Cerebral: a cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation

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

Graph visualization and navigation in information visualization: A survey

Herman, I., Mélançon, G., & Marshall, M. S. (2000) · IEEE Transactions on Visualization and Computer Graphics · doi:10.1109/2945.841119 · Cited by 1,559 · see citing works

Hierarchical Edge Bundles: Visualization of Adjacency Relations in Hierarchical Data

Holten, D. (2006) · IEEE Transactions on Visualization and Computer Graphics · doi:10.1109/tvcg.2006.147 · Cited by 986 · see citing works

prefuse

Heer, J., Card, S. K., & Landay, J. A. (2005) · ACM SIGCHI Conference on Human Factors in Computing Systems (CHI) · doi:10.1145/1054972.1055031 · Cited by 809 · see citing works

PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis

Gardy, J. L., Laird, M. R., Chen, F., Rey, S., Walsh, C. J., Ester, M., & Brinkman, F. S. L. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti057 · Cited by 719 · see citing works

Human protein reference database--2006 update

Mishra, G. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj141 · Cited by 601 · see citing works

Drawing graphs nicely using simulated annealing

Davidson, R., & Harel, D. (1996) · ACM Transactions on Graphics · doi:10.1145/234535.234538 · Cited by 486 · see citing works

Predicting subcellular localization of proteins using machine-learned classifiers

Lu, Z., Szafron, D., Greiner, R., Lu, P., Wishart, D. S., Poulin, B., Anvik, J., Macdonell, C., & Eisner, R. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg447 · Cited by 334 · see citing works

Methods for predicting bacterial protein subcellular localization

Gardy, J. L., & Brinkman, F. S. L. (2006) · Nature Reviews Microbiology · doi:10.1038/nrmicro1494 · Cited by 169 · see citing works

A grid layout algorithm for automatic drawing of biochemical networks

Li, W., & Kurata, H. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti290 · Cited by 70 · see citing works

Automatic drawing of biological networks using cross cost and subcomponent data.

Kato, M., Nagasaki, M., Doi, A., & Miyano, S. (2005) · PubMed · Cited by 16 · 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

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 · see citing works

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

Breuer, K., Foroushani, A. B. K., Laird, M. R., Chen, C. C. L., Sribnaia, A., Lo, R., Winsor, G. L., Hancock, R. E. W., Brinkman, F. S. L., & Lynn, D. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1147 · Cited by 1,224 · see citing works

CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data

Bindea, G., Galon, J., & Mlecnik, B. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt019 · Cited by 1,066 · see citing works

Visualization of omics data for systems biology

Gehlenborg, N., O’Donoghue, S. I., Baliga, N. S., Goesmann, A., Hibbs, M., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1436 · Cited by 622 · see citing works

NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration

Xia, J., Benner, M. J., & Hancock, R. E. W. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku443 · Cited by 450 · see citing works

InnateDB: facilitating systems‐level analyses of the mammalian innate immune response

Lynn, D. J., Winsor, G. L., Chan, C. C., Richard, N., Laird, M. R., Barsky, A., Gardy, J. L., Roche, F. M., Chan, T. H. W., Shah, N., et al. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.55 · Cited by 382 · see citing works

Regulatory networks define phenotypic classes of human stem cell lines

Müller, F.-J., Laurent, L. C., Kostka, D., Ulitsky, I., Williams, R., Lu, C., Park, I.-H., Rao, M. S., Shamir, R., Schwartz, P. H., et al. (2008) · Nature · doi:10.1038/nature07213 · Cited by 343 · see citing works

The Landscape of Human Proteins Interacting with Viruses and Other Pathogens

Dyer, M. D., Murali, T. M., & Sobral, B. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.0040032 · Cited by 326 · see citing works

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 · see citing works

Human Protein Reference Database and Human Proteinpedia as Discovery Tools for Systems Biology

Prasad, T. S. K., Kandasamy, K., & Pandey, A. (2009) · Methods in molecular biology · doi:10.1007/978-1-60761-232-2_6 · Cited by 276 · see citing works

