Integrative approaches for finding modular structure in biological networks

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · 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

Integrated genomic analyses of ovarian carcinoma

Perou, C. M. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/hvp3-wg08 · Cited by 7,927 · 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

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

The Cancer Genome Atlas Research Network (2008) · Nature · doi:10.1038/nature07385 · Cited by 7,735 · 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

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

BioGRID: a general repository for interaction datasets

Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960 · 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

A comprehensive two-hybrid analysis to explore the yeast protein interactome

Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566 · see citing works

Comprehensive molecular characterization of clear cell renal cell carcinoma

The Cancer Genome Atlas Research Network (2013) · Nature · doi:10.1038/nature12222 · Cited by 3,485 · see citing works

Towards a proteome-scale map of the human protein–protein interaction network

Rual, J.-F. M., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., et al. (2005) · Nature · doi:10.1038/nature04209 · Cited by 2,904 · see citing works

A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome

Stelzl, U., Worm, U., Lalowski, M. M., Haenig, C., Brembeck, F. H., Goehler, H., Strödicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.029 · Cited by 2,389 · see citing works

A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules

Stuart, J. M., Segal, E., Koller, D., & Kim, S. K. (2003) · Science · doi:10.1126/science.1087447 · Cited by 2,235 · see citing works

The Genetic Landscape of a Cell

Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L. Y., Toufighi, K., Mostafavi, S., et al. (2010) · Science · doi:10.1126/science.1180823 · Cited by 2,162 · see citing works

Hierarchical organization in complex networks

Ravasz, E., & Barabási, A.-L. (2003) · Physical Review E · doi:10.1103/physreve.67.026112 · Cited by 2,160 · see citing works

Transcriptional regulatory code of a eukaryotic genome

Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., MacIsaac, K. D., Danford, T., Hannett, N. M., Tagne, J., Reynolds, D. B., Yoo, J. Y., et al. (2004) · Nature · doi:10.1038/nature02800 · Cited by 2,116 · see citing works

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835 · see citing works

Evidence for dynamically organized modularity in the yeast protein–protein interaction network

Han, J. J., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J. M., Cusick, M. E., Roth, F. P., et al. (2004) · Nature · doi:10.1038/nature02555 · Cited by 1,789 · see citing works

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003) · Nature Genetics · doi:10.1038/ng1165 · Cited by 1,686 · see citing works

A travel guide to Cytoscape plugins

Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., Lotia, S., Pico, A. R., Bader, G. D., & Ideker, T. (2012) · Nature Methods · doi:10.1038/nmeth.2212 · Cited by 1,496 · see citing works

Protein complexes and functional modules in molecular networks

Spirin, V., & Mirny, L. A. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2032324100 · Cited by 1,468 · 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

A network-based analysis of systemic inflammation in humans

Program, I. A. H. R. T. I. L. S. C. R., Calvano, S. E., Xiao, W., Richards, D. R., Felciano, R. M., Baker, H. V., Cho, R. J., Chen, R. O., Brownstein, B. H., Cobb, J. P., et al. (2005) · Nature · doi:10.1038/nature03985 · Cited by 1,429 · see citing works

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008) · Science · doi:10.1126/science.1158684 · Cited by 1,392 · see citing works

Personal omics profiling reveals dynamic molecular and medical phenotypes

Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y. K., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.009 · Cited by 1,291 · see citing works

Discovering regulatory and signalling circuits in molecular interaction networks

Ideker, T., Ozier, O., Schwikowski, B., & Siegel, A. F. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s233 · Cited by 1,197 · see citing works

Network‐based prediction of protein function

Sharan, R., Ulitsky, I., & Ron Shamir, A. (2007) · Molecular Systems Biology · doi:10.1038/msb4100129 · Cited by 1,077 · see citing works

Genome-scale models of microbial cells: evaluating the consequences of constraints

Price, N. D., Reed, J. L., & Palsson, B. Ø. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro1023 · Cited by 1,024 · see citing works

The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes

Hillenmeyer, M. E., Fung, E., Wildenhain, J., Pierce, S. E., Hoon, S. S., Lee, W., Proctor, M. J., St.Onge, R. P., Tyers, M., Koller, D., et al. (2008) · Science · doi:10.1126/science.1150021 · Cited by 978 · see citing works

Genomic analysis of regulatory network dynamics reveals large topological changes

Luscombe, N. M., Babu, M. M., Yu, H., Snyder, M. P., Teichmann, S. A., & Gerstein, M. (2004) · Nature · doi:10.1038/nature02782 · Cited by 975 · see citing works

Protein-protein interactions: methods for detection and analysis

Phizicky, E. M., & Fields, S. (1995) · Microbiological Reviews · doi:10.1128/mr.59.1.94-123.1995 · Cited by 969 · see citing works

A systematic comparison and evaluation of biclustering methods for gene expression data

Prelić, A., Stefan Bleuler, A., Philip Zimmermann, B., Wille, A., Bühlmann, P., Gruissem, W., Hennig, L., Thiele, L., & Zitzler, E. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl060 · Cited by 916 · see citing works

