Network spectra for drug-target identification in complex diseases: new guns against old foes
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The fundamental understanding of altered complex molecular interactions in a diseased condition is the key to its cure. The overall functioning of these molecules is kind of jugglers play in the cell orchestra and to anticipate these relationships among the molecules is one of the greatest challenges in modern biology and medicine. Network science turned out to be providing a successful and simple platform to understand complex interactions among healthy and diseased tissues. Furthermore, much information about the structure and dynamics of a network is concealed in the eigenvalues of its adjacency matrix. In this review, we illustrate rapid advancements in the field of network science in combination with spectral graph theory that enables us to uncover the complexities of various diseases. Interpretations laid by network science approach have solicited insights into molecular relationships and have reported novel drug targets and biomarkers in various complex diseases.
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In silico approaches have been adopted into the drug discovery pipeline because drug discovery processes are costly and time-consuming.
“Because such processes are costly and time-consuming, in silico approaches have been adopted into the drug discovery pipeline.”
From Graph representation learning in biomedicine and healthcare (2022) · cites this paper as [32]
Modern drug discovery requires elucidating a candidate drug's chemical structure, identifying its targets, quantifying efficacy and toxicity, and detecting side effects.
“Modern drug discovery requires elucidating a candidate drug’s chemical structure, identifying its drug targets, quantifying its efficacy and toxicity, and detecting its potential side effects [13, 14, 32, 164].”
From Graph representation learning in biomedicine and healthcare (2022) · cites this paper as [32]
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Cites
Collective dynamics of ‘small-world’ networks
Watts, D. J., & Strogatz, S. H. (1998) · Nature · doi:10.1038/30918 · Cited by 43,060 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works
Emergence of Scaling in Random Networks
Barabási, A.-L., & Albert, R. (1999) · Science · doi:10.1126/science.286.5439.509 · Cited by 36,135 · see citing works
Golub, G. (2012) · doi:10.56021/9781421407944 · Cited by 34,505 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works
Statistical mechanics of complex networks
Albert, R., & Barabási, A.-L. (2002) · Reviews of Modern Physics · doi:10.1103/revmodphys.74.47 · Cited by 20,471 · see citing works
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909 · see citing works
Network biology: understanding the cell's functional organization
Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903 · see citing works
Network motifs: simple building blocks of complex networks.
Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., & Alon, U. (2002) · Science · doi:10.1126/science.298.5594.824 · Cited by 7,368 · see citing works
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw937 · Cited by 6,980 · see citing works
Chou, T.-C. (2006) · Pharmacological Reviews · doi:10.1124/pr.58.3.10 · Cited by 5,163 · see citing works
Network medicine: a network-based approach to human disease
Barabási, A.-L., Gulbahce, N., & Loscalzo, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2918 · Cited by 5,034 · see citing works
Systems biology: a brief overview
Kitano, H. (2002) · Science · doi:10.1126/science.1069492 · Cited by 4,265 · see citing works
Tumour stem cells and drug resistance
Dean, M., Fojo, T., & Bates, S. (2005) · Nature reviews. Cancer · doi:10.1038/nrc1590 · Cited by 3,668 · see citing works
From molecular to modular cell biology.
