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

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Inhibition of Mutated, Activated BRAF in Metastatic Melanoma

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The mutational landscape of lethal castration-resistant prostate cancer

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EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants

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Effects of Multi-Omics Characteristics on Identification of Driver Genes Using Machine Learning Algorithms

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Driver gene detection through Bayesian network integration of mutation and expression profiles

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Systemic circulating microRNA landscape in Lynch syndrome

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Classification and Prognosis Analysis of Pancreatic Cancer Based on DNA Methylation Profile and Clinical Information

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Whole genome and RNA sequencing analyses for 254 Taiwanese hepatocellular carcinomas

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Supervised Prediction of Aging-Related Genes From a Context-Specific Protein Interaction Subnetwork

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M6ADD: a comprehensive database of m6A modifications in diseases

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Characterizing the tumor RBP-ncRNA circuits by integrating transcriptomics, interactomics and clinical data

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How the germline informs the somatic landscape

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pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes

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Combining Mutation and Gene Network Data in a Machine Learning Approach for False-Positive Cancer Driver Gene Discovery

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OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicinePreprint

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Multi-omic stratification of the missense variant cysteinomePreprint

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DeepSom: a CNN-based approach to somatic variant calling in WGS samples without a matched normal

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Molecular Genetic Characteristics of FANCI, a Proposed New Ovarian Cancer Predisposing Gene

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Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy

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Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers

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RNA-Based Strategies for Cancer Therapy: In Silico Design and Evaluation of ASOs for Targeted Exon Skipping

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An atlas of cell-type-specific interactome networks across 44 human tumor types

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PARP inhibitors suppress tumours via centrosome error-induced senescence independent of DNA damage response

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Genetic variants for head size share genes and pathways with cancer

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Molecular models of bidirectional promoter regulation

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Proteogenomic insights into the biology and treatment of pan-melanoma

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Clinical and molecular risk factors for repeat interventions due to symptomatic uterine leiomyomas

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Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit

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Multiview representation learning for identification of novel cancer genes and their causative biological mechanisms

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Clonal Hematopoiesis and Clinical Outcomes in Metastatic Castration-Resistant Prostate Cancer Patients Given Androgen Receptor Pathway Inhibitors (Alliance A031201)

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Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets

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Strategies to include prior knowledge in omics analysis with deep neural networks

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Validation of an AI-enabled exome/transcriptome liquid biopsy platform for early detection, MRD, disease monitoring, and therapy selection for solid tumors

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Whole-Genome Methylation Study of Congenital Lung Malformations in Children

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Germline and somatic genetic variability of oxysterol-related genes in breast cancer patients with early disease of the luminal subtype

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End-to-End Learning for Image-Based Detection of Molecular Alterations in Digital Pathology

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Network Biology-Inspired Machine Learning Features Predict Cancer Gene Targets and Reveal Target Coordinating Mechanisms

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Predicting drug response through tumor deconvolution by cancer cell lines

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Estimating the Frequency of Single Point Driver Mutations across Common Solid Tumours

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Tumor suppressor genes and allele-specific expression: mechanisms and significance

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Prevalence and Spectrum of Pathogenic Germline Variants in Japanese Patients With Early-Onset Colorectal, Breast, and Prostate Cancer

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Implementing gene curation for hereditary cancer susceptibility in Australia: achieving consensus on genes with clinical utility

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Pan-Cancer Analysis of Head-to-Head Gene Pairs in Terms of Transcriptional Activity, Co-expression and Regulation

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Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis

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CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia

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A New Insight for the Identification of Oncogenic Variants in Breast and Prostate Cancers in Diverse Human Populations, With a Focus on Latinos

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driveR: a novel method for prioritizing cancer driver genes using somatic genomics data

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Clonal populations of a human TNBC model display significant functional heterogeneity and divergent growth dynamics in distinct contexts

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Histopathological and Molecular Profiling of Clear Cell Sarcoma and Correlation with Response to Crizotinib: An Exploratory Study Related to EORTC 90101 “CREATE” Trial

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Hepatocellular carcinoma after a sustained virological response by direct‐acting antivirals harbors TP53 inactivation

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Identification of NAD+ Metabolism-Derived Gene Signatures in Ovarian Cancer Prognosis and Immunotherapy

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TRIM28 congenital predisposition to Wilms’ tumor: novel mutations and presentation in a sibling pairPreprint

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How often is each gene mutated within the cancer patient population?

