npj Precision Oncology

Article	Citations
An automated deep learning pipeline for EMVI classification and response prediction of rectal cancer using baseline MRI: a multi-centre study	289
Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers	140
Imaging and AI based chromatin biomarkers for diagnosis and therapy evaluation from liquid biopsies	127
The dynamic immune behavior of primary and metastatic ovarian carcinoma	116
KMT2C inactivation leads to PTEN downregulation and tolerance to DNA damage during cell cycle progression	113
Mucin-1: a promising pan-cancer therapeutic target	113
MYSM1 promotes lung adenocarcinoma progression via TRAF2/3-mediated activation of MAPK and non-canonical NF-κB pathways	111
Sub-regional radiomics combining multichannel 2-dimensional or 3-dimensional deep learning for predicting neoadjuvant chemo-immunotherapy response in esophageal squamous cell carcinoma: a multicenter	105
Exosome- transported FER inhibitor suppresses progression of diffuse large B-cell lymphoma via regulating AJUBA/Hippo axis	105
Improved prediction of MAPKi response duration in melanoma patients using genomic data and machine learning	86
Multi-modal characterization of metabolic and immune gene clusters in adrenocortical carcinoma treatment	70
Complement activation in tumor microenvironment after neoadjuvant therapy and its impact on pancreatic cancer outcomes	66
Constitutional mismatch repair deficiency mimicking Lynch syndrome is associated with hypomorphic mismatch repair gene variants	62
Development and testing of a polygenic risk score for breast cancer aggressiveness	62
A protein-encoding CCDC7 circular RNA inhibits the progression of prostate cancer by up-regulating FLRT3	59
Developing survival prediction models in colorectal cancer using epigenome-wide DNA methylation data from whole blood	58
A perspective on life-cycle health technology assessment and real-world evidence for precision oncology in Canada	58
Author Correction: An automated deep learning pipeline for EMVI classification and response prediction of rectal cancer using baseline MRI: a multi-centre study	56
Co-targeting KRAS G12C and EGFR reduces both mutant and wild-type RAS-GTP	55
Analyses of canine cancer mutations and treatment outcomes using real-world clinico-genomics data of 2119 dogs	55
Circulating tumor DNA in ALK-positive anaplastic large cell lymphoma: a proof-of-concept study	55
Patient-level proteomic network prediction by explainable artificial intelligence	53
Grading of lung adenocarcinomas with simultaneous segmentation by artificial intelligence (GLASS-AI)	52
Interferon signaling and ferroptosis in tumor immunology and therapy	51
Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog and NIPAL1	51

Assessment of TROP2, CEACAM5 and DLL3 in metastatic prostate cancer: Expression landscape and molecular correlates	50
Barriers and opportunities in pancreatic cancer immunotherapy	50
BRAF v600E–mutant cancers treated with vemurafenib alone or in combination with everolimus, sorafenib, or crizotinib or with paclitaxel and carboplatin (VEM-PLUS) study	48
Erigoster B targeting DECR1 induces ferroptosis of breast cancer cells via promoting phosphatidylcholine/arachidonic acid metabolism	47
Multiregional transcriptomic profiling provides improved prognostic insight in localized non-small cell lung cancer	47
User-centered design approach to visualize PROMs for molecular tumor boards	46
Enhanced efficacy of ipilimumab plus nivolumab in angiogenic subtypes of metastatic clear-cell renal cell carcinoma	45
Establishing predictive machine learning models for drug responses in patient derived cell culture	45
Histological transformation to gliosarcoma with combined BRAF/MEK inhibition in BRAF V600E mutated glioblastoma	44
Real-world experience of Molecular Tumour Boards for clinical decision-making for cancer patients	44
ECM-based molecular subtypes define prognostic, EMT status, and therapeutic diversity in IDH-mutant gliomas	43
Machine learning model for predicting tertiary lymphoid structures and treatment response in triple-negative breast cancer	42
Collagen disorder architecture features are associated with clinical, molecular, genetic factors and survival outcomes in colon cancer	42
TRIM65 regulates glucose metabolic reprogramming to promote glioma cell proliferation via ubiquitination and degradation of AMPK	42
Pan-cancer molecular tumor board experience with biomarker-driven precision immunotherapy	42
First-in-human prospective trial of sonobiopsy in high-grade glioma patients using neuronavigation-guided focused ultrasound	41
Self-supervised attention-based deep learning for pan-cancer mutation prediction from histopathology	40
Baseline biomarkers of efficacy and on-treatment immune-profile changes associated with bempegaldesleukin plus nivolumab	40
PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127+ and KLRG1+ CD8 T cells	40
