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Journal Articles

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

Lingfei Wang, Tom Michoel - 18 Aug 2017 - PLoS Computational Biology Vol: 13 Pages: e1005703

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Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

Husain A. Talukdar, Hassan Foroughi Asl, Rajeev K. Jain, Raili Ermel, Arno Ruusalepp, Oscar Franzén, Brian A. Kidd, Ben Readhead, Chiara Giannarelli, Jason C. Kovacic, Torbjörn Ivert, Joel T. Dudley, Mete Civelek, Aldons J. Lusis, Eric E. Schadt, Josefin Skogsberg, Tom Michoel, Johan L M Björkegren - 23 Mar 2016 - Cell Systems Vol: 2 Pages: 196-208

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

Hassan Foroughi Asl, Husain A Talukdar, Alida S D Kindt, Rajeev K Jain, Raili Ermel, Arno Ruusalepp, Khanh-Dung H Nguyen, Radu Dobrin, Dermot F Reilly, Heribert Schunkert, Nilesh J Samani, Ingrid Brænne, Jeanette Erdmann, Olle Melander, Jianlong Qi, Torbjörn Ivert, Josefin Skogsberg, Eric E Schadt, Tom Michoel, Johan L M Björkegren, CARDIoGRAM Consortium - 11 Jan 2015 - Circulation. Cardiovascular genetics

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Integrative multi-omics module network inference with Lemon-Tree

Eric Bonnet, Laurence Calzone, Tom Michoel - 13 Feb 2015 - PLoS Computational Biology Vol: 11

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

Ruth A Morgan, Katharina R Beck, Mark Nixon, Natalie Z M Homer, Andrew A Crawford, Diana Melchers, René Houtman, Onno C Meijer, Andreas Stomby, Anna J Anderson, Rita Upreti, Roland H Stimson, Tommy Olsson, Tom Michoel, Ariella Cohain, Arno Ruusalepp, Eric E Schadt, Johan L M Björkegren, Ruth Andrew, Christopher J Kenyon, Patrick W F Hadoke, Alex Odermatt, John A Keen, Brian R Walker - 06 Sep 2017 - Scientific Reports Vol: 7 Pages: 10633

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

Pía Francesca Loren Reyes, Tom Michoel, Anagha Joshi, Guillaume Devailly - 26 Aug 2017 - Computational and Structural Biotechnology Journal Vol: 15 Pages: 425-432

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

Lingfei Wang, Tom Michoel - 18 Aug 2017 - PLoS Computational Biology Vol: 13 Pages: e1005703

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

Oskar Schnappauf, Sven Beyes, Annika Dertmann, Vivien Freihen, Patrick Frey, Sabine Jägle, Katja Rose, Tom Michoel, Rudolf Grosschedl, Andreas Hecht - Nov 2016 - Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Vol: 1859 Pages: 1353-1367

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

Oscar Franzén, Raili Ermel, Ariella Cohain, Nicholas K Akers, Antonio Di Narzo, Husain A Talukdar, Hassan Foroughi-Asl, Claudia Giambartolomei, John F Fullard, Katyayani Sukhavasi, Sulev Köks, Li-Ming Gan, Chiara Giannarelli, Jason C Kovacic, Christer Betsholtz, Bojan Losic, Tom Michoel, Ke Hao, Panos Roussos, Josefin Skogsberg, Arno Ruusalepp, Eric E Schadt, Johan L M Björkegren - 19 Aug 2016 - Science Vol: 353 Pages: 827-30

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Human Validation of Genes Associated With a Murine Atherosclerotic Phenotype

Gerard Pasterkamp, Sander W van der Laan, Saskia Haitjema, Hassan Foroughi Asl, Marten A Siemelink, Tim Bezemer, Jessica van Setten, Martin Dichgans, Rainer Malik, Bradford B Worrall, Heribert Schunkert, Nilesh J Samani, Dominique P V de Kleijn, Hugh S Markus, Imo E Hoefer, Tom Michoel, Saskia C A de Jager, Johan L M Björkegren, Hester M den Ruijter, Folkert W Asselbergs - Jun 2016 - Arteriosclerosis, thrombosis, and vascular biology Vol: 36 Pages: 1240-1246

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Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

