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The mutational landscape of lethal castration-resistant prostate cancer

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frDriver: A Functional Region Driver Identification for Protein Sequence

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The genomic trajectory of ovarian high‐grade serous carcinoma can be observed in STIC lesions

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Molecular profiling reveals novel therapeutic targets and clonal evolution in ovarian clear cell carcinoma

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Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures

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An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer

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Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators

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Synthesis and cytotoxic activity evaluation of novel imidazopyridine carbohydrazide derivatives

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Pre-existing subclones determine radioresistance in rectal cancer organoids

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Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells

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Structure, function and disease relevance of Wnt inhibitory factor 1, a secreted protein controlling the Wnt and hedgehog pathways

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Pharmacogenomics to Predict Tumor Therapy Response: A Focus on ATP-Binding Cassette Transporters and Cytochromes P450

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Current cancer driver variant predictors learn to recognize driver genes instead of functional variants

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Estimating the predictive power of silent mutations on cancer classification and prognosis

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Single-cell transcriptomic mapping of intestinal epithelium that undergoes 3D morphogenesis and mechanodynamic stimulation in a gut-on-a-chip

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GMP-compliant iPS cell lines show widespread plasticity in a new set of differentiation workflows for cell replacement and cancer immunotherapy

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Tissue-specific iron levels modulate lipid peroxidation and the FLASH radiotherapy effect

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Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals

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Functional Characterization of TMEM127 Variants Reveals Novel Insights into Its Membrane Topology and Trafficking

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REBOOT: A STRAIGHTFORWARD APPROACH TO IDENTIFY GENES AND SPLICING ISOFORMS ASSOCIATED WITH CANCER PATIENT PROGNOSIS

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Development of an Interferon Gamma Response-Related Signature for Prediction of Survival in Clear Cell Renal Cell Carcinoma

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Inactivation of Hippo pathway characterizes a poor-prognosis subtype of esophageal cancer

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A Pan-Cancer Assessment of RB1/TP53 Co-Mutations

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From multi-omics data to the cancer druggable gene discovery: a novel machine learning-based approach

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Single-cell RNA binding protein regulatory network analyses reveal oncogenic HNRNPK-MYC signalling pathway in cancer

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Stochastic fate decisions of HSCs after transplantation: early contribution, symmetric expansion, and pool formation

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Identification of Cancer Driver Genes by Integrating Multiomics Data with Graph Neural Networks

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Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors

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A distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study

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3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients

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Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes

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Identifying potential risk genes for clear cell renal cell carcinoma with deep reinforcement learning

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Systematic in vitro analysis of therapy resistance in glioblastoma cell lines by integration of clonogenic survival data with multi-level molecular data

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Mining Drug-Target Associations in Cancer: Analysis of Gene Expression and Drug Activity Correlations

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annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

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High Concordance of Genomic Profiles between Primary and Metastatic Colorectal Cancer

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Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma

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SWAN pathway-network identification of common aneuploidy-based oncogenic drivers

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Enrichment of cancer-predisposing germline variants in adult and pediatric patients with acute lymphoblastic leukemia

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The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates

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Pan‐Cancer Single‐Nucleus Total RNA Sequencing Using snHH‐Seq

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Mutational mechanisms in multiply relapsed pediatric acute lymphoblastic leukemia

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A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer

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Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer

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Redesigning HVEM Interface for Selective Binding to LIGHT, BTLA, and CD160

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Dynamic Interactions of Transcription Factors and Enhancer Reprogramming in Cancer Progression

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The transcriptomic architecture of common cancers reflects synthetic lethal interactions

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Panels and models for accurate prediction of tumor mutation burden in tumor samples

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CXCR4 hyperactivation cooperates with TCL1 in CLL development and aggressiveness

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Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis

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Stage-differentiated ensemble modeling of DNA methylation landscapes uncovers salient biomarkers and prognostic signatures in colorectal cancer progression

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The close interaction between hypoxia-related proteins and metastasis in pancarcinomas

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Multi-omics integration analysis of GPCRs in pan-cancer to uncover inter-omics relationships and potential driver genes

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Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients

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Cis‐regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

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Preoperative ctDNA Levels Are Associated With Poor Overall Survival in Patients With Ovarian Cancer

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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data

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Towards simplified graph neural networks for identifying cancer driver genes in heterophilic networks

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Single-cell copy number calling and event history reconstruction

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Co-incidence of RCC-susceptibility polymorphisms with HIF cis-acting sequences supports a pathway tuning model of cancer

