ArticleBioinformatics (Oxford, England)2016
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Analysis of Single Circulating Tumor Cells in Renal Cell Carcinoma Reveals Phenotypic Heterogeneity and Genomic Alterations Related to Progression.International journal of molecular sciences · 2020Trial
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- A latent variable model for evaluating mutual exclusivity and co-occurrence between driver mutations in cancer.bioRxiv : the preprint server for biology · 2024Article
- Analysis of genomic and immune intratumor heterogeneity in linitis plastica via multiregional exome and T-cell receptor sequencing.Molecular oncology · 2023Article
- HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs.Bioinformatics (Oxford, England) · 2023Article
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- Stepwise evolutionary genomics of early-stage lung adenocarcinoma manifesting as pure, heterogeneous and part-solid ground-glass nodules.British journal of cancer · 2022Article
- Article
- Sequencing of Cutaneous Squamous Cell Carcinoma Primary Tumors and Patient-Matched Metastases RevealsJID innovations : skin science from molecules to population health · 2022Article
- Bayesian networks elucidate complex genomic landscapes in cancer.Communications biology · 2022Article
- Copy number alterations analysis of primary tumor tissue and circulating tumor cells from patients with early-stage triple negative breast cancer.Scientific reports · 2022Article
- Genomic Underpinnings of Tumor Behavior inAmerican journal of respiratory and critical care medicine · 2020Article
- Article
- Article
- The evolution of tumour phylogenetics: principles and practice.Nature reviews. Genetics · 2017Review
- Algorithmic methods to infer the evolutionary trajectories in cancer progression.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationWe introduce TRanslational ONCOlogy (TRONCO), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract population-level models describing the trends of accumulation of alterations in a cohort of cross-sectional samples, e.g. retrieved from publicly available databases, and individual-level models that reveal the clonal evolutionary history in single cancer patients, when multiple samples, e.g. multiple biopsies or single-cell sequencing data, are available. The resulting models can provide key hints for uncovering the evolutionary trajectories of cancer, especially for precision medicine or personalized therapy. AVAILABILITY AND IMPLEMENTATION: TRONCO is released under the GPL license, is hosted at http://bimib.disco.unimib.it/ (Software section) and archived also at bioconductor.org. CONTACT: tronco@disco.unimib.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.