Cytoscape: A Community-Based Framework for Network Modeling

Killcoyne, S., Carter, G. W., Smith, J. J., & Boyle, J. (2009) · Methods in molecular biology · doi:10.1007/978-1-60761-175-2_12 · Cited by 259 · see citing works

Tools for visually exploring biological networks

Suderman, M. J., & Hallett, M. T. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm401 · Cited by 236 · see citing works

Primary biliary cirrhosis is associated with altered hepatic microRNA expression

Padgett, K. A., Lan, R. Y., Leung, P. C., Lleò, A., Dawson, K., Pfeiff, J., Mao, T. K., Coppel, R. L., Ansari, A. A., & Gershwin, M. E. (2009) · Journal of Autoimmunity · doi:10.1016/j.jaut.2009.02.022 · Cited by 208 · see citing works

Early-Life Environmental Variation Affects Intestinal Microbiota and Immune Development in New-Born Piglets

Schokker, D., Zhang, J., Zhang, L.-L., Vastenhouw, S. A., Heilig, H. G. H. J., Smidt, H., Rebel, J. M. J., & Smits, M. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100040 · Cited by 195 · see citing works

OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space

Zhou, G., & Xia, J. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky510 · Cited by 175 · see citing works

ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

Veres, D. V., Gyurkó, D. M., Thaler, B., Szalay, K. Z., Fazekas, D., Korcsmaros, T. D., & Csermely, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1007 · Cited by 157 · see citing works

Immunoinformatics: an integrated scenario

Tomar, N., & De, R. K. (2010) · Immunology · doi:10.1111/j.1365-2567.2010.03330.x · Cited by 155 · see citing works

Nuclear Import of the Glucocorticoid Receptor-hsp90 Complex through the Nuclear Pore Complex Is Mediated by Its Interaction with Nup62 and Importin β

Echeverría, P. C., Mazaira, G., Erlejman, A., Gomez-Sanchez, C., Pilipuk, G. P., & Galigniana, M. D. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.00649-09 · Cited by 144 · see citing works

Identification of a human neonatal immune-metabolic network associated with bacterial infection

Smith, C., Dickinson, P., Forster, T., Craigon, M., Ross, A., Khondoker, M. R., France, R., Ivens, A. C., Lynn, D. J., Orme, J., et al. (2014) · Nature Communications · doi:10.1038/ncomms5649 · Cited by 134 · see citing works

Enabling a systems biology approach to immunology: focus on innate immunity.

Gardy, J., Lynn, D., Brinkman, F., & Hancock, R. (2009) · Trends in immunology · doi:10.1016/j.it.2009.03.009 · Cited by 141 · see citing works

Using biological networks to integrate, visualize and analyze genomics data

Charitou, T., Bryan, K. R., & Lynn, D. J. (2016) · Genetics Selection Evolution · doi:10.1186/s12711-016-0205-1 · Cited by 115 · see citing works

Cathelicidins and functional analogues as antisepsis molecules

Mookherjee, N., Rehaume, L. M., & Hancock, R. E. W. (2007) · Expert Opinion on Therapeutic Targets · doi:10.1517/14728222.11.8.993 · Cited by 109 · see citing works

Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context

Barsky, A., Munzner, T., Gardy, J. L., & Kincaid, R. H. (2008) · IEEE Transactions on Visualization and Computer Graphics · doi:10.1109/tvcg.2008.117 · Cited by 106 · see citing works

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

Newman, A. M., & Cooper, J. B. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-117 · Cited by 104 · see citing works

ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis

Veres, D. V., Gyurkó, M. D., Thaler, B., Szalay, K. Z., Fazekas, D., Korcsmaros, T. D., & Csermely, P. (2015) · Semmelweis University Repository (Semmelweis University) · Cited by 104 · see citing works

Complexities of targeting innate immunity to treat infection

Brown, K. L., Cosseau, C., Gardy, J. L., & Hancock, R. E. W. (2007) · Trends in Immunology · doi:10.1016/j.it.2007.04.005 · Cited by 95 · see citing works

The use of network analyses for elucidating mechanisms in cardiovascular disease

Díez, D., Wheelock, Å. M., Goto, S., Haeggström, J. Z., Paulsson‐Berne, G., Hansson, G. K., Hedin, U., Gabrielsen, A., & Wheelock, C. E. (2009) · Molecular BioSystems · doi:10.1039/b912078e · Cited by 94 · see citing works

