Ideker, Trey

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

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 51,888

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., et al. (2020) · Nature

SARS-CoV-2 and COVID-19 ResearchComputational Drug Discovery Methods

Cited by 4,405

Genome-wide methylation profiles reveal quantitative views of human aging rates

Hannum, G., Guinney, J., Zhao, L., Zhang, L., Hughes, G., Sadda, S., Klotzle, B., Bibikova, M., Fan, J.-B., Gao, Y., et al. (2013) · Molecular Cell

Epigenetics and DNA MethylationGenetics, Aging, and Longevity in Model Organisms

Cited by 4,270

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

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 2,507

Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network

Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., & Hood, L. (2001) · Science

Bioinformatics and Genomic NetworksFungal and yeast genetics research

Cited by 2,050

A N EW A PPROACH TO D ECODING L IFE : Systems Biology

Ideker, T., Galitski, T., & Hood, L. (2001) · Annual Review of Genomics and Human Genetics

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 1,664

Network‐based classification of breast cancer metastasis

Chuang, H., Lee, E., Liu, Y., Lee, D., & Ideker, T. (2007) · Molecular Systems Biology

Bioinformatics and Genomic NetworksBreast Cancer Treatment Studies

Cited by 1,431

Discovering regulatory and signalling circuits in molecular interaction networks

Ideker, T., Ozier, O., Schwikowski, B., & Siegel, A. F. (2002) · Bioinformatics

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 1,197

DNA methylation aging clocks: challenges and recommendations

Bell, C. G., Lowe, R., Adams, P. D., Baccarelli, A. A., Beck, S., Bell, J. T., Christensen, B. C., Gladyshev, V. N., Heijmans, B. T., Horvath, S., et al. (2019) · Genome Biology

Epigenetics and DNA MethylationGenetics, Aging, and Longevity in Model Organisms

Cited by 1,025

Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication

König, R., Zhou, Y., Elleder, D., Diamond, T. L., Bonamy, G. M. C., Irelan, J. T., Chiang, C.-Y., Tu, B. P., De Jesus, P. D., Lilley, C. E., et al. (2008) · Cell

HIV Research and TreatmentHIV/AIDS drug development and treatment

Cited by 960

Protein networks in disease

Ideker, T., & Sharan, R. (2008) · Genome Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 817

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

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 715

Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease

Sharma, K., Karl, B., Mathew, A. V., Gangoiti, J. A., Wassel, C. L., Saito, R., Pu, M., Sharma, S., You, Y.-H., Wang, L., et al. (2013) · Journal of the American Society of Nephrology

Chronic Kidney Disease and DiabetesMetabolomics and Mass Spectrometry Studies

Cited by 571

Predicting drug response and synergy using a deep learning model of human cancer cells

Kuenzi, B. M., Park, J., Fong, S. H., Sanchez, K. S., Lee, J., Kreisberg, J. F., Ma, J., & Ideker, T. (2020) · Cancer Cell

Computational Drug Discovery MethodsMachine Learning in Healthcare

Cited by 544

Integrative approaches for finding modular structure in biological networks

Mitra, K., Carvunis, A.-R., Ramesh, S. K., & Ideker, T. (2013) · Nature Reviews Genetics

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 535

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

Fungal and yeast genetics researchDNA Repair Mechanisms

Cited by 447

Systematic interpretation of genetic interactions using protein networks

Kelley, R., & Ideker, T. (2005) · Nature Biotechnology

Bioinformatics and Genomic NetworksFungal and yeast genetics research

Cited by 437

Using deep learning to model the hierarchical structure and function of a cell

Ma, J., Yu, M. K., Fong, S., Ono, K., Sage, E., Demchak, B., Sharan, R., & Ideker, T. (2018) · Nature Methods

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 435

Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions

Shen, J. P., Zhao, D., Sasik, R., Luebeck, J., Birmingham, A., Bojorquez-Gomez, A., Licon, K., Klepper, K., Pekin, D., Beckett, A. N., et al. (2017) · Nature Methods

CRISPR and Genetic EngineeringChromatin Remodeling and Cancer

Cited by 359

Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast

Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K., Fischer, T., Collins, S. R., Qu, H., Shales, M., Park, H.-O., Hayles, J., et al. (2008) · Science

Bioinformatics and Genomic NetworksFungal and yeast genetics research

Cited by 352

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B.-J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., et al. (2006) · Journal of Biology

Bioinformatics and Genomic NetworksFungal and yeast genetics research

Cited by 326

Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction.

Karlsson Linnér, R., Mallard, T. T., Barr, P. B., Sanchez-Roige, S., Madole, J. W., Driver, M. N., Poore, H. E., de Vlaming, R., Grotzinger, A. D., Tielbeek, J. J., et al. (2021) · Nature Neuroscience

Genetic Associations and EpidemiologyNeurotransmitter Receptor Influence on Behavior

Cited by 317

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

Huang, J. K., Carlin, D. E., Yu, M. K., Zhang, W., Kreisberg, J. F., Tamayo, P., & Ideker, T. (2018) · Cell Systems

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 289

Integrating physical and genetic maps: from genomes to interaction networks

Beyer, A., Bandyopadhyay, S., & Ideker, T. (2007) · Nature Reviews Genetics

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 207