T. Michoel

发表

Module Network Inference from a Cancer Gene Expression Data Set Identifies MicroRNA Regulated Modules

Y. van de Peer, E. Bonnet, M. Tatari, 2010, PloS one.

The Index-Based Subgraph Matching Algorithm (ISMA): Fast Subgraph Enumeration in Large Networks Using Optimized Search Trees

T. Michoel, P. Demeester, M. Pickavet, 2013, PloS one.

The Index-Based Subgraph Matching Algorithm with General Symmetries (ISMAGS): Exploiting Symmetry for Faster Subgraph Enumeration

T. Michoel, D. Colle, M. Pickavet, 2014, PloS one.

Functional transcription factor target discovery via compendia of binding and expression profiles

Anagha Joshi, Tom Michoel, A. Joshi, 2015, Scientific Reports.

Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections

T. Michoel, C. Hertz-Fowler, S. Jayaraman, 2019, PLoS neglected tropical diseases.

Characterizing regulatory path motifs in integrated networks using perturbational data

Yves Van de Peer, Anagha Joshi, Tom Michoel, 2010, Genome Biology.

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases

Tom Michoel, Claudia Giambartolomei, Eric E. Schadt, 2016, Science.

Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast

T. Michoel, Adriaan-Alexander Ludl, 2020, bioRxiv.

Causal gene regulatory network inference using enhancer activity as a causal anchor

A. Joshi, T. Michoel, G. Devailly, 2018, bioRxiv.

Causal Transcription Regulatory Network Inference Using Enhancer Activity as a Causal Anchor

A. Joshi, T. Michoel, G. Devailly, 2018, International journal of molecular sciences.

Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections

John G Kenny, T. Michoel, C. Hertz-Fowler, 2018, bioRxiv.

Graph-based data integration predicts long-range regulatory interactions across the human genome

T. Michoel, S. Demeyer, 2014, bioRxiv.

Cattle trypanosomosis: the diversity of trypanosomes and implications for disease epidemiology and control.

T. Michoel, S. Jayaraman, S. Torr, 2015, Revue scientifique et technique.

Lim Domain Binding 2: A Key Driver of Transendothelial Migration of Leukocytes and Atherosclerosis

E. Schadt, J. Björkegren, T. Michoel, 2014, Arteriosclerosis, thrombosis, and vascular biology.

Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants[W]

Steven Maere, J. Hollunder, T. Michoel, 2013, Plant Cell.

Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast

Y. van de Peer, A. Joshi, T. Michoel, 2011, Nucleic acids research.

Meta-analysis of Liver and Heart Transcriptomic Data for Functional Annotation Transfer in Mammalian Orthologs

A. Joshi, T. Michoel, G. Devailly, 2017, bioRxiv.

Meta-analysis of liver transcriptomic data to identify mammalian functional orthologs

A. Joshi, T. Michoel, G. Devailly, 2017 .

High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering

T. Michoel, P. Audenaert, Lingfei Wang, 2019, Frontiers in genetics.

Controlling false discoveries in Bayesian gene networks with lasso regression p-values

T. Michoel, Lingfei Wang, 2017, bioRxiv.

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

Piero Carninci, Y. Hayashizaki, D. Hume, 2015, Journal of leukocyte biology.

Human Validation of Genes Associated With a Murine Atherosclerotic Phenotype

N. Samani, J. Björkegren, H. Schunkert, 2014, Arteriosclerosis, thrombosis, and vascular biology.

Variation in the SERPINA6SERPINA1 locusalters morning plasma cortisol, hepatic corticosteroid binding globulin expression, gene expressionin peripheral tissues, and risk of cardiovascular disease

M. Jarvelin, C. Gieger, T. Spector, 2021 .

Variants in ALOX5, ALOX5AP and LTA4H are not associated with atherosclerotic plaque phenotypes: the Athero-Express Genomics Study.

P. D. de Bakker, J. Björkegren, T. Michoel, 2015, Atherosclerosis.

eQTLs as causal instruments for the reconstruction of hormone linked gene networks

T. Michoel, S. Bankier, 2022, Frontiers in Endocrinology.

Contribution of Regulatory-Gene Networks to Heritability of Coronary Artery Disease

J. Björkegren, H. Schunkert, T. Michoel, 2019 .

Edinburgh Research Explorer Variation in the SERPINA6SERPINA1 locusalters morning plasma cortisol, hepatic corticosteroid binding globulin expression, gene expressionin peripheral tissues, and risk of cardiovascular disease