An empirical framework for binary interactome mapping

Venkatesan, K., Rual, J.-F. M., Vázquez, A., Stelzl, U., Lemmens, I. H., Hirozane-Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K. I., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1280 · Cited by 907 · see citing works

Evidence for Network Evolution in an Arabidopsis Interactome Map

Dreze, M., Carvunis, A., Charloteaux, B., Galli, M., Pevzner, S. J., Tasan, M., Ahn, Y., Balumuri, P., Barabási, A.-Ĺ., Bautista, V., et al. (2011) · Science · doi:10.1126/science.1203877 · Cited by 895 · see citing works

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map

Collins, S. R., Miller, K. M., Maas, N. L., Roguev, A., Fillingham, J., Chu, C. S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M., et al. (2007) · Nature · doi:10.1038/nature05649 · Cited by 869 · see citing works

A literature network of human genes for high-throughput analysis of gene expression

Jenssen, T.-K., Lægreid, A., Komorowski, J., & Hovig, E. J. (2001) · Nature Genetics · doi:10.1038/88213 · Cited by 839 · see citing works

Navigating the Chaperone Network: An Integrative Map of Physical and Genetic Interactions Mediated by the Hsp90 Chaperone

Zhao, R., Davey, M., Hsu, Y.-C., Kaplanek, P., Tong, A., Parsons, A. B., Krogan, N., Cagney, G., Mai, D., Greenblatt, J., et al. (2005) · Cell · doi:10.1016/j.cell.2004.12.024 · Cited by 819 · see citing works

Protein networks in disease

Ideker, T., & Sharan, R. (2008) · Genome Research · doi:10.1101/gr.071852.107 · Cited by 817 · see citing works

Conserved patterns of protein interaction in multiple species

Sharan, R., Suthram, S., Kelley, R., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., & Ideker, T. E. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409522102 · Cited by 788 · see citing works

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

Vaske, C. J., Benz, S. C., Sanborn, J. Z., Earl, D., Szeto, C., Zhu, J., Haussler, D., & Stuart, J. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq182 · Cited by 786 · see citing works

Differential network biology

Ideker, T., & Krogan, N. J. (2012) · Molecular Systems Biology · doi:10.1038/msb.2011.99 · Cited by 784 · see citing works

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

Lewis, N. E., Nagarajan, H., & Palsson, B. O. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2737 · Cited by 779 · see citing works

An atlas of combinatorial transcriptional regulation in mouse and man

Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.044 · Cited by 715 · see citing works

Biological networks: the tinkerer as an engineer

Alon, U. (2003) · Science · doi:10.1126/science.1089072 · Cited by 706 · see citing works

Modular organization of cellular networks

Rives, A. W., & Galitski, T. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0237338100 · Cited by 695 · see citing works

Global protein function prediction from protein-protein interaction networks

Vázquez, A., Flammini, A., Maritan, A., & Vespignani, A. (2003) · Nature Biotechnology · doi:10.1038/nbt825 · Cited by 693 · see citing works

Dynamic modularity in protein interaction networks predicts breast cancer outcome

Taylor, I. W., Linding, R., Warde-Farley, D., Liu, Y., Pesquita, C., Faria, D., Bull, S. B., Pawson, T. J., Morris, Q., & Wrana, J. L. (2009) · Nature Biotechnology · doi:10.1038/nbt.1522 · Cited by 690 · see citing works

Mutual exclusivity analysis identifies oncogenic network modulesPreprint

Ciriello, G., Cerami, E. G., Sander, C., & Schultz, N. D. (2011) · Genome Research · doi:10.1101/gr.125567.111 · Cited by 676 · see citing works

Prioritizing candidate disease genes by network-based boosting of genome-wide association dataPreprint

Lee, I., Singh-Blom, U. M., Wang, P. I., Shim, J. E., & Marcotte, E. M. (2011) · Genome Research · doi:10.1101/gr.118992.110 · Cited by 673 · see citing works

Global alignment of multiple protein interaction networks with application to functional orthology detection

Singh, R. K., Xu, J., & Berger, B. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806627105 · Cited by 670 · see citing works

Relating Whole-Genome Expression Data with Protein-Protein InteractionsPreprint

Jansen, R., Greenbaum, D. S., & Gerstein, M. (2002) · Genome Research · doi:10.1101/gr.205602 · Cited by 657 · see citing works

Network-based prediction of human tissue-specific metabolism

Shlomi, T., Cabili, M. N., Herrgård, M. J., Palsson, B. Ø., & Ruppin, E. (2008) · Nature Biotechnology · doi:10.1038/nbt.1487 · Cited by 637 · see citing works

Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA RegulogsPreprint

Yu, H., Luscombe, N. M., Lu, H. X., Zhu, X., Xia, Y., Han, J. J., Bertin, N., Chung, S., Vidal, M., & Gerstein, M. (2004) · Genome Research · doi:10.1101/gr.1774904 · Cited by 563 · see citing works

Kernel methods for predicting protein–protein interactions

Ben‐Hur, A., & Noble, W. S. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1016 · Cited by 561 · see citing works

Modeling cellular machinery through biological network comparison

Sharan, R., & Ideker, T. E. (2006) · Nature Biotechnology · doi:10.1038/nbt1196 · Cited by 553 · see citing works

Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction

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

Identifying functional modules in protein–protein interaction networks: an integrated exact approach

Dittrich, M. T., Klau, G. W., Rosenwald, A., Dandekar, T., & Müller, T. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn161 · Cited by 530 · see citing works

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

Odom, D. T., Dowell, R. D., Jacobsen, E. S., Gordon, W., Danford, T. W., MacIsaac, K. D., Rolfe, P. A., Conboy, C. M., Gifford, D. K., & Fraenkel, E. (2007) · Nature Genetics · doi:10.1038/ng2047 · Cited by 506 · see citing works

The Effect of Oxygen on Biochemical Networks and the Evolution of Complex Life

Raymond, J., & Segrè, D. (2006) · Science · doi:10.1126/science.1118439 · Cited by 494 · see citing works

Identification of Potential Interaction Networks Using Sequence-Based Searches for Conserved Protein-Protein Interactions or “Interologs”Preprint

Matthews, L. R., Vaglio, P., Reboul, J., Ge, H., Davis, B. P., Garrels, J. I., Vincent, S., & Vidal, M. (2001) · Genome Research · doi:10.1101/gr.205301 · Cited by 482 · see citing works

Rewiring of Genetic Networks in Response to DNA Damage

Bandyopadhyay, S., Mehta, M., Kuo, D., Sung, M.-K., Chuang, R., Jaehnig, E. J., Bodenmiller, B., Licon, K., Copeland, W., Shales, M., et al. (2010) · Science · doi:10.1126/science.1195618 · Cited by 447 · see citing works

Evolutionary conservation of motif constituents in the yeast protein interaction network

Wuchty, S., Oltvai, Z. N., & Barabási, A.-Ĺ. (2003) · Nature Genetics · doi:10.1038/ng1242 · Cited by 445 · see citing works

Systematic interpretation of genetic interactions using protein networks

Kelley, R., & Ideker, T. (2005) · Nature Biotechnology · doi:10.1038/nbt1096 · Cited by 437 · see citing works

Tissue-specific alternative splicing remodels protein-protein interaction networks

Ellis, J. D., Barrios-Rodiles, M., Çolak, R., Irimia, M., Kim, T., Calarco, J. A., Wang, X., Pan, Q., O'Hanlon, D., Kim, P. M., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.037 · Cited by 431 · see citing works

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

Colijn, C., Brandes, A., Zucker, J., Lun, D. S., Weiner, B., Farhat, M. R., Cheng, T., Moody, D. B., Murray, M. B., & Galagan, J. E. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000489 · Cited by 431 · see citing works

Algorithms for Detecting Significantly Mutated Pathways in Cancer

Vandin, F., Upfal, E., & Raphael, B. J. (2011) · Journal of Computational Biology · doi:10.1089/cmb.2010.0265 · Cited by 427 · see citing works

PathBLAST: a tool for alignment of protein interaction networks

Kelley, B. P., Yuan, B., Lewitter, F., Sharan, R., Stockwell, B. R., & Ideker, T. E. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh411 · Cited by 421 · see citing works

Too many roads not taken

Edwards, A. M., Isserlin, R., Bader, G. D., Frye, S. V., Willson, T. M., & Yu, F. H. (2011) · Nature · doi:10.1038/470163a · Cited by 411 · see citing works

Dynamic Complex Formation During the Yeast Cell Cycle

de Lichtenberg, U., Jensen, L. J., Brunak, S., & Peer Bork, B. (2005) · Science · doi:10.1126/science.1105103 · Cited by 405 · see citing works

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis

Chandrasekaran, S., & Price, N. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005139107 · Cited by 399 · see citing works

IsoRankN: spectral methods for global alignment of multiple protein networks

Liao, C.-S., Lu, K.-H., Baym, M., Singh, R., & Berger, B. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp203 · Cited by 387 · see citing works

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data

Tanay, A., Sharan, R., Kupiec, M., & Ron Shamir, A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308661100 · Cited by 377 · see citing works

Co-clustering of biological networks and gene expression data

Hanisch, D., Zien, A., Zimmer, R., & Lengauer, T. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s145 · Cited by 317 · see citing works

Græmlin: General and robust alignment of multiple large interaction networksPreprint

Flannick, J. A., Novak, A. F., Srinivasan, B. S., McAdams, H. H., & Batzoglou, S. (2006) · Genome Research · doi:10.1101/gr.5235706 · Cited by 315 · see citing works

Identification of functional modules using network topology and high-throughput data

Ulitsky, I., & Shamir, R. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-8 · Cited by 310 · see citing works

Literature-curated protein interaction datasets

Cusick, M. E., Yu, H., Smolyar, A., Venkatesan, K., Carvunis, A., Simonis, N., Rual, J.-F. M., Borick, H., Falter‐Braun, P., Dreze, M., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1284 · Cited by 307 · see citing works

Discovering molecular pathways from protein interaction and gene expression data

Segal, E., Wang, H., & Koller, D. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1037 · Cited by 304 · see citing works

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

Yeger‐Lotem, E., Riva, L., Su, L. J., Gitler, A. D., Cashikar, A. G., King, O. D., Auluck, P. K., Geddie, M. L., Valastyan, J. S., Karger, D. R., et al. (2009) · Nature Genetics · doi:10.1038/ng.337 · Cited by 284 · see citing works

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

Scott, J., Ideker, T. E., Karp, R. M., & Sharan, R. (2006) · Journal of Computational Biology · doi:10.1089/cmb.2006.13.133 · Cited by 270 · see citing works

Pairwise Alignment of Protein Interaction Networks

Koyutürk, M., Kim, Y., Topkara, U., Subramaniam, S., Wojciech Szpankowski, A., & Grama, A. Y. (2006) · Journal of Computational Biology · doi:10.1089/cmb.2006.13.182 · Cited by 269 · see citing works

Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis

Gunsalus, K. C., Ge, H., Schetter, A. J., Goldberg, D. S., Han, J.-D. J., Hao, T., Berriz, G. F., Bertin, N., Huang, J. I., Chuang, L.-S. F., et al. (2005) · Nature · doi:10.1038/nature03876 · Cited by 269 · see citing works

A Systems Approach to Mapping DNA Damage Response Pathways

Workman, C. T., Mak, H. C., McCuine, S., Tagne, J., Agarwal, M., Ozier, O. W., Begley, T. J., Samson, L. D., & Ideker, T. E. (2006) · Science · doi:10.1126/science.1122088 · Cited by 268 · see citing works

A Genetic Interaction Map of RNA-Processing Factors Reveals Links between Sem1/Dss1-Containing Complexes and mRNA Export and Splicing

Wilmes, G. M., Bergkessel, M., Bandyopadhyay, S., Shales, M., Braberg, H., Cagney, G., Collins, S. R., Whitworth, G. B., Kress, T. L., Weissman, J. S., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.11.012 · Cited by 265 · see citing works

Integration of expression data in genome-scale metabolic network reconstructions

Blazier, A. S., & Papin, J. A. (2012) · Frontiers in Physiology · doi:10.3389/fphys.2012.00299 · Cited by 259 · see citing works

An integer linear programming approach for finding deregulated subgraphs in regulatory networks

Backes, C., Rurainski, A., Klau, G. W., Müller, O. J., Stöckel, D., Gerasch, A., Küntzer, J., Maisel, D., Ludwig, N., Hein, M., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1227 · Cited by 259 · see citing works

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

Reiss, D. J., Baliga, N. S., & Bonneau, R. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-280 · Cited by 253 · see citing works

Functional Organization of the S. cerevisiae Phosphorylation Network

Fiedler, D., Braberg, H., Mehta, M., Chechik, G., Cagney, G., Mukherjee, P., Silva, A. C., Shales, M., Collins, S. R., van Wageningen, S., et al. (2009) · Cell · doi:10.1016/j.cell.2008.12.039 · Cited by 251 · see citing works

BioNet: an R-Package for the functional analysis of biological networks

Beißer, D., Klau, G. W., Dandekar, T., Müller, T., & Dittrich, M. T. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq089 · Cited by 238 · see citing works

Simultaneous Identification of Multiple Driver Pathways in Cancer

Leiserson, M. D. M., Blokh, D., Sharan, R., & Raphael, B. J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003054 · Cited by 236 · see citing works

The human genome and drug discovery after a decade. Roads (still) not takenPreprint

Isserlin, R., Bader, G. D., Edwards, A. M., Frye, S. V., Willson, T. M., & Yu, F. H. (2011) · arXiv (Cornell University) · doi:10.48550/arxiv.1102.0448 · Cited by 236 · see citing works

Hierarchical Modularity and the Evolution of Genetic Interactomes across Species

Ryan, C. J., Roguev, A., Patrick, K. L., Xu, J., Jahari, H., Tong, Z., Beltrão, P., Shales, M., Qu, H., Collins, S. R., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.028 · Cited by 230 · see citing works

Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

Lee, J. M., Gianchandani, E. P., Eddy, J. A., & Papin, J. A. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000086 · Cited by 225 · see citing works

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiaePreprint

Herrgård, M. J., Lee, B.-S., Portnoy, V. A., & Palsson, B. Ø. (2006) · Genome Research · doi:10.1101/gr.4083206 · Cited by 224 · see citing works

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

Bisson, N., James, D. A., Ivosev, G., Tate, S. A., Bonner, R. F., Taylor, L., & Pawson, T. J. (2011) · Nature Biotechnology · doi:10.1038/nbt.1905 · Cited by 222 · see citing works

A roadmap of clustering algorithms: finding a match for a biomedical application

Andreopoulos, B., An, A., Wang, X., & Schroeder, M. (2008) · Briefings in Bioinformatics · doi:10.1093/bib/bbn058 · Cited by 221 · see citing works

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

Paull, E., Carlin, D. E., Niepel, M., et al. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt471 · Cited by 210 · see citing works

Integrating physical and genetic maps: from genomes to interaction networks

Beyer, A., Bandyopadhyay, S., & Ideker, T. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2144 · Cited by 207 · see citing works

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data

Sharan, R., Ideker, T., Kelley, B., et al. (2005) · Journal of Computational Biology · doi:10.1089/cmb.2005.12.835 · Cited by 195 · see citing works

Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiaeinteraction network

Zhang, L. V., King, O. D., Wong, S. L., Goldberg, D. S., Tong, A. H., Lesage, G., Andrews, B., Bussey, H., Boone, C. M., & Roth, F. P. (2005) · Journal of Biology · doi:10.1186/jbiol23 · Cited by 190 · see citing works

Systematic identification of functional orthologs based on protein network comparisonPreprint

Bandyopadhyay, S., Sharan, R., & Ideker, T. (2006) · Genome Research · doi:10.1101/gr.4526006 · Cited by 189 · see citing works

Integrating phenotypic and expression profiles to map arsenic-response networks

Haugen, A. C., Kelley, R., Collins, J. B., Tucker, C. J., Deng, C., Afshari, C. A., Brown, J. M., Ideker, T. E., & Houten, B. V. (2004) · Genome biology · doi:10.1186/gb-2004-5-12-r95 · Cited by 186 · see citing works

Computational analysis of the synergy among multiple interacting genes

Anastassiou, D. (2007) · Molecular Systems Biology · doi:10.1038/msb4100124 · Cited by 185 · see citing works

Co-evolution of transcriptional and post-translational cell-cycle regulation

Jensen, L. J., Jensen, T. S., de Lichtenberg, U., Brunak, S., & Bork, P. (2006) · Nature · doi:10.1038/nature05186 · Cited by 184 · see citing works

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps

Huang, H., Jedynak, B. M., & Bader, J. S. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030214 · Cited by 182 · see citing works

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

Huang, S. C., & Fraenkel, E. (2009) · Science Signaling · doi:10.1126/scisignal.2000350 · Cited by 178 · see citing works

High‐throughput two‐hybrid analysis

Fields, S. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04973.x · Cited by 172 · see citing works

A modular network model of aging

Xue, H., Xian, B., Dong, D., Xia, K., Zhu, S., Zhang, Z., Hou, L., Zhang, Q., Zhang, Y., & Han, J. J. (2007) · Molecular Systems Biology · doi:10.1038/msb4100189 · Cited by 170 · see citing works

Cross‐species chemogenomic profiling reveals evolutionarily conserved drug mode of action

Kapitzky, L., Beltrão, P., Berens, T. J., Gassner, N. C., Zhou, C., Wüster, A., Wu, J. T.-Y., Babu, M. M., Elledge, S. J., Toczyski, D. P., et al. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.107 · Cited by 160 · see citing works

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

Nibbe, R. K., Koyutürk, M., & Chance, M. R. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000639 · Cited by 153 · see citing works

Gene expression network analysis and applications to immunology

Nacu, Ş., Critchley-Thorne, R. J., Lee, P. P., et al. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm019 · Cited by 151 · see citing works

A statistical framework for differential network analysis from microarray data

Gill, R. S., Datta, S., & Datta, S. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-95 · Cited by 150 · see citing works

Cross-species analysis of biological networks by Bayesian alignment

Berg, J., & Lässig, M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602294103 · Cited by 149 · see citing works

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

Bandyopadhyay, S., Kelley, R., Krogan, N. J., & Ideker, T. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000065 · Cited by 141 · see citing works

Edge-based scoring and searching method for identifying condition-responsive protein–protein interaction sub-network

Guo, Z., Li, Y., Gong, X. Q., Yao, C., Ma, W., Wang, D., Li, Y., Zhu, J., Zhang, M., Yang, D., et al. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm294 · Cited by 136 · see citing works

NetworkBLAST: comparative analysis of protein networks

Kalaev, M., Smoot, M., Ideker, T., et al. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm630 · Cited by 135 · see citing works

Erratum: Corrigendum: Comprehensive genomic characterization defines human glioblastoma genes and core pathways

The Cancer Genome Atlas Research Network (2013) · Nature · doi:10.1038/nature11903 · Cited by 135 · see citing works

The Plasmodium protein network diverges from those of other eukaryotes

Suthram, S., Sittler, T., & Ideker, T. E. (2005) · Nature · doi:10.1038/nature04135 · Cited by 134 · see citing works

Uncovering signal transduction networks from high-throughput data by integer linear programming