Stage-dependent spatial distribution and prognostic value of CD8+ tissue-resident memory T cells in NSCLC	39
Prolonged response to dual immune checkpoint blockade in patients with advanced solid tumors: a case series	38
Single-cell landscape of bronchoalveolar immune cells in patients with immune checkpoint inhibitor-related pneumonitis	37
m6A reader IGF2BP2-stabilized lncRNA LHX1-DT inhibits renal cell carcinoma (RCC) cell proliferation and invasion by sponging miR-590-5p	37
Targeting Nrf2/PHKG2 axis to enhance radiosensitivity in NSCLC	36
Relationship among DDR gene mutations, TMB and PD-L1 in solid tumour genomes identified using clinically actionable biomarker assays	35
An international multi-institutional validation study of the algorithm for prostate cancer detection and Gleason grading	35
Discovery of prognostic lncRNAs in colorectal cancer using spatial transcriptomics	35
Genomic and transcriptomic analyses identify distinctive features of triple-negative inflammatory breast cancer	35
A universal immunohistochemistry analyzer for generalizing AI-driven assessment of immunohistochemistry across immunostains and cancer types	35
Author Correction: Imaging and AI based chromatin biomarkers for diagnosis and therapy evaluation from liquid biopsies	34
Multi-omics machine learning to study host-microbiome interactions in early-onset colorectal cancer	34
Novel molecular subtypes of METex14 non-small cell lung cancer with distinct biological and clinical significance	33
A core driver gene set identified based on geMER reveals its potential driver mechanism in pan-cancer	33
Deciphering associations between three RNA splicing-related genetic variants and lung cancer risk	33
Tumor fraction-based prognostic tool for cancer patients referred to early phase clinical trials	31
ML-based sequential analysis to assist selection between VMP and RD for newly diagnosed multiple myeloma	31
In-depth inference of transcriptional regulatory networks reveals NPM1 as a therapeutic ribosomal regulator in MYC-amplified medulloblastoma	30
Mediator kinase inhibition impedes transcriptional plasticity and prevents resistance to ERK/MAPK-targeted therapy in KRAS-mutant cancers	30
Prediction of homologous recombination deficiency identifies colorectal tumors sensitive to PARP inhibition	30
AI-driven eyelid tumor classification in ocular oncology using proteomic data	30
Leveraging patient derived models of FGFR2 fusion positive intrahepatic cholangiocarcinoma to identify synergistic therapies	30
A large-scale, multi-centre validation study of an AI-empowered blood-based test for multi-cancer early detection	30
HER3 targeting augments the efficacy of panobinostat in claudin-low triple-negative breast cancer cells	29
Progress in personalized immunotherapy for patients with brain metastasis	29
Enhancing adoptive cell therapy: future strategies for immune cell radioprotection in neuro-oncology	29
Deep learning-based quantification of eosinophils and lymphocytes shows complementary prognostic effects in colorectal cancer patients	28
Compound heterozygous MSH3 germline variants and associated tumor somatic DNA mismatch repair dysfunction	28
A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer	28
The SMARCA4R1157W mutation facilitates chromatin remodeling and confers PRMT1/SMARCA4 inhibitors sensitivity in colorectal cancer	28
Selpercatinib combination with the mitochondria-targeted antioxidant MitoQ effectively suppresses RET–mutant thyroid cancer	28

Machine learning algorithms for predicting glioma patient prognosis based on CD163+FPR3+ macrophage signature	28
Role of large language models in the multidisciplinary decision-making process for patients with renal cell carcinoma: a pilot experience	27
Predicting ROS1 and ALK fusions in NSCLC from H&E slides with a two-step vision transformer approach	27
Plasma proteomic biomarkers predict therapeutic responses in advanced biliary tract cancer patients receiving Camrelizumab plus the GEMOX treatment	27
Activation of CD44/PAK1/AKT signaling promotes resistance to FGFR1 inhibition in squamous-cell lung cancer	26
CNTNAP4 signaling regulates osteosarcoma disease progression	26
Artificial intelligence-based epigenomic, transcriptomic and histologic signatures of tobacco use in oral squamous cell carcinoma	26
ChemoID-guided therapy improves objective response rate in recurrent platinum-resistant ovarian cancer randomized clinical trial	26
Colorectal cancer risk stratification on histological slides based on survival curves predicted by deep learning	25
Multi-output prediction of dose–response curves enables drug repositioning and biomarker discovery	25
A patient-designed tissue-engineered model of the infiltrative glioblastoma microenvironment	25
Efficacy of PARP inhibitor therapy after targeted BRAF/MEK failure in advanced melanoma	25
