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For: Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási AL, Tavernier J, Hill DE, Vidal M. High-quality binary protein interaction map of the yeast interactome network. Science 2008;322:104-10. [PMID: 18719252 DOI: 10.1126/science.1158684] [Citation(s) in RCA: 977] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Number Cited by Other Article(s)
151
Jespersen N, Barbar E. Emerging Features of Linear Motif-Binding Hub Proteins. Trends Biochem Sci 2020;45:375-384. [DOI: 10.1016/j.tibs.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
152
Grbić M, Matić D, Kartelj A, Vračević S, Filipović V. A three-phase method for identifying functionally related protein groups in weighted PPI networks. Comput Biol Chem 2020;86:107246. [PMID: 32339914 DOI: 10.1016/j.compbiolchem.2020.107246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/27/2020] [Accepted: 03/03/2020] [Indexed: 01/17/2023]
153
Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere JC, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA. A reference map of the human binary protein interactome. Nature 2020;580:402-408. [PMID: 32296183 PMCID: PMC7169983 DOI: 10.1038/s41586-020-2188-x] [Citation(s) in RCA: 738] [Impact Index Per Article: 147.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 02/14/2020] [Indexed: 12/14/2022]
154
Nath K, Roy S, Nandi S. InOvIn: A fuzzy-rough approach for detecting overlapping communities with intrinsic structures in evolving networks. Appl Soft Comput 2020. [DOI: 10.1016/j.asoc.2020.106096] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
155
Carianopol CS, Chan AL, Dong S, Provart NJ, Lumba S, Gazzarrini S. An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response. Commun Biol 2020;3:145. [PMID: 32218501 PMCID: PMC7099082 DOI: 10.1038/s42003-020-0866-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/24/2020] [Indexed: 12/13/2022]  Open
156
Nomura Y, Montemayor EJ, Virta JM, Hayes SM, Butcher SE. Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1. Nucleic Acids Res 2020;48:1423-1434. [PMID: 31832688 PMCID: PMC7026655 DOI: 10.1093/nar/gkz1177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 11/28/2022]  Open
157
Yazaki J, Kawashima Y, Ogawa T, Kobayashi A, Okoshi M, Watanabe T, Yoshida S, Kii I, Egami S, Amagai M, Hosoya T, Shiroguchi K, Ohara O. HaloTag-based conjugation of proteins to barcoding-oligonucleotides. Nucleic Acids Res 2020;48:e8. [PMID: 31752022 PMCID: PMC6954424 DOI: 10.1093/nar/gkz1086] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/29/2019] [Accepted: 11/18/2019] [Indexed: 11/12/2022]  Open
158
Yugandhar K, Wang TY, Leung AKY, Lanz MC, Motorykin I, Liang J, Shayhidin EE, Smolka MB, Zhang S, Yu H. MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. Mol Cell Proteomics 2020;19:554-568. [PMID: 31839598 PMCID: PMC7050104 DOI: 10.1074/mcp.tir119.001847] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 11/06/2022]  Open
159
Nielsen CP, MacGurn JA. Coupling Conjugation and Deconjugation Activities to Achieve Cellular Ubiquitin Dynamics. Trends Biochem Sci 2020;45:427-439. [PMID: 32311336 DOI: 10.1016/j.tibs.2020.01.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/19/2022]
160
Law J, Ng K, Windram OPF. The Phenotype Paradox: Lessons From Natural Transcriptome Evolution on How to Engineer Plants. FRONTIERS IN PLANT SCIENCE 2020;11:75. [PMID: 32133018 PMCID: PMC7040092 DOI: 10.3389/fpls.2020.00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
161
Mattiazzi Usaj M, Sahin N, Friesen H, Pons C, Usaj M, Masinas MPD, Shuteriqi E, Shkurin A, Aloy P, Morris Q, Boone C, Andrews BJ. Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability. Mol Syst Biol 2020;16:e9243. [PMID: 32064787 PMCID: PMC7025093 DOI: 10.15252/msb.20199243] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/16/2019] [Accepted: 01/15/2020] [Indexed: 12/13/2022]  Open
162
