STRING swMATH ID: 23938 Software Authors: Franceschini, A.; Szklarczyk, D.; Frankild, S.; Kuhn, M.; Simonovic, M.; Roth, A.; Lin, J.; Minguez, P.; Bork, P.; Von Mering, C.; Jensen, L. J. Description: STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made—particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction data is desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism to the other; and (iii) we provide users with statistical information on any functional enrichment observed in their networks. Homepage: https://string-db.org/cgi/input.pl Related Software: KEGG; R; Cytoscape; BioGRID; IntAct; Bioconductor; GeneCards; DAVID; HIPPIE; limma; ClueGO; gcrma; MSigDB; BLAST; PSI-BLAST; I-TASSER; Reactome; Gurobi; darch; Real Cited in: 46 Publications all top 5 Cited by 155 Authors 3 Vogiatzis, Chrysafis 2 Angelopoulos, Nicos 2 Camur, Mustafa Can 2 Cowen, Lenore J. 2 Hu, Xiaozhe 2 Lagraa, Sofiane 2 Seba, Hamida 2 Wu, Kaiyi 1 Abdallah, Samer A. 1 Akhmedov, Murodzhon 1 Alanis-Lobato, Gregorio 1 Altuntas, Volkan 1 Álvarez-Miranda, Eduardo 1 Amani, Jafar 1 Anbarasu, Anand 1 Andrade-Navarro, Miguel A. 1 Babaki, Behrouz 1 Bag, Susmita 1 Barbillon, Pierre 1 Bertoni, Francesco 1 Caldarelli, Guido 1 Chiquet, Julien 1 Chitra, Uthsav 1 Cimini, Giulio 1 de Causmaecker, Patrick 1 De Niz, Carlos 1 Delgado, Alberto Santos 1 Devkota, Kapil 1 Ding, Dewu 1 El-Kebir, Mohammed 1 Ertaylan, Gökhan 1 Farhan, Hesso 1 Fattahian, Yaser 1 Fraenkel, Ernest 1 Gabrielli, Andrea 1 Gargari, Seyed Latif Mousavi 1 Garlaschelli, Diego 1 Ge, Peng 1 Giamas, Georgios 1 Gök, Murat 1 Guan, Aoran 1 Heringa, Jaap 1 Höfling, Holger 1 Hou, Mingliang 1 How, Javier J. 1 Hrga, Timotej 1 Hribar, Rok 1 Huang, Guo-Bao 1 Huang, Ping 1 Hütt, Marc-Thorsten 1 Jahangiri, Abolfazl 1 Jalali, Marziyeh 1 Janyasupab, Panisa 1 Jatana, Nidhi 1 Karakitsiou, Athanasia 1 Kheddouci, Hamamache 1 Khennoufa, Riadh 1 Klau, Gunnar W. 1 Koçal, Osman Hilmi 1 Kocheturov, Anton 1 Kong, Xiangjie 1 Kong, Yan 1 Kwee, Ivo 1 Lambert-Lacroix, Sophie 1 Lan, Wei 1 Landers, John 1 Latha, N. 1 LeNail, Alexander 1 Lesne, Annick 1 Leyman, Pieter 1 Li, Zhenpeng 1 Lin, Junyuan 1 Liu, Guixia 1 Liu, Huaping 1 Liu, Liyue 1 Liu, Xiangyu 1 Luipersbeck, Martin 1 Maji, Pradipta 1 M’Baya, Abir 1 Mier, Pablo 1 Mohammadnejad, Javad 1 Montemanni, Roberto 1 Murphy, James M. 1 Navlakha, Saket 1 Nyczka, Piotr 1 Pal, Ranadip 1 Pan, Yi 1 Panigrahi, Priya P. 1 Papa, Gregor 1 Pardalos, Panos M. 1 Park, Tae Yoon 1 Paul, Sushmita 1 Peeters, Carel F. W. 1 Petelin, Gašper 1 Picard, Franck 1 Plaimas, Kitiporn 1 Podder, Avijit 1 Povh, Janez 1 Pržulj, Nataša 1 Rahbar, Mohammad Reza ...and 55 more Authors all top 5 Cited in 30 Serials 7 Journal of Theoretical Biology 3 Annals of Operations Research 3 Algorithms 2 INFORMS Journal on Computing 1 Mathematical Biosciences 1 Physica A 1 Physics Reports 1 Bulletin of Mathematical Biology 1 Information Sciences 1 Journal of the American Statistical Association 1 Journal of Multivariate Analysis 1 Computers & Operations Research 1 International Journal of Approximate Reasoning 1 Neural Computation 1 Journal of Global Optimization 1 Applied Mathematical Modelling 1 Pattern Recognition 1 Complexity 1 Soft Computing 1 Data Mining and Knowledge Discovery 1 International Journal of Applied Mathematics and Computer Science 1 Journal of Biological Systems 1 Natural Computing 1 Mathematical Biosciences and Engineering 1 The Annals of Applied Statistics 1 International Journal of Biomathematics 1 Statistics and Computing 1 Computer Science Review 1 Methods in Molecular Biology 1 SIAM Journal on Mathematics of Data Science all top 5 Cited in 12 Fields 29 Biology and other natural sciences (92-XX) 13 Computer science (68-XX) 10 Statistics (62-XX) 8 Operations research, mathematical programming (90-XX) 4 Combinatorics (05-XX) 3 Probability theory and stochastic processes (60-XX) 2 Numerical analysis (65-XX) 2 Systems theory; control (93-XX) 1 Linear and multilinear algebra; matrix theory (15-XX) 1 Statistical mechanics, structure of matter (82-XX) 1 Game theory, economics, finance, and other social and behavioral sciences (91-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year