Publications by authors named "Yves Moreau"

100Publications

ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning.

J Chem Inf Model 2020 Sep 24. Epub 2020 Sep 24.

Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Kasteelpark Arenberg 10, Leuven 3001, Belgium.

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http://dx.doi.org/10.1021/acs.jcim.0c00459DOI Listing
September 2020

Insight into the protein solubility driving forces with neural attention.

PLoS Comput Biol 2020 04 30;16(4):e1007722. Epub 2020 Apr 30.

ESAT-STADIUS, KU Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1371/journal.pcbi.1007722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217484PMC
April 2020

Crack down on genomic surveillance.

Authors:
Yves Moreau

Nature 2019 12;576(7785):36-38

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http://dx.doi.org/10.1038/d41586-019-03687-xDOI Listing
December 2019

Predicting disease-causing variant combinations.

Proc Natl Acad Sci U S A 2019 06 24;116(24):11878-11887. Epub 2019 May 24.

Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium;

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http://dx.doi.org/10.1073/pnas.1815601116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6575632PMC
June 2019

Author Correction: Linking drug target and pathway activation for effective therapy using multi-task learning.

Sci Rep 2019 May 3;9(1):7106. Epub 2019 May 3.

RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, Germany.

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http://www.nature.com/articles/s41598-019-43503-0
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http://dx.doi.org/10.1038/s41598-019-43503-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499772PMC
May 2019

Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates.

Bioinformatics 2019 11;35(22):4617-4623

Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/btz274DOI Listing
November 2019

Towards practical privacy-preserving genome-wide association study.

BMC Bioinformatics 2018 Dec 20;19(1):537. Epub 2018 Dec 20.

imec-COSIC, Department of Electrical Engineering, KU Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1186/s12859-018-2541-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302495PMC
December 2018

Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome.

Sci Rep 2018 11 19;8(1):16980. Epub 2018 Nov 19.

Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, 1050, Brussels, Belgium.

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http://www.nature.com/articles/s41598-018-34959-7
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http://dx.doi.org/10.1038/s41598-018-34959-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242909PMC
November 2018

ECCB 2018: The 17th European Conference on Computational Biology.

Bioinformatics 2018 09;34(17):i595-i598

DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, Volos, Greece.

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http://dx.doi.org/10.1093/bioinformatics/bty740DOI Listing
September 2018

Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information.

Bioinformatics 2018 07;34(13):i447-i456

Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven and imec, Kapeldreef Leuven, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/bty289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022676PMC
July 2018

Linking drug target and pathway activation for effective therapy using multi-task learning.

Sci Rep 2018 05 29;8(1):8322. Epub 2018 May 29.

RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, Germany.

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http://dx.doi.org/10.1038/s41598-018-25947-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5974390PMC
May 2018

Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping.

Bioinformatics 2018 09;34(18):3118-3125

Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/bty309DOI Listing
September 2018

Understanding mutational effects in digenic diseases.

Nucleic Acids Res 2017 Sep;45(15):e140

Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium.

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http://dx.doi.org/10.1093/nar/gkx557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587785PMC
September 2017

Methylome analysis for spina bifida shows hypomethylation as a risk factor with evidence for a complex (epi)genetic interplay to affect neural tube development.

Clin Epigenetics 2016 13;8:108. Epub 2016 Oct 13.

Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Campus Gasthuisberg, O&N1, Herestraat 49, Box 911, 3000 Leuven, Belgium.

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http://dx.doi.org/10.1186/s13148-016-0272-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5064967PMC
April 2017

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

Candidate gene prioritization with Endeavour.

Nucleic Acids Res 2016 07 30;44(W1):W117-21. Epub 2016 Apr 30.

Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium.

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http://dx.doi.org/10.1093/nar/gkw365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987917PMC
July 2016

Genome-Wide Copy Number Variation Scan Identifies Complement Component C4 as Novel Susceptibility Gene for Crohn's Disease.