Wissberg S, Ronen M, Oren Z, Gerber D, Kalisky B. Sensitive Readout for Microfluidic High-Throughput Applications using Scanning SQUID Microscopy. Sci Rep 2020;10:1573. [PMID: 32005843 PMCID: PMC6994618 DOI: 10.1038/s41598-020-58307-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/29/2019] [Indexed: 11/08/2022]  Open
163
Sun J, Feng L, Xie J, Ma X, Wang D, Hu Y. Revealing the predictability of intrinsic structure in complex networks. Nat Commun 2020;11:574. [PMID: 31996676 PMCID: PMC6989503 DOI: 10.1038/s41467-020-14418-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/08/2020] [Indexed: 11/16/2022]  Open
164
Network of Interactions between ZIKA Virus Non-Structural Proteins and Human Host Proteins. Cells 2020;9:cells9010153. [PMID: 31936331 PMCID: PMC7016862 DOI: 10.3390/cells9010153] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/20/2019] [Accepted: 01/01/2020] [Indexed: 12/16/2022]  Open
165
Chasapis CT, Konstantinoudis G. Protein isoelectric point distribution in the interactomes across the domains of life. Biophys Chem 2020;256:106269. [PMID: 31733408 DOI: 10.1016/j.bpc.2019.106269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 01/19/2023]
166
Li S, Huang J, Liu J, Huang T, Chen H. Relative-path-based algorithm for link prediction on complex networks using a basic similarity factor. CHAOS (WOODBURY, N.Y.) 2020;30:013104. [PMID: 32013467 DOI: 10.1063/1.5094448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
167
Li Z, Nie R, You Z, Cao C, Li J. Using discriminative vector machine model with 2DPCA to predict interactions among proteins. BMC Bioinformatics 2019;20:694. [PMID: 31874626 PMCID: PMC6929273 DOI: 10.1186/s12859-019-3268-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
168
Galardini M, Busby BP, Vieitez C, Dunham AS, Typas A, Beltrao P. The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae. Mol Syst Biol 2019;15:e8831. [PMID: 31885205 PMCID: PMC6901017 DOI: 10.15252/msb.20198831] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022]  Open
169
Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J. Using INTERSPIA to Explore the Dynamics of Protein-Protein Interactions Among Multiple Species. ACTA ACUST UNITED AC 2019;68:e88. [PMID: 31751498 DOI: 10.1002/cpbi.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
170
The monothiol glutaredoxin GrxD is essential for sensing iron starvation in Aspergillus fumigatus. PLoS Genet 2019;15:e1008379. [PMID: 31525190 PMCID: PMC6762210 DOI: 10.1371/journal.pgen.1008379] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 09/26/2019] [Accepted: 08/20/2019] [Indexed: 01/17/2023]  Open
171
Lugo-Martinez J, Bar-Joseph Z, Dengjel J, Murphy RF. Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019;2019:144-153. [PMID: 32457940 DOI: 10.1145/3307339.3342150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
172
Sarkar D, Saha S. Machine-learning techniques for the prediction of protein-protein interactions. J Biosci 2019;44:104. [PMID: 31502581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
173
Choi SG, Olivet J, Cassonnet P, Vidalain PO, Luck K, Lambourne L, Spirohn K, Lemmens I, Dos Santos M, Demeret C, Jones L, Rangarajan S, Bian W, Coutant EP, Janin YL, van der Werf S, Trepte P, Wanker EE, De Las Rivas J, Tavernier J, Twizere JC, Hao T, Hill DE, Vidal M, Calderwood MA, Jacob Y. Maximizing binary interactome mapping with a minimal number of assays. Nat Commun 2019;10:3907. [PMID: 31467278 PMCID: PMC6715725 DOI: 10.1038/s41467-019-11809-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/02/2019] [Indexed: 02/06/2023]  Open
174
He S, Liu YJ, Ye FY, Li RP, Dai RJ. A new grid- and modularity-based layout algorithm for complex biological networks. PLoS One 2019;14:e0221620. [PMID: 31465473 PMCID: PMC6715240 DOI: 10.1371/journal.pone.0221620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 08/06/2019] [Indexed: 01/23/2023]  Open
175