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A full-proteome, interaction-specific characterization of mutational hotspots across human cancersPreprint

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Leveraging Gene Redundancy to Find New Histone Drivers in Cancer

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Identifying cancer driver genes in individual tumours

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Multi-layered knowledge graph neural network reveals pathway-level agreement of three breast cancer multi-gene assays

Lee, S., Park, J., Piao, Y., Lee, D., Lee, D., & Kim, S. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.04.038 · Cited by 9

Cancer drug sensitivity estimation using modular deep Graph Neural Networks

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CancerGATE: Prediction of cancer-driver genes using graph attention autoencoders

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The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model

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Full-length transcriptome atlas of gallbladder cancer reveals trastuzumab resistance conferred by ERBB2 alternative splicing

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Tamoxifen induces PI3K activation in uterine cancer

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Genetic Factors Involved in Cardiomyopathies and in Cancer

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Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells in vivo

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Recurrent splice site mutations affect key diffuse large B-cell lymphoma genes

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Multifocal organoids reveal clonal associations between synchronous intestinal tumors with pervasive heterogeneous drug responses

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Pan-precancer and cancer DNA methylation profiles revealed significant tissue specificity of interrupted biological processes in tumorigenesis

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Genomic alterations related to HPV infection status in a cohort of Chinese prostate cancer patients

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Hierarchical graph neural network with subgraph perturbations for key gene cluster discovery in cancer staging

Hou, W., Wang, Y., Zhao, Z., Cong, Y., Pang, W., & Tian, Y. (2023) · Complex & Intelligent Systems · doi:10.1007/s40747-023-01068-6 · Cited by 10

A workflow to study mechanistic indicators for driver gene prediction with Moonlight

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Duchenne muscular dystrophy treatment with lentiviral vector containing mini‐dystrophin gene in vivo

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A large-scale cancer-specific protein–DNA interaction network

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ImmuneLENS characterizes systemic immune dysregulation in aging and cancer

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Systematically Dissecting the Function of RNA-Binding Proteins During Glioma Progression

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Age‐dependent expression of cancer‐related genes in a long‐lived seabird

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Uncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform

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Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant glioma

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Survival Time Prediction of Breast Cancer Patients Using Feature Selection Algorithm Crystall

Liu, S., Li, H., Zheng, Q., Yang, L., Duan, M., Feng, X., Li, F., Huang, L., & Zhou, F. (2021) · IEEE Access · doi:10.1109/access.2021.3054823 · Cited by 9

Findings from precision oncology in the clinic: rare, novel variants are a significant contributor to scaling molecular diagnostics

Doig, K., Love, C. G., Conway, T., Seleznev, A., Ma, D. K. G., FELLOWES, A. P., Blombery, P. A., & Fox, S. B. (2022) · BMC Medical Genomics · doi:10.1186/s12920-022-01214-y · Cited by 9

ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA

Huebner, A., Black, J. R., Sarno, F., Pazo-Cid, R., Juez, I., Medina, L., García‐Carbonero, R., Guillén‐Ponce, C., Feliú, J., Alonso, C., et al. (2023) · Genome Medicine · doi:10.1186/s13073-023-01171-w · Cited by 9

Gastric cancer actionable genomic alterations across diverse populations worldwide and pharmacogenomics strategies based on precision oncology

Echeverría‐Garcés, G., Ramos-Medina, M. J., Vargas, R., Cabrera‐Andrade, A., Altamirano-Colina, A., Freire, M. P., Montalvo-Guerrero, J., Rivera-Orellana, S., Echeverría-Espinoza, P., Quiñones, L. A., et al. (2024) · Frontiers in Pharmacology · doi:10.3389/fphar.2024.1373007 · Cited by 9

Diversity spectrum analysis identifies mutation-specific effects of cancer driver genes

Dong, X., Huang, D., Yi, X., Zhang, S., Wang, Z., Yan, B., Sham, P. C., Chen, K., & Li, M. J. (2020) · Communications Biology · doi:10.1038/s42003-019-0736-4 · Cited by 9

SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants

McCoy, M., Shivakumar, V. S., Nimmagadda, S., Jafri, M. S., & Madhavan, S. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2774-9 · Cited by 9

Learning from learning machines: a new generation of AI technology to meet the needs of sciencePreprint

Pion-Tonachini, L., Bouchard, K. E., Martín, H. G., Peisert, S., Holtz, W. B., Aswani, A. J., Dwivedi, D., Wainwright, H. M., Pilania, G., Nachman, B. P., et al. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2111.13786 · Cited by 14

A Suite of Foundation Models Captures the Contextual Interplay Between CodonsPreprint

Naghipourfar, M., Chen, S., Howard, M. K., Macdonald, C. B., Khoroshkin, M., Lee, S., Saberi, A., Hagen, T., Mofrad, M. R. K., Coyote‐Maestas, W., et al. (2024) · SSRN Electronic Journal · doi:10.1101/2024.10.10.617568 · Cited by 10

CrypticProteinDB: an integrated database of proteome and immunopeptidome derived non-canonical cancer proteins

Othoum, G., & Maher, C. A. (2023) · NAR Cancer · doi:10.1093/narcan/zcad024 · Cited by 8

Comprehensive interrogation of gene lists from genome‐scale cancer screens with oncoEnrichR