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Dissecting the Functional Mechanisms of Somatic Copy-Number Alterations Based on Dysregulated ceRNA Networks across Cancers

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Genome-Wide DNA Methylation and RNA Expression Differences Correlate with Invasiveness in Melanoma Cell Lines

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A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC

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The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community

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Enhancer methylation dynamics drive core transcriptional regulatory circuitry in pan-cancer

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Rationale and Roadmap for Developing Panels of Hotspot Cancer Driver Gene Mutations as Biomarkers of Cancer Risk

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Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer’s disease microglia

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Genomic landscape and molecularly informed therapy in thymic carcinoma and other advanced thymic epithelial tumors

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Clinical utility of targeted RNA sequencing in cancer molecular diagnostics

Siddaway, R., Glembocki, A. I., Arnoldo, A., Staunton, J., Liu, A. P. Y., Yuki, K. E., Yu, M., Cohen‐Gogo, S., Shlien, A., Villani, A., et al. (2025) · Nature Medicine · doi:10.1038/s41591-025-03848-8 · Cited by 19

Prediction of Metabolic Profiles from Transcriptomics Data in Human Cancer Cell Lines

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Shallow WGS of individual CTCs identifies actionable targets for informing treatment decisions in metastatic breast cancer

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Whole-Genome Sequencing Reveals Mutational Signatures Related to Radiation-Induced Sarcomas and DNA-Damage-Repair Pathways

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Enhancer remodeling drives MLL oncogene-dependent transcriptional dysregulation in leukemia stem cells

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DeepAEG: a model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies

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Integrated analysis of optical mapping and whole-genome sequencing reveals intratumoral genetic heterogeneity in metastatic lung squamous cell carcinoma

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Predictive models for stage and risk classification in head and neck squamous cell carcinoma (HNSCC)

Kumar, S., Patnaik, S., & Dixit, A. (2020) · PeerJ · doi:10.7717/peerj.9656 · Cited by 16

A Global and Integrated Analysis of CINSARC-Associated Genetic Defects

Lesluyes, T., & Chibon, F. (2020) · Cancer Research · doi:10.1158/0008-5472.can-20-0512 · Cited by 17

e-MutPath: computational modeling reveals the functional landscape of genetic mutations rewiring interactome networks

Li, Y., Burgman, B., Khatri, I. S., Pentaparthi, S. R., Su, Z., McGrail, D. J., Li, Y., Wu, E., Eckhardt, S. G., Sahni, N., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1015 · Cited by 16

Protein signatures to distinguish aggressive from indolent prostate cancer

Garcia-Marques, F. J., Liu, S., Totten, S. M., Bermudez, A., Tanimoto, C. R., Hsu, E., Nolley, R., Hembree, A., Stoyanova, T. I., Brooks, J. D., et al. (2022) · The Prostate · doi:10.1002/pros.24307 · Cited by 16

Identifying the oncogenic potential of gene fusions exploiting miRNAs

Lovino, M., Montemurro, M., Barrese, V. S., & Ficarra, E. (2022) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2022.104057 · Cited by 16

GH Action in Prostate Cancer Cells Promotes Proliferation, Limits Apoptosis, and Regulates Cancer-related Gene Expression

Unterberger, C. J., Maklakova, V. I., Lazar, M., Arneson, P. D., McIlwain, S. J., Tsourkas, P. K., Hu, R., Kopchick, J. J., Swanson, S. M., & Marker, P. C. (2022) · Endocrinology · doi:10.1210/endocr/bqac031 · Cited by 16

Dissecting the heritable risk of breast cancer: From statistical methods to susceptibility genes

Fanfani, V., Zátopková, M., Harris, A. L., Pezzella, F., & Stracquadanio, G. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.06.001 · Cited by 15

Somatic cancer variants enriched in Alzheimer’s disease microglia-like cells drive inflammatory and proliferative states

Huang, A. Y., Zhou, Z., Talukdar, M., Enyenihi, L., Miller, M. B., Chhouk, B., Rosen, I., Zheng, M., Zhou, M., Yang, A., et al. (2026) · Cell · doi:10.1016/j.cell.2026.03.040 · Cited by 15

Comparative analysis of tongue cancer organoids among patients identifies the heritable nature of minimal residual disease

Sase, M., Sato, T., Sato, H., Miya, F., Zhang, S., Haeno, H., Kajita, M., Noguchi, T., Mori, Y., & Ohteki, T. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.10.007 · Cited by 17