Visualization of Biomedical Data

O’Donoghue, S. I., Baldi, B. F., Clark, S. J., Darling, A. E., Hogan, J. M., Kaur, S., Maier‐Hein, L., McCarthy, D. J., Moore, W. J., Stenau, E., et al. (2018) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-080917-013424 · Cited by 87 · see citing works

Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease

Talwar, P., Silla, Y., Grover, S., Gupta, M., Agarwal, R., Kushwaha, S. S., & Kukreti, R. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-199 · Cited by 85 · see citing works

A systems biology approach to understanding atherosclerosis

Ramsey, S. A., Gold, E. S., & Aderem, A. A. (2010) · EMBO Molecular Medicine · doi:10.1002/emmm.201000063 · Cited by 82 · see citing works

Immunoinformatics: A Brief Review

Tomar, N., & De, R. K. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1115-8_3 · Cited by 82 · see citing works

Node-Link or Adjacency Matrices: Old Question, New Insights

Okoe, M., Jianu, R., & Kobourov, S. (2018) · IEEE Transactions on Visualization and Computer Graphics · doi:10.1109/tvcg.2018.2865940 · Cited by 81 · see citing works

Transcriptome Analysis of Early Organogenesis in Human Embryos

Fang, H., Yang, Y., Li, C., Fu, S., Yang, Z., Jin, G., Wang, K., Zhang, J., & Jin, Y. (2010) · Developmental Cell · doi:10.1016/j.devcel.2010.06.014 · Cited by 76 · see citing works

Functional Genetic Variation in NFKBIA and Susceptibility to Childhood Asthma, Bronchiolitis, and Bronchopulmonary Dysplasia

Ali, S. M., Hirschfeld, A. F., Mayer, M. L., Fortuno, E. S., Corbett, N., Kaplan, M., Wang, S. V., Schneiderman, J., Fjell, C. D., Yan, J., et al. (2013) · The Journal of Immunology · doi:10.4049/jimmunol.1201015 · Cited by 76 · see citing works

Mapping the multiscale structure of biological systems

Schaffer, L. V., & Ideker, T. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.012 · Cited by 75 · see citing works

Curating the innate immunity interactome

Lynn, D. J., Chan, C. C., Naseer, M., Yau, M., Lo, R., Sribnaia, A., Ring, G., Que, J., Wee, K., Winsor, G. L., et al. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-117 · Cited by 75 · see citing works

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

Smith, A. M., Xu, W. X., Sun, Y., Faeder, J. R., & Marai, G. E. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-s8-s3 · Cited by 75 · see citing works

Human Protein Reference Database and Human Proteinpedia as Discovery Resources for Molecular Biotechnology

Goel, R., Muthusamy, B., Pandey, A., & Prasad, T. S. K. (2010) · Molecular Biotechnology · doi:10.1007/s12033-010-9336-8 · Cited by 72 · see citing works

Innate defense regulator peptide 1018 protects against perinatal brain injury

Bolouri, H., Sävman, K., Wang, W., Thomas, A., Maurer, N., Dullaghan, E. M., Fjell, C. D., Ek, C. J., Hagberg, H., Hancock, R. E. W., et al. (2013) · Annals of Neurology · doi:10.1002/ana.24087 · Cited by 72 · 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

Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

Karlsson, C. A. Q., Malmström, L., Aebersold, R. H., & Malmström, J. A. (2012) · Nature Communications · doi:10.1038/ncomms2297 · Cited by 66 · see citing works

The Pseudomonas aeruginosa Autoinducer 3O-C12 Homoserine Lactone Provokes Hyperinflammatory Responses from Cystic Fibrosis Airway Epithelial Cells

Mayer, M. L., Sheridan, J. A., Blohmke, C. J., Turvey, S. E., & Hancock, R. E. W. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016246 · Cited by 63 · see citing works

Atypical Activation of the Unfolded Protein Response in Cystic Fibrosis Airway Cells Contributes to p38 MAPK-Mediated Innate Immune Responses

