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Hallmarks of Cancer: The Next Generation

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Inhibition of Mutated, Activated BRAF in Metastatic Melanoma

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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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Exploring the anticancer potential of hydrogen sulfide and BAY‑876 on clear cell renal cell carcinoma cells: Uncovering novel mutations in VHL and KDR genes among ccRCC patients

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Clonal origin and genomic diversity in Lynch syndrome‐associated endometrial cancer with multiple synchronous tumors: Identification of the pathogenicity of MLH1 p. L582H

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Identification of a novel form of caspase-independent cell death triggered by BH3-mimetics in diffuse large B-cell lymphoma cell lines

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Network analysis of driver genes in human cancers

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SSCI: Self-Supervised Deep Learning Improves Network Structure for Cancer Driver Gene Identification

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Multiregional transcriptomic profiling provides improved prognostic insight in localized non-small cell lung cancer

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Comprehensive annotation of mutations in hallmark genes insights into structural and functional implications

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Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer

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Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data

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A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology

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KRAS mutation status integrated with RNA subtyping improves prognostic modeling in FOLFIRINOX-treated metastatic pancreatic cancer

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Development and validation of a transcription factor regulatory network‐based signature for individualized prognostic risk in lung adenocarcinoma

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Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection

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Joint analysis of single‐cell and bulk tissue sequencing data to infer intratumor heterogeneity

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Biomarker Identification for Liver Hepatocellular Carcinoma and Cholangiocarcinoma Based on Gene Regulatory Network Analysis

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Regulatory patterns analysis of transcription factor binding site clustered regions and identification of key genes in endometrial cancer

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A case report of malignant neuroectodermal tumor of the gastrointestinal tract without common gene fusion in a soft tissue tumor

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Systematic analysis of cancer‐specific synthetic lethal interactions provides insight into personalized anticancer therapy

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Recurrent missense variants in clonal hematopoiesis‐related genes present in the general population

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Analysis of single-nucleotide polymorphisms in genes associated with triple-negative breast cancer

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Analysis of circulating tumor DNA during checkpoint inhibition in metastatic melanoma using a tumor-agnostic panel

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Completing a genomic characterisation of microscopic tumour samples with copy number

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Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data

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Aberrant PRDM2 methylation as an early event in serrated lesions destined to evolve into microsatellite‐instable colorectal cancers

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Early Diagnostic Markers for Esophageal Squamous Cell Carcinoma: Copy Number Alteration Gene Identification and cfDNA Detection

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Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors

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Accurate differential analysis of transcription factor activity from gene expression

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The Landscape of Long Non-Coding RNA Dysregulation and Clinical Relevance in Muscle Invasive Bladder Urothelial Carcinoma

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Distribution of cancer genes in human chromosomes

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Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses

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Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation

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A phase II study of efficacy, toxicity, and the potential impact of genomic alterations on response to eribulin mesylate in combination with trastuzumab and pertuzumab in women with human epidermal growth factor receptor 2 (HER2)+ metastatic breast cancer

Balch, S., Vaz-Luís, I., Li, T., Tayob, N., Jain, E., Helvie, K. E., Buendia-Buendia, J. E., Shannon, E. E., Isakoff, S. J., Tung, N., et al. (2021) · Breast Cancer Research and Treatment · doi:10.1007/s10549-021-06329-x · Cited by 4

Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces

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Suppression of MiR130a-3p Using CRISPR/Cas9 Induces Proliferation and Migration of Non-Small Cell Lung Cancer Cell Line

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Integrative Data Analytic Framework to Enhance Cancer Precision Medicine

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An evolutionarily conserved mechanism that amplifies the effect of deleterious mutations in osteosarcoma

Jiang, Y., Ge, F., Sun, G., & Wang, H. (2022) · Molecular Genetics and Genomics · doi:10.1007/s00438-021-01852-4 · Cited by 4

The pivotal role of sampling recurrent tumors in the precision care of patients with tumors of the central nervous systemPreprint

