{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T10:04:28Z","timestamp":1774865068618,"version":"3.50.1"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,8,26]],"date-time":"2025-08-26T00:00:00Z","timestamp":1756166400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,8,26]],"date-time":"2025-08-26T00:00:00Z","timestamp":1756166400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"SGS","award":["SP2025\/018"],"award-info":[{"award-number":["SP2025\/018"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Appl Netw Sci"],"DOI":"10.1007\/s41109-025-00727-6","type":"journal-article","created":{"date-parts":[[2025,8,26]],"date-time":"2025-08-26T11:50:13Z","timestamp":1756209013000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Positive impact of structural asymmetries in PPI networks on protein complex detection"],"prefix":"10.1007","volume":"10","author":[{"given":"Lukas","family":"Papik","sequence":"first","affiliation":[]},{"given":"Eliska","family":"Ochodkova","sequence":"additional","affiliation":[]},{"given":"Eva","family":"Kriegova","sequence":"additional","affiliation":[]},{"given":"Milos","family":"Kudelka","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,8,26]]},"reference":[{"issue":"8","key":"727_CR1","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1093\/bioinformatics\/btl039","volume":"22","author":"B Adamcsek","year":"2006","unstructured":"Adamcsek B, Palla G, Farkas IJ, Der\u00e9nyi I, Vicsek T (2006) Cfinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22(8):1021\u20131023","journal-title":"Bioinformatics"},{"issue":"1","key":"727_CR2","first-page":"031","volume":"224","author":"SA Aleksander","year":"2023","unstructured":"Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL et al (2023) The gene ontology knowledgebase in 2023. Genetics 224(1):031","journal-title":"Genetics"},{"issue":"6","key":"727_CR3","first-page":"1017","volume":"18","author":"D Alvarez-Ponce","year":"2017","unstructured":"Alvarez-Ponce D (2017) Recording negative results of protein\u2013protein interaction assays: an easy way to deal with the biases and errors of interactomic data sets. Brief Bioinform 18(6):1017\u20131020","journal-title":"Brief Bioinform"},{"issue":"2","key":"727_CR4","doi-asserted-by":"publisher","first-page":"362","DOI":"10.3390\/sym14020362","volume":"14","author":"A Badel","year":"2022","unstructured":"Badel A, Breuil L, Laville P, Regad L (2022) Exploration of the structural asymmetry induced by the intrinsic flexibility of hiv-2 protease. Symmetry 14(2):362","journal-title":"Symmetry"},{"key":"727_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-4-2","volume":"4","author":"GD Bader","year":"2003","unstructured":"Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform 4:1\u201327","journal-title":"BMC Bioinform"},{"issue":"22","key":"727_CR6","doi-asserted-by":"publisher","first-page":"3045","DOI":"10.1093\/bioinformatics\/btp536","volume":"25","author":"D Binns","year":"2009","unstructured":"Binns D, Dimmer E, Huntley R, Barrell D, O\u2019donovan C, Apweiler R (2009) Quickgo: a web-based tool for gene ontology searching. Bioinformatics 25(22):3045\u20133046","journal-title":"Bioinformatics"},{"issue":"7","key":"727_CR7","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1038\/sj.embor.7401002","volume":"8","author":"J Boskovic","year":"2007","unstructured":"Boskovic J, Coloma J, Aparicio T, Zhou M, Robinson CV, Mendez J, Montoya G (2007) Molecular architecture of the human gins complex. EMBO Rep 8(7):678\u2013684","journal-title":"EMBO Rep"},{"issue":"18","key":"727_CR8","doi-asserted-by":"publisher","first-page":"2431","DOI":"10.1080\/15384101.2016.1191712","volume":"15","author":"J Boskovic","year":"2016","unstructured":"Boskovic J, Bragado-Nilsson E, Saligram Prabhakar B, Yefimenko I, Mart\u00ednez-Gago J, Munoz S, M\u00e9ndez J, Montoya G (2016) Molecular architecture of the recombinant human mcm2-7 helicase in complex with nucleotides and DNA. Cell Cycle 15(18):2431\u20132440","journal-title":"Cell Cycle"},{"issue":"7","key":"727_CR9","doi-asserted-by":"publisher","first-page":"2523","DOI":"10.1073\/pnas.1222494110","volume":"110","author":"W-H Cho","year":"2013","unstructured":"Cho W-H, Kang Y-H, An Y-Y, Tappin I, Hurwitz J, Lee J-K (2013) Human tim-tipin complex affects the biochemical properties of the replicative dna helicase and dna polymerases. Proc Natl Acad Sci 110(7):2523\u20132527","journal-title":"Proc Natl Acad