Bader, Gary D.

The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function

Warde-Farley, D., Donaldson, S. L., Comes, O., Zuberi, K., Badrawi, R., Chao, P., Franz, M., Grouios, C., Kazi, F., Lopes, C. T., et al. (2010) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

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The repertoire of mutational signatures in human cancer

Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

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Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,064

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

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

Merico, D., Isserlin, R., Stueker, O., Emili, A., & Bader, G. D. (2010) · PLoS ONE

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 2,235

A draft map of the human proteome

Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., et al. (2014) · Nature

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 2,198

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

Bioinformatics and Genomic NetworksFungal and yeast genetics research

Cited by 2,162

Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants

Tong, A. H. Y., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Pagé, N., Robinson, M., Raghibizadeh, S., Hogue, C. W. V., Bussey, H., et al. (2001) · Science

Fungal and yeast genetics researchBioinformatics and Genomic Networks

Cited by 2,138

Functional impact of global rare copy number variation in autism spectrum disorders

Pinto, D., Pagnamenta, A. T., Klei, L., Anney, R., Merico, D., Regan, R., Conroy, J., Magalhaes, T. R., Correia, C., Abrahams, B. S., et al. (2010) · Nature

Autism Spectrum Disorder ResearchGenomic variations and chromosomal abnormalities

Cited by 2,013

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

Reimand, J., Isserlin, R., Voisin, V., Kucera, M., Tannus-Lopes, C., Rostamianfar, A., Wadi, L., Meyer, M., Wong, J., Xu, C., et al. (2019) · Nature Protocols

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 1,970

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

MacParland, S. A., Liu, J. C., Ma, X.-Z., Innes, B. T., Bartczak, A. M., Gage, B. K., Manuel, J., Khuu, N., Echeverri, J., Linares, I., et al. (2018) · Nature Communications

Single-cell and spatial transcriptomicsLiver physiology and pathology

Cited by 1,552

GeneMANIA update 2018

Franz, M., Rodriguez, H., Lopes, C., Zuberi, K., Montojo, J., Bader, G. D., & Morris, Q. (2018) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 1,413

Intertumoral Heterogeneity within Medulloblastoma Subgroups

Cavalli, F. M. G., Remke, M., Rampasek, L., Peacock, J., Shih, D. J. H., Luu, B., Garzia, L., Torchia, J., Nor, C., Morrissy, A. S., et al. (2017) · Cancer Cell

Glioma Diagnosis and TreatmentCancer Genomics and Diagnostics

Cited by 1,219

A reference map of the human binary protein interactome

Luck, K., Kim, D.-K., Lambourne, L., Spirohn, K., Begg, B. E., Bian, W., Brignall, R., Cafarelli, T., Campos-Laborie, F. J., Charloteaux, B., et al. (2020) · Nature

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

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Pathway Commons, a web resource for biological pathway data

Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G. D., & Sander, C. (2011) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 1,101

The evolutionary history of 2,658 cancers

Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 1,057

Patterns of somatic structural variation in human cancer genomes

Li, Y., Roberts, N. D., Wala, J. A., Shapira, O., Schumacher, S. E., Kumar, K., Khurana, E., Waszak, S., Korbel, J. O., Haber, J. E., et al. (2020) · Nature

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 867

The BioPAX community standard for pathway data sharing

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

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Single-cell transcriptomic profiling of the aging mouse brain

Ximerakis, M., Lipnick, S. L., Innes, B. T., Simmons, S. K., Adiconis, X., Dionne, D., Mayweather, B. A., Nguyen, L., Niziolek, Z., Ozek, C., et al. (2019) · Nature Neuroscience

Single-cell and spatial transcriptomicsGenetics, Aging, and Longevity in Model Organisms

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Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Cortés-Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., et al. (2020) · Nature Genetics

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 712

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

Northcott, P. A., Lee, C., Zichner, T., Stütz, A. M., Erkek, S., Kawauchi, D., Shih, D. J. H., Hovestadt, V., Zapatka, M., Sturm, D., et al. (2014) · Nature

Glioma Diagnosis and TreatmentChromatin Remodeling and Cancer

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The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., et al. (2004) · Nature Biotechnology

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

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Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

Mack, S. C., Witt, H., Piro, R. M., Gu, L., Zuyderduyn, S., Stütz, A. M., Wang, X., Gallo, M., Garzia, L., Zayne, K., et al. (2014) · Nature

Glioma Diagnosis and TreatmentEpigenetics and DNA Methylation

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A Specificity Map for the PDZ Domain Family

Tonikian, R., Zhang, Y., Sazinsky, S. L., Currell, B., Yeh, J.-H., Reva, B., Held, H. A., Appleton, B. A., Evangelista, M., Wu, Y., et al. (2008) · PLoS Biology

Protein Structure and DynamicsChemical Synthesis and Analysis

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