Blohmke, C. J., Mayer, M. L., Tang, A., Hirschfeld, A. F., Fjell, C. D., Sze, M. A., Falsafi, R., Wang, S. V., Hsu, K., Chilvers, M. A., et al. (2012) · The Journal of Immunology · doi:10.4049/jimmunol.1103661 · Cited by 62 · see citing works

Systems Biology Approaches to Understanding the Human Immune System

Dhillon, B. K., Smith, M. L., Baghela, A. S., Lee, A. H., & Hancock, R. E. W. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.01683 · Cited by 62 · see citing works

A Systematic Approach for Analysis of Peptide Array Kinome Data

Li, Y., Arsenault, R. J., Trost, B., Slind, J., Griebel, P. J., Napper, S., & KUSALIK, A. J. (2012) · Science Signaling · doi:10.1126/scisignal.2002429 · Cited by 60 · see citing works

Lectin-Glycan Interaction Network-Based Identification of Host Receptors of Microbial Pathogenic Adhesins

Ielasi, F., Alioscha-Pérez, M., Donohue, D. S., Claes, S., Sahli, H., Schols, D., & Willaert, R. (2016) · mBio · doi:10.1128/mbio.00584-16 · Cited by 53 · see citing works

Protein-Protein Interaction Databases

Szklarczyk, D., & Jensen, L. J. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2425-7_3 · Cited by 57 · see citing works

Glycyrrhizin, silymarin, and ursodeoxycholic acid regulate a common hepatoprotective pathway in HepG2 cells

Hsiang, C., Lin, L., Kao, S.-T., Lo, H., Chou, S.-T., & Ho, T. (2015) · Phytomedicine · doi:10.1016/j.phymed.2015.05.053 · Cited by 55 · see citing works

ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma

Smit, M. A., Maddalo, G., Greig, K. T., Raaijmakers, L. M., Possik, P. A., van Breukelen, B., Cappadona, S., Heck, A. J. R., Altelaar, M. A. F., & Peeper, D. S. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145450 · Cited by 54 · see citing works

IIS – Integrated Interactome System: A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a Variety of Data Sources and Tools

Carazzolle, M. F., de Carvalho, L. M., Slepicka, H., Vidal, R. O., Pereira, G. A. G., Kobarg, J., & Meirelles, G. V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100385 · Cited by 51 · see citing works

Systems-Level Analysis of Innate Immunity

Zak, D. E., Tam, V. C., & Aderem, A. A. (2014) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032713-120254 · Cited by 49 · see citing works

Novel Modeling of Cancer Cell Signaling Pathways Enables Systematic Drug Repositioning for Distinct Breast Cancer Metastases

Zhao, H., Jin, G., Cui, K., Ren, D., Liu, T., Chen, P., Wong, S., Li, F., Fan, Y., Rodríguez, Á. L., et al. (2013) · Cancer Research · doi:10.1158/0008-5472.can-12-4617 · Cited by 47 · see citing works

Visualizing time-related data in biology, a review

Secrier, M., & Schneider, R. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbt021 · Cited by 46 · see citing works

atBioNet– an integrated network analysis tool for genomics and biomarker discovery

Ding, Y., Chen, M., Liu, Z., Ding, D., Ye, Y., Zhang, M., Kelly, R. J., Guo, L., Su, Z., Harris, S., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-325 · Cited by 46 · see citing works

Tools for protein-protein interaction network analysis in cancer research

Pamplona, R. S., Berenguer, A., Solé, X., Cordero, D., Crous‐Bou, M., Serra-Musach, J., Guinó, E., Pujana, M. Á., & Moreno, V. R. (2012) · Clinical & Translational Oncology · doi:10.1007/s12094-012-0755-9 · Cited by 43 · see citing works

The impact of modifier genes on cone-rod dystrophy heterogeneity: An explorative familial pilot study and a hypothesis on neurotransmission impairment

Donato, L., Alibrandi, S., Scimone, C., Rinaldi, C., D’Ascola, A., Calamuneri, A., D’Angelo, R., & Sidoti, A. (2022) · PLoS ONE · doi:10.1371/journal.pone.0278857 · Cited by 45 · see citing works