Inflamm Bowel Dis 2016 Mar;22(3):505-15

*Department of Clinical and Experimental Medicine, TARGID, KU Leuven, Leuven, Belgium; †Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Leuven, Belgium; ‡iMinds Department of Medical Information Technologies, KU Leuven, Leuven, Belgium; §Department of Human Genetics, KU Leuven, Leuven, Belgium; ‖Department of Gastroenterology, Ghent University Hospital, Gent, Belgium; ¶Erasmus Hospital, Free University of Brussels, Department of Gastroenterology, Brussels, Belgium; **Unit of Animal Genomics, Groupe Interdisciplinaire de Genoproteomique Appliquee (GIGA-R) and Faculty of Veterinary Medicine, University of Liege, Liege, Belgium; ††Division of Gastroenterology, Centre Hospitalier Universitaire, Université de Liege, Liège, Belgium; ‡‡Division of Gastroenterology, UZ Leuven, Leuven, Belgium; and §§Department of Electrical Engineering and Computer Science, Bioinformatics-Statistical Genetics, Montefiore Institute, Universty of Liège, Liège, Belgium.

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http://dx.doi.org/10.1097/MIB.0000000000000623DOI Listing
March 2016

Beegle: from literature mining to disease-gene discovery.

Nucleic Acids Res 2016 Jan 17;44(2):e18. Epub 2015 Sep 17.

Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001, Belgium iMinds Future Health Department, KU Leuven, Leuven 3001, Belgium.

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http://nar.oxfordjournals.org/content/early/2015/09/17/nar.g
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ftp://ftp.esat.kuleuven.be/pub/SISTA/selshal/reports/gkv905.
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv905
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http://dx.doi.org/10.1093/nar/gkv905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737179PMC
January 2016

ISMB/ECCB 2015.

Bioinformatics 2015 Jun;31(12):i1-2

Department of Biosystems Science and Engineering, ETH Zürich, Basel, SwitzerlandProceedings Chairs ISMB/ECCB 2015.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765879PMC
June 2015

Galahad: a web server for drug effect analysis from gene expression.

Nucleic Acids Res 2015 Jul 4;43(W1):W208-12. Epub 2015 May 4.

Interdisciplinary Research Facility Life Sciences, Department of Development and Regeneration, KU Leuven Kulak, Kortrijk, 8500, Belgium

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http://dx.doi.org/10.1093/nar/gkv436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489261PMC
July 2015

NGS-Logistics: federated analysis of NGS sequence variants across multiple locations.

Genome Med 2014 17;6(9):71. Epub 2014 Sep 17.

KU Leuven, Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, Kasteelpark Arenberg 10, Box 2446, 3001 Leuven, Belgium ; iMinds Medical IT Department, Kasteelpark Arenberg 10, Box 2446, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1186/s13073-014-0071-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198698PMC
October 2014

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome.

Sci Transl Med 2014 Sep;6(252):252ra123

Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany. Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany.

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http://dx.doi.org/10.1126/scitranslmed.3009262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512639PMC
September 2014

ECCB 2014: The 13th European Conference on Computational Biology.

Bioinformatics 2014 Sep;30(17):i345-8

(ECCB'14 Co-Chair) University of Leuven, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/btu512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147932PMC
September 2014

Protein fold recognition using geometric kernel data fusion.

Bioinformatics 2014 Jul 3;30(13):1850-7. Epub 2014 Mar 3.

Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, iMinds Medical IT and Department of Computer Science, KU Leuven, 3001 Leuven, BelgiumDepartment of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, iMinds Medical IT and Department of Computer Science, KU Leuven, 3001 Leuven, BelgiumDepartment of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, iMinds Medical IT and Department of Computer Science, KU Leuven, 3001 Leuven, Belgium.

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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btu118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071197PMC
July 2014

In vitro screening of embryos by whole-genome sequencing: now, in the future or never?

Hum Reprod 2014 Apr 2;29(4):842-51. Epub 2014 Feb 2.

Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1093/humrep/deu005DOI Listing
April 2014

eXtasy: variant prioritization by genomic data fusion.

Nat Methods 2013 Nov 29;10(11):1083-4. Epub 2013 Sep 29.

1] Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Leuven, Belgium. [2] iMinds Future Health Department, Leuven, Belgium. [3].

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http://www.nature.com/articles/nmeth.2656
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http://dx.doi.org/10.1038/nmeth.2656DOI Listing
November 2013

Concordance of gene expression in human protein complexes reveals tissue specificity and pathology.

Nucleic Acids Res 2013 Oct 5;41(18):e171. Epub 2013 Aug 5.

Department of Electrical Engineering, ESAT-SCD, IBBT-KU Leuven Future Health Department, KU Leuven, 3001 Leuven, Belgium, Biostatistics Department, Harvard School of Public Health, Harvard University, Boston, 02115 MA, USA, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA, Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, 02142 MA, USA, Division of Endocrinology and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, 02115 MA, USA, Department of Development and Regeneration @ Kulak, KU Leuven, E. Sabbelaan 53, 8500 Kortrijk, Belgium, and NNF Center for Protein Research, Health Sciences Faculty, University of Copenhagen, DK-2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1093/nar/gkt661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794609PMC
October 2013

Unraveling genomic variation from next generation sequencing data.

BioData Min 2013 Jul 25;6(1):13. Epub 2013 Jul 25.

Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece.

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http://dx.doi.org/10.1186/1756-0381-6-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726446PMC
July 2013

Meander: visually exploring the structural variome using space-filling curves.

Nucleic Acids Res 2013 Jun 19;41(11):e118. Epub 2013 Apr 19.

Department of Electrical Engineering (ESAT/SCD), University of Leuven, Kasteelpark Arenberg 10, Box 2446, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1093/nar/gkt254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675473PMC
June 2013

Mutual inhibition among postmitotic neurons regulates robustness of brain wiring in Drosophila.

Elife 2013 Mar 5;2:e00337. Epub 2013 Mar 5.

Center for the Biology of Disease , VIB , Leuven , Belgium ; Center for Human Genetics , University of Leuven School of Medicine , Leuven , Belgium ; Doctoral Program in Molecular and Cognitive Neuroscience, Doctoral School of Biomedical Sciences , University of Leuven , Leuven , Belgium.

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http://dx.doi.org/10.7554/eLife.00337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589824PMC
March 2013

Finding the targets of a drug by integration of gene expression data with a protein interaction network.

Mol Biosyst 2013 Jul 26;9(7):1676-85. Epub 2013 Feb 26.

KU Leuven, Department of Electrical Engineering-ESAT, SCD-SISTA, Leuven, Belgium.

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http://dx.doi.org/10.1039/c3mb25438kDOI Listing
July 2013

Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains.

Nucleic Acids Res 2013 Apr 7;41(6):e66. Epub 2013 Jan 7.

Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium.

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http://dx.doi.org/10.1093/nar/gks1352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616740PMC
April 2013

An unbiased evaluation of gene prioritization tools.

Bioinformatics 2012 Dec 9;28(23):3081-8. Epub 2012 Oct 9.

Department of Electrical Engineering, ESAT-SCD, Katholieke Universiteit Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/bts581DOI Listing
December 2012

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease.

Genome Med 2012 26;4(9):73. Epub 2012 Sep 26.

KU Leuven, Department of Electrical Engineering-ESAT, SCD-SISTA, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium ; IBBT Future Health Department, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.

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http://dx.doi.org/10.1186/gm374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580443PMC
August 2014

ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings.

Bioinformatics 2012 Sep;28(18):i569-i574

IBBT Future Health Department/ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001, Heverlee-Leuven, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/bts391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436818PMC
September 2012

Computational tools for prioritizing candidate genes: boosting disease gene discovery.

Nat Rev Genet 2012 Jul 3;13(8):523-36. Epub 2012 Jul 3.

Department of Electrical Engineering ESAT-SCD and IBBT-KU Leuven Future Health Department, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium. kuleuven.be

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http://dx.doi.org/10.1038/nrg3253DOI Listing
July 2012

AliBiMotif: integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences.

