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

Hallmarks of Cancer: The Next Generation

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Cancer Genome Landscapes

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Mutation and cancer: statistical study of retinoblastoma

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Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

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Inhibition of Mutated, Activated BRAF in Metastatic Melanoma

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Processing of primary microRNAs by the Microprocessor complex

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Wnt signaling in cancer

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The mutational landscape of lethal castration-resistant prostate cancer

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MAB21L4 Deficiency Drives Squamous Cell Carcinoma via Activation of RET

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The shaping of cancer genomes with the regional impact of mutation processes

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Genome-wide in vivo screen of circulating tumor cells identifies SLIT2 as a regulator of metastasis

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Whole-exome sequencing reveals a comprehensive germline mutation landscape and identifies twelve novel predisposition genes in Chinese prostate cancer patients

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Quantitative Phosphoproteomics Analysis Uncovers PAK2- and CDK1-Mediated Malignant Signaling Pathways in Clear Cell Renal Cell Carcinoma

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Carcino-Evo-Devo, A Theory of the Evolutionary Role of Hereditary Tumors

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Paralog dispensability shapes homozygous deletion patterns in tumor genomes

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Transcriptome- and proteome-wide association studies identify genes associated with renal cell carcinoma

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A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation

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Proteogenomic analysis reveals adaptive strategies for alleviating the consequences of aneuploidy in cancer

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Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review

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Merkel Cell Polyomavirus in Merkel Cell Carcinoma: Integration Sites and Involvement of the KMT2D Tumor Suppressor Gene

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Exome of Radiation-induced Rat Mammary Carcinoma Shows Copy-number Losses and Mutations in Human-relevant Cancer Genes

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Novel Tumor-Specific Antigens for Immunotherapy Identified From Multi-omics Profiling in Thymic Carcinomas

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Predicting embryonic aneuploidy rate in IVF patients using whole-exome sequencing

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Isolation of a Human Betaretrovirus from Patients with Primary Biliary Cholangitis

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Colon cancer organoids using monoclonal organoids established in four different lesions of one cancer patient reveal tumor heterogeneity and different real-time responsiveness to anti-cancer drugs

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Individual Genetic Heterogeneity

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Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies

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TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins

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Codon bias analyses on thyroid carcinoma genes

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Circulating Cell-Free DNA-Based Detection of Tumor Suppressor Gene Copy Number Loss and Its Clinical Implication in Metastatic Prostate Cancer

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Novel patterns of complex structural variation revealed across thousands of cancer genome graphsPreprint

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Deep graph convolutional network-based multi-omics integration for cancer driver gene identification

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The earliest events in BRAF ‐mutant colorectal cancer: exome sequencing of sessile serrated lesions with a tiny focus dysplasia or cancer reveals recurring mutations in two distinct progression pathways

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Somatic mutation distribution across tumour cohorts provides a signal for positive selection in cancer

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Widespread perturbation of ETS factor binding sites in cancer

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A-to-I RNA editing shows dramatic up-regulation in osteosarcoma and broadly regulates tumor-related genes by altering microRNA target regions

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High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue

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Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins

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Analyzing the functional effects of DNA variants with gene editing

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Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries

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Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks

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Cancer pharmacoinformatics: Databases and analytical tools

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Circulating Micro-RNAs Predict the Risk of Recurrence in Triple-Negative Breast Cancer

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CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution

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Ancient Evolutionary Origin of Intrinsically Disordered Cancer Risk Regions

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LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations

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Immune subtypes and neoantigen-related immune evasion in advanced colorectal cancer

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Analysis of polymorphisms in genes associated with the FA/BRCA pathway in three patients with multiple primary malignant neoplasms

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DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks

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Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction

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PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification

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MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning

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OUP accepted manuscript

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The landscape of extrachromosomal circular DNA in medulloblastomaPreprint

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Emerging roles of cohesin-STAG2 in cancer

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Cancer genomics and bioinformatics in Latin American countries: applications, challenges, and perspectives

Torres-Narvaez, E. S., González, D., Artunduaga-Alvarado, J. A., & Ortega‐Recalde, O. (2025) · Frontiers in Oncology · doi:10.3389/fonc.2025.1584178 · Cited by 16

FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology

Li, D., Kusko, R. L., Ning, B., Tong, W., Johann, D. J., & Xu, J. (2021) · Precision Cancer Medicine · doi:10.21037/pcm-21-29 · Cited by 12

A catalog of curated breast cancer genes

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Inferring Potential Cancer Driving Synonymous Variants

Zeng, Z., & Bromberg, Y. (2022) · Genes · doi:10.3390/genes13050778 · Cited by 14