Mapping the human protein interactome

Figeys, D. (2008) · Cell Research · doi:10.1038/cr.2008.72 · Cited by 44 · see citing works

ReactionFlow: an interactive visualization tool for causality analysis in biological pathways

Dang, T. N., Murray, P., Aurisano, J., & Forbes, A. G. (2015) · BMC Proceedings · doi:10.1186/1753-6561-9-s6-s6 · Cited by 39 · see citing works

The Glomerular Transcriptome and a Predicted Protein–Protein Interaction Network

He, L., Sun, Y., Takemoto, M., Norlin, J., Tryggvason, K., Samuelsson, T., & Betsholtz, C. (2007) · Journal of the American Society of Nephrology · doi:10.1681/asn.2007050588 · Cited by 39 · see citing works

On Open Problems in Biological Network Visualization

Albrecht, M., Kerren, A., Klein, K., Kohlbacher, O., Mutzel, P., Paul, W., Schreiber, F., & Wybrow, M. (2010) · Lecture notes in computer science · doi:10.1007/978-3-642-11805-0_25 · Cited by 38 · see citing works

The Hsp90 co-chaperone p23 of Toxoplasma gondii: Identification, functional analysis and dynamic interactome determination

Echeverría, P. C., Figueras, M. J., Vogler, M., Kriehuber, T., de Miguel, N., Deng, B., Dalmasso, M. C., Matthews, D. E., Matrajt, M., Haslbeck, M., et al. (2010) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2010.04.004 · Cited by 36 · see citing works

Identification of potential markers for type 2 diabetes mellitus via bioinformatics analysis

Lu, Y., Li, Y., Li, G., & Lu, H. (2020) · Molecular Medicine Reports · doi:10.3892/mmr.2020.11281 · Cited by 34 · see citing works

Network based analyses of gene expression profile of LCN2 overexpression in esophageal squamous cell carcinoma

Wu, B., Li, C., Du, Z., Yao, Q., Wu, J., Li, F., Zhang, P., Li, S., Xu, L., & Li, E. (2014) · Scientific Reports · doi:10.1038/srep05403 · Cited by 33 · see citing works

Microarray and bioinformatics analyses of gene expression profiles in BALB/c murine macrophage polarization

Li, J., Li, X., Zhang, Y., Zhang, M., Tang, Z., & Lv, K. (2017) · Molecular Medicine Reports · doi:10.3892/mmr.2017.7511 · Cited by 33 · see citing works

A systematic analysis of human lipocalin family and its expression in esophageal carcinoma

Du, Z., Wu, B., Wu, X., Lin, X., Qiu, X., Zhan, X.-F., Wang, S., Shen, J., Zheng, C.-P., Wu, Z., et al. (2015) · Scientific Reports · doi:10.1038/srep12010 · Cited by 34 · see citing works

CellWhere: graphical display of interaction networks organized on subcellular localizations

Zhu, L., Malatras, A., Thorley, M., Aghoghogbe, I., Mer, A. S., Duguez, S., Butler-Browne, G. S., Voït, T., & Duddy, W. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv354 · Cited by 30 · see citing works

A mouse protein interactome through combined literature mining with multiple sources of interaction evidence

Li, X., Cai, H., Xu, J., Ying, S., & Zhang, Y. (2009) · Amino Acids · doi:10.1007/s00726-009-0335-7 · Cited by 30 · see citing works

Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach

Xie, W., Huang, J., Liu, Y., Jianan, R., Luo, D., & He, M. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00829 · Cited by 26 · see citing works

Reconstructed cell fate–regulatory programs in stem cells reveal hierarchies and key factors of neurogenesisPreprint

Mendoza-Parra, M. A., Malysheva, V., Saleem, M.-A. M., Lieb, M., Godel, A., & Gronemeyer, H. (2016) · Genome Research · doi:10.1101/gr.208926.116 · Cited by 26 · see citing works

XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications

Lima, D. B., Zhu, Y., & Liu, F. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00957 · Cited by 22 · see citing works

Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis

Malysheva, V., Mendoza-Parra, M. A., Saleem, M.-A. M., & Gronemeyer, H. (2016) · Genome Medicine · doi:10.1186/s13073-016-0310-3 · Cited by 22 · see citing works

An Interactive Macrophage Signal Transduction Map Facilitates Comparative Analyses of High-Throughput Data

Wentker, P., Eberhardt, M., Dreyer, F. S., Bertrams, W., Cantone, M., Griss, K., Schmeck, B., & Vera, J. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1502513 · Cited by 22 · see citing works

CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

Heberle, H., Carazzolle, M. F., Telles, G. P., Meirelles, G. V., & Minghim, R. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1787-5 · Cited by 21 · see citing works

SYNTHESIS OF PHARMACOKINETIC PATHWAYS THROUGH KNOWLEDGE ACQUISITION AND AUTOMATED REASONING

Tari, L., Anwar, S., Liang, S., Hakenberg, J., & Baral, C. R. (2009) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789814295291_0048 · Cited by 21 · see citing works

PPI Network Analysis of mRNA Expression Profile of Ezrin Knockdown in Esophageal Squamous Cell Carcinoma

Wu, B., Xie, J., Du, Z., Wu, J., Zhang, P., Xu, L., & Li, E. (2014) · BioMed Research International · doi:10.1155/2014/651954 · Cited by 21 · see citing works

Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection

Zaslavsky, E., Nudelman, G., Marquez, S., Hershberg, U., Hartmann, B., Thakar, J., Sealfon, S. C., & Kleinstein, S. H. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s6-s1 · Cited by 20 · see citing works

Network Analyses of the Differential Expression of Heat Shock Proteins in Glioma

Sun, H., Zou, H., Cai, X., Zhou, H., Li, X., Xie, W., Xie, W., Du, Z., Xu, L., Li, E., et al. (2020) · DNA and Cell Biology · doi:10.1089/dna.2020.5425 · Cited by 21 · see citing works

LCN2-interacting proteins and their expression patterns in brain tumors

Du, Z., Wu, B., Xia, Q., Zhao, Y. D., Lin, L., Cai, Z., Wang, S., Li, E., Xu, L., Li, Y., et al. (2019) · Brain Research · doi:10.1016/j.brainres.2019.146304 · Cited by 19 · see citing works

Layered Functional Network Analysis of Gene Expression in Human Heart Failure

Zhu, W., Yang, L., & Du, Z. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006288 · Cited by 19 · see citing works

Antiviral innate immunity through the lens of systems biology

Tripathi, S., & García‐Sastre, A. (2015) · Virus Research · doi:10.1016/j.virusres.2015.11.024 · Cited by 19 · see citing works

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

Lepoivre, C., Bergon, A., Lopez, F., Perumal, N. B., Nguyen, C., Imbert, J., & Puthier, D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-19 · Cited by 18 · see citing works

Functional Molecular Units for Guiding Biomarker Panel Design

Heinzel, A., Mühlberger, I., Fechete, R., Mayer, B., & Perco, P. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0709-0_7 · Cited by 18 · see citing works

Transcriptome profiling identifies p53 as a key player during calreticulin deficiency: Implications in lipid accumulation

Vig, S., Talwar, P., Kaur, K., Srivastava, R., Srivastava, R., & Datta, M. (2015) · Cell Cycle · doi:10.1080/15384101.2015.1046654 · Cited by 17 · see citing works

Tracing the footsteps of autophagy in computational biology

Sarmah, D. T., Bairagi, N., & Chatterjee, S. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa286 · Cited by 17 · see citing works

Protein Phosphatase 1γ Isoforms Linked Interactions in the Brain

Esteves, S. L. C., Korrodi‐Gregório, L., Cotrim, C. Z., van Kleeff, P. J. M., Domingues, S. C., Silva, O. A. B. D. C. E., Fardilha, M., & Silva, E. F. D. C. E. (2012) · Journal of Molecular Neuroscience · doi:10.1007/s12031-012-9902-6 · Cited by 17 · see citing works

Optimized proteomic analysis of rat liver microsomes using dual enzyme digestion with 2D-LC–MS/MS

Golizeh, M., & Sleno, L. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.02.001 · Cited by 17 · see citing works

The arachidonic acid metabolism protein-protein interaction network and its expression pattern in esophageal diseases.