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Principal component analysis of RNA-seq data unveils a novel prostate cancer-associated gene expression signaturePreprint

Perera, Y., Gonzalez, A., & Perez, R. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.26.355750 · Cited by 4

Widespread redundancy in -omics profiles of cancer mutation statesPreprint

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Somatic mutations reveal hypermutable brains and are associated with neuropsychiatric disordersPreprint

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A genetic basis for cancer sex differences revealed in Xp11 translocation renal cell carcinomaPreprint

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Histopathology-assisted proteogenomics provides foundations for stratification of melanoma metastasesPreprint

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A shift from pleiotropic to modular adaptation revealed by a high-resolution two-step adaptive walkPreprint

Kinsler, G., Li, Y., Sherlock, G. J., & Petrov, D. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.17.589938 · Cited by 4

Differential somatic coding variant landscapes between laser microdissected luminal epithelial cells from canine mammary invasive ductal solid carcinoma and comedocarcinoma

Deckwirth, V., Hundi, S., Hytönen, M. K., Hannula, S., Ellonen, P., Björkenheim, P., Sukura, A., & Lohi, H. (2024) · BMC Cancer · doi:10.1186/s12885-024-13239-w · Cited by 3

MONet: cancer driver gene identification algorithm based on integrated analysis of multi-omics data and network models

Ren, Y., Zhang, T., Liu, J., Ma, F., Chen, J., Li, P., Xiao, G., Sun, C., & Zhang, Y. (2025) · Experimental Biology and Medicine · doi:10.3389/ebm.2025.10399 · Cited by 4

A multi-objective artificial bee colony approach for identifying cancer driver pathways

Rodríguez-Bejarano, F. M., Vega-Rodríguez, M. A., & Santander‐Jiménez, S. (2025) · Expert Systems with Applications · doi:10.1016/j.eswa.2025.127071 · Cited by 3

Genetic predictors of unexpected recurrence in low-risk endometrial cancer: A comprehensive genomic analysis reveals FGFR2 as a risk factor and a rare fatal POLE-mutated recurrence

Mettälä, T., Joutsiniemi, T., Huvila, J. K., & Hietanen, S. (2025) · Gynecologic Oncology · doi:10.1016/j.ygyno.2025.03.038 · Cited by 3

Genetics of canine cancer: a guide for the veterinary oncologist

Arendt, M. L., van der Heiden, A. D., Pensch, R., & Lindblad‐Toh, K. (2025) · Veterinary oncology. · doi:10.1186/s44356-025-00021-8 · Cited by 3

A base editing platform for the correction of cancer driver mutations unmasks conserved p53 transcription programs

Wang, P., Sen, R., Buchholz, F., & Sayed, S. (2025) · Genome biology · doi:10.1186/s13059-025-03667-7 · Cited by 5

Cancer Genomic Alterations and Microenvironmental Features Encode Synergistic Interactions with Disease Outcomes

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MLGCN-Driver: a cancer driver gene identification method based on multi-layer graph convolutional neural network

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Patient-specific sequencing panels enable sensitive circulating tumor DNA analysis in rhabdomyosarcoma independent of genetic profile

Rahmqvist, I., Rudin, A. D., Mellström, E., Ibrahim, R. R., Andersson, D., Calderón, F. P., Redfors, A. O., Rostamzadeh, N., Franssila, W., Karlsson, C., et al. (2025) · npj Precision Oncology · doi:10.1038/s41698-025-01147-6 · Cited by 3

Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome

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A meta-analysis of experimentally validated neo-epitopes: patterns, biases, and opportunities

Sette, A., Carri, I., Marrama, D., Frentzen, A., Mahita, J., Blazeska, N., Vita, R., Nielsen, M., Wan, Y.-T. R., Carter, H. K., et al. (2025) · Cancer Immunology Immunotherapy · doi:10.1007/s00262-025-04209-7 · Cited by 3

ClinMAVE: a curated database for clinical application of data from multiplexed assays of variant effect