Deciphering the Increased Prevalence of TP53 Mutations in Metastatic Prostate Cancer

Zhang, W., Dong, Y., Sartor, O. A., & Zhang, K. (2022) · Cancer Informatics · doi:10.1177/11769351221087046 · Cited by 12

Strategies to inhibit FGFR4 V550L-driven rhabdomyosarcoma

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Exploratory genomic analysis of high-grade neuroendocrine neoplasms across diverse primary sites

Sun, T. Y., Zhao, L., Hummelen, P. V., Martin, B. A., Hornbacker, K., Lee, H., Xia, L. C., Padda, S. K., Ji, H. P., & Kunz, P. L. (2022) · Endocrine Related Cancer · doi:10.1530/erc-22-0015 · Cited by 12

Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers

Castro-Mondragon, J. A., Aure, M. R. R., Lingjærde, O. C., Langerød, A., Martens, J. W. M., Børresen‐Dale, A., Kristensen, V. N., & Mathelier, A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1143 · Cited by 15

NSD2 methylates AROS to promote SIRT1 activation and regulates fatty acid metabolism-mediated cancer radiotherapy

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Circadian transcriptome of pancreatic adenocarcinoma unravels chronotherapeutic targets

Sharma, D., Adnan, D., Abdel-Reheem, M. K., Anafi, R. C., Leary, D. D., & Bishehsari, F. (2024) · JCI Insight · doi:10.1172/jci.insight.177697 · Cited by 12

RedCDR: Dual Relation Distillation for Cancer Drug Response Prediction

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Lynch syndrome-associated and sporadic microsatellite unstable colorectal cancers: different patterns of clonal evolution yield highly similar tumours

Martin, S. D., Katainen, R., Taira, A., Välimäki, N., Ristimaki, A. P., Seppälä, T. T., Renkonen‐Sinisalo, L., Lepistö, A., Tahkola, K., Mattila, A. K., et al. (2024) · Human Molecular Genetics · doi:10.1093/hmg/ddae124 · Cited by 12

The amino acid composition of a protein influences its expression

Thompson, R., & Pickard, B. S. (2024) · PLoS ONE · doi:10.1371/journal.pone.0284234 · Cited by 12

Advances in cancer genomics and precision oncology

Heo, Y., Kim, W., Cho, Y., Jung, J., Kim, N., & Choi, I. (2025) · Genes & Genomics · doi:10.1007/s13258-024-01614-7 · Cited by 12

An organoid library of human esophageal squamous cell carcinomas (ESCCs) uncovers the chemotherapy-resistant ESCC features

Nakagawa, S., Sato, T., Ohashi, E., Kajita, M., Miya, F., Yamamoto, K., Yotsumata, H., Yamaguchi, K., Nakajima, Y., Miura, A., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-07869-4 · Cited by 13

ABCB1 confers resistance to carboplatin by accumulating stem-like cells in the G2/M phase of the cell cycle in p53null ovarian cancer

Lee, D., Jeong, H.-S., Hwang, S., Lee, Y., & Kang, Y. (2025) · Cell Death Discovery · doi:10.1038/s41420-025-02435-7 · Cited by 13

A rare multiple primary sarcomatoid carcinoma (SCA) of small intestine harboring driver gene mutations: a case report and a literature review

Zhu, Z., Liu, X., Li, W., Wen, Z., Ji, X., Zhou, R., Tuo, X., Chen, Y., Gong, X., Liu, G., et al. (2021) · Translational Cancer Research · doi:10.21037/tcr-20-2829 · Cited by 12

Molecular Biomarkers of Response to Eribulin in Patients with Leiomyosarcoma

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CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model

Zhao, W., Yang, J., Wu, J., Cai, G., Zhang, Y., Haltom, J., Su, W., Dong, M. J., Chen, S., Wu, J., et al. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab131 · Cited by 14

Establishment and characterization of immortalized human breast cancer cell lines from breast cancer patient-derived xenografts (PDX)

Zhuang, Y., Grainger, J., Vedell, P. T., Yu, J., Moyer, A. M., Gao, H., Fan, X.-Y., Qin, S., Liu, D., Kalari, K. R., et al. (2021) · npj Breast Cancer · doi:10.1038/s41523-021-00285-x · Cited by 12

Discovery of a novel potentially transforming somatic mutation in CSF2RB gene in breast cancer

Rashid, M., Ali, R., Almuzzaini, B., Song, H., Alhallaj, A., Abdulkarim, A. A., Baz, O., Zahrani, H. A., Sabeena, M., Alharbi, W., et al. (2021) · Cancer Medicine · doi:10.1002/cam4.4106 · Cited by 12