Nakken, S., Gundersen, S., Bernal, F. L. M., Polychronopoulos, D., Hovig, E. J., & Wesche, J. (2023) · International Journal of Cancer · doi:10.1002/ijc.34666 · Cited by 8

GLIMS: A two-stage gradual-learning method for cancer genes prediction using multi-omics data and co-splicing network

Niu, R., Guo, Y., & Shang, X. (2024) · iScience · doi:10.1016/j.isci.2024.109387 · Cited by 8

Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes

Cao, X., Huber, S., Ahari, A. J., Traube, F. R., Seifert, M., Oakes, C. C., Secheyko, P., Вилов, С. А., Scheller, I. F., Wagner, N., et al. (2024) · Genome Medicine · doi:10.1186/s13073-024-01331-6 · Cited by 9

Whole-exome Sequencing of Atypical Parathyroid Tumors Detects Novel and Common Genes Linked to Parathyroid Tumorigenesis

Pardi, E., Poma, A. M., Torregrossa, L., Pierotti, L., Borsari, S., Valentina, S. D., Marcocci, C., & Cetani, F. (2024) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/clinem/dgae441 · Cited by 8

The hallmarks of tissue-agnostic therapies and strategies for early anticancer drug discovery

Mun, J., & Lim, B. (2024) · Drug Discovery Today · doi:10.1016/j.drudis.2024.104203 · Cited by 9

The promising role of nanopore sequencing in cancer diagnostics and treatment

Su, X., Lin, Q., Liu, B., Zhou, C., Lu, L., Lin, Z., Si, J., Ding, Y., & Duan, S. (2025) · Cell Insight · doi:10.1016/j.cellin.2025.100229 · Cited by 8

Functional-proteomics-based investigation of the cellular response to farnesyltransferase inhibition in lung cancer

Pan, Y., Berkovska, O., Marathe, S., Mermelekas, G., Gudoitytė, G., Wolide, A. D., Arslan, T., Seashore-Ludlow, B. A., Lehtiö, J., & Orre, L. M. (2025) · iScience · doi:10.1016/j.isci.2025.111864 · Cited by 8

Nonstop mutations cause loss of renal tumor suppressor proteins VHL and BAP1 and affect multiple stages of protein translation

Pal, J., Riester, M., Ganner, A., Ghosh, A., Dhamija, S., Mookherjee, D., Voss, C., Frew, I. J., Kotsis, F., Neumann‐Haefelin, E., et al. (2025) · Science Advances · doi:10.1126/sciadv.adr6375 · Cited by 8

Proteogenomic Profiling of Treatment-Naïve Metastatic Malignant Melanoma

Kuras, M., Betancourt, L. H., Hong, R., Szadai, L., Murillo, J. R., Horvatovich, P. L., Plá, I., Eriksson, J. O., Szeitz, B., Deszcz, B., et al. (2025) · Cancers · doi:10.3390/cancers17050832 · Cited by 12

Variable Gene Copy Number in Cancer-Related Pathways Is Associated With Cancer Prevalence Across Mammals

Matthews, S., Fard, V. N., Tollis, M., & Seoighe, C. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf056 · Cited by 8

Detecting and quantifying clonal selection in somatic stem cells

Körber, V., Jakobsen, N. A., Ansari‐Pour, N., Moore, R., Claudino, N., Metzner, M., Thielecke, E., Esau, F., Usukhbayar, B., Salazar, M. A., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02217-y · Cited by 14

Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese

Zhou, D., Wu, M., Tan, Q., Sun, L., Tu, Y., Zheng, W., Zhu, Y., Yang, M., Hu, K., Hu, F., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-62459-6 · Cited by 8

Multimodal profiling of oral squamous cell carcinoma identifies genomic alterations and expression programs associated with betel quid chewing

Su, S.-C., Lin, C., Chen, M.-K., Lee, Y., Su, C., Bai, S., Jangir, H., Chuang, C., Chung, W., Chang, L., et al. (2025) · Neoplasia · doi:10.1016/j.neo.2025.101218 · Cited by 8

SynProtX: a large-scale proteomics-based deep learning model for predicting synergistic anticancer drug combinations

Boonyarit, B., Kositchutima, M., Phattalung, T. N., Yamprasert, N., Thuwajit, C., Rungrotmongkol, T., & Nutanong, S. Y. (2025) · GigaScience · doi:10.1093/gigascience/giaf080 · Cited by 7

Stable clonal contribution of lineage-restricted stem cells to human hematopoiesis

Yoshizato, T., Nilsson, C. C., Grasso, F., Högstrand, K., Mazzi, S., Winroth, A., Lehander, M., Barbosa, I., Walldin, G., Blanco, T. M., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02405-w · Cited by 8

Addressing the challenges of immunogenicity, heterogeneity and tumorigenicity in the clinical translation of human embryonic stem cells

Xia, L., Qin, J., & Ye, S. (2025) · Stem Cell Research & Therapy · doi:10.1186/s13287-025-04826-0 · Cited by 10

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