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

BMC bioinformatics, 2021-10, Vol.22 (1), p.1-525, Article 525

2021

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

Physical review. E, Statistical, nonlinear, and soft matter physics, 2012-11, Vol.86 (5 Pt 2), p.056111-056111, Article 056111

2012

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

PLoS computational biology, 2017-08, Vol.13 (8), p.e1005703-e1005703

2017

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Integrative multi-omics module network inference with Lemon-Tree

PLoS computational biology, 2015-02, Vol.11 (2), p.e1003983-e1003983

2015

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

Frontiers in endocrinology (Lausanne), 2022-08, Vol.13, p.949061-949061

2022

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

Science (American Association for the Advancement of Science), 2016-08, Vol.353 (6301), p.827-830

2016

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Model-based clustering of multi-tissue gene expression data

Bioinformatics, 2020-03, Vol.36 (6), p.1807-1813

2020

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Changes in the gene expression profile during spontaneous migraine attacks

Scientific reports, 2021-04, Vol.11 (1), p.8294-10, Article 8294

2021

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

Frontiers in genetics, 2019-12, Vol.10, p.1196-1196

2019

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

NPJ systems biology and applications, 2024-03, Vol.10 (1), p.24-24

2024

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An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

PloS one, 2016-01, Vol.11 (1), p.e0147078-e0147078

2016

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

International journal of molecular sciences, 2018-11, Vol.19 (11), p.3609

2018

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Accurate wisdom of the crowd from unsupervised dimension reduction

Royal Society open science, 2019-07, Vol.6 (7), p.181806-181806

2019

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

PloS one, 2014-05, Vol.9 (5), p.e97896-e97896

2014

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Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

Cell systems, 2016-03, Vol.2 (3), p.196-208

2016

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

PLoS genetics, 2014-02, Vol.10 (2), p.e1004201

2014

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MotifSuite: workflow for probabilistic motif detection and assessment

Bioinformatics, 2012-07, Vol.28 (14), p.1931-1932

2012

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

PLoS neglected tropical diseases, 2019-04, Vol.13 (4), p.e0007262-e0007262

2019

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

Frontiers in endocrinology (Lausanne), 2023, Vol.14, p.1186252-1186252

2023

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The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees

PloS one, 2013-04, Vol.8 (4), p.e61183-e61183

2013

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Causal inference in drug discovery and development

Drug discovery today, 2023-10, Vol.28 (10), p.103737-103737, Article 103737

2023

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

Proceedings of the National Academy of Sciences - PNAS, 2014-04, Vol.111 (13), p.4886-4891

2014

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

PloS one, 2010-04, Vol.5 (4), p.e10162-e10162

2010

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

Journal of leukocyte biology, 2015-05, Vol.97 (5), p.985-995

2015

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

Computational statistics & data analysis, 2016-05, Vol.97, p.60-70

Michoel, Tom

2016

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

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

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

Integrative multi-omics module network inference with Lemon-Tree

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

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

Model-based clustering of multi-tissue gene expression data

Changes in the gene expression profile during spontaneous migraine attacks

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

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

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

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

Accurate wisdom of the crowd from unsupervised dimension reduction

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

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

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

MotifSuite: workflow for probabilistic motif detection and assessment

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

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

The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees

Causal inference in drug discovery and development

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

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

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

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

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