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dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data

Scientific reports, 2018-02, Vol.8 (1), p.3384-12, Article 3384

2018

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NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms

PloS one, 2014-03, Vol.9 (3), p.e92709-e92709

2014

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Inferring regulatory networks from expression data using tree-based methods

PloS one, 2010-09, Vol.5 (9), p.e12776

2010

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Combining tree-based and dynamical systems for the inference of gene regulatory networks

Bioinformatics, 2015-05, Vol.31 (10), p.1614-1622

2015

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Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference

Cell reports (Cambridge), 2014-12, Vol.9 (6), p.2290-2303

2014

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Bridging physiological and evolutionary time‐scales in a gene regulatory network

The New phytologist, 2014-07, Vol.203 (2), p.685-696

2014

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MicroRNAs profiling in murine models of acute and chronic asthma: a relationship with mRNAs targets

PloS one, 2011-01, Vol.6 (1), p.e16509-e16509

2011

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Identification of a microRNA landscape targeting the PI3K/Akt signaling pathway in inflammation-induced colorectal carcinogenesis

American journal of physiology: Gastrointestinal and liver physiology, 2014-02, Vol.306 (3), p.G229-G243

2014

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Optimizing model-agnostic random subspace ensembles

Machine learning, 2024-02, Vol.113 (2), p.993-1042

2024

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SCENIC: single-cell regulatory network inference and clustering

Nature methods, 2017-11, Vol.14 (11), p.1083-1086

2017

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Myelin-derived lipids modulate macrophage activity by liver X receptor activation

PloS one, 2012-09, Vol.7 (9), p.e44998-e44998

2012

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Statistical interpretation of machine learning-based feature importance scores for biomarker discovery

Bioinformatics (Oxford, England), 2012-07, Vol.28 (13), p.1766-1774

2012

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Distinct blood protein profiles associated with the risk of short-term and mid/long-term clinical relapse in patients with Crohn’s disease stopping infliximab: when the remission state hides different types of residual disease activity

Gut, 2023-03, Vol.72 (3), p.443-450

2023

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Discovery of biomarker candidates associated with the risk of short-term and mid/long-term relapse after infliximab withdrawal in Crohn’s patients: a proteomics-based study

Gut, 2021-08, Vol.70 (8), p.1450-1457

2021

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Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease

Journal of proteomics, 2024-06, Vol.302, p.105199, Article 105199

2024

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External validation of serum biomarkers predicting short-term and mid/long-term relapse in patients with Crohn’s disease stopping infliximab

Gut, 2024-08, p.gutjnl-2024-332648

2024

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Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks

Methods in molecular biology (Clifton, N.J.), 2019, Vol.1883, p.161

2019

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Inferring Gene Regulatory Networks from Multiple Datasets

Methods in molecular biology (Clifton, N.J.), 2019, Vol.1883, p.251

2019

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Wisdom of crowds for robust gene network inference

Nature methods, 2012-07, Vol.9 (8), p.796-804

2012

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Strand‐specific, high‐resolution mapping of modified RNA polymerase II

Molecular systems biology, 2016-06, Vol.12 (6), p.874-n/a

2016

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Knowledge-Guided Additive Modeling for Supervised Regression

Discovery Science, 2023, p.64-78

2023

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Nets Versus Trees for Feature Ranking and Gene Network Inference

Discovery Science, p.231-245

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Machine Learning-Based Feature Ranking: Statistical Interpretation and Gene Network Inference

Huynh-Thu, Vân Anh

2011

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NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms: e92709

PloS one, 2014-03, Vol.9 (3)

2014

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Distinct biological profiles associated with the risk of short-term relapse and mid/long-term relapse in Crohn’s disease patients stopping infliximab

2023

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dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data

NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms

Inferring regulatory networks from expression data using tree-based methods

Combining tree-based and dynamical systems for the inference of gene regulatory networks

Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference

Bridging physiological and evolutionary time‐scales in a gene regulatory network

MicroRNAs profiling in murine models of acute and chronic asthma: a relationship with mRNAs targets

Identification of a microRNA landscape targeting the PI3K/Akt signaling pathway in inflammation-induced colorectal carcinogenesis

Optimizing model-agnostic random subspace ensembles

SCENIC: single-cell regulatory network inference and clustering

Myelin-derived lipids modulate macrophage activity by liver X receptor activation

Statistical interpretation of machine learning-based feature importance scores for biomarker discovery

Distinct blood protein profiles associated with the risk of short-term and mid/long-term clinical relapse in patients with Crohn’s disease stopping infliximab: when the remission state hides different types of residual disease activity

Discovery of biomarker candidates associated with the risk of short-term and mid/long-term relapse after infliximab withdrawal in Crohn’s patients: a proteomics-based study

Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease

External validation of serum biomarkers predicting short-term and mid/long-term relapse in patients with Crohn’s disease stopping infliximab

Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks

Inferring Gene Regulatory Networks from Multiple Datasets

Wisdom of crowds for robust gene network inference

Strand‐specific, high‐resolution mapping of modified RNA polymerase II

Knowledge-Guided Additive Modeling for Supervised Regression

Nets Versus Trees for Feature Ranking and Gene Network Inference

Machine Learning-Based Feature Ranking: Statistical Interpretation and Gene Network Inference

NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms: e92709

Distinct biological profiles associated with the risk of short-term relapse and mid/long-term relapse in Crohn’s disease patients stopping infliximab

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