The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers

Hallmarks of Cancer: The Next Generation

Hanahan, D., & Weinberg, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.02.013 · Cited by 66,590

The hallmarks of cancer

Hanahan, D., & Weinberg, R. A. (2000) · Cell · doi:10.1016/s0092-8674(00)81683-9 · Cited by 29,219

Cancer Genome Landscapes

Vogelstein, B., Papadopoulos, N., Velculescu, V. E., Zhou, S., Diaz, L. A., & Kinzler, K. W. (2013) · Science · doi:10.1126/science.1235122 · Cited by 7,863

Mutation and cancer: statistical study of retinoblastoma

Knudson, A. G. (1971) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.68.4.820 · Cited by 7,612

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

Dang, L., White, D. W., Gross, S., Bennett, B. D., Bittinger, M. A., Driggers, E. M., Fantin, V. R., Jang, H. G., Jin, S., Keenan, M. C., et al. (2009) · Nature · doi:10.1038/nature08617 · Cited by 4,154

A census of human cancer genes

Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., & Stratton, M. R. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1299 · Cited by 3,184

Inhibition of Mutated, Activated BRAF in Metastatic Melanoma

Flaherty, K. T., Puzanov, I., Kim, K. B., Ribas, A., McArthur, G. A., Sosman, J. A., O'Dwyer, P. J., Lee, R. J., Grippo, J. F., Nolop, K., et al. (2010) · New England Journal of Medicine · doi:10.1056/nejmoa1002011 · Cited by 3,103

Processing of primary microRNAs by the Microprocessor complex

Denli, A. M., Tops, B. B. J., Plasterk, R. H. A., Ketting, R. F., & Hannon, G. J. (2004) · Nature · doi:10.1038/nature03049 · Cited by 2,784

Wnt signaling in cancer

Zhan, T., Rindtorff, N., & Boutros, M. (2017) · Oncogene · doi:10.1038/onc.2016.304 · Cited by 2,626

The mutational landscape of lethal castration-resistant prostate cancer

Grasso, C. S., Wu, Y.-M., Robinson, D. R., Cao, X., Dhanasekaran, S. M., Khan, A. P., Quist, M. J., Jing, X., Lonigro, R. J., Brenner, J. C., et al. (2012) · Nature · doi:10.1038/nature11125 · Cited by 2,517

A gene set enrichment analysis for cancer hallmarks

Menyhárt, O., Kothalawala, W. J., & Győrffy, B. (2024) · Journal of Pharmaceutical Analysis · doi:10.1016/j.jpha.2024.101065 · Cited by 92

Pancreatic tropism of metastatic renal cell carcinoma

Singla, N., Xie, Z., Zhang, Z., Gao, M., Yousuf, Q., Onabolu, O., McKenzie, T., Tcheuyap, V. T., Ma, Y., Choi, J. S., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.134564 · Cited by 93

Interpretable identification of cancer genes across biological networks via transformer-powered graph representation learning

Su, X., Hu, P., Li, D., Zhao, B.-W., Niu, Z., Herget, T., Yu, P. S., & Hu, L. (2025) · Nature Biomedical Engineering · doi:10.1038/s41551-024-01312-5 · Cited by 101

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers

Arnedo-Pac, C., Mularoni, L., Muiños, F., González-Pérez, A., & López-Bigas, N. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz501 · Cited by 78

Drugging “undruggable” genes for cancer treatment: Are we making progress?

Duffy, M. J., & Crown, J. P. (2020) · International Journal of Cancer · doi:10.1002/ijc.33197 · Cited by 86

Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian high grade serous carcinoma

Lahtinen, A., Lavikka, K., Virtanen, A., Li, Y., Jamalzadeh, S., Skorda, A., Lauridsen, A. R., Zhang, K., Marchi, G., Isoviita, V., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.04.017 · Cited by 87

Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome

Parry, E. M., Leshchiner, I., Guièze, R., Johnson, C., Tausch, E., Parikh, S. A., Lemvigh, C. K., Broséus, J., Hergalant, S., Messer, C., et al. (2023) · Nature Medicine · doi:10.1038/s41591-022-02113-6 · Cited by 87

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity

Mangiante, L., Alcala, N., Sexton‐Oates, A., Genova, A. D., González-Pérez, A., Khandekar, A., Bergstrom, E. N., Kim, J., Liu, X., Blázquez‐Encinas, R., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01321-1 · Cited by 89