Sarkar D, Saha S. Machine-learning techniques for the prediction of protein–protein interactions. J Biosci 2019. [DOI: 10.1007/s12038-019-9909-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
176
Boulgakov AA, Ellington AD, Marcotte EM. Bringing Microscopy-By-Sequencing into View. Trends Biotechnol 2019;38:154-162. [PMID: 31416630 DOI: 10.1016/j.tibtech.2019.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 01/07/2023]
177
Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J. INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. Nucleic Acids Res 2019;46:W89-W94. [PMID: 29746660 PMCID: PMC6031021 DOI: 10.1093/nar/gky378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023]  Open
178
Schoeters F, Van Dijck P. Protein-Protein Interactions in Candida albicans. Front Microbiol 2019;10:1792. [PMID: 31440220 PMCID: PMC6693483 DOI: 10.3389/fmicb.2019.01792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/19/2019] [Indexed: 12/27/2022]  Open
179
Zhang J, Zhong C, Huang Y, Lin HX, Wang M. A method for identifying protein complexes with the features of joint co-localization and joint co-expression in static PPI networks. Comput Biol Med 2019;111:103333. [PMID: 31376777 DOI: 10.1016/j.compbiomed.2019.103333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/01/2019] [Accepted: 06/17/2019] [Indexed: 02/09/2023]
180
Su Z, Zheng X, Ai J, Shang L, Shen Y. Link prediction in recommender systems with confidence measures. CHAOS (WOODBURY, N.Y.) 2019;29:083133. [PMID: 31472512 DOI: 10.1063/1.5099565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
181
Talkish J, Igel H, Hunter O, Horner SW, Jeffery NN, Leach JR, Jenkins JL, Kielkopf CL, Ares M. Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction. RNA (NEW YORK, N.Y.) 2019;25:1020-1037. [PMID: 31110137 PMCID: PMC6633205 DOI: 10.1261/rna.070649.119] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/15/2019] [Indexed: 05/16/2023]
182
Rössler I, Embacher J, Pillet B, Murat G, Liesinger L, Hafner J, Unterluggauer JJ, Birner-Gruenberger R, Kressler D, Pertschy B. Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME. Nucleic Acids Res 2019;47:6984-7002. [PMID: 31062022 PMCID: PMC6648895 DOI: 10.1093/nar/gkz317] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/15/2019] [Accepted: 04/19/2019] [Indexed: 12/12/2022]  Open
183
Corwin T, Woodsmith J, Apelt F, Fontaine JF, Meierhofer D, Helmuth J, Grossmann A, Andrade-Navarro MA, Ballif BA, Stelzl U. Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate. Cell Syst 2019;5:128-139.e4. [PMID: 28837810 DOI: 10.1016/j.cels.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/02/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022]
184
Liu X, Zhu Y, Liu T, Xue Q, Tian F, Yuan Y, Zhao C. Exploring toxicity of perfluorinated compounds through complex network and pathway modeling. J Biomol Struct Dyn 2019;38:2604-2612. [PMID: 31244379 DOI: 10.1080/07391102.2019.1637281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
185
Guala D, Ogris C, Müller N, Sonnhammer ELL. Genome-wide functional association networks: background, data & state-of-the-art resources. Brief Bioinform 2019;21:1224-1237. [PMID: 31281921 PMCID: PMC7373183 DOI: 10.1093/bib/bbz064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 02/06/2023]  Open
186
Li M, Ni P, Chen X, Wang J, Wu FX, Pan Y. Construction of Refined Protein Interaction Network for Predicting Essential Proteins. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:1386-1397. [PMID: 28186903 DOI: 10.1109/tcbb.2017.2665482] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
187
Yugandhar K, Gupta S, Yu H. Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review. Comput Struct Biotechnol J 2019;17:805-811. [PMID: 31316724 PMCID: PMC6611912 DOI: 10.1016/j.csbj.2019.05.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 01/06/2023]  Open
188
