npj Precision Oncology

Article	Citations
Machine learning approaches to drug response prediction: challenges and recent progress	159
3D bioprinting for reconstituting the cancer microenvironment	155
Classification and mutation prediction based on histopathology H&E images in liver cancer using deep learning	117
Patient-derived organoids as a predictive biomarker for treatment response in cancer patients	113
Honeybee venom and melittin suppress growth factor receptor activation in HER2-enriched and triple-negative breast cancer	80
Genomic context of NTRK1/2/3 fusion-positive tumours from a large real-world population	77
High expression of ACE2 and TMPRSS2 and clinical characteristics of COVID-19 in colorectal cancer patients	62
PD-L1 immunohistochemistry for canine cancers and clinical benefit of anti-PD-L1 antibody in dogs with pulmonary metastatic oral malignant melanoma	55
Quantitative MRI-based radiomics for noninvasively predicting molecular subtypes and survival in glioma patients	52
Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty	51
Microbiome dysbiosis in lung cancer: from composition to therapy	51
Multiplex bioimaging of single-cell spatial profiles for precision cancer diagnostics and therapeutics	50
Pan-cancer analysis of SETD2 mutation and its association with the efficacy of immunotherapy	47
Single-cell analysis of gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity	47
GD2 CAR T cells against human glioblastoma	43
The pan-cancer landscape of crosstalk between epithelial-mesenchymal transition and immune evasion relevant to prognosis and immunotherapy response	40
Tumor microenvironment heterogeneity an important mediator of prostate cancer progression and therapeutic resistance	38
Multiplexed drug testing of tumor slices using a microfluidic platform	36
Genetic mutation and biological pathway prediction based on whole slide images in breast carcinoma using deep learning	34
Will polygenic risk scores for cancer ever be clinically useful?	34
Selective KRAS G12C inhibitors in non-small cell lung cancer: chemistry, concurrent pathway alterations, and clinical outcomes	33
Small cell transformation of ROS1 fusion-positive lung cancer resistant to ROS1 inhibition	32
Clinical application of a lung cancer organoid (tumoroid) culture system	32
The L730V/I RET roof mutations display different activities toward pralsetinib and selpercatinib	30
Dynamic roles of inflammasomes in inflammatory tumor microenvironment	30

A tumor microenvironment-specific gene expression signature predicts chemotherapy resistance in colorectal cancer patients	29
Integrated multiomics analysis of hepatoblastoma unravels its heterogeneity and provides novel druggable targets	29
High TGF-β signature predicts immunotherapy resistance in gynecologic cancer patients treated with immune checkpoint inhibition	28
Deep learning for end-to-end kidney cancer diagnosis on multi-phase abdominal computed tomography	28
Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology	27
A phase I/II study of rovalpituzumab tesirine in delta-like 3—expressing advanced solid tumors	26
Identification of gastric cancer subtypes based on pathway clustering	26
Immune microenvironment characterisation and dynamics during anti-HER2-based neoadjuvant treatment in HER2-positive breast cancer	26
Durable complete response to neoantigen-loaded dendritic-cell vaccine following anti-PD-1 therapy in metastatic gastric cancer	25
Survival improvement for patients with metastatic colorectal cancer over twenty years	25
Different pathologic responses to neoadjuvant anti-PD-1 in primary squamous lung cancer and regional lymph nodes	25
Cancer-specific immune evasion and substantial heterogeneity within cancer types provide evidence for personalized immunotherapy	24
Impressive response to dabrafenib, trametinib, and osimertinib in a metastatic EGFR-mutant/BRAF V600E lung adenocarcinoma patient	24
Bevacizumab improves tumor infiltration of mature dendritic cells and effector T-cells in triple-negative breast cancer patients	23
A blood-based miRNA signature with prognostic value for overall survival in advanced stage non-small cell lung cancer treated with immunotherapy	23
Pan-cancer analysis of genomic scar patterns caused by homologous repair deficiency (HRD)	23
Comprehensive pan-cancer genomic landscape of KRAS altered cancers and real-world outcomes in solid tumors	22
Antibody-drug conjugates in lung cancer: dawn of a new era?	22
Circulating tumor cell heterogeneity in neuroendocrine prostate cancer by single cell copy number analysis	22
Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA	21
Co-occurring genomic alterations and immunotherapy efficacy in NSCLC	21
A tyrosine kinase inhibitor-induced interferon response positively associates with clinical response in EGFR-mutant lung cancer	20
