Stein Aerts

Stein Aerts

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Stein Aerts

Stein Aerts

Publications by authors named "Stein Aerts"

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Cortical Neurogenesis Requires Bcl6-Mediated Transcriptional Repression of Multiple Self-Renewal-Promoting Extrinsic Pathways.

Neuron 2019 Sep 25;103(6):1096-1108.e4. Epub 2019 Jul 25.

Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium; VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium; Welbio, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2019.06.027DOI Listing
September 2019

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks.

Bioinformatics 2019 Jun;35(12):2159-2161

Laboratory of Computational Biology, VIB Center for Brain & Disease Research.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty916DOI Listing
June 2019

Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics.

Curr Opin Neurobiol 2019 Jun 28;56:125-134. Epub 2019 Jan 28.

VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.conb.2018.12.012DOI Listing
June 2019

Mapping gene regulatory networks from single-cell omics data.

Brief Funct Genomics 2018 07;17(4):246-254

VIB Center for Brain & Disease Research, Laboratory of Computational Biology, Leuven, Belgium.

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http://dx.doi.org/10.1093/bfgp/elx046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063279PMC
July 2018

Hippo Reprograms the Transcriptional Response to Ras Signaling.

Dev Cell 2017 09;42(6):667-680.e4

Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2017.08.013DOI Listing
September 2017

Nuclear receptors connect progenitor transcription factors to cell cycle control.

Sci Rep 2017 07 7;7(1):4845. Epub 2017 Jul 7.

CABD, Andalusian Centre for Developmental Biology, CSIC-UPO-JA, 41013, Seville, Spain.

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http://dx.doi.org/10.1038/s41598-017-04936-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501803PMC
July 2017

Decoding transcriptional states in cancer.

Curr Opin Genet Dev 2017 Apr 24;43:82-92. Epub 2017 Jan 24.

Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2017.01.003DOI Listing
April 2017

An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model.

Curr Biol 2016 08 28;26(16):2101-13. Epub 2016 Jul 28.

VIB Center for the Biology of Disease and KU Leuven Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09609822163067
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http://dx.doi.org/10.1016/j.cub.2016.06.035DOI Listing
August 2016

Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma.

BMC Cancer 2016 08 12;16:632. Epub 2016 Aug 12.

Department of Abdominal Surgical Oncology, University Hospitals Leuven, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.

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http://dx.doi.org/10.1186/s12885-016-2540-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983037PMC
August 2016

Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets.

Dev Biol 2016 07 10;415(1):157-167. Epub 2016 May 10.

Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA; Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2016.05.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4902760PMC
July 2016

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic.

Genome Res 2016 07 18;26(7):882-95. Epub 2016 May 18.

Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium;

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http://dx.doi.org/10.1101/gr.204149.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937571PMC
July 2016

CD45 antigen negativity in T-lineage ALL correlates with PTPRC mutation and sensitivity to a selective JAK inhibitor.

Br J Haematol 2015 Dec 8;171(5):884-7. Epub 2015 Apr 8.

Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy.

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http://dx.doi.org/10.1111/bjh.13448DOI Listing
December 2015

iRegulon and i-cisTarget: Reconstructing Regulatory Networks Using Motif and Track Enrichment.

Curr Protoc Bioinformatics 2015 Dec 17;52:2.16.1-39. Epub 2015 Dec 17.

Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium.

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http://dx.doi.org/10.1002/0471250953.bi0216s52DOI Listing
December 2015

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models.

PLoS Comput Biol 2015 Nov 12;11(11):e1004590. Epub 2015 Nov 12.

Laboratory of Computational Biology, KU Leuven Center for Human Genetics, Leuven, Belgium.

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http://dx.doi.org/10.1371/journal.pcbi.1004590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642938PMC
November 2015

Hindsight regulates photoreceptor axon targeting through transcriptional control of jitterbug/Filamin and multiple genes involved in axon guidance in Drosophila.

Dev Neurobiol 2015 Sep 18;75(9):1018-32. Epub 2015 Feb 18.

Laboratorio de Neurobiología Celular y Molecular, Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile.

