01/2018] [Indexed: 01/13/2023]  Open
20
Huang LC, Ross KE, Baffi TR, Drabkin H, Kochut KJ, Ruan Z, D'Eustachio P, McSkimming D, Arighi C, Chen C, Natale DA, Smith C, Gaudet P, Newton AC, Wu C, Kannan N. Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. Sci Rep 2018;8:6518. [PMID: 29695735 PMCID: PMC5916945 DOI: 10.1038/s41598-018-24457-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/23/2018] [Indexed: 11/09/2022]  Open
21
Agyei D, Tsopmo A, Udenigwe CC. Bioinformatics and peptidomics approaches to the discovery and analysis of food-derived bioactive peptides. Anal Bioanal Chem 2018. [PMID: 29516135 DOI: 10.1007/s00216-018-0974-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
22
Doellinger J, Grossegesse M, Nitsche A, Lasch P. DMSO as a mobile phase additive enhances detection of ubiquitination sites by nano-LC-ESI-MS/MS. JOURNAL OF MASS SPECTROMETRY : JMS 2018;53:183-187. [PMID: 29193534 DOI: 10.1002/jms.4049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/30/2017] [Accepted: 11/16/2017] [Indexed: 06/07/2023]
23
Sun D, Wang M, Li A. MPTM: A tool for mining protein post-translational modifications from literature. J Bioinform Comput Biol 2017;15:1740005. [PMID: 28982288 DOI: 10.1142/s0219720017400054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
24
Ross KE, Natale DA, Arighi C, Chen SC, Huang H, Li G, Ren J, Wang M, Vijay-Shanker K, Wu CH. Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology. CEUR WORKSHOP PROCEEDINGS 2016;1747:http://ceur-ws.org/Vol-1747/BIT103_ICBO2016.pdf. [PMID: 28706471 PMCID: PMC5504912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA