Topological analysis and interactive visualization of biological networks and protein structures

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

UCSF Chimera—A visualization system for exploratory research and analysis

Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,828

Collective dynamics of ‘small-world’ networks

Watts, D. J., & Strogatz, S. H. (1998) · Nature · doi:10.1038/30918 · Cited by 43,060

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

Emergence of Scaling in Random Networks

Barabási, A.-L., & Albert, R. (1999) · Science · doi:10.1126/science.286.5439.509 · Cited by 36,135

Centrality in social networks conceptual clarification

Freeman, L. C. (1978) · Social Networks · doi:10.1016/0378-8733(78)90021-7 · Cited by 17,062

The igraph software package for complex network research

Csárdi, G., & Nepusz, T. (2006) · Medical Entomology and Zoology · Cited by 10,078

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

Exploring Network Structure, Dynamics, and Function Using NetworkX

Hagberg, A. A., Schult, D. A., & Swart, P. J. (2008) · Proceedings of the Python in Science Conference · doi:10.25080/tcwv9851 · Cited by 7,477

An automated method for finding molecular complexes in large protein interaction networks

Bader, G. D., & Hogue, C. W. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-2 · Cited by 6,072

The Evolution of Random Graphs

(1986) · CBMS Regional Conference Series in Mathematics · doi:10.1090/cbms/062/06 · Cited by 5,543

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

A faster algorithm for betweenness centrality*

Brandes, U. (2001) · The Journal of Mathematical Sociology · doi:10.1080/0022250x.2001.9990249 · Cited by 4,936

Hierarchical Organization of Modularity in Metabolic Networks

Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., & Barabási, A.-L. (2002) · Science · doi:10.1126/science.1073374 · Cited by 4,224

Node centrality in weighted networks: Generalizing degree and shortest paths

Opsahl, T., Agneessens, F., & Skvoretz, J. (2010) · Social Networks · doi:10.1016/j.socnet.2010.03.006 · Cited by 3,718

Specificity and Stability in Topology of Protein Networks

Maslov, S., & Sneppen, K. (2002) · Science · doi:10.1126/science.1065103 · Cited by 3,051

Integration of biological networks and gene expression data using Cytoscape

Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., et al. (2007) · Nature Protocols · doi:10.1038/nprot.2007.324 · Cited by 2,507

A measure of betweenness centrality based on random walks

Newman, M. E. J. (2005) · Social Networks · doi:10.1016/j.socnet.2004.11.009 · Cited by 2,461

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

Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F. H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.029 · Cited by 2,387

Scale-Free Networks: A Decade and Beyond

Barabási, A.-L. (2009) · Science · doi:10.1126/science.1173299 · Cited by 2,109

Computing topological parameters of biological networks

Assenov, Y., Ramírez, F., Schelhorn, S.-E., Lengauer, T., & Albrecht, M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm554 · Cited by 1,826

On the evolution of random graphs

Erdös, P., & Rényi, A. (2011) · The Structure and Dynamics of Networks · doi:10.1515/9781400841356.38 · Cited by 1,757

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

Word, J. M., Lovell, S. C., Richardson, J. S., & Richardson, D. C. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2401 · Cited by 1,423

Pajek - Program for Large Network Analysis

Batagelj, V., & Mrvar, A. (1999) · Cited by 1,414

Scale-free networks in cell biology

Albert, R. (2005) · Journal of Cell Science · doi:10.1242/jcs.02714 · Cited by 1,215

The LEDA platform for combinatorial and geometric computing

Mehlhorn, K., Näher, S., & Uhrig, C. (1997) · Lecture Notes in Computer Science · doi:10.1007/3-540-63165-8_161 · Cited by 1,199

statnet: Software Tools for the Representation, Visualization, Analysis and Simulation of Network Data

Handcock, M. S., Hunter, D. R., Butts, C. T., Goodreau, S. M., & Morris, M. (2008) · Journal of Statistical Software · doi:10.18637/jss.v024.i01 · Cited by 926

Using graph theory to analyze biological networks

Pavlopoulos, G. A., Secrier, M., Moschopoulos, C. N., Soldatos, T. G., Kossida, S., Aerts, J., Schneider, R., & Bagos, P. G. (2011) · BioData Mining · doi:10.1186/1756-0381-4-10 · Cited by 791

The crystal structure of human deoxyhaemoglobin at 1.74 Å resolution

Fermi, G., Perutz, M. F., Shaanan, B., & Fourme, R. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90472-8 · Cited by 771

Graph Theory

Diestel, R. (2010) · Graduate Texts in Mathematics · doi:10.1007/978-3-642-14279-6 · Cited by 714

The Structure and Function of the Aspartic Proteinases

Davies, D. R. (1990) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.19.060190.001201 · Cited by 658

Getting connected: analysis and principles of biological networks

Zhu, X., Gerstein, M., & Snyder, M. (2007) · Genes & Development · doi:10.1101/gad.1528707 · Cited by 554