Zhao, X., Wang, R., Chen, L., & Aihara, K. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn145 · Cited by 132 · see citing works

Integrated genomic analyses of ovarian carcinoma

The Cancer Genome Atlas Research Network (2011) · Nature · doi:10.1038/nature10166 · Cited by 129 · see citing works

Roles for the Two-hybrid System in Exploration of the Yeast Protein Interactome

Ito, T., Ota, K., Kubota, H., Yamaguchi, Y., Chiba, T., Sakuraba, K., & Yoshida, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200005-mcp200 · Cited by 127 · see citing works

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

Miller, C. A., Settle, S. H., Sulman, E. P., Aldape, K., & Milosavljevic, A. (2011) · BMC Medical Genomics · doi:10.1186/1755-8794-4-34 · Cited by 126 · see citing works

CGI: a new approach for prioritizing genes by combining gene expression and protein–protein interaction data

Ma, X., Lee, H., Wang, L., & Sun, F. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl569 · Cited by 114 · see citing works

Differential network expression during drug and stress response

Cabusora, L., Sutton, E., Fulmer, A. W., & Forst, C. V. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti440 · Cited by 114 · see citing works

Inferring pathways from gene lists using a literature-derived network of biological relationships

Rajagopalan, D., & Agarwal, P. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti069 · Cited by 110 · see citing works

Identifying functional modules using expression profiles and confidence-scored protein interactions

Ulitsky, I., & Ron Shamir, A. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp118 · Cited by 108 · see citing works

Inferring Gene-Phenotype Associations via Global Protein Complex Network Propagation

Yang, P., Li, X., Wu, M., Kwoh, C.-K., & Ng, S.-K. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021502 · Cited by 105 · see citing works

NetWalker: a contextual network analysis tool for functional genomics

Komurov, K., Dursun, S., Erdin, S., & Ram, P. T. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-282 · Cited by 102 · see citing works

Identification of functional modules from conserved ancestral protein–protein interactions

Dutkowski, J., & Tiuryn, J. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm194 · Cited by 102 · see citing works

Measuring the Evolutionary Rewiring of Biological Networks

Shou, C., Bhardwaj, N., Lam, H. Y. K., Yan, K., Kim, P. M., Snyder, M. P., & Gerstein, M. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001050 · Cited by 101 · see citing works

Hot Spots for Modulating Toxicity Identified by Genomic Phenotyping and Localization Mapping

Begley, T. J., Rosenbach, A., Ideker, T. E., & Samson, L. D. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.09.005 · Cited by 101 · see citing works

COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method

Ma, H., Schadt, E. E., Kaplan, L. M., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr136 · Cited by 99 · see citing works

Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks

Ulitsky, I., & Ron Shamir, A. (2007) · Molecular Systems Biology · doi:10.1038/msb4100144 · Cited by 98 · see citing works

Optimally discriminative subnetwork markers predict response to chemotherapy

Dao, P., Wang, K., Collins, C. C., Ester, M., Lapuk, A. V., & Şahinalp, S. C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr245 · Cited by 98 · see citing works

Graph-based iterative Group Analysis enhances microarray interpretation

Breitling, R., Amtmann, A., & Herzyk, P. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-100 · Cited by 96 · see citing works

Dissection of DNA Damage Responses Using Multiconditional Genetic Interaction Maps

Guénolé, A., Srivas, R., Vreeken, K., Wang, Z. Z., Wang, S., Krogan, N. J., Ideker, T., & van Attikum, H. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.11.023 · Cited by 95 · see citing works

Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data

Komurov, K., White, M. A., & Ram, P. T. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000889 · Cited by 92 · see citing works

Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

Lee, J. M., Gianchandani, E. P., Eddy, J. A., & Papin, J. A. (2008) · PLoS Computational Biology · doi:10.1371/annotation/5594348b-de00-446a-bdd0-ec56e70b3553 · Cited by 89 · see citing works

Fast and Accurate Alignment of Multiple Protein Networks

Kalaev, M., Bafna, V., & Sharan, R. (2009) · Journal of Computational Biology · doi:10.1089/cmb.2009.0136 · Cited by 85 · see citing works

ANAT: A Tool for Constructing and Analyzing Functional Protein Networks

Yosef, N., Zalckvar, E., Rubinstein, A. D., Homilius, M., Atias, N., Vardi, L., Berman, I., Zur, H., Kimchi, A., Ruppin, E., et al. (2011) · Science Signaling · doi:10.1126/scisignal.2001935 · Cited by 82 · see citing works

Detecting disease associated modules and prioritizing active genes based on high throughput data

Qiu, Y., Zhang, S., Zhang, X., et al. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-26 · Cited by 80 · see citing works

A systems biology approach to identify effective cocktail drugs

Wu, Z., Zhao, X., & Chen, L. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-s2-s7 · Cited by 80 · see citing works

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions

Ulitsky, I., Shlomi, T., Kupiec, M., & Shamir, R. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.42 · Cited by 80 · see citing works

