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For: Yeger-Lotem E, Sharan R. Human protein interaction networks across tissues and diseases. Front Genet 2015;6:257. [PMID: 26347769 PMCID: PMC4541328 DOI: 10.3389/fgene.2015.00257] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/17/2015] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Harrigan WL, Ferrell BD, Wommack KE, Polson SW, Schreiber ZD, Belcaid M. Improvements in viral gene annotation using large language models and soft alignments. BMC Bioinformatics 2024;25:165. [PMID: 38664627 PMCID: PMC11046836 DOI: 10.1186/s12859-024-05779-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024]  Open
2
Monzon AM, Arrías PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Fornasari MS, Parisi G, Piovesan D, Kajava AV, Tosatto SCE. A STRP-ed definition of Structured Tandem Repeats in Proteins. J Struct Biol 2023;215:108023. [PMID: 37652396 DOI: 10.1016/j.jsb.2023.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/31/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
3
Ginsberg SD, Sharma S, Norton L, Chiosis G. Targeting stressor-induced dysfunctions in protein-protein interaction networks via epichaperomes. Trends Pharmacol Sci 2023;44:20-33. [PMID: 36414432 PMCID: PMC9789192 DOI: 10.1016/j.tips.2022.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022]
4
García-Vaquero ML, Gama-Carvalho M, Pinto FR, De Las Rivas J. Biological interacting units identified in human protein networks reveal tissue-functional diversification and its impact on disease. Comput Struct Biotechnol J 2022;20:3764-3778. [PMID: 35891788 PMCID: PMC9304429 DOI: 10.1016/j.csbj.2022.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 12/29/2022]  Open
5
Li Q, Milenkovic T. Supervised Prediction of Aging-Related Genes From a Context-Specific Protein Interaction Subnetwork. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2484-2498. [PMID: 33929964 DOI: 10.1109/tcbb.2021.3076961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
6
Saha S, Halder AK, Bandyopadhyay SS, Chatterjee P, Nasipuri M, Basu S. Computational modeling of human-nCoV protein-protein interaction network. Methods 2022;203:488-497. [PMID: 34902553 PMCID: PMC8662836 DOI: 10.1016/j.ymeth.2021.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 01/25/2023]  Open
7
Mukherjee SB, Mukherjee S, Frenkel-Morgenstern M. Fusion proteins mediate alternation of protein interaction networks in cancers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022;131:165-176. [PMID: 35871889 DOI: 10.1016/bs.apcsb.2022.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
8
Hou S, Zhang P, Yang K, Wang L, Ma C, Li Y, Li S. Decoding multilevel relationships with the human tissue-cell-molecule network. Brief Bioinform 2022;23:6585388. [PMID: 35551347 DOI: 10.1093/bib/bbac170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/09/2022] [Accepted: 04/16/2022] [Indexed: 02/01/2023]  Open
9
Nussinov R, Jang H, Nir G, Tsai CJ, Cheng F. Open Structural Data in Precision Medicine. Annu Rev Biomed Data Sci 2022;5:95-117. [PMID: 35483346 DOI: 10.1146/annurev-biodatasci-122220-012951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
10
Panday S, Alexov E. Protein-Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation. ACS OMEGA 2022;7:11057-11067. [PMID: 35415339 PMCID: PMC8991903 DOI: 10.1021/acsomega.1c07037] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
11
Newaz K, Milenkovic T. Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:974-988. [PMID: 32897864 DOI: 10.1109/tcbb.2020.3022767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
12
Joshi S, Gomes ED, Wang T, Corben A, Taldone T, Gandu S, Xu C, Sharma S, Buddaseth S, Yan P, Chan LYL, Gokce A, Rajasekhar VK, Shrestha L, Panchal P, Almodovar J, Digwal CS, Rodina A, Merugu S, Pillarsetty N, Miclea V, Peter RI, Wang W, Ginsberg SD, Tang L, Mattar M, de Stanchina E, Yu KH, Lowery M, Grbovic-Huezo O, O'Reilly EM, Janjigian Y, Healey JH, Jarnagin WR, Allen PJ, Sander C, Erdjument-Bromage H, Neubert TA, Leach SD, Chiosis G. Pharmacologically controlling protein-protein interactions through epichaperomes for therapeutic vulnerability in cancer. Commun Biol 2021;4:1333. [PMID: 34824367 PMCID: PMC8617294 DOI: 10.1038/s42003-021-02842-3] [Citation(s) in RCA: 3] [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: 01/29/2021] [Accepted: 11/03/2021] [Indexed: 12/03/2022]  Open
