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Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization

BMC bioinformatics, 2023-05, Vol.24 (1), p.187-187, Article 187

2023

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Detecting archaic introgression using an unadmixed outgroup

PLoS genetics, 2018-09, Vol.14 (9), p.e1007641-e1007641

2018

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Multivariate phase-type theory for the site frequency spectrum

Journal of mathematical biology, 2021-12, Vol.83 (6-7), p.63-63, Article 63

2021

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Graph-based algorithms for phase-type distributions

Statistics and computing, 2022-12, Vol.32 (6), Article 103

2022

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Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

Genome research, 2011-03, Vol.21 (3), p.349-356

2011

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Comparative and demographic analysis of orang-utan genomes

Nature (London), 2011-01, Vol.469 (7331), p.529-533

2011

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Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

eLife, 2017-03, Vol.6

2017

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Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model

PLoS genetics, 2007-02, Vol.3 (2), p.e7-e7

2007

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Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains

BMC bioinformatics, 2011-12, Vol.12 (1), p.465-465, Article 465

2011

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Significance evaluation in factor graphs

BMC bioinformatics, 2017-03, Vol.18 (1), p.199-199, Article 199

2017

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A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species

PLoS genetics, 2012-12, Vol.8 (12), p.e1003125-e1003125

2012

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A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data

BMC bioinformatics, 2018-04, Vol.19 (1), p.147-147, Article 147

2018

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Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model

PLoS genetics, 2011-03, Vol.7 (3), p.e1001319-e1001319

2011

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Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach

Genetics (Austin), 2009-09, Vol.183 (1), p.259-274

2009

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Maximum likelihood estimation and natural pairwise estimating equations are identical for three sequences and a symmetric 2-state substitution model

Theoretical population biology, 2024-04, Vol.156, p.1-4

2024

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Extreme selective sweeps independently targeted the X chromosomes of the great apes

Proceedings of the National Academy of Sciences - PNAS, 2015-05, Vol.112 (20), p.6413-6418

2015

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Extensive X-linked adaptive evolution in central chimpanzees

Proceedings of the National Academy of Sciences - PNAS, 2012-02, Vol.109 (6), p.2054-2059

2012

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Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments

Algorithms for molecular biology, 2018-12, Vol.13 (1), p.17-17, Article 17

2018

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Studying models of balancing selection using phase-type theory

Genetics (Austin), 2021-06, Vol.218 (2)

2021

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An alternative derivation of the stationary distribution of the multivariate neutral Wright–Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data

Theoretical population biology, 2017-04, Vol.114, p.88-94

2017

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A Sampling Algorithm to Compute the Set of Feasible Solutions for NonNegative Matrix Factorization with an Arbitrary Rank

SIAM journal on matrix analysis and applications, 2022-01, Vol.43 (1), p.257-273

2022

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Flexible model-based non-negative matrix factorization with application to mutational signatures

Statistical applications in genetics and molecular biology, 2024-01, Vol.23 (1)

2024

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Statistical Inference in the Wright–Fisher Model Using Allele Frequency Data

Systematic biology, 2017-01, Vol.66 (1), p.e30-e46

2017

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Phase-type distributions in population genetics

Theoretical population biology, 2019-06, Vol.127, p.16-32

2019

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The multivariate Wright–Fisher process with mutation: Moment-based analysis and inference using a hierarchical Beta model

Theoretical population biology, 2016-04, Vol.108, p.36-50

2016

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Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization

Detecting archaic introgression using an unadmixed outgroup

Multivariate phase-type theory for the site frequency spectrum

Graph-based algorithms for phase-type distributions

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

Comparative and demographic analysis of orang-utan genomes

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model

Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains

Significance evaluation in factor graphs

A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species

A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data

Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model

Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach

Maximum likelihood estimation and natural pairwise estimating equations are identical for three sequences and a symmetric 2-state substitution model

Extreme selective sweeps independently targeted the X chromosomes of the great apes

Extensive X-linked adaptive evolution in central chimpanzees

Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments

Studying models of balancing selection using phase-type theory

An alternative derivation of the stationary distribution of the multivariate neutral Wright–Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data

A Sampling Algorithm to Compute the Set of Feasible Solutions for NonNegative Matrix Factorization with an Arbitrary Rank

Flexible model-based non-negative matrix factorization with application to mutational signatures

Statistical Inference in the Wright–Fisher Model Using Allele Frequency Data

Phase-type distributions in population genetics

The multivariate Wright–Fisher process with mutation: Moment-based analysis and inference using a hierarchical Beta model

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