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A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression
2019
Algorithms for Molecular Biology
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We introduce a new dissimilarity measure between a pair of "clonal trees", each representing the progression and mutational heterogeneity of a tumor sample, constructed by the use of single cell or bulk ...
Given two clonal trees, our multi-labeled tree dissimilarity (MLTD) measure is defined as the minimum number of mutation/label deletions, (empty) leaf deletions, and vertex (clonal) expansions, applied ...
One of the most widely used ways of depicting mutational heterogeneity and tumor progression over time is by the use of a clonal tree of tumor evolution. ...
doi:10.1186/s13015-019-0152-9
pmid:31372179
pmcid:PMC6661107
fatcat:7ozycr2qpbhfde74n6vdxfc64e
A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression
2018
Workshop on Algorithms in Bioinformatics
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We introduce a new edit distance measure between a pair of "clonal trees", each representing the progression and mutational heterogeneity of a tumor sample, constructed by the use of single cell or bulk ...
Given two clonal trees, our multi-labeled tree edit distance (MLTED) measure is defined as the minimum number of mutation/label deletions, (empty) leaf deletions, and vertex (clonal) expansions, applied ...
WA B I 2 0 1 8
22:6 Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression Proof. The first equation easily follows from the fact that A(i, 0) ⊆ ∅ and A(0, j) ⊆ ∅. ...
doi:10.4230/lipics.wabi.2018.22
dblp:conf/wabi/KarpovMRS18
fatcat:4dr2tygncbfd3jrbd2on5jocme
Distance Measures for Tumor Evolutionary Trees
2019
Bioinformatics
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Quantitative measures that compare such trees are vital to a number of different applications including benchmarking tree inference methods and evaluating common inheritance patterns across patients. ...
Motivation There has been recent increased interest in using algorithmic methods to infer the evolutionary tree underlying the developmental history of a tumor. ...
Acknowledgements We thank Jack Kupiers for useful conversations related to this work. ...
doi:10.1093/bioinformatics/btz869
pmid:31750900
pmcid:PMC7141873
fatcat:l2kiwyirirdjzjungkhhodya3a
Distance Measures for Tumor Evolutionary Trees
[article]
2019
bioRxiv
pre-print
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Quantitative measures that compare such trees are then vital to benchmarking these algorithmic tree inference methods, understanding the structure of the space of possible trees for a given dataset, and ...
inheritance patterns characteristic of tumor evolutionary trees. ...
A tumor evolution distance measure is a function d : T × T −→ R ≥0 for which a value of d(·, ·) that is close to 0 indicates that the two input clonal trees are very similar and progressively larger values ...
doi:10.1101/591107
fatcat:ajev6u3ihjdpxgjdypyj5xass4
PhISCS - A Combinatorial Approach for Sub-perfect Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data
[article]
2018
bioRxiv
pre-print
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We express our formulation both in the form of an integer linear program (ILP) and - for the first time in the context of tumor phylogeny reconstruction - a boolean constraint satisfaction problem (CSP ...
Available computational methods for tumor phylogeny inference via SCS typically aim to identify the most likely perfect phylogeny tree satisfying infinite sites assumption (ISA). ...
Danko for fruitful discussions on the formulations. ...
doi:10.1101/376996
fatcat:fvpohlcyt5c6rnnkfs77tnj52a
Reconstructing the evolutionary history of a BCR lineage with minimum spanning tree and clonotype abundances
[article]
2022
bioRxiv
pre-print
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There are a few phylogenetic methods for reconstructing the evolutionary history of B cell lineages; best-performing solutions are time-demanding and restricted to analyze a reduced number of BCR sequences ...
Using both simulated and experimental data, we demonstrated that ClonalTree outperforms MST-based algorithms and achieves a similar performance compared to a method that explores tree generating space ...
Acknowledgements Authors are grateful to Lucile Jeusset and Thibaud Verny for their insightful comments and fruitful discussion. ...
doi:10.1101/2022.02.27.481992
fatcat:74ratmzmu5affowidaumcu7zba
Inferring tumour evolution from single-cell and multi-sample data
2018
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This dissertation focuses on computational methods for inferring trees of tumour evolution from single-cell and multi-sample sequencing data. ...
The first part of the dissertation describes OncoNEM, a novel probabilistic method to infer clonal lineage trees from noisy single nucleotide variants of single cells. ...
Thank you also to past and present members of the Markowetz lab for their friendship and for stimulating discussions. ...
doi:10.17863/cam.21747
fatcat:63e6vpdaqvgphmcznvuthcav2q