13
Gong S, Duan Y, Wu C, Osterhoff G, Schopow N, Kallendrusch S. A Human Pan-Cancer System Analysis of Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3 (PLOD3). Int J Mol Sci 2021;22:ijms22189903. [PMID: 34576068 PMCID: PMC8467482 DOI: 10.3390/ijms22189903] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/07/2021] [Accepted: 09/11/2021] [Indexed: 01/11/2023]  Open
14
Hollander M, Do T, Will T, Helms V. Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data. FRONTIERS IN BIOINFORMATICS 2021;1:724297. [PMID: 36303788 PMCID: PMC9581068 DOI: 10.3389/fbinf.2021.724297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/23/2021] [Indexed: 12/25/2022]  Open
15
Chen H, Shaw D, Bu D, Jiang T. FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. NAR Genom Bioinform 2021;3:lqab057. [PMID: 34169280 PMCID: PMC8219044 DOI: 10.1093/nargab/lqab057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/18/2021] [Accepted: 06/03/2021] [Indexed: 12/24/2022]  Open
16
Ginsberg SD, Neubert TA, Sharma S, Digwal CS, Yan P, Timbus C, Wang T, Chiosis G. Disease-specific interactome alterations via epichaperomics: the case for Alzheimer's disease. FEBS J 2021;289:2047-2066. [PMID: 34028172 DOI: 10.1111/febs.16031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/23/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022]
17
Du Y, Cai M, Xing X, Ji J, Yang E, Wu J. PINA 3.0: mining cancer interactome. Nucleic Acids Res 2021;49:D1351-D1357. [PMID: 33231689 PMCID: PMC7779002 DOI: 10.1093/nar/gkaa1075] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022]  Open
18
Dynamics of a Protein Interaction Network Associated to the Aggregation of polyQ-Expanded Ataxin-1. Genes (Basel) 2020;11:genes11101129. [PMID: 32992839 PMCID: PMC7600199 DOI: 10.3390/genes11101129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022]  Open
19
Salnikova LE, Khadzhieva MB, Kolobkov DS, Gracheva AS, Kuzovlev AN, Abilev SK. Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits. Sci Rep 2020;10:14740. [PMID: 32895400 PMCID: PMC7477549 DOI: 10.1038/s41598-020-71018-6] [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: 03/24/2020] [Accepted: 07/28/2020] [Indexed: 12/02/2022]  Open
20
Polaske NW, Kelly BD, Smith MA, Haura EB, Belosludtsev YY. Fully Automated Protein Proximity Assay in Formalin-Fixed, Paraffin-Embedded Tissue Using Caged Haptens. Bioconjug Chem 2020;31:1635-1640. [PMID: 32395983 DOI: 10.1021/acs.bioconjchem.0c00193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
21
Niss K, Gomez-Casado C, Hjaltelin JX, Joeris T, Agace WW, Belling KG, Brunak S. Complete Topological Mapping of a Cellular Protein Interactome Reveals Bow-Tie Motifs as Ubiquitous Connectors of Protein Complexes. Cell Rep 2020;31:107763. [PMID: 32553166 DOI: 10.1016/j.celrep.2020.107763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/03/2020] [Accepted: 05/21/2020] [Indexed: 11/18/2022]  Open
22
Basha O, Mauer O, Simonovsky E, Shpringer R, Yeger-Lotem E. ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues. Nucleic Acids Res 2020;47:W242-W247. [PMID: 31114913 PMCID: PMC6602570 DOI: 10.1093/nar/gkz421] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/23/2019] [Accepted: 05/06/2019] [Indexed: 12/13/2022]  Open
23
Bajpai AK, Davuluri S, Tiwary K, Narayanan S, Oguru S, Basavaraju K, Dayalan D, Thirumurugan K, Acharya KK. Systematic comparison of the protein-protein interaction databases from a user's perspective. J Biomed Inform 2020;103:103380. [DOI: 10.1016/j.jbi.2020.103380] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 11/08/2019] [Accepted: 01/27/2020] [Indexed: 01/08/2023]
24
Gulfidan G, Turanli B, Beklen H, Sinha R, Arga KY. Pan-cancer mapping of differential protein-protein interactions. Sci Rep 2020;10:3272. [PMID: 32094374 PMCID: PMC7039988 DOI: 10.1038/s41598-020-60127-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 02/04/2020] [Indexed: 01/02/2023]  Open
