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Prognostic genome and transcriptome signatures in colorectal cancers

Nunes, L., Li, F., Wu, M., Luo, T., Hammarström, K., Torell, E., Ljuslinder, I., Mezheyeuski, A., Edqvist, P.-H. D., Löfgren‐Burström, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07769-3 · Cited by 164 · see citing works

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

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Molecular map of chronic lymphocytic leukemia and its impact on outcome

Knisbacher, B. A., Lin, Z., Hahn, C. K., Nadeu, F., Duran‐Ferrer, M., Stevenson, K. E., Tausch, E., Delgado, J., Barbera-Mourelle, A., Taylor-Weiner, A. N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01140-w · Cited by 156 · see citing works

Laying the foundation for genomically-based risk assessment in chronic myeloid leukemia

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PTEN as a Prognostic/Predictive Biomarker in Cancer: An Unfulfilled Promise?

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Multi-omics analysis identifies osteosarcoma subtypes with distinct prognosis indicating stratified treatment

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Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer

Cotto, K. C., Feng, Y.-Y., Ramu, A., Richters, M. M., Freshour, S. L., Skidmore, Z. L., Xia, H., McMichael, J. F., Kunisaki, J., Campbell, K. M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37266-6 · Cited by 131 · see citing works

Polysaccharides of mushroom Pleurotus spp.: New extraction techniques, biological activities and development of new technologies

Barbosa, J. R., Freitas, M. M. D. S., Martins, L. H. D. S., & de Carvalho, R. N. (2019) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2019.115550 · Cited by 127 · see citing works

In silico saturation mutagenesis of cancer genes

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GraphCDR: a graph neural network method with contrastive learning for cancer drug response prediction

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CancerSCEM: a database of single-cell expression map across various human cancers

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Integrative clinical and molecular characterization of translocation renal cell carcinoma

Bakouny, Z., Sadagopan, A., Ravi, P. K., Metaferia, N. Y., Li, J., AbuHammad, S., Tang, S., Denize, T., Garner, E. R., Gao, X. Y., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2021.110190 · Cited by 123 · see citing works

Mutational landscape of cancer-driver genes across human cancers

Sinkala, M. (2023) · Scientific Reports · doi:10.1038/s41598-023-39608-2 · Cited by 130 · see citing works

Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation

Kinsler, G., Geiler‐Samerotte, K., & Petrov, D. A. (2020) · eLife · doi:10.7554/elife.61271 · Cited by 110 · see citing works

Clinical Application of Cytokines in Cancer Immunotherapy

Qiu, Y., Su, M., Liu, L., Tang, Y., Pan, Y., & Sun, J. (2021) · Drug Design Development and Therapy · doi:10.2147/dddt.s308578 · Cited by 120 · see citing works

Molecular classification of hormone receptor-positive HER2-negative breast cancer

Jin, X., Zhou, Y.-F., Ma, D., Zhao, S., Lin, C., Xiao, Y., Fu, T., Liu, C., Chen, Y., Xiao, W.-X., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01507-7 · Cited by 117 · see citing works

Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma

Megquier, K., Turner-Maier, J., Swofford, R., Kim, J. H., Sarver, A. L., Wang, C., Sakthikumar, S., Johnson, J., Koltookian, M., Lewellen, M., et al. (2019) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-19-0221 · Cited by 118 · see citing works

Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin

Tedesco, M., Giannese, F., Lazarević, D., Giansanti, V., Rosano, D., Monzani, S., Catalano, I., Grassi, E., Zanella, E. R., Botrugno, O. A., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-01031-1 · Cited by 112 · see citing works

Cross-species oncogenic signatures of breast cancer in canine mammary tumors

Kim, T., Yang, I. S., Seung, B., Lee, S., Kim, D., Ha, Y.-J. J., Seo, M.-K., Kim, K.-K., Kim, H. S., Cheong, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17458-0 · Cited by 116 · see citing works

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

Tian, L., Li, Y., Edmonson, M. N., Zhou, X., Newman, S., McLeod, C., Thrasher, A., Liu, Y., Tang, B., Rusch, M., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02043-x · Cited by 115 · see citing works

Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource

Dreßler, L., Bortolomeazzi, M., Keddar, M. R., Mišetić, H., Sartini, G., Acha‐Sagredo, A., Montorsi, L., Wijewardhane, N., Repana, D., Nulsen, J., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02607-z · Cited by 113 · see citing works

Pan-cancer proteogenomics connects oncogenic drivers to functional states

Li, Y., Porta‐Pardo, E., Tokheim, C. J., Bailey, M. H., Yaron, T. M., Stathias, V., Geffen, Y., Imbach, K. J., Cao, S., Anand, S. K., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.014 · Cited by 114 · see citing works

New insight into circRNAs: characterization, strategies, and biomedical applications