Unlocking the potential of TIGIT in enhancing therapeutic strategies for acute myeloid leukemia through combined azacitidine therapy	25
MDM2 inhibition is associated with the emergence of TP53-altered clonal hematopoiesis	25
Augmented reality microscopy to bridge trust between AI and pathologists	24
Artificial intelligence-based assessment of PD-L1 expression in diffuse large B cell lymphoma	24
Potential of pre-diagnostic metabolomics for colorectal cancer risk assessment or early detection	24
Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration	24
A multimodal fusion system predicting survival benefits of immune checkpoint inhibitors in unresectable hepatocellular carcinoma	24
A multi-cancer early detection blood test using machine learning detects early-stage cancers lacking USPSTF-recommended screening	23
ALK fusions in the pan-cancer setting: another tumor-agnostic target?	23
Perfusion-based ex vivo culture of frozen ovarian cancer tissues with preserved tumor microenvironment	23
Personalized prediction of anticancer potential of non-oncology drugs through learning from genome derived molecular pathways	22
PUM1-TRAF3 fusion protein activates non-canonical NF-κB signaling via rescued NIK in biliary tract cancer	22
Multicenter radio-multiomic analysis for predicting breast cancer outcome and unravelling imaging-biological connection	22
Cancer-related cells and oncosomes in the liquid biopsy of pancreatic cancer patients undergoing surgery	22
Genetic and oncogenic features of RASGRF fusions	22
Striking efficacy of a vaccine targeting TOP2A for triple-negative breast cancer immunoprevention	22
Transcriptional profiling clarifies a program of enzalutamide extreme non-response in lethal prostate cancer	22
Potential utility of risk stratification for multicancer screening with liquid biopsy tests	22
Germline pathogenic variants in DNA repair pathways: a key feature in a significant subset of translocation-associated sarcomas	22
Complete morphologic response to gilteritinib in ALK-rearranged acute myeloid leukemia	22
LINE1 insertion into the NACC2 locus disrupts the HDM2 axis and activates lung oncogenic signaling	21
ARHGAP4/MYH9/β-catenin/c-Jun positive feedback loop promotes colorectal cancer stemness	21
Chemokine expression predicts T cell-inflammation and improved survival with checkpoint inhibition across solid cancers	21
Personalized circulating tumor DNA dynamics inform survival and response to immune checkpoint blockade in recurrent/metastatic head and neck cancer	21
APOE-high myeloid cells are uniquely associated with metastatic intrathoracic lymph nodes obtained by EBUS-TBNA in primary lung cancer	21
Clock pathway inhibitor overcomes tumor immune-exclusion via regulation of fibrocyte differentiation	21
Author Correction: A targetable OSGIN1–AMPK–SLC2A3 axis controls the vulnerability of ovarian cancer to ferroptosis	21
Functional cure with single agent olutasidenib in relapsed IDH1/NPM1 co-mutated AML	20
Use of PSMA PET/CT to detect prostate cancer metastatic to a preexisting thyroid nodule	20
High TGF-β signature predicts immunotherapy resistance in gynecologic cancer patients treated with immune checkpoint inhibition	20
Whole-genome analysis of an aggressive metastatic pancreatic solid pseudopapillary neoplasm	20
Ligand-receptor interactions combined with histopathology for improved prognostic modeling in HPV-negative head and neck squamous cell carcinoma	20
Development and interpretation of a multimodal predictive model for prognosis of gastrointestinal stromal tumor	20
Novel paediatric case of a spinal high-grade astrocytoma with piloid features in a patient with Noonan Syndrome	19
GD2: hopes and challenges for the treatment of pediatric patients with tumors of the central nervous system	19
Progress and challenges of artificial intelligence in lung cancer clinical translation	19
Integrative analysis of KEAP1/NFE2L2 alterations across 3600+ tumors reveals an NRF2 expression signature as a prognostic biomarker in cancer	19
Evaluating cell culture reliability in pediatric brain tumor primary cells through DNA methylation profiling	19
Predicting survival in prospective clinical trials using weakly-supervised QSP	19
Complete response to fifth-line anti-PD-1 rechallenge in fumarate hydratase-mutated papillary renal cell carcinoma	19
Exceptional response to the ATR inhibitor, camonsertib, in a patient with ALT+ metastatic melanoma	19
Multi-omics analyses reveal interactions between GREM1+ fibroblasts and SPP1+ macrophages in gastric cancer	19
Tertiary lymphoid structures potentially promote immune checkpoint inhibitor response in SMARCB1-deficient medullary renal cell carcinoma	19
Opportunities and challenges for patient-derived models of brain tumors in functional precision medicine	18
Imaging immunity in patients with cancer using positron emission tomography	18