Systematic characterization of mutations altering protein degradation in human cancers

Tokheim, C. J., Wang, X., Timms, R. T., Zhang, B., Mena, E. L., Wang, B., Chen, C., Ge, J., Chu, J., Zhang, W., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.01.020 · Cited by 85

Recombination of repeat elements generates somatic complexity in human genomes

Pascarella, G., Hon, C. C., Hashimoto, K., Busch, A., Luginbühl, J., Parr, C., Hin Yip, W., Abe, K., Kratz, A., Bonetti, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.032 · Cited by 77

The forces driving cancer extracellular vesicle secretion

Bebelman, M. P., Janssen, E., Pegtel, D. M., & Crudden, C. (2020) · Neoplasia · doi:10.1016/j.neo.2020.11.011 · Cited by 86

Expanding the human proteome with microproteins and peptideins

Deutsch, E. W., Kok, L. W., Mudge, J. M., Valls, C., Jungreis, I., Ruiz‐Orera, J., Sun, Z., Kusebauch, U., Fierro-Monti, I., Abelin, J. G., et al. (2026) · Nature · doi:10.1038/s41586-026-10459-x · Cited by 98

In-depth cell-free DNA sequencing reveals genomic landscape of Hodgkin’s lymphoma and facilitates ultrasensitive residual disease detection

Sobesky, S., Mammadova, L., Cirillo, M., Drees, E. E. E., Mattlener, J., Dörr, H., Altmüller, J., Shi, Z., Bröckelmann, P. J., Weiss, J. M., et al. (2021) · Med · doi:10.1016/j.medj.2021.09.002 · Cited by 79

Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation

Noureen, N., Wu, S., Lv, Y., Yang, J., Yung, W. K. A., Gelfond, J., Wang, X., Koul, D., Ludlow, A. T., & Zheng, S. (2021) · Nature Communications · doi:10.1038/s41467-020-20474-9 · Cited by 78

Complex synthetic lethality in cancer

Ryan, C. J., Devakumar, L. J. P. S., Pettitt, S. J., & Lord, C. J. (2023) · Nature Genetics · doi:10.1038/s41588-023-01557-x · Cited by 82

The mutational landscape of the SCAN‐B real‐world primary breast cancer transcriptome

Brueffer, C., Gladchuk, S., Winter, C., Vallon‐Christersson, J., Hegardt, C., Häkkinen, J., George, A. M., Chen, Y., Ehinger, A., Larsson, C., et al. (2020) · EMBO Molecular Medicine · doi:10.15252/emmm.202012118 · Cited by 72

Integration of Online Omics-Data Resources for Cancer Research

Das, T., Andrieux, G., Ahmed, M., & Chakraborty, S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.578345 · Cited by 77

Whole-exome sequencing reveals germline-mutated small cell lung cancer subtype with favorable response to DNA repair–targeted therapies

Tlemsani, C., Takahashi, N., Pongor, L. S., Rajapakse, V. N., Tyagi, M. G., Wen, X., Fasaye, G., Schmidt, K. T., Desai, P. A., Kim, C., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abc7488 · Cited by 75

Comprehensive profiling of 1015 patients’ exomes reveals genomic-clinical associations in colorectal cancer

Zhao, Q., Wang, F., Chen, Y., Chen, S., Yao, Y.-C., Zeng, Z.-L., Jiang, T., Wang, Y., Wu, C., Jing, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30062-8 · Cited by 75

Chronological genome and single-cell transcriptome integration characterizes the evolutionary process of adult T cell leukemia-lymphoma

Yamagishi, M., Kubokawa, M., Kuze, Y., Suzuki, A., Yokomizo, A., Kobayashi, S., Nakashima, M., Makiyama, J., Iwanaga, M., Fukuda, T., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25101-9 · Cited by 77

Assessing CSF ctDNA to Improve Diagnostic Accuracy and Therapeutic Monitoring in Breast Cancer Leptomeningeal Metastasis

Fitzpatrick, A., Iravani, M., Mills, A., Childs, L., Alaguthurai, T., Clifford, A., García-Murillas, I., Laere, S. V., Dirix, L. Y., Harries, M., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-3017 · Cited by 74

Prediction of biomarkers and therapeutic combinations for anti-PD-1 immunotherapy using the global gene network association

Wu, C.-C., Wang, Y., Livingston, J. A., Zhang, J., & Futreal, P. A. (2022) · Nature Communications · doi:10.1038/s41467-021-27651-4 · Cited by 80

Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability

Bae, T., Fasching, L., Wang, Y., Shin, J. H., Šuvakov, M., Jang, Y., Norton, S., Dias, C., Mariani, J., Jourdon, A., et al. (2022) · Science · doi:10.1126/science.abm6222 · Cited by 78

The genomic landscape of cholangiocarcinoma reveals the disruption of post-transcriptional modifiers

Zhang, Y., Ma, Z., Li, C., Wang, C., Jiang, W., Chang, J., Han, S., Lu, Z., Shao, Z., Wang, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30708-7 · Cited by 74

A highly efficient transgene knock-in technology in clinically relevant cell types

Allen, A. G., Khan, S., Margulies, C. M., Viswanathan, R., Lele, S. S., Blaha, L. C., Scott, S. N., Izzo, K. M., Gerew, A., Pattali, R. K., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01779-8 · Cited by 71

Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma

Chapman, O. S., Luebeck, J., Sridhar, S., Wong, I. T., Dixit, D., Wang, S., Prasad, G., Rajkumar, U., Pagadala, M., Larson, J. D., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01551-3 · Cited by 77

MTR-Viewer: identifying regions within genes under purifying selection

Silk, M. A., Petrovski, S., & Ascher, D. B. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz457 · Cited by 72

Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer

von Loga, K., Woolston, A., Punta, M., Barber, L. J., Griffiths, B. L., Semiannikova, M., Spain, G., Challoner, B. R., Fenwick, K., Simon, R., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13915-7 · Cited by 74

CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection

Li, H., Han, Z., Sun, Y., Wang, F., Hu, P., Gao, Y., Bai, X., Peng, S., Ren, C., Xu, X., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50426-6 · Cited by 73

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns

Emperle, M., Adam, S., Kunert, S., Dukatz, M., Baude, A., Plass, C., Rathert, P., Bashtrykov, P., & Jeltsch, A. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz911 · Cited by 69

Clonal evolution in liver cancer at single-cell and single-variant resolution

Su, X., Zhao, L., Shi, Y. Y., Zhang, R., Long, Q., Bai, S., Luo, Q., Lin, Y., Zou, X., Ghazanfar, S., et al. (2021) · Journal of Hematology & Oncology · doi:10.1186/s13045-021-01036-y · Cited by 71

Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma

Meiller, C., Montagne, F., Hirsch, T. Z., Caruso, S., Wolf, J. D., Bayard, Q., Assié, J., Meunier, L., Blum, Y., Quetel, L., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00931-w · Cited by 75

Nanoparticles-Based Strategies to Improve the Delivery of Therapeutic Small Interfering RNA in Precision Oncology

Huang, J., & Xiao, K. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics14081586 · Cited by 73

Pan-cancer analysis reveals molecular patterns associated with age

Shah, Y., Verma, A., Marderstein, A. R., White, J. B., Bhinder, B., Medina, J. S. G., & Elemento, O. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110100 · Cited by 71

High-throughput functional evaluation of human cancer-associated mutations using base editors

Kim, Y., Lee, S., Cho, S., Park, J., Chae, D., Park, T., Minna, J. D., & Kim, S. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01276-4 · Cited by 66

Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv

Shiraishi, Y., Koya, J., Chiba, K., Okada, A., Arai, Y., Saito, Y., Shibata, T., & Kataoka, K. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad526 · Cited by 66

Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk

Wilcox, N., Dumont, M., González‐Neira, A., Carvalho, S., Beauparlant, C. J., Crotti, M., Luccarini, C., Soucy, P., Dubois, S., Núñez‐Torres, R., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01466-z · Cited by 69

A Comprehensive Review of Deep Learning Applications with Multi-Omics Data in Cancer Research

Sartori, F., Codicè, F., Caranzano, I., Rollo, C., Birolo, G., Fariselli, P., & Pancotti, C. (2025) · Genes · doi:10.3390/genes16060648 · Cited by 78

Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance

Casolino, R., Beer, P. A., Chakravarty, D., Davis, M. B., Malapelle, U., Mazzarella, L., Normanno, N., Pauli, C., Subbiah, V., Turnbull, C., et al. (2024) · CA A Cancer Journal for Clinicians · doi:10.3322/caac.21825 · Cited by 69