M. Jarvelin, C. Gieger, T. Spector, 2021 .

Causal inference in drug discovery and development

T. Michoel, J. Zhang, 2022, Drug discovery today.

Changes in the gene expression profile during spontaneous migraine attacks

J. Olesen, A. Buil, T. Michoel, 2020, Scientific Reports.

Variable reproducibility in genome-scale public data

A. Joshi, T. Michoel, G. Devailly, 2015 .

Towards system level modeling of functional modules and regulatory pathways using genome-scale data

Y. Peer, E. Bonnet, A. Joshi, 2010 .

Goldstone Boson Normal Coordinates in Interacting Bose Gases

T. Michoel, A. Verbeure, 1999, math-ph/9903003.

Model-based clustering of multi-tissue gene expression data. Bioinformatics

J. Björkegren, T. Michoel, Pau Erola, 2019 .

Goldstone Boson Normal Coordinates

T. Michoel, A. Verbeure, 2000, math-ph/0001033.

Central limit theorems for the large-spin asymptotics of quantum spins

T. Michoel, B. Nachtergaele, 2003, math-ph/0310027.

The large-spin asymptotics of the ferromagnetic XXZ chain

T. Michoel, B. Nachtergaele, 2003, math-ph/0307051.

Mathematical structure of magnons in quantum ferromagnets

T. Michoel, A. Verbeure, 1999, math-ph/9903004.

Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data

Yves Van de Peer, Tom Michoel, Eric Bonnet, 2010, Bioinform..

Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets

N. Samani, J. Björkegren, J. Erdmann, 2018, Scientific Reports.

Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast

Tom Michoel, Adriaan-Alexander Ludl, T. Michoel, 2020, bioRxiv.

Alignment and integration of complex networks by hypergraph-based spectral clustering

Tom Michoel, Bruno Nachtergaele, T. Michoel, 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks

Piet Demeester, Mario Pickavet, Yves Van de Peer, 2011, Bioinform..

A Scalable Method for Molecular Network Reconstruction Identifies Properties of Targets and Mutations in Acute Myeloid Leukemia

Anagha Joshi, Tom Michoel, Yvonne Beck, 2014, J. Comput. Biol..

Human Y Chromosome Exerts Pleiotropic Effects on Susceptibility to Atherosclerosis

James M. Eales, M. Jobling, N. Samani, 2019, Arteriosclerosis, thrombosis, and vascular biology.

Carbonyl reductase 1 catalyzes 20β-reduction of glucocorticoids, modulating receptor activation and metabolic complications of obesity

E. Schadt, J. Björkegren, T. Michoel, 2017, Scientific Reports.

Enhancer decommissioning by Snail1-induced competitive displacement of TCF7L2 and down-regulation of transcriptional activators results in EPHB2 silencing.

T. Michoel, R. Grosschedl, A. Hecht, 2016, Biochimica et biophysica acta.

A Graph Feature Auto-Encoder for the prediction of unobserved node features on biological networks

Tom Michoel, Ramin Hasibi, T. Michoel, 2021, BMC Bioinformatics.

Microglial brain region-dependent diversity and selective regional sensitivities to ageing

Tom Michoel, Mark P Stevens, Sara Clohisey, 2015, Nature Neuroscience.

Microglial brain regiondependent diversity and selective regional sensitivities to aging

T. Michoel, B. McColl, T. Freeman, 2015 .

High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering

Tom Michoel, Pieter Audenaert, Lingfei Wang, 2018, bioRxiv.

Smoking is Associated to DNA Methylation in Atherosclerotic Carotid Lesions

J. Björkegren, T. Michoel, M. van Iterson, 2018, Circulation. Genomic and precision medicine.

SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer

T. Michoel, R. Schüle, S. Lassmann, 2015, Molecular oncology.

Silencing of the EPHB3 tumor-suppressor gene in human colorectal cancer through decommissioning of a transcriptional enhancer

T. Michoel, M. Werner, S. Lassmann, 2014, Proceedings of the National Academy of Sciences.

Variation in the SERPINA6/SERPINA1 locus alters morning plasma cortisol, hepatic corticosteroid binding globulin expression, gene expression in peripheral tissues, and risk of cardiovascular disease

M. Jarvelin, C. Gieger, T. Spector, 2021, Journal of Human Genetics.

A mechanistic framework for cardiometabolic and coronary artery diseases

E. Schadt, J. Björkegren, H. Schunkert, 2022, Nature Cardiovascular Research.

Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks.

Anagha Joshi, Tom Michoel, Bruno Nachtergaele, 2011, Molecular bioSystems.

Software regulatory path motifs in integrated networks using perturbational data

Yves Van de Peer, Tom Michoel, Thomas Van Parys, 2010 .