The drug efficacy testing in 3D cultures platform identifies effective drugs for ovarian cancer patients	18
NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology	18
Design of self-assembled micelles based on natural dual-targeting strategies and evaluation of their anti-liver cancer effects as drug delivery systems	18
Author Correction: Predicting the tumor microenvironment composition and immunotherapy response in non-small cell lung cancer from digital histopathology images	18
Machine learning-driven multi-targeted drug discovery in colon cancer using biomarker signatures	18
Real life outcome analysis of breast cancer brain metastases treated with Trastuzumab Deruxtecan	18
A review of machine learning methods for cancer characterization from microbiome data	18
Development of potent antibody drug conjugates against ICAM1+ cancer cells in preclinical models of cholangiocarcinoma	18
Tackling FGFR3-driven bladder cancer with a promising synergistic FGFR/HDAC targeted therapy	18
Towards precision radiation oncology: endocrine therapy response as a biomarker for personalization of breast radiotherapy	17
Integrative whole slide image and spatial transcriptomics analysis with QuST and QuPath	17
HDAC6 facilitates LUAD progression by inducing EMT and enhancing macrophage polarization towards the M2 phenotype	17
A destabilizing Y891D mutation in activated EGFR impairs sensitivity to kinase inhibition	17
Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning	17
An appraisal of genetic testing for prostate cancer susceptibility	17
Element-specific estimation of background mutation rates in whole cancer genomes through transfer learning	17
Secrets of DNA-PKcs beyond DNA repair	17
A comprehensive analysis of minimally differentially methylated regions common to pediatric and adult solid tumors	17
Biallelic EPCAM deletions induce tissue-specific DNA repair deficiency and cancer predisposition	17
Impact of TP53 mutations in Triple Negative Breast Cancer	17
Precision immuno-oncology approach for four malignant tumors in siblings with constitutional mismatch repair deficiency syndrome	17
Single-cell transcriptome analysis identifies MIF as a novel tumor-associated neutrophil marker for pancreatic ductal adenocarcinoma	16
Comprehensive genetic profiling and molecularly guided treatment for patients with primary CNS tumors	16

DNA methylation at quantitative trait loci (mQTLs) varies with cell type and nonheritable factors and may improve breast cancer risk assessment	16
Integrative molecular analyses define correlates of high B7-H3 expression in metastatic castrate-resistant prostate cancer	16
Single-cell analysis of gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity	16
Plasma epigenomic profiling reveals treatment-emergent squamous transformation in prostate cancer	16
Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma	16
Defining the extracellular matrix for targeted immunotherapy in adult and pediatric brain cancer	15
Single-cell transcriptome sequencing reveals spatial distribution of IL34+ cancer-associated fibroblasts in hepatocellular carcinoma tumor microenvironment	15
Pre-radiotherapy ctDNA liquid biopsy for risk stratification of oligometastatic non-small cell lung cancer	15
Multi-omics analysis reveals NNMT as a master metabolic regulator of metastasis in esophageal squamous cell carcinoma	15
Spatial tumor immune microenvironment phenotypes in ovarian cancer	15
Multimodal spatial proteomic profiling in acute myeloid leukemia	15
A phase II trial of mTORC1/2 inhibition in STK11 deficient non small cell lung cancer	15
Deep learning-based detection and semi-quantitative model for spread through air spaces (STAS) in lung adenocarcinoma	15
HAPIR: a refined Hallmark gene set-based machine learning approach for predicting immunotherapy response in cancer patients	14
Author Correction: An interpretable machine learning system for colorectal cancer diagnosis from pathology slides	14
Identification of novel prognostic and predictive biomarkers in salivary duct carcinoma via comprehensive molecular profiling	14
Survival-inferred fragility of statistical significance in phase III oncology trials	14
Complete response to alectinib in ALK-fusion metastatic salivary ductal carcinoma	14
All models are wrong and yours are useless: making clinical prediction models impactful for patients	14
Collision of germline POLE and PMS2 variants in a young patient treated with immune checkpoint inhibitors	14
Multi-omics analysis deciphers intercellular communication regulating oxidative stress to promote oral squamous cell carcinoma progression	14
Accurate prediction of disease-free and overall survival in non-small cell lung cancer using patient-level multimodal weakly supervised learning	14
Integrating histopathology and transcriptomics for spatial tumor microenvironment profiling in a melanoma case study	14