Liquid biopsy mutation panel for non-small cell lung cancer: analytical validation and clinical concordance	20
Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma	20
Targeting CDK1 in cancer: mechanisms and implications	20
Cell graph neural networks enable the precise prediction of patient survival in gastric cancer	20
Image analysis reveals molecularly distinct patterns of TILs in NSCLC associated with treatment outcome	20
Comprehensive functional evaluation of variants of fibroblast growth factor receptor genes in cancer	20
A genomic mutation signature predicts the clinical outcomes of immunotherapy and characterizes immunophenotypes in gastrointestinal cancer	20
Predictive and prognostic transcriptomic biomarkers in soft tissue sarcomas	19
Self-supervised attention-based deep learning for pan-cancer mutation prediction from histopathology	19
Pan-cancer prognostic genetic mutations and clinicopathological factors associated with survival outcomes: a systematic review	19
A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images	19
Combined FGFR and Akt pathway inhibition abrogates growth of FGFR1 overexpressing EGFR-TKI-resistant NSCLC cells	19
Efficacy of MEK inhibition in a recurrent malignant peripheral nerve sheath tumor	19
Pre-treatment serum albumin and mutational burden as biomarkers of response to immune checkpoint blockade	18
Super-enhancer in prostate cancer: transcriptional disorders and therapeutic targets	18
Vaginal microbiota, genital inflammation, and neoplasia impact immune checkpoint protein profiles in the cervicovaginal microenvironment	18
Association of mismatch repair status with survival and response to neoadjuvant chemo(radio)therapy in rectal cancer	18
Decreased cytotoxic T cells and TCR clonality in organ transplant recipients with squamous cell carcinoma	18
Targeting the epichaperome as an effective precision medicine approach in a novel PML-SYK fusion acute myeloid leukemia	18
Artificial intelligence reveals features associated with breast cancer neoadjuvant chemotherapy responses from multi-stain histopathologic images	18
Prostate cancer polygenic risk score and prediction of lethal prostate cancer	18
Complete response to PD-1 blockade following EBV-specific T-cell therapy in metastatic nasopharyngeal carcinoma	18
Just Add Data: automated predictive modeling for knowledge discovery and feature selection	18
Deep learning for diagnosis of acute promyelocytic leukemia via recognition of genomically imprinted morphologic features	17
Mendelian randomization analyses of genetically predicted circulating levels of cytokines with risk of breast cancer	17
Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies	17
Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury	17
Crizotinib in patients with tumors harboring ALK or ROS1 rearrangements in the NCI-MATCH trial	17

Characterizing advanced breast cancer heterogeneity and treatment resistance through serial biopsies and comprehensive analytics	17
Applications and clinical trial landscape using Toll-like receptor agonists to reduce the toll of cancer	17
The identification and functional analysis of CD8+PD-1+CD161+ T cells in hepatocellular carcinoma	17
Early identification of disease progression in ALK-rearranged lung cancer using circulating tumor DNA analysis	17
Genomic features and tumor immune microenvironment alteration in NSCLC treated with neoadjuvant PD-1 blockade	17
Feasibility and first reports of the MATCH-R repeated biopsy trial at Gustave Roussy	16
Circulating tumor cell copy-number heterogeneity in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors	16
Small extracellular vesicle PD-L1 in cancer: the knowns and unknowns	16
Molecular pathogenesis of desmoid tumor and the role of γ-secretase inhibition	16
A subset of lung cancer cases shows robust signs of homologous recombination deficiency associated genomic mutational signatures	16
Genomic characterization and outcome evaluation of kinome fusions in lung cancer revealed novel druggable fusions	16
Accurate surgical navigation with real-time tumor tracking in cancer surgery	16
Inflation of tumor mutation burden by tumor-only sequencing in under-represented groups	16
Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients	16
A computational method for prioritizing targeted therapies in precision oncology: performance analysis in the SHIVA01 trial	15
Artificial intelligence for the next generation of precision oncology	15
Splice-switching of the insulin receptor pre-mRNA alleviates tumorigenic hallmarks in rhabdomyosarcoma	15
Clinical, genetic and pharmacological data support targeting the MEK5/ERK5 module in lung cancer	15
An international working group consensus report for the prioritization of molecular biomarkers for Ewing sarcoma	15
Association of pro-inflammatory soluble cytokine receptors early during hepatocellular carcinoma stereotactic radiotherapy with liver toxicity	15