Hartwell, L. H., Hopfield, J. J., Leibler, S., & Murray, A. W. (1999) · Nature · doi:10.1038/35011540 · Cited by 3,632 · see citing works
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395 · see citing works
Goh, K.-I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., & Barabási, A.-L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701361104 · Cited by 3,242 · see citing works
Human Protein Reference Database--2009 update
Prasad, T. S. K., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, R. B., Venugopal, A., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn892 · Cited by 3,205 · see citing works
HMDB 3.0—The Human Metabolome Database in 2013
Wishart, D. S., Jewison, T., Guo, A. C., Wilson, M., Knox, C., Liu, Y., Djoumbou-Feunang, Y., Mandal, R., Aziat, F., Dong, E., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1065 · Cited by 2,845 · see citing works
Epigenetic modifications and human disease
Portela, A., & Esteller, M. (2010) · Nature Biotechnology · doi:10.1038/nbt.1685 · Cited by 2,843 · see citing works
Mechanisms of Cancer Drug Resistance
Gottesman, M. M. (2002) · Annual Review of Medicine · doi:10.1146/annurev.med.53.082901.103929 · Cited by 2,643 · see citing works
Kitano, H. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1471 · Cited by 2,278 · see citing works
The causes and consequences of genetic heterogeneity in cancer evolution
Burrell, R. A., McGranahan, N., Bartek, J., & Swanton, C. (2013) · Nature · doi:10.1038/nature12625 · Cited by 2,262 · see citing works
Pan-cancer patterns of somatic copy number alteration
Zack, T. I., Schumacher, S. E., Carter, S. L., Cherniack, A. D., Saksena, G., Tabak, B., Lawrence, M. S., Zhang, C., Wala, J. A., Mermel, C. H., et al. (2013) · Nature Genetics · doi:10.1038/ng.2760 · Cited by 1,843 · see citing works
Reactome: a database of reactions, pathways and biological processes
Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1018 · Cited by 1,751 · see citing works
A N <scp>EW</scp> A <scp>PPROACH TO</scp> D <scp>ECODING</scp> L <scp>IFE</scp> : Systems Biology
Ideker, T., Galitski, T., & Hood, L. (2001) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.2.1.343 · Cited by 1,664 · see citing works
Characteristic Vectors of Bordered Matrices With Infinite Dimensions
Wigner, E. P. (1955) · Annals of Mathematics · doi:10.2307/1970079 · Cited by 1,581 · see citing works
BIND--The Biomolecular Interaction Network Database
Bader, G. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.242 · Cited by 1,556 · see citing works
Uncovering disease-disease relationships through the incomplete interactome
Menche, J., Sharma, A., Kitsak, M., Ghiassian, S. D., Vidal, M., Loscalzo, J., & Barabási, A.-L. (2015) · Science · doi:10.1126/science.1257601 · Cited by 1,546 · see citing works
Network‐based classification of breast cancer metastasis
Chuang, H., Lee, E., Liu, Y., Lee, D., & Ideker, T. (2007) · Molecular Systems Biology · doi:10.1038/msb4100180 · Cited by 1,431 · see citing works
Recent Segmental Duplications in the Human Genome
Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W., & Eichler, E. E. (2002) · Science · doi:10.1126/science.1072047 · Cited by 1,355 · see citing works
MIPS: a database for genomes and protein sequences
Mewes, H. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.37 · Cited by 1,276 · see citing works
A systems biology approach for pathway level analysisPreprint
Drăghici, S., Khatri, P., Tarca, A. L., Amin, K., Done, A., Voichiţa, C., Georgescu, C., & Romero, R. J. (2007) · Genome Research · doi:10.1101/gr.6202607 · Cited by 1,250 · see citing works
The IntAct molecular interaction database in 2012
Kerrien, S., Aranda, B., Breuza, L., Bridge, A. J., Broackes-Carter, F., Chen, C. C. L., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U. G., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1088 · Cited by 1,151 · see citing works
DIP: the Database of Interacting Proteins
Xénarios, I. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.289 · Cited by 1,125 · see citing works
BIND: the Biomolecular Interaction Network Database
Bader, G. D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg056 · Cited by 1,113 · see citing works
Mitigation strategies for pandemic influenza in the United States
Germann, T. C., Kadau, K., Longini, I. M., & Macken, C. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601266103 · Cited by 1,047 · see citing works
Universal and Nonuniversal Properties of Cross Correlations in Financial Time Series
Plerou, V., Gopikrishnan, P., Rosenow, B., et al. (1999) · Physical Review Letters · doi:10.1103/physrevlett.83.1471 · Cited by 1,027 · see citing works
Cancer heterogeneity: implications for targeted therapeutics
Fisher, R. A., Pusztai, L., & Swanton, C. (2013) · British Journal of Cancer · doi:10.1038/bjc.2012.581 · Cited by 980 · see citing works
The BioGRID interaction database: 2017 update
Chatr‐aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas, N. K., O’Donnell, L., Oster, S. K., Theesfeld, C. L., Sellam, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1102 · Cited by 960 · see citing works
Ideker, T., & Sharan, R. (2008) · Genome Research · doi:10.1101/gr.071852.107 · Cited by 817 · see citing works
MIPS: a database for genomes and protein sequences
Mewes, H. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.31 · Cited by 784 · see citing works
Modeling interactome: scale-free or geometric?
