List of works - Tom Michoel

Accurate wisdom of the crowd from unsupervised dimension reduction

scientific article published on 31 July 2019

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

scientific article published on 26 November 2012

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

scientific article published on 21 January 2016

An Integrative Approach to Infer Regulation Programs in a Transcription Regulatory Module Network ⬇️

scientific article published on April 11, 2012

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

scientific article

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

scientific article published on 03 April 2019

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

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

scientific article published on 6 September 2017

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

scientific article published on August 2016

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

scientific article

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

scientific article published on 15 November 2018

Characterizing regulatory path motifs in integrated networks using perturbational data

scientific article

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

scientific article

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

scientific article published in September 2012

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

scientific article published on 3 March 2016

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

scientific article

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

scientific article

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

scientific article published on 05 August 2016

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

article published in 2011

Expression quantitative trait Loci acting across multiple tissues are enriched in inherited risk for coronary artery disease

scientific article

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

scientific article published on 09 February 2016

Helicoidal transfer matrix model for inhomogeneous DNA melting

scientific article

Human Validation of Genes Associated With a Murine Atherosclerotic Phenotype

scientific article

Integrative multi-omics module network inference with Lemon-Tree ⬇️

scientific article published on 13 February 2015

Learning Differential Module Networks Across Multiple Experimental Conditions

scientific article published on 01 January 2019

Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis

scientific article

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

scientific article

Meta-analysis of liver and heart transcriptomic data for functional annotation transfer in mammalian orthologs

Microglial brain region-dependent diversity and selective regional sensitivities to aging.

scientific article published on 18 January 2016

Model-based clustering of multi-tissue gene expression data

scientific article published on 01 March 2020

Module network inference from a cancer gene expression data set identifies microRNA regulated modules

scientific article

Module networks revisited: computational assessment and prioritization of model predictions

scientific article

MotifSuite: workflow for probabilistic motif detection and assessment

scientific article published on 15 May 2012

Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila ⬇️

scientific article published on April 2015

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

scientific article published on 21 February 2018

Plasma cholesterol-induced lesion networks activated before regression of early, mature, and advanced atherosclerosis

scientific article

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

scientific article published on 10 April 2012

Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants

scientific article published on 13 August 2013

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

scientific article

Reverse-engineering transcriptional modules from gene expression data

scientific article

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

scientific article published on 16 September 2014

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

scientific article published on 18 March 2014

Smoking is Associated to DNA Methylation in Atherosclerotic Carotid Lesions

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

scientific article

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

scientific article published on 25 February 2015

The Index-based Subgraph Matching Algorithm with General Symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration

scientific article (publication date: 2014)

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

scientific article published on 17 July 2009

Validating module network learning algorithms using simulated data

scientific article

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

scientific article

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

scientific article published on 20 January 2015

Whole-Transcriptome Causal Network Inference with Genomic and Transcriptomic Data

scientific article published on 01 January 2019

Whole-transcriptome causal network inference with genomic and transcriptomic data

kruX: matrix-based non-parametric eQTL discovery

scientific article published on 14 January 2014

List of works by Tom Michoel

Accurate wisdom of the crowd from unsupervised dimension reduction

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

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

An Integrative Approach to Infer Regulation Programs in a Transcription Regulatory Module Network ⬇️

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

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

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

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

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

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

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

Characterizing regulatory path motifs in integrated networks using perturbational data

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

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

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

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

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

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

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

Expression quantitative trait Loci acting across multiple tissues are enriched in inherited risk for coronary artery disease

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

Helicoidal transfer matrix model for inhomogeneous DNA melting

Human Validation of Genes Associated With a Murine Atherosclerotic Phenotype

Integrative multi-omics module network inference with Lemon-Tree ⬇️

Learning Differential Module Networks Across Multiple Experimental Conditions

Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis

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

Meta-analysis of liver and heart transcriptomic data for functional annotation transfer in mammalian orthologs

Microglial brain region-dependent diversity and selective regional sensitivities to aging.

Model-based clustering of multi-tissue gene expression data

Module network inference from a cancer gene expression data set identifies microRNA regulated modules

Module networks revisited: computational assessment and prioritization of model predictions

MotifSuite: workflow for probabilistic motif detection and assessment

Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila ⬇️

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

Plasma cholesterol-induced lesion networks activated before regression of early, mature, and advanced atherosclerosis

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

Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants

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

Reverse-engineering transcriptional modules from gene expression data

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

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

Smoking is Associated to DNA Methylation in Atherosclerotic Carotid Lesions

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

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

The Index-based Subgraph Matching Algorithm with General Symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration

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

Validating module network learning algorithms using simulated data

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

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

Whole-Transcriptome Causal Network Inference with Genomic and Transcriptomic Data

Whole-transcriptome causal network inference with genomic and transcriptomic data

kruX: matrix-based non-parametric eQTL discovery