Analyzing biological network parameters with CentiScaPe

Scardoni, G., Petterlini, M., & Laudanna, C. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp517 · Cited by 543

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms 1 1Edited by J. Thornton

Word, J. M., Lovell, S. C., LaBean, T. H., Taylor, H. C., Zalis, M. E., Presley, B. K., Richardson, J. S., & Richardson, D. C. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2400 · Cited by 529

Structural parameters of communication networks

Shimbel, A. (1953) · Bulletin of Mathematical Biology · doi:10.1007/bf02476438 · Cited by 498

Social Network Analysis with sna

Butts, C. T. (2008) · Journal of Statistical Software · doi:10.18637/jss.v024.i06 · Cited by 468

Understanding network concepts in modules

Dong, J., & Horvath, S. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-24 · Cited by 455

Analysis of Biological Networks

(2008) · Wiley eBooks · doi:10.1002/9780470253489 · Cited by 363

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, B. R., & Albrecht, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq405 · Cited by 322

A Decade of Systems Biology

Chuang, H.-Y., Hofree, M., & Ideker, T. (2010) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100109-104122 · Cited by 319

Random walks and the effective resistance of networks

Tetali, P. (1991) · Journal of Theoretical Probability · doi:10.1007/bf01046996 · Cited by 310

GLay: community structure analysis of biological networks

Su, G., Kuchinsky, A., Morris, J. H., States, D. J., & Meng, F. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq596 · Cited by 275

Next-generation sequencing to generate interactome datasets

Yu, H., Tardivo, L., Tam, S., Weiner, E., Gebreab, F., Fan, C., Svrzikapa, N., Hirozane-Kishikawa, T., Rietman, E., Yang, X., et al. (2011) · Nature Methods · doi:10.1038/nmeth.1597 · Cited by 259

Analyzing and visualizing residue networks of protein structures

Doncheva, N. T., Klein, K., Domingues, F. S., & Albrecht, M. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.01.002 · Cited by 257

Toward the dynamic interactome: it's about time

Przytycka, T. M., Singh, M., & Slonim, D. K. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp057 · Cited by 254

Evolution of biomolecular networks — lessons from metabolic and protein interactions

Yamada, T., & Bork, P. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2787 · Cited by 252

Tools for visually exploring biological networks

Suderman, M., & Hallett, M. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm401 · Cited by 237

An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality

Yoon, J., Blumer, A., & Lee, K. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl533 · Cited by 235

Network analysis of protein dynamics

Böde, C., Kovács, I. A., Szalay, M. S., Palotai, R., Korcsmáros, T., & Csermely, P. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.05.021 · Cited by 223

A survey of visualization tools for biological network analysis

Pavlopoulos, G. A., Wegener, A.-L., & Schneider, R. (2008) · BioData Mining · doi:10.1186/1756-0381-1-12 · Cited by 218

Graph-based analysis and visualization of experimental results with ONDEX

Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rüegg, A., Rawlings, C., Verrier, P., & Philippi, S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl081 · Cited by 211

The Powerful Law of the Power Law and Other Myths in Network Biology

Lima-Mendez, G., & van Helden, J. (2009) · Molecular BioSystems · doi:10.1039/b908681a · Cited by 210

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

VisANT: data-integrating visual framework for biological networks and modules

Hu, Z., Mellor, J., Wu, J., Yamada, T., Holloway, D., & DeLisi, C. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki431 · Cited by 178

Intra and Inter-Molecular Communications Through Protein Structure Network

Vishveshwara, S., Ghosh, A., & Hansia, P. (2009) · Current Protein & Peptide Science · doi:10.2174/138920309787847590 · Cited by 174

PRIN: a predicted rice interactome network

Gu, H., Zhu, P., Jiao, Y., Meng, Y., & Chen, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-161 · Cited by 159

Synthetic Lethal Screen of an EGFR-Centered Network to Improve Targeted Therapies

Astsaturov, I. A., Ratushny, V., Sukhanova, A. L., Einarson, M. B., Bagnyukova, T., Zhou, Y., Devarajan, K., Silverman, J. S., Tikhmyanova, N., Skobeleva, N., et al. (2010) · Science Signaling · doi:10.1126/scisignal.2001083 · Cited by 144

RING: networking interacting residues, evolutionary information and energetics in protein structures

Martín, A. J. M., Vidotto, M., Boscariol, F., Domenico, T. D., Walsh, I., & Tosatto, S. C. E. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr191 · Cited by 138

Biological impacts and context of network theory

Almaas, E. (2007) · Journal of Experimental Biology · doi:10.1242/jeb.003731 · Cited by 133

Creative elements: network-based predictions of active centres in proteins and cellular and social networks

Csermely, P. (2008) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2008.09.006 · Cited by 132

NeMo: Network Module identification in Cytoscape

Rivera, C. G., Vakil, R. M., & Bader, J. S. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-s1-s61 · Cited by 130

Discovering functions and revealing mechanisms at molecular level from biological networks