Pentraxin 3 is a stromally-derived biomarker for detection of pancreatic ductal adenocarcinoma	15
Secondary IDH1 resistance mutations and oncogenic IDH2 mutations cause acquired resistance to ivosidenib in cholangiocarcinoma	15
Acetylation of ELF5 suppresses breast cancer progression by promoting its degradation and targeting CCND1	15
The Aurora kinase/β-catenin axis contributes to dexamethasone resistance in leukemia	15
Progression of prostate carcinoma is promoted by adipose stromal cell-secreted CXCL12 signaling in prostate epithelium	15
Usability of deep learning and H&E images predict disease outcome-emerging tool to optimize clinical trials	14
Rare deleterious germline variants and risk of lung cancer	14
Spatially variant immune infiltration scoring in human cancer tissues	14
Harnessing the immunotherapeutic potential of CDK4/6 inhibitors in melanoma: is timing everything?	14
HER3 activation contributes toward the emergence of ALK inhibitor-tolerant cells in ALK-rearranged lung cancer with mesenchymal features	13
Targeted biologic inhibition of both tumor cell-intrinsic and intercellular CLPTM1L/CRR9-mediated chemotherapeutic drug resistance	13
Real-world data analyses unveiled the immune-related adverse effects of immune checkpoint inhibitors across cancer types	13
On-treatment measurements of circulating tumor DNA during FOLFOX therapy in patients with colorectal cancer	13
Imaging immunity in patients with cancer using positron emission tomography	13
Overcoming resistance to BRAFV600E inhibition in melanoma by deciphering and targeting personalized protein network alterations	13
Characterization of evolution trajectory and immune profiling of brain metastasis in lung adenocarcinoma	12
Multiscale-omic assessment of EWSR1-NFATc2 fusion positive sarcomas identifies the mTOR pathway as a potential therapeutic target	12
Circulating stromal cells in resectable pancreatic cancer correlates to pathological stage and predicts for poor clinical outcomes	12
Immunosuppression for immune-related adverse events during checkpoint inhibition: an intricate balance	12
Computer extracted gland features from H&E predicts prostate cancer recurrence comparably to a genomic companion diagnostic test: a large multi-site study	12
Genomic landscape and immune-related gene expression profiling of epithelial ovarian cancer after neoadjuvant chemotherapy	11
Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies	11
Collision of germline POLE and PMS2 variants in a young patient treated with immune checkpoint inhibitors	11
Somatic copy number profiling from hepatocellular carcinoma circulating tumor cells	11
Precision medicine: preliminary results from the Initiative for Molecular Profiling and Advanced Cancer Therapy 2 (IMPACT2) study	11
Genomic investigation of co-targeting tumor immune microenvironment and immune checkpoints in pan-cancer immunotherapy	11
Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia	11
A perspective on life-cycle health technology assessment and real-world evidence for precision oncology in Canada	11
Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors	11
Clonal dynamics of BRAF-driven drug resistance in EGFR-mutant lung cancer	11
Favorable immune checkpoint inhibitor outcome of patients with melanoma and NSCLC harboring FAT1 mutations	11
A DNA methylation-based liquid biopsy for triple-negative breast cancer	11
Acquired JAK2 mutations confer resistance to JAK inhibitors in cell models of acute lymphoblastic leukemia	10
Co-targeting CDK2 and CDK4/6 overcomes resistance to aromatase and CDK4/6 inhibitors in ER+ breast cancer	10
Identification of epithelial and mesenchymal circulating tumor cells in clonal lineage of an aggressive prostate cancer case	10
Adaptive resistance to lorlatinib via EGFR signaling in ALK-rearranged lung cancer	10
Models that combine transcriptomic with spatial protein information exceed the predictive value for either single modality	10
Targeting extracellular and juxtamembrane FGFR2 mutations in chemotherapy-refractory cholangiocarcinoma	10
Preoperative immune landscape predisposes adverse outcomes in hepatocellular carcinoma patients with liver transplantation	10
PALB2 or BARD1 loss confers homologous recombination deficiency and PARP inhibitor sensitivity in prostate cancer	10
Genomic landscape of 891 RET fusions detected across diverse solid tumor types	10
Expanded genetic testing of GIST patients identifies high proportion of non-syndromic patients with germline alterations	10
Prediction of early-stage melanoma recurrence using clinical and histopathologic features	10
Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity	10
DNA-based copy number analysis confirms genomic evolution of PDX models	10
Deletions on 9p21 are associated with worse outcomes after anti-PD-1/PD-L1 monotherapy but not chemoimmunotherapy	10