Feng, X., Zhu, S.-X., Pu, K., Huang, H., Chen, Y., & Wang, W. (2023) · Experimental Hematology and Oncology · doi:10.1186/s40164-023-00451-w · Cited by 118 · see citing works

De novo detection of somatic mutations in high-throughput single-cell profiling data sets

Muyas, F., Sauer, C. M., Valle-Inclán, J. E., Li, R., Rahbari, R., Mitchell, T. J., Hormoz, S., & Cortés‐Ciriano, I. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01863-z · Cited by 112 · see citing works

Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities

Nichols, C. A., Gibson, W. J., Brown, M. S., Kosmicki, J. A., Busanovich, J. P., Wei, H. Y., Urbanski, L. M., Currimjee, N., Berger, A. C., Gao, G. F., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16399-y · Cited by 103 · see citing works

Transcriptional effects of copy number alterations in a large set of human cancers

Bhattacharya, A., Bense, R. D., Urzúa-Traslaviña, C. G., de Vries, E. G. E., van Vugt, M. A. T. M., & Fehrmann, R. S. N. (2020) · Nature Communications · doi:10.1038/s41467-020-14605-5 · Cited by 102 · see citing works

Linking pollution and cancer in aquatic environments: A review

Baines, C., Lerebours, A., Frédéric Thomas, A., Fort, J., Kreitsberg, R., Gentès, S., Meitern, R., Saks, L., Újvári, B., Giraudeau, M., et al. (2021) · Environment International · doi:10.1016/j.envint.2021.106391 · Cited by 105 · see citing works

The concurrence of DNA methylation and demethylation is associated with transcription regulation

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Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencingPreprint

Aganezov, S. S., Goodwin, S., Sherman, R. M., Sedlazeck, F. J., Arun, G., Bhatia, S., Lee, I., Kirsche, M., Wappel, R. L., Kramer, M., et al. (2020) · Genome Research · doi:10.1101/gr.260497.119 · Cited by 101 · see citing works

Genomic profiling of primary histiocytic sarcoma reveals two molecular subgroups

Egan, C., Nicolae, A., Lack, J., Chung, H., Skarshaug, S., Pham, T., Navarro, W., Abdullaev, Z., Aguilera, N. S. I., Xi, L., et al. (2019) · Haematologica · doi:10.3324/haematol.2019.230375 · Cited by 100 · see citing works

CysDB: a human cysteine database based on experimental quantitative chemoproteomics

Boatner, L. M., Palafox, M. F., Schweppe, D. K., & Backus, K. M. (2023) · Cell chemical biology · doi:10.1016/j.chembiol.2023.04.004 · Cited by 97 · see citing works

Discovering the drivers of clonal hematopoiesis

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Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial

Hunt, S. E., Moore, B., Amode, R., Armean, I. M., Lemos, D., Mushtaq, A., Parton, A., Schuilenburg, H., Szpak, M., Thormann, A., et al. (2021) · Human Mutation · doi:10.1002/humu.24298 · Cited by 96 · see citing works

Cancer aneuploidies are shaped primarily by effects on tumour fitness

Shih, J., Sarmashghi, S., Zhakula-Kostadinova, N., Zhang, S., Georgis, Y., Hoyt, S. H., Cuoco, M. S., Gao, G. F., Spurr, L. F., Berger, A. C., et al. (2023) · Nature · doi:10.1038/s41586-023-06266-3 · Cited by 101 · see citing works

RosettaDDGPrediction for high‐throughput mutational scans: From stability to binding

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Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data

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Japanese version of The Cancer Genome Atlas, JCGA, established using fresh frozen tumors obtained from 5143 cancer patients

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Integrative spatial analysis reveals tumor heterogeneity and immune colony niche related to clinical outcomes in small cell lung cancer

Chen, H., Deng, C., Gao, J., Wang, J., Fu, F., Wang, Q., Wang, Q., Zhang, S., Zhang, S., Fan, F., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.01.012 · Cited by 94 · see citing works

Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes

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Abstract 2469: The COSMIC Cancer Gene Census - a comprehensive study of all mutated cancer-driving genes

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Abstract 2599: COSMIC Cancer Gene Census: expert descriptions across genes in oncogenesis

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COSMIC: the Catalogue Of Somatic Mutations In Cancer

Tate, J. G., Bamford, S., Jubb, H. C., Sondka, Z., Beare, D. M., Bindal, N., Boutselakis, H., Cole, C. G., Creatore, C., Dawson, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1015 · Cited by 4,867 · see citing works

Abstract 5285: COSMIC: comprehensively exploring oncogenomics

Forbes, S. A., Bindal, N., Beare, D. M., Bamford, S., Cole, C. G., Ward, S. A., Leung, K., Kok, C. Y., Jia, M., De, T., et al. (2016) · Cancer Research · doi:10.1158/1538-7445.am2016-5285 · Cited by 1 · see citing works

The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screensPreprint

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