Sci"},{"issue":"3","key":"727_CR10","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1074\/mcp.M600381-MCP200","volume":"6","author":"SR Collins","year":"2007","unstructured":"Collins SR, Kemmeren P, Zhao X-C, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ (2007) Toward a comprehensive atlas of the physical interactome of saccharomyces cerevisiae. Mol Cell Proteom 6(3):439\u2013450","journal-title":"Mol Cell Proteom"},{"issue":"1","key":"727_CR11","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1007\/s41109-024-00639-x","volume":"9","author":"E Dopater","year":"2024","unstructured":"Dopater E, Ochodkova E, Kudelka M (2024) Network embedding based on depdist contraction. Appl Netw Sci 9(1):28","journal-title":"Appl Netw Sci"},{"key":"727_CR12","doi-asserted-by":"crossref","unstructured":"D\u00f6rig C, Marulli C, Peskett T, Volkmar N, Pantolini L, Studer G, Paleari C, Frommelt F, Schwede T, Souza N, et al (2024) Global profiling of protein complex dynamics with an experimental library of protein interaction markers. Nature Biotechnology, 1\u201315","DOI":"10.1038\/s41587-024-02432-8"},{"key":"727_CR13","doi-asserted-by":"crossref","unstructured":"Gnanasekaran P, Pappu HR (2023) Affinity purification-mass spectroscopy (ap-ms) and co-immunoprecipitation (co-ip) technique to study protein\u2013protein interactions. In: Protein-Protein Interactions: Methods and Protocols, pp. 81\u201385. Springer, Berlin","DOI":"10.1007\/978-1-0716-3327-4_7"},{"issue":"7","key":"727_CR14","doi-asserted-by":"publisher","first-page":"3932","DOI":"10.1021\/acs.chemrev.3c00550","volume":"124","author":"G Grassmann","year":"2024","unstructured":"Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E (2024) Computational approaches to predict protein-protein interactions in crowded cellular environments. Chem Rev 124(7):3932\u20133977","journal-title":"Chem Rev"},{"key":"727_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-8-236","volume":"8","author":"GT Hart","year":"2007","unstructured":"Hart GT, Lee I, Marcotte EM (2007) A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinform 8:1\u201311","journal-title":"BMC Bioinform"},{"issue":"1","key":"727_CR16","doi-asserted-by":"publisher","first-page":"1240","DOI":"10.1038\/s41467-019-09177-y","volume":"10","author":"IA Kov\u00e1cs","year":"2019","unstructured":"Kov\u00e1cs IA, Luck K, Spirohn K, Wang Y, Pollis C, Schlabach S, Bian W, Kim D-K, Kishore N, Hao T et al (2019) Network-based prediction of protein interactions. Nat Commun 10(1):1240","journal-title":"Nat Commun"},{"issue":"7084","key":"727_CR17","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/nature04670","volume":"440","author":"NJ Krogan","year":"2006","unstructured":"Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP et al (2006) Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature 440(7084):637\u2013643","journal-title":"Nature"},{"issue":"1","key":"727_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s41109-019-0192-6","volume":"4","author":"M Kudelka","year":"2019","unstructured":"Kudelka M, Ochodkova E, Zehnalova S, Plesnik J (2019) Ego-zones: Non-symmetric dependencies reveal network groups with large and dense overlaps. Appl Netw Sci 4(1):1\u201349","journal-title":"Appl Netw Sci"},{"issue":"6","key":"727_CR19","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/s41589-020-0529-6","volume":"16","author":"JH Lorent","year":"2020","unstructured":"Lorent JH, Levental KR, Ganesan L, Rivera-Longsworth G, Sezgin E, Doktorova M, Lyman E, Levental I (2020) Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape. Nat Chem Biol 16(6):644\u2013652","journal-title":"Nat Chem Biol"},{"issue":"4","key":"727_CR20","doi-asserted-by":"publisher","first-page":"948","DOI":"10.1002\/prot.21071","volume":"64","author":"Z Lubovac","year":"2006","unstructured":"Lubovac Z, Gamalielsson J, Olsson B (2006) Combining functional and topological properties to identify core modules in protein interaction networks. Proteins: Struct, Funct, Bioinf 64(4):948\u2013959","journal-title":"Proteins: Struct, Funct, Bioinf"},{"issue":"1","key":"727_CR21","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1186\/s12859-022-04960-z","volume":"23","author":"J Lyu","year":"2022","unstructured":"Lyu J, Yao Z, Liang B, Liu Y, Zhang Y (2022) Small protein complex prediction algorithm based on protein-protein interaction network segmentation. BMC Bioinform 23(1):405","journal-title":"BMC Bioinform"},{"issue":"3","key":"727_CR22","doi-asserted-by":"publisher","first-page":"1592","DOI":"10.1109\/TCBB.2021.3050102","volume":"19","author":"X