Int J Data Min Bioinform 2012 ;6(2):196-215

Knowledge Discovery and Bioinformatics (KDBIO), INESC-ID Computer Science Department, IST, Technical University of Lisbon, Rua Alves Redol 9, 1000-029 Lisboa, Portugal.

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http://dx.doi.org/10.1504/ijdmb.2012.048198DOI Listing
September 2012

Optimized data fusion for kernel k-means clustering.

IEEE Trans Pattern Anal Mach Intell 2012 May;34(5):1031-9

Knapp Center for Biomedical Discovery, Department of Medicine, Institute for Genomics and Systems Biology, University of Chicago, 900 E. 57th St. Room 10148, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1109/TPAMI.2011.255DOI Listing
May 2012

Congenital heart defects in a novel recurrent 22q11.2 deletion harboring the genes CRKL and MAPK1.

Am J Med Genet A 2012 Mar 8;158A(3):574-80. Epub 2012 Feb 8.

Center for Human Genetics, University Hospitals Leuven, Herestraat, Leuven, Belgium.

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http://dx.doi.org/10.1002/ajmg.a.35217DOI Listing
March 2012

Microarray analysis of copy number variation in single cells.

Nat Protoc 2012 Jan 19;7(2):281-310. Epub 2012 Jan 19.

Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1038/nprot.2011.426DOI Listing
January 2012

Single-cell copy number variation detection.

Genome Biol 2011 Aug 29;12(8):R80. Epub 2011 Aug 29.

Department of Electrical Engineering, Esat-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven 3001, Belgium.

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http://dx.doi.org/10.1186/gb-2011-12-8-r80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245619PMC
August 2011

Predicting receptor-ligand pairs through kernel learning.

BMC Bioinformatics 2011 Aug 11;12:336. Epub 2011 Aug 11.

SCD-ESAT, Department of Electrical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven 3001, Belgium.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199765PMC
August 2011

PINTA: a web server for network-based gene prioritization from expression data.

Nucleic Acids Res 2011 Jul 20;39(Web Server issue):W334-8. Epub 2011 May 20.

Department of Electrical Engineering (ESAT-SCD), Katholieke Universiteit Leuven, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1093/nar/gkr289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125740PMC
July 2011

A guide to web tools to prioritize candidate genes.

Brief Bioinform 2011 Jan 21;12(1):22-32. Epub 2010 Mar 21.

Katholieke Universiteit Leuven, Belgium.

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http://dx.doi.org/10.1093/bib/bbq007DOI Listing
January 2011

Optimized data fusion for K-means Laplacian clustering.

Bioinformatics 2011 Jan 26;27(1):118-26. Epub 2010 Oct 26.

Signals, Identification, System Theory and Automation, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven-Heverlee, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/btq569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008636PMC
January 2011

Candidate gene prioritization by network analysis of differential expression using machine learning approaches.

BMC Bioinformatics 2010 Sep 14;11:460. Epub 2010 Sep 14.

Department of Electrical Engineering (ESAT-SCD) Katholieke Universiteit Leuven, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1186/1471-2105-11-460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945940PMC
September 2010

Novel insights into the global proteome responses of insulin-producing INS-1E cells to different degrees of endoplasmic reticulum stress.

J Proteome Res 2010 Oct;9(10):5142-52

Laboratory for Experimental Medicine and Endocrinology (LEGENDO), University Hospital Gasthuisberg, Catholic University of Leuven, Herestraat 49, Leuven, Belgium.

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http://pubs.acs.org/doi/abs/10.1021/pr1004086
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http://dx.doi.org/10.1021/pr1004086DOI Listing
October 2010

YTPdb: a wiki database of yeast membrane transporters.

Biochim Biophys Acta 2010 Oct 19;1798(10):1908-12. Epub 2010 Jun 19.

ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium.

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October 2010

Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.

Bioinformatics 2010 Sep 30;26(17):2210-1. Epub 2010 Jun 30.

ESAT-SCD. Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/btq348DOI Listing
September 2010

Large-scale benchmark of Endeavour using MetaCore maps.