Ma, C., Zhao, L., Tang, X., Li, P., Li, L., Wang, S., Wu, J., Luo, L., Liu, Y., Zhang, Z., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1102 · Cited by 7

A novel statistical feature selection framework for biomarker discovery and cancer classification via multiomics integration

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DNA mutation rates in evolution, longevity, and disease: An evolutionary and biological trade-off

Cao, D., Zeng, C., & Ren, R. (2026) · Cell investigation. · doi:10.1016/j.clnves.2026.100061 · Cited by 3

An interpretable molecular framework for predicting cancer driver missense mutations

Yang, Y., Sun, W., Liu, Y., Zhang, J., & Li, M. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2524289123 · Cited by 3

Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types

Everall, A., Tapinos, A., Hawari, A., Cornish, A. J., Sud, A., Chubb, D., Kinnersley, B., Frangou, A., Barquín, M., Jung, J., et al. (2026) · Nature Genetics · doi:10.1038/s41588-025-02474-x · Cited by 27

Acute megakaryoblastic leukaemia shows high frequency of chromosome 1q aberrations and dismal outcome

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Detecting biased validation of predictive models in the positive-unlabeled setting: disease gene prioritization case study

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A framework for considering prior information in network‐based approaches to omics data analysis

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Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models

Han, Z., Yu, G., & Yang, Y. (2023) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm58861.2023.10385593 · Cited by 3

Identifying genes associated with disease outcomes using joint sparse canonical correlation analysis—An application in renal clear cell carcinoma

Dutta, D., Sen, A., & Satagopan, J. M. (2024) · Genetic Epidemiology · doi:10.1002/gepi.22566 · Cited by 3

The longitudinal kinetics of AAV5 vector integration profiles and evaluation of clonal expansion in mice

Ismail, A. M., Witt, E., Bouwman, T., Clark, W. T., Yates, B., Franco, M., & Fong, S. (2024) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2024.101294 · Cited by 3

Evaluation of the gene fusion landscape in early onset sporadic rectal cancer reveals association with chromatin architecture and genome stability

Gupta, A., Avadhanula, S., & Bashyam, M. D. (2024) · Oncogene · doi:10.1038/s41388-024-03088-z · Cited by 4

INDELpred: Improving the prediction and interpretation of indel pathogenicity within the clinical genome

Wei, Y., Zhang, T., Wang, B., Jiang, X., Ling, F., Fang, M., Jin, X., & Bai, Y. (2024) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2024.100325 · Cited by 3

Evolutionary dependency of cancer mutations in gene pairs inferred by nonsynonymous-synonymous mutation ratios

Han, D., Kim, S., Lee, S., Moon, Y., Kang, S. J., Yoo, J., Jeong, H. Y., Cho, H. J., Jeon, J. Y., Sim, B. C., et al. (2024) · Genome Medicine · doi:10.1186/s13073-024-01376-7 · Cited by 3

A review and perspective paper: Ras oncogene gets modest, from kingpin to mere henchman

Camonis, J., Aushev, V. N., Zueva, E., & Zalcman, G. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05449-z · Cited by 3

Whole-exome sequencing reveals novel genomic signatures and potential therapeutic targets during the progression of rectal neuroendocrine neoplasm

Shi, X., Zhai, Z. Y., Zhou, P., Xue, X. F., Huang, Z. Y., Li, X. X., Yang, G. H., Bao, C. J., You, L. J., Cui, X. B., et al. (2024) · Cell Death and Disease · doi:10.1038/s41419-024-07232-1 · Cited by 3

Proximity Proteomics Reveals USP44 Forms a Complex with BRCA2 in Neuroblastoma Cells and Is Required to Prevent Chromosome Breakage

Ali, A., Hussain, S., Bedekovics, T., Jeon, R. H., May, D. G., Roux, K. J., & Galardy, P. J. (2024) · Biomedicines · doi:10.3390/biomedicines12122901 · Cited by 3

An ensemble machine learning-based performance evaluation identifies top In-Silico pathogenicity prediction methods that best classify driver mutations in cancer

