PO2RDF: representation of real-world data for precision oncology using resource description framework.
PMID:35907849
Genomic Landscape, Clinical Features and Outcomes of Non-Small Cell Lung Cancer Patients Harboring BRAF Alterations of Distinct Functional Classes.
PMID:35884534
Genetic variation associated with condensate dysregulation in disease.
PMID:35809564
Targeted Therapy for Adrenocortical Carcinoma: A Genomic-Based Search for Available and Emerging Options.
PMID:35681700
scAmpi-A versatile pipeline for single-cell RNA-seq analysis from basics to clinics.
PMID:35658001
Multi-Omic Data Improve Prediction of Personalized Tumor Suppressors and Oncogenes.
PMID:35620468
CancerVar: An artificial intelligence-empowered platform for clinical interpretation of somatic mutations in cancer.
PMID:35544644
A pan-cancer survey of cell line tumor similarity by feature-weighted molecular profiles.
PMID:35475239
Bioinformatic Challenges Detecting Genetic Variation in Precision Medicine Programs.
PMID:35463004
Standardized evidence-based approach for assessment of oncogenic and clinical significance of NTRK fusions.
PMID:35366592
Liquid Biopsy and Artificial Intelligence as Tools to Detect Signatures of Colorectal Malignancies: A Modern Approach in Patient's Stratification.
PMID:35356214
Whole exome sequencing of pediatric leukemia reveals a novel InDel within FLT-3 gene in AML patient from Mizo tribal population, Northeast India.
PMID:35350997
Findings from precision oncology in the clinic: rare, novel variants are a significant contributor to scaling molecular diagnostics.
PMID:35346197
Distinct Genomic Profiles Are Associated with Treatment Response and Survival in Ovarian Cancer.
PMID:35326660
The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification.
PMID:35311178
Anaplastic thyroid cancer: genome-based search for new targeted therapy options.
PMID:35275096
Single-Cell Sequencing Technologies in Precision Oncology.
PMID:35230694
Computational Resources for the Interpretation of Variations in Cancer.
PMID:35230689
Pathway Analysis for Cancer Research and Precision Oncology Applications.
PMID:35230687
The Architecture of a Precision Oncology Platform.
PMID:35230680
The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.
PMID:35221333
Effective drug combinations in breast, colon and pancreatic cancer cells.
PMID:35197630
The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization.
PMID:35193494
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer.
PMID:35148171
A platform for oncogenomic reporting and interpretation.
PMID:35140225
Integrative Genomic Analyses of 1,145 Patient Samples Reveal New Biomarkers in Esophageal Squamous Cell Carcinoma.
PMID:35127817
Discovery through clinical sequencing in oncology.
PMID:35122052
Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology.
PMID:35121878
Moving pan-cancer studies from basic research toward the clinic.
PMID:35121865
Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).
PMID:35101336
Landscape of driver gene events, biomarkers, and druggable targets identified by whole-genome sequencing of glioblastomas.
PMID:35047820
NETME: on-the-fly knowledge network construction from biomedical literature.
PMID:35013714
Artificial intelligence in clinical research of cancers.
PMID:34929741
The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics.
PMID:34873156
Genomic and molecular features distinguish young adult cancer from later-onset cancer.
PMID:34788626
Patient similarity network of newly diagnosed multiple myeloma identifies patient subgroups with distinct genetic features and clinical implications.
PMID:34788103
The Human Disease Ontology 2022 update.
PMID:34755882
Development and Validation of Targeted Gene Sequencing Panel Based Companion Diagnostic for Korean Patients with Solid Tumors.
PMID:34680263
Targeted Therapy of Papillary Thyroid Cancer: A Comprehensive Genomic Analysis.
PMID:34630336
JCGA: the Japanese version of the Cancer Genome Atlas and its contribution to the interpretation of gene alterations detected in clinical cancer genome sequencing.
PMID:34588443
Validation of an NGS Panel Designed for Detection of Actionable Mutations in Tumors Common in Latin America.
PMID:34575676
VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases.
PMID:34570217
ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer.
PMID:34529669
Gene Mutation Analysis in Papillary Thyroid Carcinoma Using a Multi-Gene Panel in China.
PMID:34511996
Information Retrieval Using Machine Learning for Biomarker Curation in the Exposome-Explorer.
PMID:34490412
Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.
PMID:34429404
Comparative analysis of nuclear and mitochondrial DNA from tissue and liquid biopsies of colorectal cancer patients.
PMID:34408162
Merida: a novel boolean logic based integer linear program for personalized cancer therapy.
PMID:34352075
Identification of Variants Associated With Rare Hematological Disorder Erythrocytosis Using Targeted Next-Generation Sequencing Analysis.
PMID:34349782
The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets.