Meng","year":"2021","unstructured":"Meng X, Xiang J, Zheng R, Wu F-X, Li M (2021) Dpcmne: detecting protein complexes from protein-protein interaction networks via multi-level network embedding. IEEE\/ACM Trans Comput Biol Bioinf 19(3):1592\u20131602","journal-title":"IEEE\/ACM Trans Comput Biol Bioinf"},{"issue":"3","key":"727_CR23","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1042\/EBC20200108","volume":"66","author":"R Morris","year":"2022","unstructured":"Morris R, Black KA, Stollar EJ (2022) Uncovering protein function: from classification to complexes. Essays Biochem 66(3):255\u2013285","journal-title":"Essays Biochem"},{"issue":"5","key":"727_CR24","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1038\/nmeth.1938","volume":"9","author":"T Nepusz","year":"2012","unstructured":"Nepusz T, Yu H, Paccanaro A (2012) Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods 9(5):471\u2013472","journal-title":"Nat Methods"},{"key":"727_CR25","doi-asserted-by":"publisher","first-page":"5255","DOI":"10.1016\/j.csbj.2021.09.014","volume":"19","author":"S Omranian","year":"2021","unstructured":"Omranian S, Angeleska A, Nikoloski Z (2021) Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. Comput Struct Biotechnol J 19:5255\u20135263","journal-title":"Comput Struct Biotechnol J"},{"key":"727_CR26","doi-asserted-by":"publisher","first-page":"2699","DOI":"10.1016\/j.csbj.2022.05.049","volume":"20","author":"S Omranian","year":"2022","unstructured":"Omranian S, Nikoloski Z, Grimm DG (2022) Computational identification of protein complexes from network interactions: present state, challenges, and the way forward. Comput Struct Biotechnol J 20:2699\u20132712","journal-title":"Comput Struct Biotechnol J"},{"issue":"D1","key":"727_CR27","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1093\/nar\/gky1079","volume":"47","author":"R Oughtred","year":"2019","unstructured":"Oughtred R, Stark C, Breitkreutz B-J, Rust J, Boucher L, Chang C, Kolas N, O\u2019Donnell L, Leung G, McAdam R et al (2019) The biogrid interaction database: 2019 update. Nucleic Acids Res 47(D1):529\u2013541","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"727_CR28","doi-asserted-by":"publisher","first-page":"0262056","DOI":"10.1371\/journal.pone.0262056","volume":"16","author":"MV Palukuri","year":"2021","unstructured":"Palukuri MV, Marcotte EM (2021) Super. complex: a supervised machine learning pipeline for molecular complex detection in protein-interaction networks. PLoS ONE 16(12):0262056","journal-title":"PLoS ONE"},{"key":"727_CR29","doi-asserted-by":"crossref","unstructured":"Papik L, Ochodkova E, Kriegova E, Kudelka M (2024) Structural asymmetries in ppi networks as a tool to improve the detection of protein complexes. In: International Conference on Complex Networks and Their Applications. Springer, Berlin pp. 27\u201338","DOI":"10.1007\/978-3-031-82439-5_3"},{"issue":"7","key":"727_CR30","doi-asserted-by":"publisher","first-page":"1000443","DOI":"10.1371\/journal.pcbi.1000443","volume":"5","author":"C Pesquita","year":"2009","unstructured":"Pesquita C, Faria D, Falcao AO, Lord P, Couto FM (2009) Semantic similarity in biomedical ontologies. PLoS Comput Biol 5(7):1000443","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"727_CR31","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1093\/nar\/gkn1005","volume":"37","author":"S Pu","year":"2009","unstructured":"Pu S, Wong J, Turner B, Cho E, Wodak SJ (2009) Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res 37(3):825\u2013831","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"727_CR32","first-page":"17","volume":"7","author":"N Safari-Alighiarloo","year":"2014","unstructured":"Safari-Alighiarloo N, Taghizadeh M, Rezaei-Tavirani M, Goliaei B, Peyvandi AA (2014) Protein-protein interaction networks (ppi) and complex diseases. Gastroenterol Hepatol Bed Bench 7(1):17","journal-title":"Gastroenterol Hepatol Bed Bench"},{"key":"727_CR33","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.ymeth.2016.06.010","volume":"110","author":"X Shen","year":"2016","unstructured":"Shen X, Yi L, Jiang X, Zhao Y, Hu X, He T, Yang J (2016) Neighbor affinity based algorithm for discovering temporal protein complex from dynamic PPI network. Methods 110:90\u201396","journal-title":"Methods"},{"issue":"D1","key":"727_CR34","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1093\/nar\/gku1003","volume":"43","author":"D