Wu, B., Bai, C., Du, Z., Zou, H., Wu, J., Xie, W., Zhang, P., Xu, L., & Li, E. (2018) · PubMed Central · Cited by 16 · see citing works

Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation

Echeverria, P. C., Forafonov, F., Pandey, D., Muhlebach, G., & Picard, D. (2011) · BioData Mining · doi:10.1186/1756-0381-4-15 · Cited by 15 · see citing works

Fast grid layout algorithm for biological networks with sweep calculation

Kojima, K., Nagasaki, M., & Miyano, S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn196 · Cited by 15 · see citing works

Layered Signaling Regulatory Networks Analysis of Gene Expression Involved in Malignant Tumorigenesis of Non-Resolving Ulcerative Colitis via Integration of Cross-Study Microarray Profiles

Fan, S., Pan, Z., Geng, Q., Li, X., Wang, Y., An, Y., Xu, Y. H., Tie, L., Pan, Y., & Li, X. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067142 · Cited by 14 · see citing works

A Study of Colormaps in Network Visualization

Karim, R. M., Kwon, O.-H., Park, C., & Lee, K. (2019) · Applied Sciences · doi:10.3390/app9204228 · Cited by 14 · see citing works

A Network-Based Approach on Elucidating the Multi-Faceted Nature of Chronological Aging in S. cerevisiae

Börklü, E., & Ülgen, K. Ö. (2011) · PLoS ONE · doi:10.1371/journal.pone.0029284 · Cited by 13 · see citing works

Revisited Experimental Comparison of Node-Link and Matrix Representations

Okoe, M., Jianu, R., & Kobourov, S. (2018) · Lecture notes in computer science · doi:10.1007/978-3-319-73915-1_23 · Cited by 13 · see citing works

The Protein Architecture of Human Secretory Vesicles Reveals Differential Regulation of Signaling Molecule Secretion by Protein Kinases

Bark, S. J., Wegrzyn, J., Taupenot, L., Ziegler, M. G., O’Connor, D. T., Ma, Q., Smoot, M. E., Ideker, T. E., & HOOK, V. Y. H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041134 · Cited by 12 · see citing works

The Involvement of Cholesterol in Sepsis and Tolerance to Lipopolysaccharide Highlighted by the Transcriptome Analysis of Zebrafish ( Danio rerio )

Dios, S., Balseiro, P., Costa, M. M., Romero, A., Boltaña, S., Roher, N., MacKenzie, S. A., Figueras, A. J., & Novoa, B. (2014) · Zebrafish · doi:10.1089/zeb.2014.0995 · Cited by 12 · see citing works

In silico model of atherosclerosis with individual patient calibration to enable precision medicine for cardiovascular disease

Buckler, A. J., Marlevi, D., Skenteris, N. T., Lengquist, M., Kronqvist, M., Matic, L. P., & Hedin, U. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.106364 · Cited by 11 · see citing works

Visualization of the interactome: What are we looking at?

Fung, D. C. Y., Li, S. S., Goel, A., Hong, S., & Wilkins, M. R. (2012) · PROTEOMICS · doi:10.1002/pmic.201100454 · Cited by 11 · see citing works

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

Inoue, K., Shimozono, S., Yoshida, H., & Kurata, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037739 · Cited by 10 · see citing works

BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm057 Systems biology Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation

Barsky, A., Gardy, J. L., Hancock, R. E. W., Munzner, T., & Wong, L. (2006)

CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization

Frias, S., Bryan, K. R., Brinkman, F. S. L., & Lynn, D. J. (2015) · Database · doi:10.1093/database/bav041 · Cited by 9 · see citing works

Database tool CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization

Frias, S., Bryan, K., Brinkman, F. S. L., & Lynn, D. J. (2016)

CellWhere: graphical display of interaction networks organized on subcellular localizations

Zhu, L., Malatras, A., Thorley, M., Aghoghogbe, I., Mer, A. S., Duguez, S., Butler-Browne, G. S., Voït, T., & Duddy, W. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv354 · Cited by 30 · see citing works

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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