Sander, Chris

Pathway Commons, a web resource for biological pathway data

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Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

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Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Abeshouse, A., Adebamowo, C., Adebamowo, S. N., Akbani, R., Akeredolu, T., Ally, A., Anderson, M. L., Anur, P., Appelbaum, E. L., Armenia, J., et al. (2017) · Cell

Sarcoma Diagnosis and TreatmentChromatin Remodeling and Cancer

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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

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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

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The systems biology graphical notation.

Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., et al. (2009) · Nature Biotechnology

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

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Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal

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Cancer Genomics and DiagnosticsBioinformatics and Genomic Networks

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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

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Correlated mutations and residue contacts in proteins

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Protein Structure and DynamicsEnzyme Structure and Function

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An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins.

Bork, P., Sander, C., & Valencia, A. (1992) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

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Mutation effects predicted from sequence co-variation

Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P. I., Springer, M., Sander, C., & Marks, D. S. (2017) · Nature Biotechnology

Genomics and Rare DiseasesEvolution and Genetic Dynamics

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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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Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy

Barretina, J., Taylor, B. S., Banerji, S., Ramos, A. H., Lagos-Quintana, M., DeCarolis, P. L., Shah, K., Socci, N. D., Weir, B. A., Ho, A., et al. (2010) · Nature Genetics

Sarcoma Diagnosis and TreatmentChromatin Remodeling and Cancer

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The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma

Bott, M., Brevet, M., Taylor, B. S., Shimizu, S., Ito, T., Wang, L., Creaney, J., Lake, R. A., Zakowski, M. F., Reva, B., et al. (2011) · Nature Genetics

Occupational and environmental lung diseasesChromatin Remodeling and Cancer

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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

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Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

Zheng, S., Cherniack, A. D., Dewal, N., Moffitt, R. A., Danilova, L., Murray, B. A., Lerario, A. M., Else, T., Knijnenburg, T. A., Ciriello, G., et al. (2016) · Cancer Cell

Adrenal and Paraganglionic TumorsChromatin 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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Protein structure prediction from sequence variation

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Protein Structure and DynamicsEnzyme Structure and Function

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Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Hmeljak, J., Sanchez-Vega, F., Hoadley, K. A., Shih, J., Stewart, C., Heiman, D., Tarpey, P., Danilova, L., Drill, E., Gibb, E. A., et al. (2018) · Cancer Discovery

Occupational and environmental lung diseasesIntraperitoneal and Appendiceal Malignancies

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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

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Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

Khan, A. A., Betel, D., Miller, M. L., Sander, C., Leslie, C. S., & Marks, D. S. (2009) · Nature Biotechnology

MicroRNA in disease regulationRNA Interference and Gene Delivery

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Sequence co-evolution gives 3D contacts and structures of protein complexes

Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S. (2014) · eLife

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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

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Genome-wide analysis of noncoding regulatory mutations in cancer

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Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

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A Specificity Map for the PDZ Domain Family

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