Impact of TP53 mutations in Triple Negative Breast Cancer	10
Induction immune-checkpoint inhibitors for resectable oncogene-mutant NSCLC: A multicenter pooled analysis	10
Combination venetoclax and selinexor effective in relapsed refractory multiple myeloma with translocation t(11;14)	10
Integrated molecular characterisation of endometrioid ovarian carcinoma identifies opportunities for stratification	10
Analyses of canine cancer mutations and treatment outcomes using real-world clinico-genomics data of 2119 dogs	10
Integrative molecular analyses define correlates of high B7-H3 expression in metastatic castrate-resistant prostate cancer	10
A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival	9
Benefits of local consolidative treatment in oligometastases of solid cancers: a stepwise-hierarchical pooled analysis and systematic review	9
Comprehensive clinicopathological and genomic profiling of gallbladder cancer reveals actionable targets in half of patients	9
Molecular characterization of low-grade serous ovarian carcinoma identifies genomic aberrations according to hormone receptor expression	9
Precision medicine: affording the successes of science	9
Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology	9
Racial and ethnic disparities in a real-world precision oncology data registry	9
Stabilization of p18 by deubiquitylase CYLD is pivotal for cell cycle progression and viral replication	9

PARP inhibitors promote stromal fibroblast activation by enhancing CCL5 autocrine signaling in ovarian cancer	9
Patient-level proteomic network prediction by explainable artificial intelligence	9
Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer	9
Mutated clones driving leukemic transformation are already detectable at the single-cell level in CD34-positive cells in the chronic phase of primary myelofibrosis	9
Comprehensive RNA analysis of CSF reveals a role for CEACAM6 in lung cancer leptomeningeal metastases	9
Gas6 expression is reduced in advanced breast cancers	9
Molecular differences between lymph nodes and distant metastases compared with primaries in colorectal cancer patients	9
Advances in NK cell therapy for brain tumors	8
Multimodal analysis suggests differential immuno-metabolic crosstalk in lung squamous cell carcinoma and adenocarcinoma	8
TCERG1L allelic variation is associated with cisplatin-induced hearing loss in childhood cancer, a PanCareLIFE study	8
STAT3 inhibition suppresses adaptive survival of ALK-rearranged lung cancer cells through transcriptional modulation of apoptosis	8
MatchMiner: an open-source platform for cancer precision medicine	8
Epigenomics and immunotherapeutic advances in pediatric brain tumors	8
A patient-designed tissue-engineered model of the infiltrative glioblastoma microenvironment	8
Inter-eye genomic heterogeneity in bilateral retinoblastoma via aqueous humor liquid biopsy	8
MEK inhibitor resistance in lung adenocarcinoma is associated with addiction to sustained ERK suppression	8
FOXP3+ T cells in uterine sarcomas are associated with favorable prognosis, low extracellular matrix expression and reduced YAP activation	8
Multi-site desmoplastic small round cell tumors are genetically related and immune-cold	8
Preoperative clinical and tumor genomic features associated with pathologic lymph node metastasis in clinical stage I and II lung adenocarcinoma	8
Drug sensitivity profiling of 3D tumor tissue cultures in the pediatric precision oncology program INFORM	8
Synergistic activation of mutant TERT promoter by Sp1 and GABPA in BRAFV600E-driven human cancers	7
Radiomics for characterization of the glioma immune microenvironment	7
Deep learning generates synthetic cancer histology for explainability and education	7
Deep computational image analysis of immune cell niches reveals treatment-specific outcome associations in lung cancer	7
Disease progression patterns and molecular resistance mechanisms to crizotinib of lung adenocarcinoma harboring ROS1 rearrangements	7
Comparative biomarker analysis of PALOMA-2/3 trials for palbociclib	7
Targeting Mre11 overcomes platinum resistance and induces synthetic lethality in XRCC1 deficient epithelial ovarian cancers	7
Emerging precision diagnostics in advanced cutaneous squamous cell carcinoma	7
Panels and models for accurate prediction of tumor mutation burden in tumor samples	7
BAP1 methylation: a prognostic marker of uveal melanoma metastasis	7
ESCCAL-1 promotes cell-cycle progression by interacting with and stabilizing galectin-1 in esophageal squamous cell carcinoma	6
Microfluidic-based dynamic BH3 profiling predicts anticancer treatment efficacy	6
Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration	6
SRC-RAC1 signaling drives drug resistance to BRAF inhibition in de-differentiated cutaneous melanomas	6
An appraisal of genetic testing for prostate cancer susceptibility	6