PMID:34326338
Tumor Mutation Burden Prediction Model in Egyptian Breast Cancer patients based on Next Generation Sequencing.
PMID:34319027
Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis.
PMID:34316711
MUSTARD-a comprehensive resource of mutation-specific therapies in cancer.
PMID:34309639
The mutational profile of immune surveillance genes in diagnostic and refractory/relapsed DLBCLs.
PMID:34275438
Prevalence and Landscape of Actionable Genomic Alterations in Renal Cell Carcinoma.
PMID:34261695
ctDNA MRD Detection and Personalized Oncogenomic Analysis in Oligometastatic Colorectal Cancer From Plasma and Urine.
PMID:34250420
Identification and monitoring of mutations in circulating cell-free tumor DNA in hepatocellular carcinoma treated with lenvatinib.
PMID:34174931
Criteria-based curation of a therapy-focused compendium to support treatment recommendations in precision oncology.
PMID:34162978
Therapeutic Implications of Germline Testing in Patients With Advanced Cancers.
PMID:34133209
Prognostic Genetic Biomarkers Based on Oncogenic Signaling Pathways for Outcome Prediction in Patients with Oral Cavity Squamous Cell Carcinoma.
PMID:34070941
A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine.
PMID:34050359
Comprehensive analysis of oncogenic signatures and consequent repurposed drugs in TMPRSS2:ERG fusion-positive prostate cancer.
PMID:34047472
The Human Salivary Proteome Wiki: A Community-Driven Research Platform.
PMID:34032471
Knowledge bases and software support for variant interpretation in precision oncology.
PMID:33971666
Molecular Profiling-Based Assignment of Cancer Therapy (NCI-MPACT): A Randomized Multicenter Phase II Trial.
PMID:33928209
APICURON: a database to credit and acknowledge the work of biocurators.
PMID:33882120
Development and Analytical Validation of a Targeted Next-Generation Sequencing Panel to Detect Actionable Mutations for Targeted Therapy.
PMID:33854338
OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations.
PMID:33771218
Clinical cancer genomic profiling.
PMID:33762738
Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology.
PMID:33737716
A showcase study on personalized in silico drug response prediction based on the genetic landscape of muscle invasive bladder cancer.
PMID:33712636
Comparison of Open-access Databases for Clinical Variant Interpretation in Cancer: A Case Study of MDS/AML.
PMID:33608312
Development and validation of a multigene variant profiling assay to guide targeted and immuno therapy selection in solid tumors.
PMID:33556149
Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.
PMID:33535033
Artificial Intelligence Pipeline to Bridge the Gap between Bench Researchers and Clinical Researchers in Precision Medicine.
PMID:33511289
Online informatics resources to facilitate cancer target and chemical probe discovery.
PMID:33479663
VarStack: a web tool for data retrieval to interpret somatic variants in cancer.
PMID:33247936
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts.
PMID:33237278
Factors influencing cancer genetic somatic mutation test ordering by cancer physician.
PMID:33183308
Linking Pharmacogenomic Information on Drug Safety and Efficacy with Ethnic Minority Populations.
PMID:33113799
CNCDatabase: a database of non-coding cancer drivers.
PMID:33095860
Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies.
PMID:33083132
Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma.
PMID:33046443
Comparison of three commercial decision support platforms for matching of next-generation sequencing results with therapies in patients with cancer.
PMID:32967919
Mouse-human co-clinical trials demonstrate superior anti-tumour effects of buparlisib (BKM120) and cetuximab combination in squamous cell carcinoma of head and neck.
PMID:32963347
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome.
PMID:32926574
Comparison of Annotation Services for Next-Generation Sequencing in a Large-Scale Precision Oncology Program.
PMID:32923873
Next-Generation Sequencing and the Clinical Oncology Workflow: Data Challenges, Proposed Solutions, and a Call to Action.
PMID:32923847
Comparative Analysis of Public Knowledge Bases for Precision Oncology.
PMID:32914021
KAT6A amplifications are associated with shorter progression-free survival and overall survival in patients with endometrial serous carcinoma.
PMID:32877461
From Patient Engagement to Precision Oncology: Leveraging Informatics to Advance Cancer Care.
PMID:32823322
OncoPDSS: an evidence-based clinical decision support system for oncology pharmacotherapy at the individual level.
PMID:32770988
A comprehensive DNA panel next generation sequencing approach supporting diagnostics and therapy prediction in neurooncology.
PMID:32758285
Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors.
PMID:32738923
Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data.
PMID:32734171
Patient-derived ovarian cancer organoids capture the genomic profiles of primary tumours applicable for drug sensitivity and resistance testing.
PMID:32724113
Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices.
