Cargando…

CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples

Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, an...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lu, Bingxin, Curtius, Kit, Graham, Trevor A., Yang, Ziheng, Barnes, Chris P.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2023
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10283241/ https://www.ncbi.nlm.nih.gov/pubmed/37340508 http://dx.doi.org/10.1186/s13059-023-02983-0

Ejemplares similares

Correcting for Sequencing Error in Maximum Likelihood Phylogeny Inference
por: Kuhner, Mary K., et al.
Publicado: (2014)

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
por: Nguyen, Lam-Tung, et al.
Publicado: (2015)

ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
por: Sashittal, Palash, et al.
Publicado: (2023)

Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty
por: Togkousidis, Anastasis, et al.
Publicado: (2023)

‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees
por: Dencker, Thomas, et al.
Publicado: (2019)

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
por: Kaufmann, Tom L., et al.
Publicado: (2022)

SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss
por: Morel, Benoit, et al.
Publicado: (2022)

An investigation of irreproducibility in maximum likelihood phylogenetic inference
por: Shen, Xing-Xing, et al.
Publicado: (2020)

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets
por: Zhou, Xiaofan, et al.
Publicado: (2018)

Detecting differential copy number variation between groups of samples
por: Lowe, Craig B., et al.
Publicado: (2018)

The Effect of Nonreversibility on Inferring Rooted Phylogenies
por: Cherlin, Svetlana, et al.
Publicado: (2018)

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data
por: Kessner, Darren, et al.
Publicado: (2013)

The identification of mediating effects using genome-based restricted maximum likelihood estimation
por: Rietveld, Cornelius A., et al.
Publicado: (2023)

Variational inference using approximate likelihood under the coalescent with recombination
por: Liu, Xinhao, et al.
Publicado: (2021)

Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
por: Rasmussen, Markus, et al.
Publicado: (2011)

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
por: Ha, Gavin, et al.
Publicado: (2014)

Controls for Phylogeny and Robust Analysis in Pareto Task Inference
por: Adler, Miri, et al.
Publicado: (2021)

Maximum likelihood estimation of a social relations structural equation model
por: Nestler, Steffen, et al.
Publicado: (2020)

High resolution copy number inference in cancer using short-molecule nanopore sequencing
por: Baslan, Timour, et al.
Publicado: (2021)

A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data
por: Jiang, Xiaoqian, et al.
Publicado: (2018)

A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences
por: Grimm, Guido W., et al.
Publicado: (2007)

Random Effects Multinomial Processing Tree Models: A Maximum Likelihood Approach
por: Nestler, Steffen, et al.
Publicado: (2023)

Single-cell copy number variation detection
por: Cheng, Jiqiu, et al.
Publicado: (2011)

Maximum Likelihood Estimation and Inference: With Examples in R, SAS and ADMB
por: Millar, Russell B
Publicado: (2011)

Maximum Likelihood Inference of Small Trees in the Presence of Long Branches
por: Parks, Sarah L., et al.
Publicado: (2014)

Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis
por: Letouzé, Eric, et al.
Publicado: (2010)

Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees
por: Wang, Yaxuan, et al.
Publicado: (2020)

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia
por: Jones, Matthew G, et al.
Publicado: (2020)

Maximum Augmented Empirical Likelihood Estimation of Categorical Marginal Models for Large Sparse Contingency Tables
por: van der Ark, L. Andries, et al.
Publicado: (2023)

Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria
por: Park, Hyun Jung, et al.
Publicado: (2012)

Transfering Targeted Maximum Likelihood Estimation for Causal Inference into Sports Science
por: Dijkhuis, Talko B., et al.
Publicado: (2022)

NetRAX: accurate and fast maximum likelihood phylogenetic network inference
por: Lutteropp, Sarah, et al.
Publicado: (2022)

Negative Binomial mixed models estimated with the maximum likelihood method can be used for longitudinal RNAseq data
por: Tsonaka, Roula, et al.
Publicado: (2020)

Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study
por: Bhutkar, Arjun, et al.
Publicado: (2007)

A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples
por: Saunderson, Emily A, et al.
Publicado: (2019)

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling
por: Hall, Matthew D, et al.
Publicado: (2019)

Inferring excitation-inhibition dynamics using a maximum entropy model unifying brain structure and function
por: Fortel, Igor, et al.
Publicado: (2022)

Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples
por: Hostetter, Galen, et al.
Publicado: (2010)

Analysis of molecular inversion probe performance for allele copy number determination
por: Wang, Yuker, et al.
Publicado: (2007)

Copy number variation detection and genotyping from exome sequence data
por: Krumm, Niklas, et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_rtqvrsjjhlpku5qhociabele7u