Husain A. Talukdar, Hassan Foroughi Asl, Rajeev K. Jain, Raili Ermel, Arno Ruusalepp, Oscar Franzén, Brian A. Kidd, Ben Readhead, Chiara Giannarelli, Jason C. Kovacic, Torbjörn Ivert, Joel T. Dudley, Mete Civelek, Aldons J. Lusis, Eric E. Schadt, Josefin Skogsberg, Tom Michoel, Johan L M Björkegren - 23 Mar 2016 - Cell Systems Vol: 2 Pages: 196-208

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Microglial brain region−dependent diversity and selective regional sensitivities to aging

Kathleen Renault, Tom Michoel, Michail Karavolos, Sara Clohisey, John Baillie, Mark Stevens, Thomas Freeman, Kim Summers, Barry McColl - Mar 2016 - Nature Neuroscience Vol: 19 Pages: 504-516

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An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

Ine Melckenbeeck, Pieter Audenaert, Tom Michoel, Didier Colle, Mario Pickavet - 21 Jan 2016 - PLoS One Vol: 11

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

Christopher J. Banks, Anagha Joshi, Tom Michoel - 2016 - Scientific Reports Vol: 6

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

Guillaume Devailly, Anna Mantsoki, Tom Michoel, Anagha Joshi - 21 Dec 2015 - FEBS Letters Vol: 589 Pages: 3866–3870

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

Harriet K Auty, Steven J. Torr, Siddharth Jayaraman, Tom Michoel, Liam Morrison - Aug 2015 - Revue scientifique et technique-Office international des epizooties Vol: 34 Pages: 587-598

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

Sander W. Van Der Laan, Hassan Foroughi Asl, Pleunie van den Borne, Jessica van Setten, M. E Madeleine van der Perk, Sander M. van de Weg, Arjan H. Schoneveld, Dominique P V de Kleijn, Tom Michoel, Johan L M Björkegren, Hester M. den Ruijter, Folkert W. Asselbergs, Paul I W de Bakker, Gerard Pasterkamp - 01 Apr 2015 - Atherosclerosis Vol: 239 Pages: 528-538

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

Anagha Joshi, Yvonne Beck, Tom Michoel - Apr 2015 - Journal of Computational Biology Vol: 22 Pages: 253-65

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

Anagha Joshi, Christopher Pooley, Tom C Freeman, Andreas Lennartsson, Magda Babina, Christian Schmidl, Teunis Geijtenbeek, Tom Michoel, Jessica Severin, Masayoshi Itoh, Timo Lassmann, Hideya Kawaji, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Michael Rehli, David A Hume, the FANTOM Consortium - 25 Feb 2015 - Journal of Leukocyte Biology Vol: 97 Pages: 985-995

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Integrative multi-omics module network inference with Lemon-Tree

Eric Bonnet, Laurence Calzone, Tom Michoel - 13 Feb 2015 - PLoS Computational Biology Vol: 11

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

Kerstin Rönsch, Sabine Jägle, Katja Rose, Maximilian Seidl, Francis Baumgartner, Vivien Freihen, Afsheen Yousaf, Eric Metzger, Silke Lassmann, Roland Schüle, Robert Zeiser, Tom Michoel, Andreas Hecht - Feb 2015 - Molecular Oncology Vol: 9 Pages: 335-354

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

Hassan Foroughi Asl, Husain A Talukdar, Alida S D Kindt, Rajeev K Jain, Raili Ermel, Arno Ruusalepp, Khanh-Dung H Nguyen, Radu Dobrin, Dermot F Reilly, Heribert Schunkert, Nilesh J Samani, Ingrid Brænne, Jeanette Erdmann, Olle Melander, Jianlong Qi, Torbjörn Ivert, Josefin Skogsberg, Eric E Schadt, Tom Michoel, Johan L M Björkegren, CARDIoGRAM Consortium - 11 Jan 2015 - Circulation. Cardiovascular genetics

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Microglial transcriptome diversity in the healthy adult brain reveals regional heterogeneity in immunoregulatory and metabolic function and selective sensitivity to ageing

K. Renault, T. Michoel, M. Karavolos, M. Stevens, T. Freeman, K. Summers, B. McColl - 2015 - Glia Vol: 63 Pages: E192-E192

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Plasma cholesterol-induced regression of early, mature, and advanced atherosclerosis

J. L. M. Bjorkegren, S. Hagg, H. A. Talukdar, H. Foroughi Asl, R. K. Jain, C. Cedergren, M. M. Shang, A. Rossignoli, R. Takolander, O. Melander, A. Hamsten, T. Michoel, J. Skogsberg - Aug 2014 - Atherosclerosis Vol: 235 Pages: E29-E29