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

Lan, A., Smoly, I. Y., Rapaport, G., Lindquist, S., Fraenkel, E., & Yeger‐Lotem, E. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr359 · Cited by 79 · see citing works

New methods for joint analysis of biological networks and expression data

Sohler, F., Hanisch, D., & Zimmer, R. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth112 · Cited by 71 · see citing works

Subnetwork State Functions Define Dysregulated Subnetworks in Cancer

Chowdhury, S. A., Nibbe, R. K., Chance, M. R., & Koyutürk, M. (2011) · Journal of Computational Biology · doi:10.1089/cmb.2010.0269 · Cited by 69 · see citing works

Integrated cellular network of transcription regulations and protein-protein interactions

Wang, Y., & Chen, B. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-20 · Cited by 68 · see citing works

Evolution thinks modular

Vespignani, A. (2003) · Nature Genetics · doi:10.1038/ng1003-118 · Cited by 63 · see citing works

Network biology methods integrating biological data for translational science

Bebek, G., Koyutürk, M., Price, N. D., & Chance, M. R. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbr075 · Cited by 63 · see citing works

Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis

Gu, J., Chen, Y., Li, S., & Li, Y. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-47 · Cited by 60 · see citing works

Integrating siRNA and protein–protein interaction data to identify an expanded insulin signaling networkPreprint

Tu, Z., Argmann, C., Wong, K. K., Mitnaul, L. J., Edwards, S. W., Sach, I. C., Zhu, J., & Schadt, E. E. (2009) · Genome Research · doi:10.1101/gr.087890.108 · Cited by 59 · see citing works

The promise and the peril.

Whelan, D. B. (1998) · PubMed · Cited by 59 · see citing works

Rewiring makes the difference

Califano, A. (2011) · Molecular Systems Biology · doi:10.1038/msb.2010.117 · Cited by 58 · see citing works

Transcriptional regulation of protein complexes within and across species

Tan, K., Shlomi, T., Feizi, H., Ideker, T., & Sharan, R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606914104 · Cited by 58 · see citing works

Evolution of metabolic network organization

Mazurie, A., Bonchev, D., Schwikowski, B., & Buck, G. A. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-59 · Cited by 55 · see citing works

The expanded human disease network combining protein–protein interaction information

Zhang, X., Zhang, R., Jiang, Y., et al. (2011) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.30 · Cited by 54 · see citing works

Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegansaging

Fortney, K., Kotlyar, M., & Jurišica, I. (2010) · Genome biology · doi:10.1186/gb-2010-11-2-r13 · Cited by 52 · see citing works

IDENTIFICATION OF COORDINATELY DYSREGULATED SUBNETWORKS IN COMPLEX PHENOTYPES

Chowdhury, S. A., & Koyutürk, M. (2009) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789814295291_0016 · Cited by 49 · see citing works

Identifying Responsive Functional Modules from Protein-Protein Interaction Network

Wu, Z., Zhao, X., & Chen, L. (2009) · Molecules and Cells · doi:10.1007/s10059-009-0035-x · Cited by 46 · see citing works

Gene Expression: Protein Interaction Systems Network Modeling Identifies Transformation-Associated Molecules and Pathways in Ovarian Cancer

Bapat, S. A., Krishnan, A., Ghanate, A. D., Kusumbe, A. P., & Kalra, R. S. (2010) · Cancer Research · doi:10.1158/0008-5472.can-10-0447 · Cited by 46 · see citing works

DDN: a caBIG® analytical tool for differential network analysis

Zhang, B., Tian, Y., Lu, J., Li, H., Shih, I., Madhavan, S., Clarke, R. C., Hoffman, E. P., Xuan, J., Hilakivi-Clarke, L. A., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr052 · Cited by 41 · see citing works

Integrative gene network construction for predicting a set of complementary prostate cancer genes

Ahn, J., Yoon, Y., Park, C., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr283 · Cited by 37 · see citing works

Differential C3NET reveals disease networks of direct physical interactions

Altay, G., Asim, M., Markowetz, F. M., & Neal, D. E. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-296 · Cited by 36 · see citing works

A Differential Network Approach to Exploring Differences between Biological States: An Application to Prediabetes

Valcárcel, B., Würtz, P., al Basatena, N.-K. S., Tukiainen, T., Kangas, A. J., Soininen, P., Järvelin, M., Ala‐Korpela, M., Ebbels, T. M. D., & Iorio, M. D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024702 · Cited by 35 · see citing works

Identification of differentially expressed subnetworks based on multivariate ANOVA

Hwang, T., & Park, T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-128 · Cited by 34 · see citing works

Identifying differentially regulated subnetworks from phosphoproteomic data

Klammer, M., Godl, K., Tebbe, A., et al. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-351 · Cited by 33 · see citing works

Dynamical Systems for Discovering Protein Complexes and Functional Modules from Biological Networks

Li, W., Liu, Y., Huang, H.-C., et al. (2007) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2007.070210 · Cited by 32 · see citing works