Bioinformatics 2010 Aug 10;26(15):1922-3. Epub 2010 Jun 10.

Novartis Pharma AG, Postfach, Basel, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btq307DOI Listing
August 2010

L2-norm multiple kernel learning and its application to biomedical data fusion.

BMC Bioinformatics 2010 Jun 8;11:309. Epub 2010 Jun 8.

Bioinformatics Group, Department of Electrical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Heverlee B-3001, Belgium.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906488PMC
June 2010

Detection of novel 3' untranslated region extensions with 3' expression microarrays.

BMC Genomics 2010 Mar 26;11:205. Epub 2010 Mar 26.

Gene Expression Unit, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1186/1471-2164-11-205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858751PMC
March 2010

Gene prioritization and clustering by multi-view text mining.

BMC Bioinformatics 2010 Jan 14;11:28. Epub 2010 Jan 14.

Bioinformatics Group, Department of Electrical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Heverlee B3001, Belgium.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098068PMC
January 2010

Bridging the gap between systems biology and medicine.

Genome Med 2009 Sep 29;1(9):88. Epub 2009 Sep 29.

Department of Critical Care Medicine and CRISMA laboratory, University of Pittsburgh School of Medicine, Scaife 602, 3550 Terrace, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1186/gm88DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768995PMC
September 2009

Proteome analysis demonstrates profound alterations in human dendritic cell nature by TX527, an analogue of vitamin D.

Proteomics 2009 Jul;9(14):3752-64

Laboratory for Experimental Medicine and Endocrinology (LEGENDO), University Hospital Gasthuisberg, Catholic University of Leuven, B-3000 Leuven, Belgium.

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http://doi.wiley.com/10.1002/pmic.200800848
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July 2009

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.

Am J Hum Genet 2009 Apr 2;84(4):524-33. Epub 2009 Apr 2.

Cambridge University Department of Medical Genetics, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.

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http://dx.doi.org/10.1016/j.ajhg.2009.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667985PMC
April 2009

Integrating computational biology and forward genetics in Drosophila.

PLoS Genet 2009 Jan 23;5(1):e1000351. Epub 2009 Jan 23.

Department of Molecular and Developmental Genetics, Laboratory of Neurogenetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium.

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http://dx.doi.org/10.1371/journal.pgen.1000351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628282PMC
January 2009

Protein-induced changes during the maturation process of human dendritic cells: A 2-D DIGE approach.

Proteomics Clin Appl 2008 Sep 21;2(9):1349-60. Epub 2008 Jul 21.

Laboratory for Experimental Medicine and Endocrinology, University Hospital Gasthuisberg, Catholic University of Leuven, Leuven, Belgium.

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http://doi.wiley.com/10.1002/prca.200800110
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September 2008

Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining.

Bioinformatics 2008 Aug;24(16):i119-25

Department of Electrical Engineering, Bioinformatics Group, SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium.

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August 2008

ENDEAVOUR update: a web resource for gene prioritization in multiple species.

Nucleic Acids Res 2008 Jul 28;36(Web Server issue):W377-84. Epub 2008 May 28.

Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, Belgium.

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http://dx.doi.org/10.1093/nar/gkn325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447805PMC
July 2008

Detecting cis-regulatory binding sites for cooperatively binding proteins.

Nucleic Acids Res 2008 May 9;36(8):e46. Epub 2008 Apr 9.

Department of Electrical Engineering, ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1093/nar/gkn140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377448PMC
May 2008

Using ribosomal protein genes as reference: a tale of caution.

PLoS One 2008 Mar 26;3(3):e1854. Epub 2008 Mar 26.

Gene Expression Unit, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267211PMC
March 2008

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions.

Nucleic Acids Res 2008 Apr 16;36(7):e43. Epub 2008 Mar 16.

Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium.

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http://dx.doi.org/10.1093/nar/gkn114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367735PMC
April 2008

Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo.

J Comput Biol 2007 Oct;14(8):1105-14

Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1089/cmb.2007.0073DOI Listing
October 2007