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Approximation and inference methods for stochastic biochemical kinetics-a tutorial review

Journal of physics. A, Mathematical and theoretical, 2017-01, Vol.50 (9), p.93001

2017

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BRIE: transcriptome-wide splicing quantification in single cells

Genome Biology, 2017-06, Vol.18 (1), p.123-123, Article 123

2017

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BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments

Genome Biology, 2021-08, Vol.22 (1), p.251-251, Article 251

2021

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Comparison of different moment-closure approximations for stochastic chemical kinetics

The Journal of chemical physics, 2015-11, Vol.143 (18), p.185101-185101

2015

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Melissa: Bayesian clustering and imputation of single-cell methylomes

Genome Biology, 2019-03, Vol.20 (1), p.61-61, Article 61

2019

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SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data

Genome Biology, 2024-02, Vol.25 (1), p.55-17, Article 55

2024

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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

Nature communications, 2018-02, Vol.9 (1), p.781-9, Article 781

2018

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Model reduction for the Chemical Master Equation: An information-theoretic approach

The Journal of chemical physics, 2023-03, Vol.158 (11), p.114113-114113

2023

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Validity conditions for moment closure approximations in stochastic chemical kinetics

The Journal of chemical physics, 2014-08, Vol.141 (8), p.084103-084103

2014

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Single-trial classification of EEG in a visual object task using ICA and machine learning

Journal of neuroscience methods, 2014-05, Vol.228, p.1-14

2014

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Multi-omics profiling of mouse gastrulation at single-cell resolution

Nature (London), 2019-12, Vol.576 (7787), p.487-491

2019

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The complex chemical Langevin equation

The Journal of chemical physics, 2014-07, Vol.141 (2), p.024103-024103

2014

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Network of epistatic interactions within a yeast snoRNA

Science (American Association for the Advancement of Science), 2016-05, Vol.352 (6287), p.840-844

2016

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Point process modelling of the Afghan War Diary

Proceedings of the National Academy of Sciences - PNAS, 2012-07, Vol.109 (31), p.12414-12419

2012

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Transcription factor binding predicts histone modifications in human cell lines

Proceedings of the National Academy of Sciences - PNAS, 2014-09, Vol.111 (37), p.13367-13372

2014

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Cox process representation and inference for stochastic reaction–diffusion processes

Nature communications, 2016-05, Vol.7 (1), p.11729-11729, Article 11729

2016

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SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data

PLoS computational biology, 2022-06, Vol.18 (6), p.e1010163-e1010163

2022

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Subclonal reconstruction of tumors by using machine learning and population genetics

Nature genetics, 2020-09, Vol.52 (9), p.898-907

2020

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scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution

Genome Biology, 2021-04, Vol.22 (1), p.114-114, Article 114

2021

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diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data

Genome Biology, 2021-05, Vol.22 (1), p.165-165, Article 165

2021

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The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data

BMC bioinformatics, 2020-11, Vol.21 (1), p.531-531, Article 531

2020

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Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing

PLoS genetics, 2020-10, Vol.16 (10), p.e1009087-e1009087

2020

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MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain

PLoS genetics, 2017-05, Vol.13 (5), p.e1006793

2017

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Unbiased Bayesian inference for population Markov jump processes via random truncations

Statistics and computing, 2017, Vol.27 (4), p.991-1002

2017

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Modeling Conflict Dynamics with Spatio-Temporal Data

2013, 2013

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Approximation and inference methods for stochastic biochemical kinetics-a tutorial review

BRIE: transcriptome-wide splicing quantification in single cells

BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments

Comparison of different moment-closure approximations for stochastic chemical kinetics

Melissa: Bayesian clustering and imputation of single-cell methylomes

SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

Model reduction for the Chemical Master Equation: An information-theoretic approach

Validity conditions for moment closure approximations in stochastic chemical kinetics

Single-trial classification of EEG in a visual object task using ICA and machine learning

Multi-omics profiling of mouse gastrulation at single-cell resolution

The complex chemical Langevin equation

Network of epistatic interactions within a yeast snoRNA

Point process modelling of the Afghan War Diary

Transcription factor binding predicts histone modifications in human cell lines

Cox process representation and inference for stochastic reaction–diffusion processes

SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data

Subclonal reconstruction of tumors by using machine learning and population genetics

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution

diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data

The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data

Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing

MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain

Unbiased Bayesian inference for population Markov jump processes via random truncations

Modeling Conflict Dynamics with Spatio-Temporal Data

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