Pržulj, N., Corneil, D. G., & Jurišica, I. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth436 · Cited by 709 · see citing works
Characteristic Vectors of Bordered Matrices with Infinite Dimensions II
Wigner, E. P. (1993) · Springer eBooks · doi:10.1007/978-3-662-02781-3_36 · Cited by 693 · see citing works
Economic Consequences of Diabetes Mellitus in the U.S. in 1997
American Diabetes Association (1998) · Diabetes Care · doi:10.2337/diacare.21.2.296 · Cited by 654 · see citing works
On the Distinction between Disease and Illness
Boorse, C. (1999) · Philosophy & Public Affairs · doi:10.4324/9780203823415-4 · Cited by 646 · see citing works
Network-based in silico drug efficacy screening
Guney, E., Menche, J., Vidal, M., & Barábasi, A.-L. (2016) · Nature Communications · doi:10.1038/ncomms10331 · Cited by 625 · see citing works
Network modeling links breast cancer susceptibility and centrosome dysfunction
Pujana, M. Á., Han, J.-D. J., Starita, L. M., Purrington, K. S., Tewari, M., Ahn, J. S., Rennert, G., Moreno, V. R., Kirchhoff, T., Gold, B., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.2 · Cited by 611 · see citing works
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Schellenberger, J., Park, J. O., Conrad, T. M., & Palsson, B. Ø. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-213 · Cited by 585 · see citing works
Caspi, R. R., Foerster, H., Fulcher, C., Kaipa, P., Krummenacker, M., Latendresse, M., Paley, S., Rhee, S. Y., Shearer, A. G., Tissier, C. P., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm900 · Cited by 581 · see citing works
ConsensusPathDB--a database for integrating human functional interaction networks
Kamburov, A., Wierling, C., Lehrach, H., & Herwig, R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn698 · Cited by 565 · see citing works
From big data analysis to personalized medicine for all: challenges and opportunities
Alyass, A., Turcotte, M., & Meyre, D. (2015) · BMC Medical Genomics · doi:10.1186/s12920-015-0108-y · Cited by 557 · see citing works
Getting connected: analysis and principles of biological networksPreprint
Zhu, X., Gerstein, M., & Snyder, M. P. (2007) · Genes & Development · doi:10.1101/gad.1528707 · Cited by 549 · see citing works
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
Orchard, S. E., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S. L., Bridge, A. J., Briganti, L., Brinkman, F. S. L., Cesareni, G., et al. (2012) · Nature Methods · doi:10.1038/nmeth.1931 · Cited by 538 · see citing works
Yeger‐Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R. Y., Alon, U. S., & Margalit, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0306752101 · Cited by 536 · see citing works
Defective protein folding as a basis of human disease
Thomas, P., Qu, B.-H., & Pedersen, P. L. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89100-8 · Cited by 531 · see citing works
WikiPathways: building research communities on biological pathways
Kelder, T., van Iersel, M., Hanspers, K., Kutmon, M., Conklin, B. R., Evelo, C. T., & Pico, A. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1074 · Cited by 521 · see citing works
Gene regulatory network growth by duplication
Teichmann, S. A., & Babu, M. M. (2004) · Nature Genetics · doi:10.1038/ng1340 · Cited by 516 · see citing works
Physical approach to complex systems
Kwapień, J., & Drożdż, S. (2012) · Physics Reports · doi:10.1016/j.physrep.2012.01.007 · Cited by 514 · see citing works
MINT, the molecular interaction database: 2009 update
Ceol, A. G. M., Chatr‐aryamontri, A., Licata, L., Peluso, D., Briganti, L., Perfetto, L., Castagnoli, L., & Cesareni, G. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp983 · Cited by 507 · see citing works