Zhang, S., Jin, G., Zhang, X., & Chen, L. (2007) · PROTEOMICS · doi:10.1002/pmic.200700095 · Cited by 120

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

Lorenz, W. W., Alba, R., Yu, Y.-S., Bordeaux, J. M., Simões, M., & Dean, J. F. D. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-264 · Cited by 118

Network Analysis Tools: from biological networks to clusters and pathways

Brohée, S., Faust, K., Lima‐Mendez, G., Vanderstocken, G., & van Helden, J. (2008) · Nature Protocols · doi:10.1038/nprot.2008.100 · Cited by 109

Proteins As Networks: Usefulness of Graph Theory in Protein Science

Giuliani, A., Krishnan, A. V., Zbilut, J. P., & Tomita, M. (2008) · Current Protein and Peptide Science · doi:10.2174/138920308783565705 · Cited by 106

MINE: Module Identification in Networks

Rhrissorrakrai, K., & Gunsalus, K. C. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-192 · Cited by 96

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

Radrich, K., Tsuruoka, Y., Dobson, P. D., Gevorgyan, A., Swainston, N., Baart, G. J. E., & Schwartz, J. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-114 · Cited by 94

Biana: a software framework for compiling biological interactions and analyzing networks

García-García, J., Güney, E., Aragüés, R., Planas-Iglesias, J., & Oliva, B. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-56 · Cited by 93

Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus

Welsch, C., Domingues, F. S., Süsser, S., Antes, I., Hartmann, C., Mayr, G., Schlicker, A., Sarrazin, C., Albrecht, M., Zeuzem, S., et al. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r16 · Cited by 81

Protein‐protein interactions: Making sense of networks via graph‐theoretic modeling

Pržulj, N. (2010) · BioEssays · doi:10.1002/bies.201000044 · Cited by 78

Crystal structure of a complex of HIV‐1 protease with a dihydroxyethylene‐containing inhibitor: Comparisons with molecular modeling

Thanki, N., Rao, J., Foundling, S. I., Wlodawer, A., Howe, W. J., Moon, J. B., Hui, J. O., Tomasselli, A. G., Heinrikson, R. L., & Thaisrivongs, S. (1992) · Protein Science · doi:10.1002/pro.5560010811 · Cited by 70

QuACN: an R package for analyzing complex biological networks quantitatively

Mueller, L. A. J., Kugler, K., Dander, A., Graber, A., & Dehmer, M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq606 · Cited by 54

Comprehensive cluster analysis with Transitivity Clustering

Wittkop, T., Emig, D., Truß, A., Albrecht, M., Böcker, S., & Baumbach, J. (2011) · Nature Protocols · doi:10.1038/nprot.2010.197 · Cited by 52

Expression profile and specific network features of the apoptotic machinery explain relapse of acute myeloid leukemia after chemotherapy

Ragusa, M., Avola, G., Angelica, R., Barbagallo, D., Guglielmino, M. R., Duro, L. R., Majorana, A., Statello, L., Salito, L., Consoli, C., et al. (2010) · BMC Cancer · doi:10.1186/1471-2407-10-377 · Cited by 28

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 24

Computational Tools for the Interactive Exploration of Proteomic and Structural Data

Morris, J. H., Meng, E. C., & Ferrin, T. E. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r000007-mcp201 · Cited by 11

Application of computational approaches to study signalling networks of nuclear and Tyrosine kinase receptors

Choura, M., & Rebaï, A. (2010) · Biology Direct · doi:10.1186/1745-6150-5-58 · Cited by 9

Protein-protein interactions: analysis and prediction

Frishman, D., Albrecht, M., Blankenburg, H., Bork, P., Harrington, E. D., Hermjakob, H., Jensen, L. J., Juan, D., Lengauer, T., Pagel, P., et al. (2008) · Springer eBooks · doi:10.1007/978-3-211-75123-7_17 · Cited by 6

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

Csermely, P., Korcsmáros, T., Kiss, H. J. M., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 892

Selectivity determinants of GPCR–G-protein binding

Flock, T., Hauser, A. S., Lund, N., Gloriam, D. E., Balaji, S., & Babu, M. M. (2017) · Nature · doi:10.1038/nature22070 · Cited by 384

The role of protein dynamics in the evolution of new enzyme function

Campbell, E., Kaltenbach, M., Correy, G. J., Carr, P. D., Porebski, B. T., Livingstone, E. K., Afriat-Jurnou, L., Buckle, A. M., Weik, M., Hollfelder, F., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2175 · Cited by 311

xiNET: cross-link network maps with residue resolution

Combe, C. W., Fischer, L., & Rappsilber, J. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.042259 · Cited by 296

Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets

Vinayagam, A., Gibson, T. E., Lee, H.-J., Yilmazel, B., Roesel, C., Hu, Y., Kwon, Y., Sharma, A., Liu, Y.-Y., Perrimon, N., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603992113 · Cited by 257