PMID:32644817
The Community Oncology and Academic Medical Center Alliance in the Age of Precision Medicine: Cancer Genetics and Genomics Considerations.
PMID:32640668
Identification of Altered Genes in Gallbladder Cancer as Potential Driver Mutations for Diagnostic and Prognostic Purposes: A Computational Approach.
PMID:32546937
Landscape and function of multiple mutations within individual oncogenes.
PMID:32494066
Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations.
PMID:32365829
Targeted next generation sequencing identifies somatic mutations in a cohort of Egyptian breast cancer patients.
PMID:32322420
Establishment and characterization of patient-derived xenografts as paraclinical models for head and neck cancer.
PMID:32293356
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.
PMID:32246132
CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase.
PMID:32191543
Wikidata as a knowledge graph for the life sciences.
PMID:32180547
OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.
PMID:32142370
A Review of Precision Oncology Knowledgebases for Determining the Clinical Actionability of Genetic Variants.
PMID:32117976
Identification of targeted therapy options for gastric adenocarcinoma by comprehensive analysis of genomic data.
PMID:32107691
Adopting solutions for annotation and reporting of next generation sequencing in clinical practice.
PMID:32099889
Requirements Analysis and Specification for a Molecular Tumor Board Platform Based on cBioPortal.
PMID:32050609
A virtual molecular tumor board to improve efficiency and scalability of delivering precision oncology to physicians and their patients.
PMID:32025647
AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting.
PMID:32019565
Development of a Precision Medicine Workflow in Hematological Cancers, Aalborg University Hospital, Denmark.
PMID:32013121
Evidence-Based Network Approach to Recommending Targeted Cancer Therapies.
PMID:31990579
Molecular profiling for precision cancer therapies.
PMID:31937368
Future of Evidence Synthesis in Precision Oncology: Between Systematic Reviews and Biocuration.
PMID:31930186
Generation and characterization of a mitotane-resistant adrenocortical cell line.
PMID:31910152
Genome analysis and knowledge-driven variant interpretation with TGex.
PMID:31888639
Japanese version of The Cancer Genome Atlas, JCGA, established using fresh frozen tumors obtained from 5143 cancer patients.
PMID:31863614
ClinVAP: a reporting strategy from variants to therapeutic options.
PMID:31830259
GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis.
PMID:31811943
Text-mining clinically relevant cancer biomarkers for curation into the CIViC database.
PMID:31796060
Standard operating procedure for curation and clinical interpretation of variants in cancer.
PMID:31779674
Molecular characterization of lung adenocarcinoma from Korean patients using next generation sequencing.
PMID:31765373
The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact.
PMID:31748536
Next-generation sequencing reveals unique combination of mutations in cis of CSF3R in atypical chronic myeloid leukemia.
PMID:31692115
Pan-cancer whole-genome analyses of metastatic solid tumours.
PMID:31645765
A case for expert curation: an overview of cancer curation in the Clinical Genome Resource (ClinGen).
PMID:31645350
Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes.
PMID:31618044
Precision oncology: lessons learned and challenges for the future.
PMID:31616176
Tracking longitudinal genetic changes of circulating tumor DNA (ctDNA) in advanced Lung adenocarcinoma treated with chemotherapy.
PMID:31597567
Integrated genomic profiling expands clinical options for patients with cancer.
PMID:31570899
The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies.
PMID:31570896
Dissecting molecular mechanisms of resistance to NOTCH1-targeted therapy in T-cell acute lymphoblastic leukemia xenografts.
PMID:31467126
Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants.
PMID:31443733
Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants.
PMID:31439692
Identification of key genes in osteosarcoma by meta‑analysis of gene expression microarray.
PMID:31432118
VIST - a Variant-Information Search Tool for precision oncology.
PMID:31419935
The pivotal role of sampling recurrent tumors in the precision care of patients with tumors of the central nervous system.
PMID:31371350
Clinical Applications of Next-Generation Sequencing in Precision Oncology.
PMID:31335390
Semalytics: a semantic analytics platform for the exploration of distributed and heterogeneous cancer data in translational research.
PMID:31287543
Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives.
PMID:31263868
Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines.
PMID:31262303
A Decade of Translational Bioinformatics: A Retrospective Analysis of "Year-in-Review" Presentations.
PMID:31258986
ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer.
PMID:31169290
RHOA in Gastric Cancer: Functional Roles and Therapeutic Potential.
PMID:31156701
Computational analysis of data from a genome-wide screening identifies new PARP1 functional interactors as potential therapeutic targets.
PMID:31105872
The incidence of consecutive manifestations in Von Hippel-Lindau disease.
PMID:31087189
AlloDriver: a method for the identification and analysis of cancer driver targets.
PMID:31069394
ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification.
PMID:31038669
[Detection and interpretation of somatic variants in molecular pathology].