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http://dx.doi.org/10.1002/dneu.22271DOI Listing
September 2015

Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models.

Mol Biol Evol 2015 Sep 4;32(9):2441-55. Epub 2015 May 4.

Laboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium

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http://dx.doi.org/10.1093/molbev/msv107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540964PMC
September 2015

p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response.

Cell Cycle 2014 ;13(16):2572-86

a University of Cambridge; Medical Research Council Cancer Unit; Hutchison/MRC Research Center ; Cambridge , UK.

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http://dx.doi.org/10.4161/15384101.2015.942209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4601526PMC
August 2015

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.

Nucleic Acids Res 2015 Jul 29;43(W1):W57-64. Epub 2015 Apr 29.

Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium

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http://dx.doi.org/10.1093/nar/gkv395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489282PMC
July 2015

Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.

Cell Rep 2014 Dec 18;9(6):2290-303. Epub 2014 Dec 18.

Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, Leuven 3000, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.11.038DOI Listing
December 2014

JAK3 mutants transform hematopoietic cells through JAK1 activation, causing T-cell acute lymphoblastic leukemia in a mouse model.

Blood 2014 Nov 5;124(20):3092-100. Epub 2014 Sep 5.

Vlaams Instituut voor Biotechnologie Center for the Biology of the Disease, Leuven, Belgium; Katholieke Universiteit Leuven Center for Human Genetics, Leuven, Belgium;

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http://dx.doi.org/10.1182/blood-2014-04-566687DOI Listing
November 2014

Reduced synaptic vesicle protein degradation at lysosomes curbs TBC1D24/sky-induced neurodegeneration.

J Cell Biol 2014 Nov;207(4):453-62

VIB Center for the Biology of Disease and Center for Human Genetics Laboratory of Neuronal Communication, KU Leuven, 3000 Leuven, Belgium VIB Center for the Biology of Disease and Center for Human Genetics Laboratory of Neuronal Communication, KU Leuven, 3000 Leuven, Belgium

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http://dx.doi.org/10.1083/jcb.201406026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242831PMC
November 2014

Alteration of the microRNA network during the progression of Alzheimer's disease.

EMBO Mol Med 2013 10 9;5(10):1613-34. Epub 2013 Sep 9.

VIB Center for the Biology of Disease, Leuven, Belgium; Center for Human Genetics, Leuven Institute for Neurodegenerative Disorders (LIND) University Hospitals Leuven, and University of Leuven, O&N4, Herestraat, Leuven, Belgium.

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http://dx.doi.org/10.1002/emmm.201201974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799583PMC
October 2013

Cancer: Mutations close in on gene regulation.

Nature 2013 Jul;499(7456):35-6

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http://dx.doi.org/10.1038/499035aDOI Listing
July 2013

Variations in the exome of the LNCaP prostate cancer cell line.

Prostate 2012 Sep 27;72(12):1317-27. Epub 2011 Dec 27.

Molecular Endocrinology Laboratory, Department of Molecular Cell Biology, University of Leuven, 3000 Leuven, Belgium.

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http://dx.doi.org/10.1002/pros.22480DOI Listing
September 2012

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.

Nucleic Acids Res 2012 Aug 20;40(15):e114. Epub 2012 Jun 20.

TAGC - Inserm U1090 and Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France.

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http://dx.doi.org/10.1093/nar/gks543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424583PMC
August 2012

Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets.

Authors:
Stein Aerts

Curr Top Dev Biol 2012 ;98:121-45

Laboratory of Computational Biology, Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1016/B978-0-12-386499-4.00005-7DOI Listing
April 2012

Using cisTargetX to predict transcriptional targets and networks in Drosophila.

Methods Mol Biol 2012 ;786:291-314

TAGC Inserm U928 and Université de la Mediterranée, Marseille, France.

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http://dx.doi.org/10.1007/978-1-61779-292-2_18DOI Listing
February 2012

Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation.

Fly (Austin) 2011 Jul-Sep;5(3):221-3. Epub 2011 Jul 1.

Laboratory of Computational Biology, KU Leuven School of Medicine, Leuven, Belgium.