Multi-species integrative biclustering

Waltman, P., Kacmarczyk, T. J., Bate, A. R., Kearns, D. B., Reiss, D. J., Eichenberger, P., & Bonneau, R. (2010) · Genome biology · doi:10.1186/gb-2010-11-9-r96 · Cited by 32 · see citing works

Algorithmic and analytical methods in network biology

Koyutürk, M. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.61 · Cited by 31 · see citing works

A Scalable Approach for Discovering Conserved Active Subnetworks across Species

Deshpande, R., Sharma, S., Verfaillie, C. M., Hu, W.-S., & Myers, C. L. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001028 · Cited by 26 · see citing works

DISCOVERING REGULATED NETWORKS DURING HIV-1 LATENCY AND REACTIVATION

Bandyopadhyay, S., KELLEY, R., & Ideker, T. (2005) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812701626_0033 · Cited by 26 · see citing works

CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data

Zhang, K. X., & Ouellette, B. F. F. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001114 · Cited by 25 · see citing works

Module Discovery by Exhaustive Search for Densely Connected, Co-Expressed Regions in Biomolecular Interaction Networks

Çolak, R., Moser, F., Chu, J. S.-C., Schönhuth, A., Chen, N., & Ester, M. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013348 · Cited by 24 · see citing works

Assembling global maps of cellular function through integrative analysis of physical and genetic networks

Srivas, R., Hannum, G., Ruscheinski, J., Ono, K., Wang, P., Smoot, M. E., & Ideker, T. (2011) · Nature Protocols · doi:10.1038/nprot.2011.368 · Cited by 23 · see citing works

ToPNet—an application for interactive analysis of expression data and biological networks

Hanisch, D., Sohler, F., & Zimmer, R. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth096 · Cited by 21 · see citing works

Plant networks

Muers, M. R. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3058 · Cited by 12 · see citing works

Contextual analysis of RNAi-based functional screens using interaction networks

Gonzalez, O., & Zimmer, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr469 · Cited by 10 · see citing works

Integrative omics for health and disease

Karczewski, K. J., & Snyder, M. P. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2018.4 · Cited by 1,158 · see citing works

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

Mostafavi, S., Gaiteri, C., Sullivan, S. E., White, C. C., Tasaki, S., Xu, J., Taga, M., Klein, H.-U., Patrick, E., Komashko, V., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0154-9 · Cited by 509 · see citing works

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

Parikshak, N. N., Gandal, M. J., & Geschwind, D. H. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3934 · Cited by 430 · see citing works

Network biology concepts in complex disease comorbidities

Hu, J. X., Thomas, C. E., & Brunak, S. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.87 · Cited by 328 · see citing works

The discovery of integrated gene networks for autism and related disorders

Hormozdiari, F., Penn, O., Borenstein, E., & Eichler, E. E. (2015) · Genome Research · doi:10.1101/gr.178855.114 · Cited by 249 · see citing works

Modules, networks and systems medicine for understanding disease and aiding diagnosis

Gustafsson, M., Nestor, C. E., Zhang, H., Barabási, A.-L., Baranzini, S., Brunak, S., Chung, K. F., Federoff, H. J., Gavin, A.-C., Meehan, R. R., et al. (2014) · Genome Medicine · doi:10.1186/s13073-014-0082-6 · Cited by 194 · see citing works

Systematic Functional Annotation and Visualization of Biological Networks

Baryshnikova, A. (2016) · Cell Systems · doi:10.1016/j.cels.2016.04.014 · Cited by 148 · see citing works

DINGO: differential network analysis in genomics

Ha, M. J., Baladandayuthapani, V., & Do, K.-A. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv406 · Cited by 120 · see citing works

De novo mutations from whole exome sequencing in neurodevelopmental and psychiatric disorders: From discovery to application

Wang, W., Corominas, R., & Lin, G. N. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00258 · Cited by 70 · see citing works

Network biology bridges the gaps between quantitative genetics and multi-omics to map complex diseases

Wu, S., Chen, D., & Snyder, M. P. (2022) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2021.102101 · Cited by 25 · see citing works

Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders

Mozzi, A., Forni, D., Cagliani, R., Pozzoli, U., Clerici, M., & Sironi, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-06440-4 · Cited by 19 · see citing works

Biomolecular network querying: a promising approach in systems biology

Zhang, S., Zhang, X., & Chen, L. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-5 · Cited by 33 · see citing works

Reconstruction of Biological Networks for Integrative Analysis

Österlund, T. (2014) · Chalmers Publication Library (Chalmers University of Technology)

Network biology and applications

Redhu, N. S., & Thakur, Z. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-89775-4.00024-9 · Cited by 8 · see citing works

An Overview of Systems Biology

Albert, R., & Assmann, S. M. (2017) · Annual Plant Reviews online · doi:10.1002/9781119312994.apr0373

Biological Networks

Lecca, P., & Carpentieri, B. (2023) · Techniques in life science and biomedicine for the non-expert · doi:10.1007/978-3-031-36566-9_2