Spectra of “real-world” graphs: Beyond the semicircle law
Farkas, I. J., Derényi, I., Barabási, A.-Ĺ., & Vicsek, T. (2001) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.64.026704 · Cited by 502 · see citing works
Global topological features of cancer proteins in the human interactome
Jonsson, P. F., & Bates, P. A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl390 · Cited by 490 · see citing works
Detecting functional modules in the yeast protein–protein interaction network
Chen, J., & Yuan, B. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl370 · Cited by 440 · see citing works
Ekman, D. S., Light, S., Björklund, Å. K., & Elofsson, A. (2006) · Genome biology · doi:10.1186/gb-2006-7-6-r45 · Cited by 377 · see citing works
Schoeberl, B., Pace, E. A., Fitzgerald, J. B., Harms, B. D., Xu, L., Nie, L., Linggi, B. E., Kalra, A. V., Paragas, V. B., Bukhalid, R. A., et al. (2009) · Science Signaling · doi:10.1126/scisignal.2000352 · Cited by 358 · see citing works
Localization and Spreading of Diseases in Complex Networks
Goltsev, A. V., Dorogovtsev, S. N., Oliveira, J. G., et al. (2012) · Physical Review Letters · doi:10.1103/physrevlett.109.128702 · Cited by 350 · see citing works
HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores
Schaefer, M. H., Fontaine, J., Vinayagam, A., Porras, P., Wanker, E. E., & Andrade-Navarro, M. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031826 · Cited by 334 · see citing works
Pathway and network analysis of cancer genomes
Creixell, P., Linding, R., Reimand, J., Bader, G. D., Haider, S., Wu, G., Ouellette, B. F. F., Boutros, P. C., Stein, L. D., Shibata, T., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3440 · Cited by 326 · see citing works
Chapter 5: Network Biology Approach to Complex Diseases
Cho, D.-Y., Kim, Y.-A., & Przytycka, T. M. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002820 · Cited by 283 · see citing works
Dorogovtsev, S. N., Goltsev, A. V., Mendes, J. F. F., & Samukhin, A. N. (2003) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.68.046109 · Cited by 281 · see citing works
The structure and function of networks
Newman, M. E. J. (2002) · Computer Physics Communications · doi:10.1016/s0010-4655(02)00201-1 · Cited by 271 · see citing works
Defining ‘health’ and ‘disease’
Ereshefsky, M. (2009) · Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences · doi:10.1016/j.shpsc.2009.06.005 · Cited by 257 · see citing works
Linear Algebra: A Modern Introduction
Poole, D. (2002) · Medical Entomology and Zoology · Cited by 250 · see citing works
Spectra and eigenvectors of scale-free networks
Goh, K.-I., Kahng, B., & Kim, D. (2001) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.64.051903 · Cited by 237 · see citing works
SIGNOR: a database of causal relationships between biological entities
Perfetto, L., Briganti, L., Calderone, A., Perpetuini, A. C., Iannuccelli, M., Langone, F., Licata, L., Marinkovic, M., Mattioni, A., Pavlidou, T., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1048 · Cited by 235 · see citing works
Human Cancer Protein-Protein Interaction Network: A Structural Perspective
Kar, G., Gursoy, A., & Keskin, O. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000601 · Cited by 235 · see citing works
APID: Agile Protein Interaction DataAnalyzer
Prieto, C. A. V., & Rivas, J. D. L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl128 · Cited by 224 · see citing works
Sneha, P., & Doss, C. G. P. (2015) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2015.09.004 · Cited by 205 · see citing works
SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks
Fazekas, D., Koltai, M., Türei, D., Módos, D., Pálfy, M., Dúl, Z., Zsákai, L., Szalay-Bekő, M., Lenti, K., Farkas, I. J., et al. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-7 · Cited by 198 · see citing works
Human diseases through the lens of network biology
Furlong, L. I. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.11.004 · Cited by 194 · see citing works
Modena, B. D., Bleecker, E. R., Busse, W. W., ERZURUM, S. C., Gaston, B. M., Jarjour, N. N., Meyers, D. A., Milošević, J., Tedrow, J. R., Wu, W., et al. (2017) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201607-1407oc · Cited by 157 · see citing works
Colloquium : Random matrices and chaos in nuclear spectra
Papenbrock, T., & Weidenmüller, H. A. (2007) · Reviews of Modern Physics · doi:10.1103/revmodphys.79.997 · Cited by 107 · see citing works
Tissue Specificity of Human Disease Module
Kitsak, M., Sharma, A., Menche, J., Güney, E., Ghiassian, S. D., Loscalzo, J., & Barabási, A.-Ĺ. (2016) · Scientific Reports · doi:10.1038/srep35241 · Cited by 101 · see citing works
Biana: a software framework for compiling biological interactions and analyzing networks
Garcı́a-Garcı́a, J., Güney, E., Aragüés, R., Planas-Iglesias, J., & Oliva, B. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-56 · Cited by 91 · see citing works
Effect of localization on the stability of mutualistic ecological networks
Suweis, S. S., Grilli, J., Banavar, J. R., Stefano Allesina, A., & Maritan, A. (2015) · Nature Communications · doi:10.1038/ncomms10179 · Cited by 89 · see citing works
Universality in complex networks: Random matrix analysis
Bandyopadhyay, J. N., & Jalan, S. (2007) · Physical Review E · doi:10.1103/physreve.76.026109 · Cited by 85 · see citing works
Self-citationSpectral analysis and the dynamic response of complex networks
de Aguiar, M. A. M., & Yaneer Bar-yam, A. (2005) · Physical Review E · doi:10.1103/physreve.71.016106 · Cited by 85 · see citing works
The state of global health in 2014
Sepúlveda, J., & Murray, C. J. L. (2014) · Science · doi:10.1126/science.1257099 · Cited by 78 · see citing works
Random-matrix theory and eigenmodes of dynamical systems
Haake, F., & Życzkowski, K. (1990) · Physical Review A · doi:10.1103/physreva.42.1013 · Cited by 74 · see citing works
Discriminating Different Classes of Biological Networks by Analyzing the Graphs Spectra Distribution
Takahashi, D. Y., Sato, J. R., Ferreira, C. E., & Fujita, A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049949 · Cited by 74 · see citing works
Ayers, D., & Day, P. J. (2015) · Molecular Biology International · doi:10.1155/2015/698169 · Cited by 73 · see citing works
Hsieh, J. C. F., Berg, D. V. D., Kang, H., Hsieh, C., & Lieber, M. R. (2013) · Aging Cell · doi:10.1111/acel.12053 · Cited by 71 · see citing works
The distribution of genetic variance across phenotypic space and the response to selection
Blows, M. W., & McGuigan, K. (2014) · Molecular Ecology · doi:10.1111/mec.13023 · Cited by 65 · see citing works
Spectral properties of complex networks
Sarkar, C., & Jalan, S. (2018) · Chaos An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/1.5040897 · Cited by 62 · see citing works
Self-citationAlQuraishi, M., Koytiger, G., Jenney, A., MacBeath, G., & Sorger, P. K. (2014) · Nature Genetics · doi:10.1038/ng.3138 · Cited by 59 · see citing works
Gibson, S. M., Ficklin, S. P., Isaacson, S., Luo, F., Feltus, F. A., & Smith, M. C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0055871 · Cited by 58 · see citing works
Role of clinical bioinformatics in the development of network-based Biomarkers
Wang, X. (2011) · Journal of Clinical Bioinformatics · doi:10.1186/2043-9113-1-28 · Cited by 58 · see citing works
Complexity in cancer biology: is systems biology the answer?
