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A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression

Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, S. Cenk Sahinalp
2019 Algorithms for Molecular Biology  
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

Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, S. Cenk Sahinalp, Michael Wagner
2018 Workshop on Algorithms in Bioinformatics  
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

Zach DiNardo, Kiran Tomlinson, Anna Ritz, Layla Oesper, Yann Ponty
2019 Bioinformatics  
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]

Zach DiNardo, Kiran Tomlinson, Anna Ritz, Layla Oesper
2019 bioRxiv   pre-print
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]

Salem Malikic, Simone Ciccolella, Farid Rashidi Mehrabadi, Camir Ricketts, Md. Khaledur Rahman, Ehsan Haghshenas, Daniel Seidman, Faraz Hach, Iman Hajirasouliha, S. Cenk Sahinalp
2018 bioRxiv   pre-print
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]

Nika Abdollahi, Anne de Septenville, Frederic Davi, Juliana Silva Bernardes
2022 bioRxiv   pre-print
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

Edith Ross, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Florian Markowetz
2018
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