Das, S. K., Patel, V., Chakravarty, S., Ghosh, A., Mukhopadhyay, A., & Biswas, N. K. (2025) · BioData Mining · doi:10.1186/s13040-024-00420-x · Cited by 6

Biophysical Properties of Somatic Cancer Mutations in the S4 Transmembrane Segment of the Human Voltage-Gated Proton Channel hHV1

Jardin, C., Derst, C., Franzen, A., Mahorivska, I., DeCoursey, T. E., Musset, B., & Chaves, G. (2025) · Biomolecules · doi:10.3390/biom15020156 · Cited by 5

Integrating edge features and complementary attention mechanism for drug response prediction

Li, C., Wang, M., Tang, C., & Zhu, Y. (2025) · Knowledge-Based Systems · doi:10.1016/j.knosys.2025.113508 · Cited by 3

Progression of Follicular Thyroid Carcinomas to Anaplastic Thyroid Carcinomas: Molecular and Clinicopathologic Characteristics with Comparison to Papillary Thyroid Carcinoma-Derived Anaplastic Thyroid Carcinomas

Odate, T., Kondo, T., Katoh, R., Ito, K., Ueno, T., Yatabe, Y., & Mori, T. (2025) · Endocrine Pathology · doi:10.1007/s12022-025-09875-y · Cited by 3

Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples

Zhang, C., El-Kebir, M., & Ochoa, I. (2021) · Nature Communications · doi:10.1038/s41467-021-22466-9 · Cited by 3

Network-Based Analysis to Identify Drivers of Metastatic Prostate Cancer Using GoNetic

van Brienen, L. D. S., Miclotte, G., Larmuseau, M., den Eynden, J. V., & Kathleen Marchal, D. (2021) · Cancers · doi:10.3390/cancers13215291 · Cited by 3

A Network-Centric Framework for the Evaluation of Mutual Exclusivity Tests on Cancer Drivers

Ahmed, R., Erten, C., Houdjedj, A., Kazan, H., & Yalçın, C. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.746495 · Cited by 3

Design of a targeted next‐generation DNA sequencing panel for pediatric T‐cell lymphoblastic lymphoma to unravel biology and optimize treatment

Ruether, C., Wünsch, C., Randau, G., Michgehl, U., Trautmann, M., Hartmann, W., Sandmann, S., Dugas, M., Khanam, T., & Burkhardt, B. (2022) · Genes Chromosomes and Cancer · doi:10.1002/gcc.23037 · Cited by 3

Comparative Analysis Between Cellular Oncogenes and Viral Oncogenes

(2020) · Biointerface Research in Applied Chemistry · doi:10.33263/briac113.99399951 · Cited by 3

Complex Disease Genes Identification Using a Heterogeneous Network Embedding Approach

Ghasemi, M., Rahgozar, M., & Kavousi, K. (2022) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2022.3175598 · Cited by 3

Characterization of the Functional Interplay between the BRD7 and BRD9 Homologues in mSWI/SNF Complexes

Agbo, L., Loehr, J., Tchara, P.-E. K., & Lambert, J. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00464 · Cited by 3

Functional Profiling of Soft Tissue Sarcoma Using Mechanistic Models

Payá‐Milans, M., Peña-Chilet, M., Loucera, C., Esteban‐Medina, M., & Dopazo, J. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241914732 · Cited by 3

DriverMP enables improved identification of cancer driver genes

Liu, Y., Han, J., Kong, T., Xiao, N., Mei, Q., & Liu, J. (2022) · GigaScience · doi:10.1093/gigascience/giad106 · Cited by 2

KDProg: A Knowledge distillation graph neural network for cancer prognosis prediction and analysis

Xiong, S., Wang, Z., Zhang, J., Luo, H., Zhang, Y., & Zou, Q. (2023) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm58861.2023.10386037 · Cited by 3

STAT3 is a genetic modifier of TGF-beta induced EMT in KRAS mutant pancreatic cancer