Koutsogiannouli, E. A., Papavassiliou, A. G., & Papanikolaou, N. A. (2013) · Cancer Medicine · doi:10.1002/cam4.62 · Cited by 49 · see citing works
Understanding cancer complexome using networks, spectral graph theory and multilayer framework
Rai, A., Pradhan, P., Nagraj, J., Lohitesh, K., Chowdhury, R., & Jalan, S. (2017) · Scientific Reports · doi:10.1038/srep41676 · Cited by 45 · see citing works
Self-citationRandom matrix analysis of localization properties of gene coexpression network
Jalan, S., Solymosi, N., Vattay, G., & Li, B. (2010) · Physical Review E · doi:10.1103/physreve.81.046118 · Cited by 44 · see citing works
Self-citationRecent Progress and Modern Challenges in Applied Mathematics, Modeling and Computational Science
Melnik, R., Makarov, R. N., & Bélair, J. (2017) · Fields Institute communications · doi:10.1007/978-1-4939-6969-2 · Cited by 43 · see citing works
Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology
Aguirre‐Plans, J., Piñero, J., Menche, J., Sanz, F., Furlong, L. I., Schmidt, H. H. H. W., Oliva, B., & Güney, E. (2018) · Pharmaceuticals · doi:10.3390/ph11030061 · Cited by 43 · see citing works
Community of protein complexes impacts disease association
Wang, Q., Liu, W., Ning, S., Ye, J., Huang, T., Li, Y., Wang, P., Shi, H., & Li, X. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.74 · Cited by 41 · see citing works
Spectral plots and the representation and interpretation of biological data
Banerjee, A., & Jost, J. (2007) · Theory in Biosciences · doi:10.1007/s12064-007-0005-9 · Cited by 36 · see citing works
Shinde, P., & Jalan, S. (2015) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/112/58001 · Cited by 34 · see citing works
Self-citationSpectral analysis of protein-protein interactions inDrosophila melanogaster
Kamp, C., & Christensen, K. (2005) · Physical Review E · doi:10.1103/physreve.71.041911 · Cited by 31 · see citing works
Spectral properties of directed random networks with modular structure
Jalan, S., Zhu, G., & Li, B. (2011) · Physical Review E · doi:10.1103/physreve.84.046107 · Cited by 29 · see citing works
Self-citationRandomness and preserved patterns in cancer network
Rai, A., Menon, A. V., & Jalan, S. (2014) · Scientific Reports · doi:10.1038/srep06368 · Cited by 29 · see citing works
Self-citationSpectral transitions in networks
Palla, G., & Vattay, G. (2006) · New Journal of Physics · doi:10.1088/1367-2630/8/12/307 · Cited by 28 · see citing works
Agrawal, A., Sarkar, C., Dwivedi, S. K., Dhasmana, N., & Jalan, S. (2013) · Physica A Statistical Mechanics and its Applications · doi:10.1016/j.physa.2013.12.005 · Cited by 24 · see citing works
Self-citationEmergence of clustering: Role of inhibition
Dwivedi, S. K., & Jalan, S. (2014) · Physical Review E · doi:10.1103/physreve.90.032803 · Cited by 24 · see citing works
Self-citationOrigin and implications of zero degeneracy in networks spectra
Yadav, A., & Jalan, S. (2015) · Chaos An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/1.4917286 · Cited by 24 · see citing works
Self-citationParenclitic Network Analysis of Methylation Data for Cancer Identification
Karsakov, A., Bartlett, T. E., Ryblov, A., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169661 · Cited by 23 · see citing works
Optimized evolution of networks for principal eigenvector localization
Pradhan, P., Yadav, A., Dwivedi, S. K., et al. (2017) · Physical review. E · doi:10.1103/physreve.96.022312 · Cited by 23 · see citing works
Analysing degeneracies in networks spectra
Marrec, L., & Jalan, S. (2017) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/117/48001 · Cited by 22 · see citing works
Self-citationComparisons of gene coexpression network modules in breast cancer and ovarian cancer
Zhang, S. (2018) · BMC Systems Biology · doi:10.1186/s12918-018-0530-9 · Cited by 20 · see citing works
Güney, E., & Oliva, B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0094686 · Cited by 17 · see citing works
Random Matrix Analysis for Gene Interaction Networks in Cancer Cells
Kikkawa, A. (2018) · Scientific Reports · doi:10.1038/s41598-018-28954-1 · Cited by 15 · see citing works
Codon based co-occurrence network motifs in human mitochondria
Shinde, P. S., Sarkar, C., & Jalan, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-21454-2 · Cited by 15 · see citing works