Assessment of 13 in silico pathogenicity methods on cancer-related variants

Yazar, M., & Özbek, P. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105434 · Cited by 12

The Cellular and Molecular Landscape of Synchronous Pediatric Sialoblastoma and Hepatoblastoma

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Bioinformatics Prediction and Machine Learning on Gene Expression Data Identifies Novel Gene Candidates in Gastric Cancer

Kori, M., & Göv, E. (2022) · Genes · doi:10.3390/genes13122233 · Cited by 12

Using genomic scars to select immunotherapy beneficiaries in advanced non-small cell lung cancer

Donker, H. C., van Es, B., Tamminga, M., Lunter, G. A., van Kempen, L. C. L. T., Schuuring, E. M. D., Hiltermann, T. J. N., & Groen, H. J. M. (2023) · Scientific Reports · doi:10.1038/s41598-023-32499-3 · Cited by 12

Mutational signatures and increased retrotransposon insertions in xeroderma pigmentosum variant skin tumors

Corradi, C., Vilar, J. B., Buzatto, V. C., de Souza, T. A., Castro, L. P., Munford, V., Vecchi, R. D., Galante, P. A. F., do Rego, F. O. R., Miller, T. L. A., et al. (2023) · Carcinogenesis · doi:10.1093/carcin/bgad030 · Cited by 13

Data curation-research: practices of data standardization and exploration in a precision medicine database

Tempini, N. (2020) · New Genetics and Society · doi:10.1080/14636778.2020.1853513 · Cited by 12

A computational approach for the discovery of significant cancer genes by weighted mutation and asymmetric spreading strength in networks

Cutigi, J. F., Evangelista, A. F., Reis, R. M., & Simao, A. D. S. (2021) · Scientific Reports · doi:10.1038/s41598-021-02671-8 · Cited by 12

Revealing the contribution of somatic gene mutations to shaping tumor immune microenvironment

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ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers

Nath, A., Cohen, A. L., & Bild, A. (2022) · Molecular Systems Biology · doi:10.15252/msb.202110558 · Cited by 12

MiR-4458-loaded gelatin nanospheres target COL11A1 for DDR2/SRC signaling pathway inactivation to suppress the progression of estrogen receptor-positive breast cancer

Liu, J., Yang, C., Chen, Q., Yu, T., Zhang, S., Guo, W., Luo, L.-H., Zhao, G., Yin, D., & Zhang, C. (2022) · Biomaterials Science · doi:10.1039/d2bm00543c · Cited by 12

Comparative study of the evolution of cancer gene duplications across fish

Baines, C., Meitern, R., Kreitsberg, R., & Sepp, T. (2022) · Evolutionary Applications · doi:10.1111/eva.13481 · Cited by 14

Aplastic anemia in a patient with CVID due to NFKB1 haploinsufficiencyPreprint

Sklarz, T., Hurwitz, S. N., Stanley, N. L., Juusola, J., Bagg, A., & Babushok, D. V. (2020) · Molecular Case Studies · doi:10.1101/mcs.a005769 · Cited by 12

Expansion of gastric intestinal metaplasia with copy number aberrations contributes to field cancerization

Kumagai, K. (2022) · Institutional Repositories DataBase (IRDB) · doi:10.14989/doctor.k24138 · Cited by 12

Modeling and predicting cancer clonal evolution with reinforcement learningPreprint

Ivanovic, S. S., & El-Kebir, M. (2023) · Genome Research · doi:10.1101/gr.277672.123 · Cited by 12

The mutagenic forces shaping the genomic landscape of lung cancer in never smokersPreprint

Díaz‐Gay, M., Zhang, T., Hoang, P. H., Khandekar, A., Zhao, W., Steele, C. D., Otlu, B., Nandi, S. P., Vangara, R., Bergstrom, E. N., et al. (2024) · medRxiv · doi:10.1101/2024.05.15.24307318 · Cited by 12

Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation

Hao, Y., Lee, H., Baraboo, M., Burch, K., Maurer, T. M., Somarelli, J. A., & Conant, G. C. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa026 · Cited by 11

A patient-driven clinicogenomic partnership for metastatic prostate cancer

Crowdis, J. P., Balch, S., Sterlin, L., Thomas, B. S., Camp, S. Y., Dunphy, M., Anastasio, E., Shah, S., Damon, A. L., Ramos, R., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100169 · Cited by 11

Acute Myeloid Leukemia Expresses a Specific Group of Olfactory Receptors

Guardia, G. D. A., Naressi, R. G., Buzatto, V. C., da Costa, J. B., Zalcberg, I. R., Ramires, J., Malnic, B., Gutiyama, L. M., & Galante, P. A. F. (2023) · Cancers · doi:10.3390/cancers15123073 · Cited by 12