Brant JO, Boatwright JL, Davenport R, Sandoval AGW, Maden M, Barbazuk WB. Comparative transcriptomic analysis of dermal wound healing reveals de novo skeletal muscle regeneration in Acomys cahirinus. PLoS One 2019;14:e0216228. [PMID: 31141508 PMCID: PMC6541261 DOI: 10.1371/journal.pone.0216228] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/16/2019] [Indexed: 01/14/2023]  Open
189
Rasti S, Vogiatzis C. A survey of computational methods in protein–protein interaction networks. ANNALS OF OPERATIONS RESEARCH 2019;276:35-87. [DOI: 10.1007/s10479-018-2956-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
190
Straightforward Protein-Protein Interaction Interface Mapping via Random Mutagenesis and Mammalian Protein Protein Interaction Trap (MAPPIT). Int J Mol Sci 2019;20:ijms20092058. [PMID: 31027327 PMCID: PMC6539206 DOI: 10.3390/ijms20092058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/08/2019] [Accepted: 04/13/2019] [Indexed: 01/18/2023]  Open
191
Liu X, Liu Z, Dziulko AK, Li F, Miller D, Morabito RD, Francois D, Levy SF. iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast. Cell Syst 2019;8:338-344.e8. [PMID: 30954477 PMCID: PMC6483859 DOI: 10.1016/j.cels.2019.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/10/2019] [Accepted: 03/06/2019] [Indexed: 11/24/2022]
192
Höpfler M, Kern MJ, Straub T, Prytuliak R, Habermann BH, Pfander B, Jentsch S. Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance. EMBO J 2019;38:embj.2018100368. [PMID: 31015336 PMCID: PMC6545562 DOI: 10.15252/embj.2018100368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 12/27/2022]  Open
193
Bing X, Bunea F, Royer M, Das J. Latent Model-Based Clustering for Biological Discovery. iScience 2019;14:125-135. [PMID: 30954780 PMCID: PMC6449745 DOI: 10.1016/j.isci.2019.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/26/2018] [Accepted: 03/18/2019] [Indexed: 11/27/2022]  Open
194
Detecting intrinsic communities in evolving networks. SOCIAL NETWORK ANALYSIS AND MINING 2019. [DOI: 10.1007/s13278-019-0552-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
195
Liu H, Pfirrmann T. The Gid-complex: an emerging player in the ubiquitin ligase league. Biol Chem 2019;400:1429-1441. [DOI: 10.1515/hsz-2019-0139] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/20/2019] [Indexed: 12/16/2022]
196
Macossay-Castillo M, Marvelli G, Guharoy M, Jain A, Kihara D, Tompa P, Wodak SJ. The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. J Mol Biol 2019;431:1650-1670. [PMID: 30878482 DOI: 10.1016/j.jmb.2019.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/25/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
197
Collective influencers in protein interaction networks. Sci Rep 2019;9:3948. [PMID: 30850642 PMCID: PMC6408499 DOI: 10.1038/s41598-019-40410-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/31/2019] [Indexed: 11/28/2022]  Open
198
Nguyen H, Shrestha S, Tran D, Shafi A, Draghici S, Nguyen T. A Comprehensive Survey of Tools and Software for Active Subnetwork Identification. Front Genet 2019;10:155. [PMID: 30891064 PMCID: PMC6411791 DOI: 10.3389/fgene.2019.00155] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/13/2019] [Indexed: 12/13/2022]  Open
199
Tian B, Duan Q, Zhao C, Teng B, He Z. Reinforce: An Ensemble Approach for Inferring PPI Network from AP-MS Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:365-376. [PMID: 28534782 DOI: 10.1109/tcbb.2017.2705060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
200
Gay S, Piccini D, Bruhn C, Ricciardi S, Soffientini P, Carotenuto W, Biffo S, Foiani M. A Mad2-Mediated Translational Regulatory Mechanism Promoting S-Phase Cyclin Synthesis Controls Origin Firing and Survival to Replication Stress. Mol Cell 2019;70:628-638.e5. [PMID: 29775579 PMCID: PMC5972228 DOI: 10.1016/j.molcel.2018.04.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/26/2018] [Accepted: 04/23/2018] [Indexed: 11/03/2022]
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