Emerging innovations in theranostics for pancreatic neuroendocrine tumors	14
Latent class analysis-derived classification improves the cancer-specific death stratification of molecular subtyping in colorectal cancer	14
Methylation cytometric pretreatment blood immune profiles with tumor mutation burden as prognostic indicators for survival outcomes in head and neck cancer patients on anti-PD-1 therapy	14
Prediction and analysis of tumor infiltrating lymphocytes across 28 cancers by TILScout using deep learning	14
Trans-ancestry transcriptome-wide association and functional studies to uncover novel susceptibility genes and therapeutic targets for colorectal cancer	14
Author Correction: Naltriben promotes tumor growth by activating the TRPM7-mediated development of the anti-inflammatory M2 phenotype	14
Integration of pre-treatment computational radiomics, deep radiomics, and transcriptomics enhances soft-tissue sarcoma patient prognosis	14
RadGLO: an interactive platform for radiomic feature analysis and prognostic modeling in glioma	14
High risk clear cell renal cell carcinoma microenvironments contain protumour immunophenotypes lacking specific immune checkpoints	13
A morphometric signature to identify ductal carcinoma in situ with a low risk of progression	13
Revealing neuroendocrine transformation in gynecological cancers through genomic analysis	13
Development of a deep learning model for cancer diagnosis by inspecting cell-free DNA end-motifs	13
Locoregional tumor burden and risk of mortality in metastatic breast cancer	13
Molecular characterization of low-grade serous ovarian carcinoma identifies genomic aberrations according to hormone receptor expression	13
Cell graph neural networks enable the precise prediction of patient survival in gastric cancer	13
Comprehensive analysis of targetable mutations and tumor microenvironment in urachal cancer	13
Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities	13
Illuminating the future of precision cancer surgery with fluorescence imaging and artificial intelligence convergence	13
Neoadjuvant therapy-induced immune dynamics and myeloid-associated resistance in advanced head and neck cancer	13
Adaptive Darwinian off-target resistance mechanisms to selective RET inhibition in RET driven cancer	13
Upregulation of POLE and proficient DNA repair are features of CIC::DUX4 sarcomas	13
A multiparameter liquid biopsy approach allows to track melanoma dynamics and identify early treatment resistance	13
MC1R signaling through the cAMP-CREB/ATF-1 and ERK-NFκB pathways accelerates G1/S transition promoting breast cancer progression	13
Challenges and opportunities associated with the MD Anderson IMPACT2 randomized study in precision oncology	13
Bayesian risk prediction model for colorectal cancer mortality through integration of clinicopathologic and genomic data	13
RNF4 mediated degradation of PDHA1 promotes colorectal cancer metabolism and metastasis	12
Pharmacogenomic discovery of genetically targeted cancer therapies optimized against clinical outcomes	12
Sotorasib resistance in KRAS G12C-mutant invasive mucinous adenocarcinoma with implications for VEGF-A	12
A multi-modal deep learning model for prediction of Ki-67 for meningiomas using pretreatment MR images	12
Multi-omics analysis unveils immunosuppressive microenvironment in the occurrence and development of multiple pulmonary lung cancers	12
Prediction of early-stage melanoma recurrence using clinical and histopathologic features	12
Applying a multi-task and multi-instance framework to predict axillary lymph node metastases in breast cancer	12
Multimodal analysis suggests differential immuno-metabolic crosstalk in lung squamous cell carcinoma and adenocarcinoma	12
Molecular landscape of ERBB2 alterations in 3000 advanced NSCLC patients	12
ALDH1A1 promotes PARP inhibitor resistance by enhancing retinoic acid receptor-mediated DNA polymerase θ expression	12
Biopsy image-based deep learning for predicting pathologic response to neoadjuvant chemotherapy in patients with NSCLC	12
Genomic landscape of liquid biopsy mutations in TP53 and DNA damage genes in cancer patients	12
FOXA1-dependent NSUN2 facilitates the advancement of prostate cancer by preserving TRIM28 mRNA stability in a m5C-dependent manner	12
A deep learning model, NAFNet, predicts adverse pathology and recurrence in prostate cancer using MRIs	12
Intraoperative margin assessment for basal cell carcinoma with deep learning and histologic tumor mapping to surgical site	12
G0S2: a potential target for NSCLC identified through prognostic models from multi-Omic analysis of regulatory T cell metabolic genes	12
Identification of breast cancer subtypes and drug response prediction through forward and reverse translation	12
Immunologic correlates in a CIC::DUX4 fusion-positive sarcoma responsive to dual immune checkpoint blockade	12