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BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process

Genome Biology, 2018-05, Vol.19 (1), p.65-65, Article 65

2018

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Evolution of IgE responses to multiple allergen components throughout childhood

Journal of allergy and clinical immunology, 2018-10, Vol.142 (4), p.1322-1330

2018

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miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

PLoS computational biology, 2021-08, Vol.17 (8), p.e1009290-e1009290

2021

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Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5' to 3' degradation

PLoS biology, 2023-01, Vol.21 (1), p.e3001956-e3001956

2023

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MIDER: network inference with mutual information distance and entropy reduction

PloS one, 2014-05, Vol.9 (5), p.e96732-e96732

2014

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Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression

PloS one, 2015-03, Vol.10 (3), p.e0119821-e0119821

2015

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Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis

Nature communications, 2019-06, Vol.10 (1), p.2835-19, Article 2835

2019

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Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis

Nature communications, 2020-09, Vol.11 (1), p.4402-4402, Article 4402

2020

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Murine AGM single-cell profiling identifies a continuum of hemogenic endothelium differentiation marked by ACE

Blood, 2022-01, Vol.139 (3), p.343-356

2022

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OscoNet: inferring oscillatory gene networks

BMC bioinformatics, 2020-08, Vol.21 (Suppl 10), p.351-351, Article 351

2020

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A genetic study of Wilson's disease in the United Kingdom

Brain (London, England : 1878), 2013-05, Vol.136 (Pt 5), p.1476-1487

2013

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Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

Proceedings of the National Academy of Sciences - PNAS, 2015-10, Vol.112 (42), p.13115-13120

2015

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Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference

PLoS computational biology, 2016-11, Vol.12 (11), p.e1005212-e1005212

2016

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DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment

PLoS computational biology, 2021-10, Vol.17 (10), p.e1009465-e1009465

2021

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Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples

PloS one, 2011-11, Vol.6 (11), p.e27156-e27156

2011

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HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation

PLoS genetics, 2020-12, Vol.16 (12), p.e1009162-e1009162

2020

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C9ORF72 GGGGCC Expanded Repeats Produce Splicing Dysregulation which Correlates with Disease Severity in Amyotrophic Lateral Sclerosis

PloS one, 2015-05, Vol.10 (5), p.e0127376

2015

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Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005479-e1005479

2017

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Modulation of transcription burst amplitude underpins dosage compensation in the Drosophila embryo

Cell reports (Cambridge), 2023-04, Vol.42 (4), p.112382-112382, Article 112382

2023

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Gene regulatory network reconstruction using Bayesian networks, the Dantzig Selector, the Lasso and their meta-analysis

PloS one, 2011-12, Vol.6 (12), p.e29165-e29165

2011

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The Circadian Clock in Murine Chondrocytes Regulates Genes Controlling Key Aspects of Cartilage Homeostasis

Arthritis & rheumatology (Hoboken, N.J.), 2013-09, Vol.65 (9), p.2334-2345

2013

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Identification of differences in CD4 + T-cell gene expression between people with asthma and healthy controls

Scientific reports, 2023-12, Vol.13 (1), p.22796-22796, Article 22796

2023

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A systems immunology approach to investigate cytokine responses to viruses and bacteria and their association with disease

Scientific reports, 2022-08, Vol.12 (1), p.13463-13463, Article 13463

2022

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Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks

PloS one, 2011-05, Vol.6 (5), p.e19729-e19729

2011

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Sex differences in innate anti-viral immune responses to respiratory viruses and in their clinical outcomes in a birth cohort study

Scientific reports, 2021-12, Vol.11 (1), p.23741-23741, Article 23741

2021

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BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process

Evolution of IgE responses to multiple allergen components throughout childhood

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5' to 3' degradation

MIDER: network inference with mutual information distance and entropy reduction

Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression

Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis

Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis

Murine AGM single-cell profiling identifies a continuum of hemogenic endothelium differentiation marked by ACE

OscoNet: inferring oscillatory gene networks

A genetic study of Wilson's disease in the United Kingdom

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference

DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment

Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation

C9ORF72 GGGGCC Expanded Repeats Produce Splicing Dysregulation which Correlates with Disease Severity in Amyotrophic Lateral Sclerosis

Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes

Modulation of transcription burst amplitude underpins dosage compensation in the Drosophila embryo

Gene regulatory network reconstruction using Bayesian networks, the Dantzig Selector, the Lasso and their meta-analysis

The Circadian Clock in Murine Chondrocytes Regulates Genes Controlling Key Aspects of Cartilage Homeostasis

Identification of differences in CD4 + T-cell gene expression between people with asthma and healthy controls

A systems immunology approach to investigate cytokine responses to viruses and bacteria and their association with disease

Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks

Sex differences in innate anti-viral immune responses to respiratory viruses and in their clinical outcomes in a birth cohort study

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