Biosystem Analysis of the Hypoxia Inducible Domain Family Member 2A: Implications in Cancer Biology

Salazar, C., Yáñez, O., Elorza, Á. A., Cortés, N., García‐Beltrán, O., Tiznado, W., & Ruíz, L. M. (2020) · Genes · doi:10.3390/genes11020206 · Cited by 14

Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability

Roberts, A. G. K., Catchpoole, D. R., & Kennedy, P. J. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab124 · Cited by 15

Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues

Borgsmüller, N., Valecha, M. V., Kuipers, J., Beerenwinkel, N., & Posada, D. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100380 · Cited by 16

Distinct mutational processes shape selection of MHC class I and class II mutations across primary and metastatic tumors

Mumphrey, M. B., Hosseini, N., Parolia, A., Geng, J., Zou, W., Raghavan, M., Chinnaiyan, A. M., & Cieslik, M. P. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112965 · Cited by 15

Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer

He, F., Bandyopadhyay, A. M., Klesse, L. J., Rogojina, A. T., Chun, S. H., Butler, E. B., Hartshorne, T., Holland, T., Garcia, D. K., Weldon, K. S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43373-1 · Cited by 16

Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer

Lykoskoufis, N. M. R., Planet, E., Ongen, H., Trono, D., & Dermitzakis, E. T. (2024) · Nature Communications · doi:10.1038/s41467-023-42405-0 · Cited by 14

Protein structural context of cancer mutations reveals molecular mechanisms and candidate driver genes

Pino, D. C., Badonyi, M., Semple, C. A. M., & Marsh, J. A. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114905 · Cited by 15

Deep learning analysis of histopathological images predicts immunotherapy prognosis and reveals tumour microenvironment features in non-small cell lung cancer

Wang, Y., Ju, X., Hua, R., Chen, J., Dai, X., Liu, L., Wang, G., Bai, Y., Hu, H., & Li, X. (2024) · British Journal of Cancer · doi:10.1038/s41416-024-02856-8 · Cited by 18

Aspects of Gene Therapy Products Using Current Genome-Editing Technology in Japan

Yamaguchi, T., Uchida, E., Okada, T., Ozawa, K., Onodera, M., Kume, A., Shimada, T., Takahashi, S., Tani, K., Nasu, Y., et al. (2020) · Human Gene Therapy · doi:10.1089/hum.2020.156 · Cited by 16

mTOR Inhibition Leads to Src-Mediated EGFR Internalisation and Degradation in Glioma Cells

Colella, B., Colardo, M., Iannone, G., Contadini, C., Sáiz-Ladera, C., Fuoco, C., Barilà, D., Velasco, G., Segatto, M., & Bartolomeo, S. D. (2020) · Cancers · doi:10.3390/cancers12082266 · Cited by 16

Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network

Zeng, Z., Fu, J., Cibulskis, C., Jhaveri, A., Gumbs, C. E., Das, B., Sánchez‐Espiridión, B., Janssens, S., Taing, L., Wang, J., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3251 · Cited by 14

Detection of Rare Germline Variants in the Genomes of Patients with B-Cell Neoplasms

Orgueira, A. M., López, M. C., Raíndo, A. P., Arias, J. Á. D., Rodríguez, B. A., Pérez, L. B., Vence, N. A., López, Á. B., Blanco, A. A., Valentín, P. M., et al. (2021) · Cancers · doi:10.3390/cancers13061340 · Cited by 15

Analysis of rare disruptive germline mutations in 2135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes

Loveday, C., Garrett, A., Law, P., Hanks, S., Poyastro-Pearson, E., Adlard, J., Barwell, J., Berg, J., Brady, A. F., Brewer, C., et al. (2022) · Annals of Oncology · doi:10.1016/j.annonc.2022.09.152 · Cited by 13

DiffBrainNet: Differential analyses add new insights into the response to glucocorticoids at the level of genes, networks and brain regions

Gerstner, N., Krontira, A. C., Cruceanu, C., Roeh, S., Pütz, B., Sauer, S., Rex‐Haffner, M., Schmidt, M. V., Binder, E. B., & Arloth, J. (2022) · Neurobiology of Stress · doi:10.1016/j.ynstr.2022.100496 · Cited by 10

A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects

Miller, D. B., & Piccolo, S. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.640242 · Cited by 15

Improved supervised prediction of aging-related genes via weighted dynamic network analysis

Li, Q., Newaz, K., & Milenković, T. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04439-3 · Cited by 16

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