Prediction of human population responses to toxic compounds by a collaborative competition

Ana L. Teixeira, Eleni G. Christodoulou, Jeffrey T. Chang, 2015, Nature Biotechnology.

Module networks revisited: computational assessment and prioritization of model predictions

Kathleen Marchal, Yves Van de Peer, Anagha Joshi, 2009, Bioinform..

Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development.

Anagha Joshi, Tom Michoel, Eric Bonnet, 2009, Molecular bioSystems.

Plasma Cholesterol–Induced Lesion Networks Activated before Regression of Early, Mature, and Advanced Atherosclerosis

J. Björkegren, T. Michoel, O. Melander, 2014, PLoS genetics.

Detection of Regulator Genes and eQTLs in Gene Networks

Tom Michoel, Lingfei Wang, T. Michoel, 2015, 1512.05574.

Post‐transcriptional regulatory networks play a key role in noise reduction that is conserved from micro‐organisms to mammals

Anagha Joshi, Tom Michoel, A. Joshi, 2012, The FEBS journal.

Expression Quantitative Trait Loci Acting Across Multiple Tissues Are Enriched in Inherited Risk for Coronary Artery Disease

Tom Michoel, Eric E Schadt, Olle Melander, 2015, Circulation. Cardiovascular genetics.

Model-based clustering of multi-tissue gene expression data

Tom Michoel, Pau Erola, Johan L M Björkegren, 2018, Bioinform..

Context-specific transcriptional regulatory network inference from global gene expression maps using double two-way t-tests

Tom Michoel, Jianlong Qi, T. Michoel, 2012, Bioinform..

Reverse‐Engineering Transcriptional Modules from Gene Expression Data

Kathleen Marchal, Tom Michoel, Riet De Smet, 2009, Annals of the New York Academy of Sciences.

Gene networks driven by genetic variation for plasma cortisol in hepatic and adipose tissues implicate corticosteroid binding globulin in modulating tissue glucocorticoid action and cardiovascular risk

J. Björkegren, T. Michoel, B. Walker, 2023, bioRxiv.

Contribution of Gene Regulatory Networks to Heritability of Coronary Artery Disease.

E. Schadt, J. Björkegren, H. Schunkert, 2019, Journal of the American College of Cardiology.

A regression tree-based Gibbs sampler to learn the regulation programs in a transcription regulatory module network

Gregory Butler, Tom Michoel, Jianlong Qi, 2010, 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

Whole-Transcriptome Causal Network Inference with Genomic and Transcriptomic Data.

Tom Michoel, Lingfei Wang, T. Michoel, 2018, Methods in molecular biology.

Nonextensive Bose–Einstein condensation model

T. Michoel, A. Verbeure, 1999, math-ph/0011047.

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

Tom Michoel, Ben Readhead, Brian A. Kidd, 2016, Cell systems.

Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data

Tom Michoel, Lingfei Wang, T. Michoel, 2016, bioRxiv.

RFPHEN2GEN: A MACHINE LEARNING BASED ASSOCIATION STUDY OF BRAIN IMAGING PHENOTYPES TO GENOTYPES

Muhammad Ammar Malik, T. Michoel, A. Lundervold, 2022, European Neuropsychopharmacology.

Tesla-Rapture: A Lightweight Gesture Recognition System From mmWave Radar Sparse Point Clouds

P. Popovski, T. Michoel, S. Sigg, 2023, IEEE Transactions on Mobile Computing.

kruX: matrix-based non-parametric eQTL discovery

Tom Michoel, Jianlong Qi, Johan Björkegren, 2013, BMC Bioinformatics.

J. Björkegren, T. Michoel, B. Walker, 2023, bioRxiv.

Cross-TissueRegulatory G eneNetworks in Coronary Artery Disease Graphical Abstract Highlights

E. Schadt, J. Dudley, J. Björkegren, 2016 .

Integrative Multi-omics Module Network Inference with Lemon-Tree

Tom Michoel, Eric Bonnet, Laurence Calzone, 2014, PLoS Comput. Biol..

Accurate wisdom of the crowd from unsupervised dimension reduction

Tom Michoel, Lingfei Wang, T. Michoel, 2017, Royal Society Open Science.

Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource

Guillaume Devailly, Anna Mantsoki, Anagha Joshi, 2015, FEBS letters.

Learning Differential Module Networks Across Multiple Experimental Conditions.

Tom Michoel, Eric Bonnet, Pau Erola, 2017, Methods in molecular biology.

Validating module network learning algorithms using simulated data

Kathleen Marchal, Yvan Saeys, Koenraad Van Leemput, 2007, BMC Bioinformatics.