Computational analysis of protein–protein interactions of cancer drivers in renal cell carcinoma

Pei, J., Zhang, J., & Cong, Q. (2023) · FEBS Open Bio · doi:10.1002/2211-5463.13732 · Cited by 11

Not Only RET but NF1 and Chromosomal Instability Are Seen in Young Patients with Sporadic Medullary Thyroid Carcinoma

Castroneves, L. A., Mangone, F. R., Lerário, A. M., Mercante, A. M. D. C., Batista, R. L., Barros, L. R. C., Ferreira, C. V., Farias, E. C., Vanderlei, F. A. B., Maia, A. L., et al. (2024) · Journal of the Endocrine Society · doi:10.1210/jendso/bvae059 · Cited by 11

Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution

Dietzen, M., Zhai, H.-R., Lucas, O., Pich, O., Barrington, C., Lu, W.-T., Ward, S., Guo, Y., Hynds, R. E., Zaccaria, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50107-4 · Cited by 15

Proteogenomic characterization of pancreatic neuroendocrine tumors uncovers hypoxia and immune signatures in clinically aggressive subtypes

Tanaka, A., Ogawa, M., Zhou, Y., Otani, Y., Hendrickson, R. C., Miele, M. M., Li, Z., Klimstra, D. S., Wang, J. Y., & Roehrl, M. H. A. (2024) · iScience · doi:10.1016/j.isci.2024.110544 · Cited by 14

AI-derived comparative assessment of the performance of pathogenicity prediction tools on missense variants of breast cancer genes

Ahmad, R. M., Ali, B. R., Al-Jasmi, F. A., Dhaheri, N. A., Turki, S. H. A., Kizhakkedath, P., & Mohamad, M. S. (2024) · Human Genomics · doi:10.1186/s40246-024-00667-9 · Cited by 12

DEMINING: A deep learning model embedded framework to distinguish RNA editing from DNA mutations in RNA sequencing data

Fu, Z.-C., Gao, B., Fang, N., Ma, X.-K., & Yang, L. C. (2024) · Genome biology · doi:10.1186/s13059-024-03397-2 · Cited by 11

VACCIMEL, an allogeneic melanoma vaccine, efficiently triggers T cell immune responses against neoantigens and alloantigens, as well as against tumor-associated antigens

Carri, I., Schwab, E., Triviño, J. C., von Euw, E. M., Nielsen, M., Mordoh, J., & Barrio, M. M. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1496204 · Cited by 11

PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor

Husremović, T., Meier, V., Piëch, L., Siess, K. M., Antonioli, S., Grishkovskaya, I., Kircheva, N., Angelova, S., Wenzl, K., Brandstätter, A., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2417218122 · Cited by 13

Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability

Espiritu, D., Sheng, Y., Peng, Y., Ostroverkhova, D. S., Li, S., Landsman, D., Aristizabal, M. J., & Panchenko, A. R. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf899 · Cited by 11

PNNandKCNQ1OT1Can Predict the Efficacy of Adjuvant Fluoropyrimidine-Based Chemotherapy in Colorectal Cancer Patients

Lapucci, A., Perrone, G., Paolo, A. D., Napoli, C., Landini, I., Roviello, G., Calosi, L., Naccarato, A. G., Falcone, A., Bani, D., et al. (2020) · Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics · doi:10.3727/096504020x16056983169118 · Cited by 11

Identifying Key Somatic Copy Number Alterations Driving Dysregulation of Cancer Hallmarks in Lower-Grade Glioma

Zhou, Y., Wang, S., Yan, H., Pang, B., Zhang, X., Pang, L., Wang, Y., Xu, J., Hu, J. R., Lan, Y., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.654736 · Cited by 11

Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data

Ianevski, A., Giri, A. K., & Aittokallio, T. A. (2022) · RePEc: Research Papers in Economics · Cited by 11

Set1 Targets Genes with Essential Identity and Tumor-Suppressing Functions in Planarian Stem Cells

Verma, P., Waterbury, C. K. M., & Duncan, E. M. (2021) · Genes · doi:10.3390/genes12081182 · Cited by 11

Integrated molecular profiling of patient‐derived ovarian cancer models identifies clinically relevant signatures and tumor vulnerabilities

Lupia, M., Melocchi, V., Bizzaro, F., Riso, P. L., Dama, E., Baronio, M., Ranghiero, A., Barberis, M. C. P., Bernard, L., Bertalot, G., et al. (2022) · International Journal of Cancer · doi:10.1002/ijc.33983 · Cited by 11

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