Knijnenburg, Theo

The Immune Landscape of Cancer

Thorsson, V., Gibbs, D. L., Brown, S. D., Wolf, D., Bortone, D. S., Ou Yang, T.-H., Porta-Pardo, E., Gao, G. F., Plaisier, C. L., Eddy, J. A., et al. (2018) · Immunity

Cancer Immunotherapy and BiomarkersImmune cells in cancer

Cited by 5,870

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

Liu, J., Lichtenberg, T., Hoadley, K. A., Poisson, L. M., Lazar, A. J., Cherniack, A. D., Kovatich, A. J., Benz, C. C., Levine, D. A., Lee, A. V., et al. (2018) · Cell

Cancer Genomics and DiagnosticsGene expression and cancer classification

Cited by 3,725

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Sanchez-Vega, F., Mina, M., Armenia, J., Chatila, W. K., Luna, A., La, K. C., Dimitriadoy, S., Liu, D. L., Kantheti, H. S., Saghafinia, S., et al. (2018) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,201

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

Hoadley, K. A., Yau, C., Hinoue, T., Wolf, D. M., Lazar, A. J., Drill, E., Shen, R., Taylor, A. M., Cherniack, A. D., Thorsson, V., et al. (2018) · Cell

Cancer Genomics and DiagnosticsGene expression and cancer classification

Cited by 2,546

Comprehensive Characterization of Cancer Driver Genes and Mutations

Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell

Cancer Genomics and DiagnosticsGenomics and Rare Diseases

Cited by 2,256

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

Malta, T. M., Sokolov, A., Gentles, A. J., Burzykowski, T., Poisson, L., Weinstein, J. N., Kamińska, B., Huelsken, J., Omberg, L., Gevaert, O., et al. (2018) · Cell

Cancer Cells and MetastasisPluripotent Stem Cells Research

Cited by 2,180

A Landscape of Pharmacogenomic Interactions in Cancer

Iorio, F., Knijnenburg, T. A., Vis, D. J., Bignell, G. R., Menden, M. P., Schubert, M., Aben, N., Gonçalves, E., Barthorpe, S., Lightfoot, H., et al. (2016) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 2,090

The chromatin accessibility landscape of primary human cancers

Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,230

Spatial organization and molecular correlation of tumor-infiltrating lymphocytes using deep learning on pathology images

Saltz, J., Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., Samaras, D., Shroyer, K. R., Zhao, T., Batiste, R., et al. (2018) · Cell Reports

AI in cancer detectionCancer Immunotherapy and Biomarkers

Cited by 1,027

Comprehensive Characterization of Cancer Driver Genes and Mutations

Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 552

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer

Wang, Y., Xu, X., Maglic, D., Dill, M. T., Mojumdar, K., Ng, P. K.-S., Jeong, K. J., Tsang, Y. H., Moreno, D., Bhavana, V. H., et al. (2018) · Cell Reports

Hippo pathway signaling and YAP/TAZCancer-related molecular mechanisms research

Cited by 500

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Schaub, F. X., Dhankani, V., Berger, A. C., Trivedi, M., Richardson, A. B., Shaw, R., Zhao, W., Zhang, X., Ventura, A., Liu, Y., et al. (2018) · Cell Systems

Cancer Genomics and DiagnosticsCancer-related Molecular Pathways

Cited by 431

MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-β Receptor Signaling

Huang, S., Hölzel, M., Knijnenburg, T., Schlicker, A., Roepman, P., McDermott, U., Garnett, M., Grernrum, W., Sun, C., Prahallad, A., et al. (2012) · Cell

TGF-β signaling in diseasesLung Cancer Treatments and Mutations

Cited by 430

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Ding, L., Bailey, M. H., Porta-Pardo, E., Thorsson, V., Colaprico, A., Bertrand, D., Gibbs, D. L., Weerasinghe, A., Huang, K.-L., Tokheim, C., et al. (2018) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 399

Integrated intracellular organization and its variations in human iPS cells

Viana, M. P., Chen, J., Knijnenburg, T. A., Vasan, R., Yan, C., Arakaki, J. E., Bailey, M., Berry, B., Borensztejn, A., Brown, E. M., et al. (2023) · Nature

Cell Image Analysis TechniquesPluripotent Stem Cells Research

Cited by 132

Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

Zhou, J. X., Taramelli, R., Pedrini, E., Knijnenburg, T., & Huang, S. (2017) · Scientific Reports

Bioinformatics and Genomic NetworksSingle-cell and spatial transcriptomics

Cited by 85

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

Knijnenburg, T. A., Klau, G. W., Iorio, F., Garnett, M. J., McDermott, U., Shmulevich, I., & Wessels, L. F. A. (2016) · Scientific Reports

Gene Regulatory Network AnalysisExplainable Artificial Intelligence (XAI)

Cited by 74

Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Gerbin, K. A., Grancharova, T., Donovan-Maiye, R., Hendershott, M. C., Brown, J., Dinh, S. Q., Gehring, J. L., Hirano, M., Johnson, G. R., Nath, A., et al. (2020) · Cell Systems

Single-cell and spatial transcriptomicsPluripotent Stem Cells Research

Cited by 59

Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Gerbin, K. A., Grancharova, T., Donovan-Maiye, R. M., Hendershott, M. C., Anderson, H. G., Brown, J. M., Chen, J., Dinh, S. Q., Gehring, J. L., Johnson, G. R., et al. (2021) · Cell Systems

Single-cell and spatial transcriptomicsPluripotent Stem Cells Research

Cited by 59

A deep generative model of 3D single-cell organization

Donovan-Maiye, R. M., Brown, J. M., Chan, C. K., Ding, L., Yan, C., Gaudreault, N., Theriot, J. A., Maleckar, M. M., Knijnenburg, T. A., & Johnson, G. R. (2022) · PLOS Computational Biology

Cell Image Analysis TechniquesSingle-cell and spatial transcriptomics

Cited by 44

A deep generative model of 3D single-cell organization

Donovan-Maiye, R. M., Brown, J. M., Chan, C. K., Ding, L., Yan, C., Gaudreault, N., Theriot, J. A., Maleckar, M. M., Knijnenburg, T. A., & Johnson, G. R. (2021) · PLoS Computational Biology

Cell Image Analysis TechniquesSingle-cell and spatial transcriptomics

Cited by 44

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

Mirzaei, H., Knijnenburg, T. A., Kim, B., Robinson, M., Picotti, P., Carter, G. W., Li, S., Dilworth, D. J., Eng, J. K., Aitchison, J. D., et al. (2013) · Proceedings of the National Academy of Sciences

Advanced Proteomics Techniques and ApplicationsGenomics and Chromatin Dynamics

Cited by 30