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http://dx.doi.org/10.4161/fly.5.3.15542DOI Listing
November 2011

The atonal proneural transcription factor links differentiation and tumor formation in Drosophila.

PLoS Biol 2009 Feb;7(2):e40

Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium.

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http://dx.doi.org/10.1371/journal.pbio.1000040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652389PMC
February 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

Sequencing the regulatory genome.

Genome Biol 2008 19;9(6):313. Epub 2008 Jun 19.

Department of Molecular and Developmental Genetics, Laboratory of Neurogenetics, VIB, Leuven B-3000, Belgium.

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http://dx.doi.org/10.1186/gb-2008-9-6-313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481419PMC
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

Text-mining assisted regulatory annotation.

Genome Biol 2008 13;9(2):R31. Epub 2008 Feb 13.

Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B-3000, Belgium.

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http://dx.doi.org/10.1186/gb-2008-9-2-r31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374703PMC
May 2008

Fine-tuning enhancer models to predict transcriptional targets across multiple genomes.

PLoS One 2007 Nov 7;2(11):e1115. Epub 2007 Nov 7.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001115PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2047340PMC
November 2007

Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus.

BMC Bioinformatics 2006 Aug 2;7:367. Epub 2006 Aug 2.

Laboratory of Transcription Regulation, Department of Cell Biology, The Nencki Institute of Experimental Biology, Pasteura 3, 02-093 Warsaw, Poland.

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http://dx.doi.org/10.1186/1471-2105-7-367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560171PMC
August 2006

Gene prioritization through genomic data fusion.

Nat Biotechnol 2006 May;24(5):537-44

Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology (VIB), University of Leuven, Herestraat 49, bus 602, 3000 Leuven, Belgium.

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https://endeavour.esat.kuleuven.be/files/pdfs/Paris_Curie09_
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http://cbio.ensmp.fr/~jvert/svn/bibli/local/Aerts2006Gene.pd
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ftp://ftp.esat.kuleuven.be/pub/SISTA/ida/reports/11-114.pdf
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http://dx.doi.org/10.1038/nbt1203DOI Listing
May 2006

Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro.

J Neurochem 2006 Apr;97 Suppl 1:87-91

Laboratory of Transcription Regulation, Department of Cell Biology, The Nencki Institute of Experimental Biology, Warsaw, Poland.

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http://dx.doi.org/10.1111/j.1471-4159.2005.03537.xDOI Listing
April 2006

TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W393-6

Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium.

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http://dx.doi.org/10.1093/nar/gki354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160115PMC
July 2005

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes.

Bioinformatics 2004 Aug 25;20(12):1974-6. Epub 2004 Mar 25.

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

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http://dx.doi.org/10.1093/bioinformatics/bth179DOI Listing
August 2004

Comprehensive analysis of the base composition around the transcription start site in Metazoa.

BMC Genomics 2004 Jun 1;5(1):34. Epub 2004 Jun 1.

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

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http://dx.doi.org/10.1186/1471-2164-5-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC436054PMC
June 2004

Computational detection of cis -regulatory modules.

Bioinformatics 2003 Oct;19 Suppl 2:ii5-14

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

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http://dx.doi.org/10.1093/bioinformatics/btg1052DOI Listing
October 2003

Comparison and meta-analysis of microarray data: from the bench to the computer desk.

Trends Genet 2003 Oct;19(10):570-7

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

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http://dx.doi.org/10.1016/j.tig.2003.08.006DOI Listing
October 2003

Gene profiling of hippocampal neuronal culture.

J Neurochem 2003 Jun;85(5):1279-88

Laboratory for Neuronal Cell Biology, Center for Human Genetics, and Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven and VIB (Flemish Interuniversity Institute for Biotechnology), Leuven, Belgium.

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http://dx.doi.org/10.1046/j.1471-4159.2003.01753.xDOI Listing
June 2003

Toucan: deciphering the cis-regulatory logic of coregulated genes.

Nucleic Acids Res 2003 Mar;31(6):1753-64

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC152870PMC
http://dx.doi.org/10.1093/nar/gkg268DOI Listing
March 2003