PMID:31037375
The Evolving Landscape of Cancer Stem Cells and Ways to Overcome Cancer Heterogeneity.
PMID:31013960
Elucidation of Novel Therapeutic Targets for Acute Myeloid Leukemias with RUNX1-RUNX1T1 Fusion.
PMID:30959925
Precision oncogenomics.
PMID:30936200
Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways.
PMID:30889380
Precision Medicine for Relapsed Multiple Myeloma on the Basis of an Integrative Multiomics Approach.
PMID:30706044
D3Oncoprint: Stand-Alone Software to Visualize and Dynamically Explore Annotated Genomic Mutation Files.
PMID:30652557
Knowledge base toward understanding actionable alterations and realizing precision oncology.
PMID:30542800
Database of evidence for precision oncology portal.
PMID:30535306
PDX Finder: A portal for patient-derived tumor xenograft model discovery.
PMID:30535239
Variant information systems for precision oncology.
PMID:30463544
Human Disease Ontology 2018 update: classification, content and workflow expansion.
PMID:30407550
PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs.
PMID:30407536
BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform.
PMID:30402350
A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data.
PMID:30397337
ClinGen Allele Registry links information about genetic variants.
PMID:30311374
Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.
PMID:30311370
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples.
PMID:30287923
SMART Cancer Navigator: A Framework for Implementing ASCO Workshop Recommendations to Enable Precision Cancer Medicine.
PMID:30238071
Cancer Informatics in 2017: A New Beginning and a Bright Future.
PMID:30157527
Novel clinicopathological and molecular characterization of metanephric adenoma: a study of 28 cases.
PMID:30111351
Computational resources associating diseases with genotypes, phenotypes and exposures.
PMID:30102366
Making the right calls in precision oncology.
PMID:30080824
Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning.
PMID:30059508
BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery.
PMID:30053270
Computational Approaches to Prioritize Cancer Driver Missense Mutations.
PMID:30037003
A systematic assessment of the availability and clinical drug information coverage of machine-readable clinical drug data sources for building knowledge translation products.
PMID:29982512
Standardizing And Democratizing Access To Cancer Molecular Diagnostic Test Data From Patients To Drive Translational Research.
PMID:29888062
Investigating the Feasibility of Targeted Next-Generation Sequencing to Guide the Treatment of Head and Neck Squamous Cell Carcinoma.
PMID:29747488
Genomics and electronic health record systems.
PMID:29741693
The emerging clinical relevance of genomics in cancer medicine.
PMID:29599476
Sample-Index Misassignment Impacts Tumour Exome Sequencing.
PMID:29593270
Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations.
PMID:29592813
Disease Ontology: improving and unifying disease annotations across species.
PMID:29590633
From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards.
PMID:29544535
Unexplored therapeutic opportunities in the human genome.
PMID:29472638
Classifying cancer genome aberrations by their mutually exclusive effects on transcription.
PMID:29322935
Interactive or static reports to guide clinical interpretation of cancer genomics.
PMID:29315417
Using single-cell multiple omics approaches to resolve tumor heterogeneity.
PMID:29285690
Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.
PMID:29276046
Personal Cancer Genome Reporter: variant interpretation report for precision oncology.
PMID:29272339
Bioinformatics for precision oncology.
PMID:29272324
eGARD: Extracting associations between genomic anomalies and drug responses from text.
PMID:29261751
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.
PMID:29254494
Informatics for cancer immunotherapy.
PMID:29253114
ClinGen Cancer Somatic Working Group - standardizing and democratizing access to cancer molecular diagnostic data to drive translational research.
PMID:29218886
Personalized cancer therapy-leveraging a knowledge base for clinical decision-making.
PMID:29212833
DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.
PMID:29156001
Comprehensive genomic analysis of Oesophageal Squamous Cell Carcinoma reveals clinical relevance.
PMID:29127303
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
PMID:29123641
Resources for Interpreting Variants in Precision Genomic Oncology Applications.
PMID:28975082
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine.
PMID:28968638
OncoKB: A Precision Oncology Knowledge Base.
PMID:28890946
Precision Oncology: The Road Ahead.
PMID:28887051
Managing the genomic revolution in cancer diagnostics.
PMID:28639053
Toward Molecularly Driven Precision Medicine in Lung Adenocarcinoma.
PMID:28576842
A knowledge-based framework for the discovery of cancer-predisposing variants using large-scale sequencing breast cancer data.
PMID:28569218
mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers.
PMID:28482068
PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories.
PMID:28438193
Genomics pipelines and data integration: challenges and opportunities in the research setting.
PMID:28092471
Somatic cancer variant curation and harmonization through consensus minimum variant level data.
PMID:27814769