Szklarczyk","year":"2015","unstructured":"Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP et al (2015) String v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43(D1):447\u2013452","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"727_CR35","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1093\/nar\/gkac1000","volume":"51","author":"D Szklarczyk","year":"2023","unstructured":"Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S et al (2023) The string database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res 51(D1):638\u2013646","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"727_CR36","doi-asserted-by":"publisher","first-page":"10131","DOI":"10.1038\/s41598-020-66699-y","volume":"10","author":"A Tareen","year":"2020","unstructured":"Tareen A, Wingreen NS, Mukhopadhyay R (2020) Asymmetry between activators and deactivators in functional protein networks. Sci Rep 10(1):10131","journal-title":"Sci Rep"},{"issue":"D1","key":"727_CR37","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1093\/nar\/gkac1015","volume":"51","author":"G Tsitsiridis","year":"2023","unstructured":"Tsitsiridis G, Steinkamp R, Giurgiu M, Brauner B, Fobo G, Frishman G, Montrone C, Ruepp A (2023) Corum: the comprehensive resource of mammalian protein complexes-2022. Nucleic Acids Res 51(D1):539\u2013545","journal-title":"Nucleic Acids Res"},{"key":"727_CR38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1477-5956-11-S1-S18","volume":"11","author":"S Wang","year":"2013","unstructured":"Wang S, Wu F (2013) Detecting overlapping protein complexes in PPI networks based on robustness. Proteome Sci 11:1\u20138","journal-title":"Proteome Sci"},{"issue":"10","key":"727_CR39","doi-asserted-by":"publisher","first-page":"1274","DOI":"10.1093\/bioinformatics\/btm087","volume":"23","author":"JZ Wang","year":"2007","unstructured":"Wang JZ, Du Z, Payattakool R, Yu PS, Chen C-F (2007) A new method to measure the semantic similarity of go terms. Bioinformatics 23(10):1274\u20131281","journal-title":"Bioinformatics"},{"key":"727_CR40","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-018-2565-8","volume":"20","author":"R Wang","year":"2019","unstructured":"Wang R, Liu G, Wang C (2019) Identifying protein complexes based on an edge weight algorithm and core-attachment structure. BMC Bioinform 20:1\u201320","journal-title":"BMC Bioinform"},{"key":"727_CR41","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2024.3429546","author":"W Wang","year":"2024","unstructured":"Wang W, Meng X, Xiang J, Bedru HD, Li M (2024) Dopcc: detecting overlapping protein complexes via multi-metrics and co-core attachment method. IEEE\/ACM Trans Comput Biol Bioinform. https:\/\/doi.org\/10.1109\/TCBB.2024.3429546","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"7","key":"727_CR42","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1093\/bioinformatics\/btq064","volume":"26","author":"G Yu","year":"2010","unstructured":"Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S (2010) Gosemsim: an R package for measuring semantic similarity among go terms and gene products. Bioinformatics 26(7):976\u2013978","journal-title":"Bioinformatics"},{"issue":"1","key":"727_CR43","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.ygeno.2019.01.011","volume":"112","author":"J Zahiri","year":"2020","unstructured":"Zahiri J, Emamjomeh A, Bagheri S, Ivazeh A, Mahdevar G, Tehrani HS, Mirzaie M, Fakheri BA, Mohammad-Noori M (2020) Protein complex prediction: a survey. Genomics 112(1):174\u2013183","journal-title":"Genomics"}],"container-title":["Applied Network Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s41109-025-00727-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s41109-025-00727-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s41109-025-00727-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T16:31:42Z","timestamp":1757435502000},"score":1,"resource":{"primary":{"URL":"https:\/\/appliednetsci.springeropen.com\/articles\/10.1007\/s41109-025-00727-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,26]]},"references-count":43,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["727"],"URL":"https:\/\/doi.org\/10.1007\/s41109-025-00727-6","relation":{},"ISSN":["2364-8228"],"issn-type":[{"value":"2364-8228","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,26]]},"assertion":[{"value":"31 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 July 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 August 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"38"}}