Evolutionary Routes in Metastatic Uveal Melanomas Depend on MBD4 Alterations

Rodrigues, M. J., Mobuchon, L., Houy, A., Alsafadi, S., Baulande, S., Mariani, O., Marande, B., Raïs, K. A., van der Kooij, M. K., Kapiteijn, E., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-1215 · Cited by 65

Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types

Boot, A., Ng, A. W. T., Chong, F. T., Ho, S.-C., Yu, W., Tan, D. S. W., Iyer, N. G., & Rozen, S. G. (2020) · Genome Research · doi:10.1101/gr.255620.119 · Cited by 58

Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas

Harbers, L., Agostini, F., Nicoś, M., Poddighe, D., Bienko, M., & Crosetto, N. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.700568 · Cited by 64

Direct targeting of oncogenic RAS mutants with a tumor-specific cytosol-penetrating antibody inhibits RAS mutant–driven tumor growth

Shin, S., Kim, J., Park, S.-W., Jun, S.-Y., Kweon, H.-J., Choi, D.-K., Lee, D., Cho, Y. B., & Kim, Y. (2020) · Science Advances · doi:10.1126/sciadv.aay2174 · Cited by 63

Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells

Robinson, P. S., Thomas, L. E., Abascal, F., Jung, H., Harvey, L. M. R., West, H. D., Ólafsson, S., Lee, B. C. H., Coorens, T. H. H., Lee-Six, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31341-0 · Cited by 63

A hybrid machine learning model for classifying gene mutations in cancer using LSTM, BiLSTM, CNN, GRU, and GloVe

Aburass, S., Dorgham, O. M., & Shaqsi, J. A. (2024) · Systems and Soft Computing · doi:10.1016/j.sasc.2024.200110 · Cited by 71

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment

Kovaka, S., Hook, P. W., Jenike, K. M., Shivakumar, V. S., Morina, L. B., Razaghi, R., Timp, W., & Schatz, M. C. (2025) · Nature Methods · doi:10.1038/s41592-025-02631-4 · Cited by 63

Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression

Lau, E., McCoy, P. J., Reeves, F., Chow, K., Clarkson, M. J., Kwan, E. M., Packwood, K., Northen, H., He, M., Kingsbury, Z., et al. (2020) · Genome Medicine · doi:10.1186/s13073-020-00770-1 · Cited by 62

Inferring subgroup-specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication

Xi, J., Yuan, X., Wang, M., Li, A., Li, X., & Huang, Q. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz793 · Cited by 63

Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy

Subramanian, A., Nemat‐Gorgani, N., Ellis-Caleo, T. J., van IJzendoorn, D. G. P., Sears, T. J., Somani, A., Luca, B. A., Zhou, M. Y., Bradić, M., Torres, I. A., et al. (2024) · Nature Cancer · doi:10.1038/s43018-024-00743-y · Cited by 66

The mutagenic forces shaping the genomes of lung cancer in never smokers

Díaz‐Gay, M., Zhang, T., Hoang, P. H., Leduc, C., Baine, M. K., Travis, W. D., Sholl, L. M., Joubert, P., Khandekar, A., Wei, Z., et al. (2025) · Nature · doi:10.1038/s41586-025-09219-0 · Cited by 85

Association of Damaging Variants in Genes With Increased Cancer Risk Among Patients With Congenital Heart Disease

Morton, S. U., Shimamura, A., Newburger, P. E., Opotowsky, A. R., Quiat, D., Pereira, A. C., Jin, S. C., Gurvitz, M., Brueckner, M., Chung, W. K., et al. (2021) · JAMA Cardiology · doi:10.1001/jamacardio.2020.4947 · Cited by 62

Comprehensive genomic and epigenomic analysis in cancer of unknown primary guides molecularly-informed therapies despite heterogeneity

Möhrmann, L., Werner, M., Oleś, M., Möck, A., Uhrig, S., Jahn, A., Kreutzfeldt, S., Fröhlich, M., Hutter, B., Paramasivam, N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31866-4 · Cited by 63

The evolution of hematopoietic cells under cancer therapy

Pich, O., Cortés‐Bullich, A., Muiños, F., Pratcorona, M., González-Pérez, A., & López-Bigas, N. (2021) · Nature Communications · doi:10.1038/s41467-021-24858-3 · Cited by 60

The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2

Tutuncuoglu, B., Çakır, M., Batra, J., Bouhaddou, M., Eckhardt, M., Gordon, D. E., & Krogan, N. J. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0559 · Cited by 58

The multifaceted roles of cohesin in cancer

Nardo, M. D., Pallotta, M. M., & Musio, A. (2022) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-022-02321-5 · Cited by 62

DRPreter: Interpretable Anticancer Drug Response Prediction Using Knowledge-Guided Graph Neural Networks and Transformer

Shin, J., Piao, Y., Bang, D., Kim, S., & Jo, K. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232213919 · Cited by 60

Targeting synthetic lethal paralogs in cancer

Ryan, C. J., Mehta, I., Kebabci, N., & Adams, D. J. (2023) · Trends in cancer · doi:10.1016/j.trecan.2023.02.002 · Cited by 59

Comprehensive characterization of distinct genetic alterations in metastatic breast cancer across various metastatic sites

Cha, S., Lee, E., & Won, H. (2021) · npj Breast Cancer · doi:10.1038/s41523-021-00303-y · Cited by 56

A proteogenomics data-driven knowledge base of human cancer

Liao, Y., Savage, S. R., Dou, Y., Shi, Z., Yi, X., Jiang, W., Lei, J. T., & Zhang, B. (2023) · Cell Systems · doi:10.1016/j.cels.2023.07.007 · Cited by 60

Targeting Tumor Heterogeneity with Neoantigen-Based Cancer Vaccines

Pounraj, S., Chen, S., Ma, L., Mazzieri, R., Dolcetti, R., & Rehm, B. H. A. (2023) · Cancer Research · doi:10.1158/0008-5472.can-23-2042 · Cited by 61

The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution

Nguyen, D., Hooper, W. F., Liu, W., Chu, T. R., Geiger, H. M., Shelton, J. M., Shah, M. J., Goldstein, Z. R., Winterkorn, L. H., Helland, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07955-3 · Cited by 62

Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma

Zhao, X., Xing, P., Song, X., Zhao, M., Zhao, L., Dang, Y., Lei, L.-L., Xu, R., Han, W.-L., Wang, P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26745-3 · Cited by 55

Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

Álvarez, E. G., Demeulemeester, J., Otero, P., Jolly, C., García‐Souto, D., Pequeño‐Valtierra, A., Zamora, J., Tojo, M., Temes, J., Baez‐Ortega, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26805-8 · Cited by 61

RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancerPreprint

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. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/436634 · Cited by 59

Targeting Loss of Heterozygosity: A Novel Paradigm for Cancer Therapy

Zhang, X., & Sjöblom, T. (2021) · Pharmaceuticals · doi:10.3390/ph14010057 · Cited by 58

Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer

Nath, A., Cosgrove, P. A., Mirsafian, H., Christie, E. L., Pflieger, L. T., Copeland, B., Majumdar, S., Cristea, M. C., Han, E. S., Lee, S. J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23171-3 · Cited by 59

Predictive biomarkers for 5-fluorouracil and oxaliplatin-based chemotherapy in gastric cancers via profiling of patient-derived xenografts

Na, D., Chae, J., Cho, S., Kang, W., Lee, A., Min, S., Kang, J., Kim, M. J., Choi, J., Lee, W., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25122-4 · Cited by 56

Somatic and Germline Genomic Alterations in Very Young Women with Breast Cancer

Waks, A. G., Kim, D., Jain, E., Snow, C., Kirkner, G. J., Rosenberg, S. M., Oh, C., Poorvu, P. D., Ruddy, K. J., Tamimi, R. M., et al. (2022) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-2572 · Cited by 56

Functional effects of protein variants

Vihinen, M. (2020) · Biochimie · doi:10.1016/j.biochi.2020.10.009 · Cited by 56

Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancersPreprint

Symer, D. E., Akagi, K., Geiger, H. M., Yang, S. T., Li, G., Emde, A., Xiao, W., Jiang, B., Corvelo, A., Toussaint, N. C., et al. (2021) · Genome Research · doi:10.1101/gr.275911.121 · Cited by 58

Genome-wide profiling of non-smoking-related lung cancer cells reveals common RB1 rearrangements associated with histopathologic transformation in EGFR-mutant tumors

Pros, E., Saigí, M., Alameda, D., Gómez‐Mariano, G., Martínez–Delgado, B., Alburquerque-Béjar, J. J., Carretero, J., Tonda, R., Esteve‐Codina, A., Català, I., et al. (2020) · Annals of Oncology · doi:10.1016/j.annonc.2019.09.001 · Cited by 55

Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era

Porta‐Pardo, E., Valencia, A., & Godzik, A. (2020) · FEBS Letters · doi:10.1002/1873-3468.13781 · Cited by 57

Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis

Farshidfar, F., Rhrissorrakrai, K., Levovitz, C., Peng, C., Knight, J., Bacchiocchi, A., Su, J., Yin, M., Sznol, M., Ariyan, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28566-4 · Cited by 59

Liver cancer heterogeneity modeled by in situ genome editing of hepatocytes

Tang, M., Zhao, Y., Zhao, J., Wei, S., Liu, M., Zheng, N., Geng, D., Han, S., Zhang, Y., Zhong, G., et al. (2022) · Science Advances · doi:10.1126/sciadv.abn5683 · Cited by 54

Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns

Watson, E. V., Lee, J. J.-K., Gulhan, D., Melloni, G. E. M., Venev, S. V., Magesh, R. Y., Frederick, A., Chiba, K., Wooten, E. C., Naxerova, K., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01665-2 · Cited by 53

Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer

Martínez-Jiménez, F., Muiños, F., López‐Arribillaga, E., López-Bigas, N., & González-Pérez, A. (2019) · Nature Cancer · doi:10.1038/s43018-019-0001-2 · Cited by 55

The Evolution of Human Cancer Gene Duplications across Mammals

Tollis, M., Schneider‐Utaka, A. K., & Maley, C. C. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa125 · Cited by 56

Clonal lineage from normal endometrium to ovarian clear cell carcinoma through ovarian endometriosis

Suda, K., Diaz, L. A. C., Yoshihara, K., Nakaoka, H., Yachida, N., Motoyama, T., Inoue, I., & Enomoto, T. (2020) · Cancer Science · doi:10.1111/cas.14507 · Cited by 53

Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium

Yamaguchi, M., Nakaoka, H., Suda, K., Yoshihara, K., Ishiguro, T., Yachida, N., Saito, K., Ueda, H., Sugino, K., Mori, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28568-2 · Cited by 54

Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants

He, M. M., Li, Q., Yan, M., Cao, H., Hu, Y., He, K., Cao, K., Li, M. M., & Wang, K. (2019) · Genome Medicine · doi:10.1186/s13073-019-0664-4 · Cited by 58

Whole Genome Analysis of Ovarian Granulosa Cell Tumors Reveals Tumor Heterogeneity and a High-Grade TP53-Specific Subgroup

Roze, J. F., Monroe, G. R., Kutzera, J., Groeneweg, J. W., Stelloo, E., Paijens, S. T., Nijman, H. W., van Meurs, H. S., van Lonkhuijzen, L. R. C. W., Piek, J. M. J., et al. (2020) · Cancers · doi:10.3390/cancers12051308 · Cited by 54

easyCLIP analysis of RNA-protein interactions incorporating absolute quantification

Porter, D. F., Miao, W., Yang, X., Goda, G. A., Ji, A. L., Donohue, L. K. H., Aleman, M. M., Dominguez, D., & Khavari, P. A. (2021) · Nature Communications · doi:10.1038/s41467-021-21623-4 · Cited by 52

Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling

Hobor, S., Bakir, M. A., Hiley, C. T., Skrzypski, M. T., Frankell, A. M., Bakker, B., Watkins, T. B. K., Markovets, A. A., Dry, J. R., Brown, A. P., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47606-9 · Cited by 51

Molecular determinants of sotorasib clinical efficacy in KRASG12C-mutated non-small-cell lung cancer

Skoulidis, F., Li, B. T., Langen, A. J. D., Hong, D. S., Léna, H., Wolf, J., Dy, G. K., Fontecedro, A. C., Tomasini, P., Velcheti, V., et al. (2025) · Nature Medicine · doi:10.1038/s41591-025-03732-5 · Cited by 54

Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Tong, Y., Sun, M., Chen, L., Wang, Y., Yan, L., Li, L., Zhang, X., Cai, Y., Qie, J., Pang, Y., et al. (2022) · Journal of Hematology & Oncology · doi:10.1186/s13045-022-01384-3 · Cited by 52

FS–GBDT: identification multicancer-risk module via a feature selection algorithm by integrating Fisher score and GBDT

Zhang, J., Xu, D., Hao, K., Zhang, Y., Chen, W., Liu, J., Gao, R., Wu, C., & Marinis, Y. Z. D. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa189 · Cited by 51

Multi-omics profiling of primary small cell carcinoma of the esophagus reveals RB1 disruption and additional molecular subtypes