D’Amico, S., Kirillov, V., Petrenko, O., & Reich, N. C. (2024) · eLife · doi:10.7554/elife.92559 · Cited by 11

CRISPR/Cas9 targeting of passenger single nucleotide variants in haploinsufficient or essential genes expands cancer therapy prospects

Kim, H.-D., Han, J. H., Kim, M., Kim, M., Jo, S.-I., Lee, N., Cha, S., Oh, M. J., Choi, G., & Kim, H. S. (2024) · Scientific Reports · doi:10.1038/s41598-024-58094-8 · Cited by 3

Rev1 overexpression accelerates N‐methyl‐N‐nitrosourea (MNU)‐induced thymic lymphoma by increasing mutagenesis

Sasatani, M., Xi, Y., Daino, K., Ishikawa, A., Masuda, Y., Kajimura, J., Piao, J., Zaharieva, E. K., Honda, H., Zhou, G., et al. (2024) · Cancer Science · doi:10.1111/cas.16159 · Cited by 3

Enhanced Sampling Molecular Dynamics Simulations Reveal Transport Mechanism of Glycoconjugate Drugs through GLUT1

Liu, Z., Cao, X., Ma, Z., Xu, L., Wang, L., Li, J., Xiao, M., & Jiang, X. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25105486 · Cited by 4

Clinical relevance of somatic mutations in Chinese lung adenocarcinoma and their prognostic implications for survival

Li, T., Liu, J., Zhou, Y., Huang, S., Wang, D., Chen, J., Fu, Y., & He, P. (2024) · Cancer Medicine · doi:10.1002/cam4.7227 · Cited by 2

Mutations, substitutions, and selection: Linking mutagenic processes to cancer using evolutionary theory

Cannataro, V. L., Glasmacher, K. A., & Hampson, C. E. (2024) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2024.167268 · Cited by 3

Identifying actionable synthetically lethal cancer gene pairs using mutual exclusivity

Wooller, S. K., Pearl, L. H., & Pearl, F. M. G. (2024) · FEBS Letters · doi:10.1002/1873-3468.14950 · Cited by 3

HYENA detects oncogenes activated by distal enhancers in cancer

Yu, A., Yesilkanal, A. E., Thakur, A., Wang, F., Yang, Y., Phillips, W., Wu, X., Muir, A., He, X., Spitz, F., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae646 · Cited by 2

Predictive biomarkers for metachronous gastric cancer development after endoscopic resection of early gastric cancer

Kim, B., Chun, H., Lee, J. W., Park, M., Kwak, Y., Kim, J. M., Kim, S. G., Ryu, J. K., Choi, J., & Cho, S. (2024) · Cancer Medicine · doi:10.1002/cam4.70104 · Cited by 3

ECGA: A web server to explore and analyze extrachromosomal gene in cancer

Zhou, N., Peng, L., Zhang, Z., Luo, Q., Sun, H., Bao, J., Ning, Y., & Yuan, X. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.11.009 · Cited by 3

Characterization of cancer-driving nucleotides (CDNs) across genes, cancer types, and patients

Zhang, L., Deng, T., Liufu, Z., Chen, X., Wu, S., Liu, X., Shi, C., Chen, B., Hu, Z., Cai, Q., et al. (2024) · eLife · doi:10.7554/elife.99341.3 · Cited by 3

Personalized prediction of anticancer potential of non-oncology drugs through learning from genome derived molecular pathways

Dong, X., Liu, H., Tong, T., Wu, L., Wang, J., You, T., Wei, Y., Yi, X., Yang, H., Hu, J., et al. (2025) · npj Precision Oncology · doi:10.1038/s41698-025-00813-z · Cited by 4

Clinical syndromes linked to biallelic germline variants in MCM8 and MCM9

Helderman, N. C., Yang, T., Palles, C., Terlouw, D., Mei, H., Vorderman, R. H. P., Cats, D., Díaz‐Gay, M., Jongmans, M. C. J., Ramdien, A., et al. (2025) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2025.100480 · Cited by 3

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