25
Basha O, Argov CM, Artzy R, Zoabi Y, Hekselman I, Alfandari L, Chalifa-Caspi V, Yeger-Lotem E. Differential network analysis of multiple human tissue interactomes highlights tissue-selective processes and genetic disorder genes. Bioinformatics 2020;36:2821-2828. [DOI: 10.1093/bioinformatics/btaa034] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 01/19/2023]  Open
26
Hekselman I, Yeger-Lotem E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat Rev Genet 2020;21:137-150. [DOI: 10.1038/s41576-019-0200-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2019] [Indexed: 02/07/2023]
27
Cowman T, Coşkun M, Grama A, Koyutürk M. Integrated querying and version control of context-specific biological networks. Database (Oxford) 2020;2020:baaa018. [PMID: 32294194 PMCID: PMC7158887 DOI: 10.1093/database/baaa018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/13/2020] [Accepted: 02/21/2020] [Indexed: 01/26/2023]
28
Alanis-Lobato G, Schaefer MH. Generation and Interpretation of Context-Specific Human Protein-Protein Interaction Networks with HIPPIE. Methods Mol Biol 2020;2074:135-144. [PMID: 31583636 DOI: 10.1007/978-1-4939-9873-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
29
Zhu L, Hofestadt R, Ester M. Tissue-Specific Subcellular Localization Prediction Using Multi-Label Markov Random Fields. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:1471-1482. [PMID: 30736003 DOI: 10.1109/tcbb.2019.2897683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
30
Cicaloni V, Trezza A, Pettini F, Spiga O. Applications of in Silico Methods for Design and Development of Drugs Targeting Protein-Protein Interactions. Curr Top Med Chem 2019;19:534-554. [PMID: 30836920 DOI: 10.2174/1568026619666190304153901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/02/2019] [Accepted: 01/25/2019] [Indexed: 11/22/2022]
31
Giudice G, Petsalaki E. Proteomics and phosphoproteomics in precision medicine: applications and challenges. Brief Bioinform 2019;20:767-777. [PMID: 29077858 PMCID: PMC6585152 DOI: 10.1093/bib/bbx141] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/21/2017] [Indexed: 12/11/2022]  Open
32
Latysheva NS, Babu MM. Molecular Signatures of Fusion Proteins in Cancer. ACS Pharmacol Transl Sci 2019;2:122-133. [PMID: 32219217 PMCID: PMC7088938 DOI: 10.1021/acsptsci.9b00019] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Indexed: 01/07/2023]
33
Allahyar A, Ubels J, de Ridder J. A data-driven interactome of synergistic genes improves network-based cancer outcome prediction. PLoS Comput Biol 2019;15:e1006657. [PMID: 30726216 PMCID: PMC6380593 DOI: 10.1371/journal.pcbi.1006657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 02/19/2019] [Accepted: 11/20/2018] [Indexed: 12/13/2022]  Open
34
Tay AP, Liang A, Wilkins MR, Pang CNI. Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle. ACTA ACUST UNITED AC 2019;66:e71. [PMID: 30653846 DOI: 10.1002/cpbi.71] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
35
Oughtred R, Stark C, Breitkreutz BJ, Rust J, Boucher L, Chang C, Kolas N, O’Donnell L, Leung G, McAdam R, Zhang F, Dolma S, Willems A, Coulombe-Huntington J, Chatr-aryamontri A, Dolinski K, Tyers M. The BioGRID interaction database: 2019 update. Nucleic Acids Res 2019;47:D529-D541. [PMID: 30476227 PMCID: PMC6324058 DOI: 10.1093/nar/gky1079] [Citation(s) in RCA: 836] [Impact Index Per Article: 167.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/15/2018] [Accepted: 11/22/2018] [Indexed: 12/17/2022]  Open
36
Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly. Sci Rep 2018;8:13712. [PMID: 30209338 PMCID: PMC6135828 DOI: 10.1038/s41598-018-32009-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/24/2018] [Indexed: 01/27/2023]  Open
37
Spiniello M, Knoener RA, Steinbrink MI, Yang B, Cesnik AJ, Buxton KE, Scalf M, Jarrard DF, Smith LM. HyPR-MS for Multiplexed Discovery of MALAT1, NEAT1, and NORAD lncRNA Protein Interactomes. J Proteome Res 2018;17:3022-3038. [PMID: 29972301 DOI: 10.1021/acs.jproteome.8b00189] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