Self-citationSato, J. R., Balardin, J. B., Vidal, M. C., & Fujita, A. (2016) · Journal of Psychiatry and Neuroscience · doi:10.1503/jpn.140364 · Cited by 14 · see citing works
Dissortativity and duplications in oral cancer
Shinde, P., Yadav, A., Rai, A., & Jalan, S. (2015) · The European Physical Journal B · doi:10.1140/epjb/e2015-60426-5 · Cited by 12 · see citing works
Self-citationBurz, D. S., & Shekhtman, A. G. (2009) · Nature · doi:10.1038/458037a · Cited by 12 · see citing works
Network Topologies Decoding Cervical Cancer
Jalan, S., Kanhaiya, K., Rai, A., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135183 · Cited by 11 · see citing works
Self-citationPrognostic interaction patterns in diabetes mellitus II: A random-matrix-theory relation
Rai, A., Pawar, A. K., & Jalan, S. (2015) · Physical Review E · doi:10.1103/physreve.92.022806 · Cited by 9 · see citing works
Self-citationRandomness and Structure in Collaboration Networks: A Random Matrix Analysis
Sarkar, C., & Jalan, S. (2016) · IEEE Transactions on Computational Social Systems · doi:10.1109/tcss.2016.2591778 · Cited by 8 · see citing works
Self-citationDetection of epigenomic network community oncomarkers
Bartlett, T. E., & Zaikin, A. A. (2016) · The Annals of Applied Statistics · doi:10.1214/16-aoas939 · Cited by 7 · see citing works
Predicting protein networks in cancer
Califano, A. (2014) · Nature Genetics · doi:10.1038/ng.3156 · Cited by 6 · see citing works
Gohil, D. J., Kothari, S., Shinde, P. S., et al. (2014) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2014.11.005 · Cited by 3 · see citing works
Self-citationApplication of Random Matrix Theory to Complex Networks
Rai, A., & Jalan, S. (2015) · Understanding complex systems · doi:10.1007/978-3-319-17037-4_6 · Cited by 2 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 6
- Mehta M Random Matrices. second ed. 1991 New York Academic Press
- Melnik R Makarov R Belair J Recent Progress and Modern Challenges in Applied Mathematics 2017 NY Springer
- Mieghem P Graph spectra for complex networks. first ed. 2011 New York Cambridge University Press
- Rai, A, Jalan S (2015). In: Banerjee S Rondoni L (eds)Applications of chaos and Nonlinear Dynamics in Science and Engineering, Vol.4, Understanding Complex Systems, pp 195–212.. Springer. Cham.
- Rai, A (2017) Network topologies unraveling randomness and preserved patterns in disease complexome. Dissertation, Indian Institute of Technology Indore. Nat Sci Rep (Springer Nature).
- Shinde, P, et al. (2018) Symmetry in disease networks identified: Proposal for multicancer biomarkers (Under review in Network Science).
Cited by
Sorted by citations
Graph representation learning in biomedicine and healthcare
Li, M. M., Huang, K., & Zitnik, M. (2022) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00942-x · Cited by 294 · see citing works
“…17,18 ; graph neural networks 19–21 (GNNs); representation learning for homogeneous and heterogeneous graphs 22–24 , solely heterogeneous graphs 25 and dynamic graphs 26 ; data fusion 27 ; network propagation 28 ; topological data analysis 29 (TDA); and the creation of biomedical networks 9,29–32 .”
- Authors
- Rai, A., Shinde, P., & Jalan, S.
- Affiliations
- Indian Institute of Technology Guwahati (IN)
- Indian Institute of Technology Indore (IN)
- Corresponding author
- Rai, Aparna
- Venue
- Applied Network Science
- Published
- 2018-12
- Volume
- 3
- Issue
- 1
- Pages
- 51-51
- ISSN
- 2364-8228 (ISSN-L)
- PMC
- PMC6297166
- OpenAlex
- W2904862283
- Cited by
- 12
- References
- 129
- Citations by year
- 2023: 3 · 2022: 3 · 2021: 2 · 2020: 1 · 2019: 2 · 2018: 1
- FWCI
- 0.15
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Applied Network Science (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Department of Science and Technology, Ministry of Science and Technology, India
- Ministry of Education and Science of the Russian Federation (074-02-2018-330)
- Indian Institute of Technology Guwahati
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Physics and Astronomy › Statistical and Nonlinear Physics › Complex Network Analysis Techniques
- Keywords
- drug target identification, complex diseases, spectral graph theory, adjacency matrix eigenvalues, network science, biomarkers, molecular interactions, network dynamics
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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