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

Ming-Mei Shang, Husain A Talukdar, Jennifer J Hofmann, Colin Niaudet, Hassan Foroughi Asl, Rajeev K Jain, Aranzazu Rossignoli, Cecilia Cedergren, Angela Silveira, Bruna Gigante, Karin Leander, Ulf de Faire, Anders Hamsten, Arno Ruusalepp, Olle Melander, Torbjörn Ivert, Tom Michoel, Eric E Schadt, Christer Betsholtz, Josefin Skogsberg, Johan L M Björkegren - 12 Jun 2014 - Arteriosclerosis, thrombosis, and vascular biology Vol: 34 Pages: 2068-2077

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

Maarten Houbraken, Sofie Demeyer, Tom Michoel, Pieter Audenaert, Didier Colle, Mario Pickavet - 30 May 2014 - PLoS One Vol: 9

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

S. Jägle, K. Rönsch, S. Timme, H. Andrlová, M. Bertrand, M. Jäger, A. Proske, M. Schrempp, A. Yousaf, T. Michoel, R. Zeiser, M. Werner, S. Lassmann, A. Hecht - 01 Apr 2014 - Proceedings of the National Academy of Sciences Vol: 111 Pages: 4886-4891

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

Johan L M Björkegren, Sara Hägg, Husain A Talukdar, Hassan Foroughi Asl, Rajeev K Jain, Cecilia Cedergren, Ming-Mei Shang, Aránzazu Rossignoli, Rabbe Takolander, Olle Melander, Anders Hamsten, Tom Michoel, Josefin Skogsberg - 27 Feb 2014 - PLoS Genetics Vol: 10 Pages: e1004201

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kruX: Matrix-based non-parametric eQTL discovery

Jianlong Qi, Hassan Foroughi Asl, Johan Bjorkegren, Tom Michoel - 14 Jan 2014 - BMC Bioinformatics Vol: 15

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

Rahul Bhosale, Jeremy B Jewell, Jens Hollunder, Abraham J K Koo, Marnik Vuylsteke, Tom Michoel, Pierre Hilson, Alain Goossens, Gregg A Howe, John Browse, Steven Maere - 13 Aug 2013 - The Plant Cell

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

Sofie Demeyer, Tom Michoel, Jan Fostier, Pieter Audenaert, Mario Pickavet, Piet Demeester - 2013 - PLoS One Vol: 8 Pages: e61183

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

Tom Michoel, Bruno Nachtergaele - 26 Nov 2012 - Physical Review E - Statistical, Nonlinear and Soft Matter Physics Vol: 86

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

Jianlong Qi, Tom Michoel - 15 Sep 2012 - Bioinformatics Vol: 28 Pages: 2325-2332

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An integrative approach to infer regulation programs in a transcription regulatory module network

Jianlong Qi, Tom Michoel, Gregory Butler - 2012 - Journal of Biomedicine and Biotechnology Vol: 2012 Pages: 245968

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

Anagha Joshi, Yvonne Beck, Tom Michoel - 2012 - Febs Journal Vol: 279 Pages: 3501-3512

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

Jianlong Qi, Tom Michoel, Gregory Butler - 2012 - Journal of Biomedicine and Biotechnology Pages: -

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MotifSuite: workflow for probabilistic motif detection and assessment

Marleen Claeys, Valerie Storms, Hong Sun, Tom Michoel, Kathleen Marchal - 2012 - Bioinformatics Vol: 28 Pages: 1931-1932

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

Anagha Joshi, Yves Van de Peer, Tom Michoel - Nov 2011 - Nucleic Acids Research Vol: 39 Pages: 9108-9117

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

Pieter Audenaert, Thomas Van Parys, Florian Brondel, Mario Pickavet, Piet Demeester, Yves Van de Peer, Tom Michoel - 01 Jun 2011 - Bioinformatics Vol: 27 Pages: 1587-1588

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ATHEROSCLEROSIS REGRESSION IN A MOUSE MODEL WITH HUMAN-LIKE HYPERCHOLESTEROLEMIA

J. Bjoerkegren, S. Haegg, S. Maleki, M. Shang, T. Michoel, J. Skogsberg - Jun 2011 - Atherosclerosis supplements Vol: 12 Pages: 64-64

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

Tom Michoel, Anagha Joshi, Bruno Nachtergaele, Yves Van de Peer - 2011 - Molecular Biosystems Vol: 7 Pages: 2769-2778

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