Accurate wisdom of the crowd from unsupervised dimension reduction

Tom Michoel, Lingfei Wang, T. Michoel, 2017, Royal Society Open Science.

Restricted maximum-likelihood method for learning latent variance components in gene expression data with known and unknown confounders

Muhammad Ammar Malik, T. Michoel, 2020, bioRxiv.

Analytic solution and stationary phase approximation for the Bayesian lasso and elastic net

Tom Michoel, T. Michoel, 2017, NeurIPS.

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

Didier Colle, Mario Pickavet, Tom Michoel, 2016, PloS one.

Analysis of a Gibbs sampler method for model-based clustering of gene expression data

Yves Van de Peer, Anagha Joshi, Tom Michoel, 2008, Bioinform..

Validating module network learning algorithms using simulated data

Y. Saeys, Steven Maere, M. Kuiper, 2007, BMC Bioinformatics.

Gene expression Analysis of a Gibbs sampler method for model-based clustering of gene expression data

Yves Van de Peer, Anagha Joshi, Tom Michoel, 2008 .

MotifSuite: workflow for probabilistic motif detection and assessment

Kathleen Marchal, Hong Sun, Tom Michoel, 2012, Bioinform..

A pr 2 00 0 Preprint-KUL-TF-2000 / 12 Interferencing in coupled Bose-Einstein condensates

T. Michoel, A. Verbeure, 2000 .

Interferencing in Coupled Bose–Einstein Condensates

T. Michoel, A. Verbeure, 2000, math-ph/0004004.

Validating module network learning algorithms using simulated data

Y. Saeys, Steven Maere, Y. Peer, 2007, BMC Bioinformatics.

Whole-transcriptome causal network inference with genomic and transcriptomic data

Tom Michoel, Lingfei Wang, T. Michoel, 2017, bioRxiv.

Functional transcription factor target discovery via compendia of binding and expression profiles

T. Michoel, A. Joshi, C. J. Banks, 2015, Scientific Reports.

Characterizing regulatory path motifs in integrated networks using perturbational data

Thomas Van Parys, Y. Peer, T. Michoel, 2017 .

Lim Domain Binding 2: A Key Driver of Transendothelial Migration of Leukocytes and Atherosclerosis

E. Schadt, J. Björkegren, T. Michoel, 2014, Arteriosclerosis, thrombosis, and vascular biology.

Natural coordinate descent algorithm for L1-penalised regression in generalised linear models

Tom Michoel, T. Michoel, 2014, Comput. Stat. Data Anal..

Comparable variable selection with Lasso

Tom Michoel, Lingfei Wang, T. Michoel, 2017, 1701.07011.

Module networks revisited: computational assessment and prioritization of model predictions

Riet De Smet, Y. Peer, T. Michoel, 2009, Bioinform..

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Kathleen Marchal, Yves Van de Peer, Anagha Joshi, 2009, BMC Systems Biology.

Integrating Sensing and Communication in Cellular Networks via NR Sidelink pdf

Tom Michoel, Stephan Sigg, Stefano Savazzi, 2021, ArXiv.

Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data

T. Michoel, Lingfei Wang, 2016, bioRxiv.

Efficient causal inference with hidden confounders from genome-transcriptome variation data

Tom Michoel, Lingfei Wang, T. Michoel, 2016 .

Plasma cortisol-linked gene networks in hepatic and adipose tissues implicate corticosteroid-binding globulin in modulating tissue glucocorticoid action and cardiovascular risk

J. Björkegren, T. Michoel, A. Ruusalepp, 2023, Frontiers in endocrinology.

Tesla-Rapture: A Lightweight Gesture Recognition System From mmWave Radar Sparse Point Clouds pdf

Petar Popovski, Tom Michoel, Stephan Sigg, 2021, IEEE Transactions on Mobile Computing.

Efficient query-driven biclustering of gene expression data using Probabilistic Relational Models

Tim Van den Bulcke, B. Moor, T. Michoel, 2008 .

Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality

T. Michoel, D. Oyarzún, Ramin Hasibi, 2023, bioRxiv.

Implementing quantum gates using the ferromagnetic spin-J XXZ chain with kink boundary conditions

T. Michoel, B. Nachtergaele, Jaideep Mulherkar, 2009, 0902.1276.

Functional transcription factor target discovery via compendia of binding and expression profiles

T. Michoel, Anagha Joshi, Christopher J. Banks, 2015, Scientific Reports.

Predicting gene expression from network topology using graph neural networks pdf

Tom Michoel, Ramin Hasibi, T. Michoel, 2020, ArXiv.