Evolution of acquired resistance in a ROS1+ KRAS G12C+ NSCLC through the MAPK pathway	6
Extraordinary clinical response to ibrutinib in low-grade ovarian cancer guided by organoid drug testing	6
PERK mediates resistance to BRAF inhibition in melanoma with impaired PTEN	6
Challenges and opportunities associated with the MD Anderson IMPACT2 randomized study in precision oncology	6
Clinical implications of systemic and local immune responses in human angiosarcoma	6
Multi-omics data integration and modeling unravels new mechanisms for pancreatic cancer and improves prognostic prediction	6
Durable responses to alectinib in murine models of EML4-ALK lung cancer requires adaptive immunity	6
Comprehensive molecular profiling of pulmonary pleomorphic carcinoma	6
Hypermutated phenotype in gliosarcoma of the spinal cord	5
Clinical prospects of WRN inhibition as a treatment for MSI tumours	5
Drivers of genomic loss of heterozygosity in leiomyosarcoma are distinct from carcinomas	5
Potential pathogenic germline variant reporting from tumor comprehensive genomic profiling complements classic approaches to germline testing	5
Digital Display Precision Predictor: the prototype of a global biomarker model to guide treatments with targeted therapy and predict progression-free survival	5
Criteria-based curation of a therapy-focused compendium to support treatment recommendations in precision oncology	5
Systemic immune modulation by stereotactic radiotherapy in early-stage lung cancer	5
PBRM1 mutations might render a subtype of biliary tract cancers sensitive to drugs targeting the DNA damage repair system	5
Identification of novel prognostic and predictive biomarkers in salivary duct carcinoma via comprehensive molecular profiling	5
Landscape of potentially targetable receptor tyrosine kinase fusions in diverse cancers by DNA-based profiling	5
The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells	5
ALK fusions in the pan-cancer setting: another tumor-agnostic target?	5
Polygenic risk scores to stratify cancer screening should predict mortality not incidence	5
Single-cell atlas of diverse immune populations in the advanced biliary tract cancer microenvironment	5
Leveraging patient derived models of FGFR2 fusion positive intrahepatic cholangiocarcinoma to identify synergistic therapies	5
Artificial intelligence in ovarian cancer histopathology: a systematic review	5
Evolution of MET and NRAS gene amplification as acquired resistance mechanisms in EGFR mutant NSCLC	5
Peripheral blood DNA methylation profiles predict future development of B-cell Non-Hodgkin Lymphoma	5
Tumor-associated macrophage-related strategies for glioma immunotherapy	5
Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition	5
Activation of CD44/PAK1/AKT signaling promotes resistance to FGFR1 inhibition in squamous-cell lung cancer	5
Gross tumour volume radiomics for prognostication of recurrence & death following radical radiotherapy for NSCLC	4
Single-cell transcriptomic profiling for inferring tumor origin and mechanisms of therapeutic resistance	4
A single-cell based precision medicine approach using glioblastoma patient-specific models	4
An analysis of research biopsy core variability from over 5000 prospectively collected core samples	4
The tumor mutational landscape of BRCA2-deficient primary and metastatic prostate cancer	4
Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma	4
Integrated molecular and clinical analysis of BRAF-mutant glioma in adults	4
A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes	4
ALDH1A1 promotes PARP inhibitor resistance by enhancing retinoic acid receptor-mediated DNA polymerase θ expression	4
Proximity of immune and tumor cells underlies response to BRAF/MEK-targeted therapies in metastatic melanoma patients	4
GSK3 inhibition circumvents and overcomes acquired lorlatinib resistance in ALK-rearranged non-small-cell lung cancer	4
ML-based sequential analysis to assist selection between VMP and RD for newly diagnosed multiple myeloma	4
BRAF v600E–mutant cancers treated with vemurafenib alone or in combination with everolimus, sorafenib, or crizotinib or with paclitaxel and carboplatin (VEM-PLUS) study	4
Targeting CD47-SIRPa axis shows potent preclinical anti-tumor activity as monotherapy and synergizes with PARP inhibition	4
Author Correction: Genomic context of NTRK1/2/3 fusion-positive tumours from a large real-world population	4
Downregulation of KEAP1 in melanoma promotes resistance to immune checkpoint blockade	4
AKT/mTOR signaling modulates resistance to endocrine therapy and CDK4/6 inhibition in metastatic breast cancers	4
Circulating tumor DNA sequencing provides comprehensive mutation profiling for pediatric central nervous system tumors	4
Pan-cancer molecular tumor board experience with biomarker-driven precision immunotherapy	4