Li, R., Yang, Z., Shao, F., Cheng, H. S., Wen, Y., Sun, S., Guo, W., Li, Z., Zhang, F., Xue, L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24043-6 · Cited by 54

Splicing is an alternate oncogenic pathway activation mechanism in glioma

Siddaway, R., Milos, S., Vadivel, A. K. A., Dobson, T., Swaminathan, J., Ryall, S. T., Pajovic, S., Patel, P. G., Nazarian, J., Becher, O. J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28253-4 · Cited by 52

Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction

Bacolla, A., Ye, Z., Ahmed, Z., & Tainer, J. A. (2019) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2019.03.004 · Cited by 52

Mortality and risk of progression to adult T cell leukemia/lymphoma in HTLV-1–associated myelopathy/tropical spastic paraparesis

Nagasaka, M., Yamagishi, M., Yagishita, N., Araya, N., Kobayashi, S., Makiyama, J., Kubokawa, M., Yamauchi, J., Hasegawa, D., Coler-Reilly, A. L. G., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1920346117 · Cited by 50

Exploring the Allosteric Territory of Protein Function

Tee, W.-V., Tan, Z. W., Lee, K., Guarnera, E., & Berezovsky, I. N. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c00540 · Cited by 50

Recurrent mutations in topoisomerase IIα cause a previously undescribed mutator phenotype in human cancers

Boot, A., Liu, M., Stantial, N., Shah, V. R., Yu, W., Nitiss, K. C., Nitiss, J. L., Jinks-Robertson, S., & Rozen, S. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2114024119 · Cited by 50

Deep learning for cancer type classification and driver gene identification

Zeng, Z., Mao, C., Vo, A. H., Li, X., Nugent, J. O., Khan, S. A., Clare, S. E., & Luo, Y. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04400-4 · Cited by 57

An atlas of transposable element-derived alternative splicing in cancer

Clayton, E. A., Rishishwar, L., Huang, T.-C., Gulati, S., Ban, D., McDonald, J. F., & Jordan, I. K. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0342 · Cited by 48

A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers

Han, Y., Huang, L., & Zhou, F. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab055 · Cited by 48

CMC: Cancer miRNA Census – a list of cancer-related miRNA genes

Suszyńska, M., Machowska, M., Fraszczyk, E., Michalczyk, M., Philips, A., Galka-Marciniak, P., & Kozłowski, P. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae017 · Cited by 49

Transcriptionally active enhancers in human cancer cells

Lidschreiber, K., Jung, L. A., von der Emde, H., Dave, K., Taipale, J., Cramer, P., & Lidschreiber, M. (2021) · Molecular Systems Biology · doi:10.15252/msb.20209873 · Cited by 49

Multifocal Organoid Capturing of Colon Cancer Reveals Pervasive Intratumoral Heterogenous Drug Responses

Kim, S., Park, J. W., Seo, H., Kim, M. J., Park, J., Kim, G., Lee, J. O., Shin, Y., Bae, J. M., Koo, B., et al. (2021) · Advanced Science · doi:10.1002/advs.202103360 · Cited by 48

Integrative proteomic characterization of adenocarcinoma of esophagogastric junction

Li, S., Li, Y., Xu, Z., Xu, J., Chen, G., Guan, X., Pan, G.-Z., Hu, C., Dong, J., Du, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36462-8 · Cited by 46

Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers

ter Brugge, P., Moser, S. C., Bièche, I., Kristel, P., Ibadioune, S., Eeckhoutte, A., de Bruijn, R., van der Burg, E., Lutz, C., Annunziato, S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37537-2 · Cited by 47

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

Sońdka, Z., Speedy, H. E., Bamford, S., Cole, C. G., Ward, S. A., & Forbes, S. A. (2019) · Cancer Research · doi:10.1158/1538-7445.am2019-2469 · Cited by 1

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

Sońdka, Z., Bamford, S., Cole, C. G., Dawson, E., Ponting, L., Stefancsik, R., Ward, S. A., Tate, J. G., Campbell, P. J., & Forbes, S. A. (2017) · Cancer Research · doi:10.1158/1538-7445.am2017-2599

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

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

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

Repana, D., Nulsen, J., Dreßler, L., Bortolomeazzi, M., Venkata, S. K., Tourna, A., Yakovleva, A., Palmieri, T., & Ciccarelli, F. D. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/389858 · Cited by 38