38
Zitnik M, Leskovec J. Predicting multicellular function through multi-layer tissue networks. Bioinformatics 2018;33:i190-i198. [PMID: 28881986 PMCID: PMC5870717 DOI: 10.1093/bioinformatics/btx252] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
39
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst 2018;6:484-495.e5. [PMID: 29605183 DOI: 10.1016/j.cels.2018.03.001] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/19/2017] [Accepted: 02/28/2018] [Indexed: 12/27/2022]
40
Basha O, Shpringer R, Argov CM, Yeger-Lotem E. The DifferentialNet database of differential protein-protein interactions in human tissues. Nucleic Acids Res 2018;46:D522-D526. [PMID: 29069447 PMCID: PMC5753382 DOI: 10.1093/nar/gkx981] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/19/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022]  Open
41
Laddach A, Ng JCF, Chung SS, Fraternali F. Genetic variants and protein-protein interactions: a multidimensional network-centric view. Curr Opin Struct Biol 2018;50:82-90. [PMID: 29306755 DOI: 10.1016/j.sbi.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 01/18/2023]
42
Havugimana PC, Hu P, Emili A. Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks. Expert Rev Proteomics 2017;14:845-855. [PMID: 28918672 DOI: 10.1080/14789450.2017.1374179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Mohammadi S, Grama A. A convex optimization approach for identification of human tissue-specific interactomes. Bioinformatics 2017;32:i243-i252. [PMID: 27307623 PMCID: PMC4908329 DOI: 10.1093/bioinformatics/btw245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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Boezio B, Audouze K, Ducrot P, Taboureau O. Network-based Approaches in Pharmacology. Mol Inform 2017;36. [PMID: 28692140 DOI: 10.1002/minf.201700048] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/21/2017] [Indexed: 12/23/2022]
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Caldera M, Buphamalai P, Müller F, Menche J. Interactome-based approaches to human disease. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Will T, Helms V. Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare. BMC SYSTEMS BIOLOGY 2017;11:44. [PMID: 28376810 PMCID: PMC5379774 DOI: 10.1186/s12918-017-0400-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/26/2017] [Indexed: 12/24/2022]
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Yang J, Yang T, Wu D, Lin L, Yang F, Zhao J. The integration of weighted human gene association networks based on link prediction. BMC SYSTEMS BIOLOGY 2017;11:12. [PMID: 28137253 PMCID: PMC5282786 DOI: 10.1186/s12918-017-0398-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/25/2017] [Indexed: 12/27/2022]
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Basha O, Barshir R, Sharon M, Lerman E, Kirson BF, Hekselman I, Yeger-Lotem E. The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. Nucleic Acids Res 2016;45:D427-D431. [PMID: 27899616 PMCID: PMC5210565 DOI: 10.1093/nar/gkw1088] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023]  Open
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Oliviero G, Brien GL, Waston A, Streubel G, Jerman E, Andrews D, Doyle B, Munawar N, Wynne K, Crean J, Bracken AP, Cagney G. Dynamic Protein Interactions of the Polycomb Repressive Complex 2 during Differentiation of Pluripotent Cells. Mol Cell Proteomics 2016. [DOI: https://doi.org/10.1074/mcp.m116.062240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
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Oliviero G, Brien GL, Waston A, Streubel G, Jerman E, Andrews D, Doyle B, Munawar N, Wynne K, Crean J, Bracken AP, Cagney G. Dynamic Protein Interactions of the Polycomb Repressive Complex 2 during Differentiation of Pluripotent Cells. Mol Cell Proteomics 2016;15:3450-3460. [PMID: 27634302 DOI: 10.1074/mcp.m116.062240] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Indexed: 01/08/2023]  Open
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