Stein Aerts - Publications

Katholieke Universiteit Leuven, Leuven, Vlaanderen, Belgium 
regualtory genomics, computational biology

56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Adriaens C, Standaert L, Barra J, Latil M, Verfaillie A, Kalev P, Boeckx B, Wijnhoven PW, Radaelli E, Vermi W, Leucci E, Lapouge G, Beck B, van den Oord J, Nakagawa S, ... ... Aerts S, et al. p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nature Medicine. PMID 27376578 DOI: 10.1038/nm.4135  0.8
2016 Jin M, Aibar S, Ge Z, Chen R, Aerts S, Mardon G. Identification of Novel Direct Targets of Drosophila Sine Oculis by Integration of Genome-wide Data Sets. Developmental Biology. PMID 27178668 DOI: 10.1016/j.ydbio.2016.05.007  0.8
2015 Naval-Sánchez M, Potier D, Hulselmans G, Christiaens V, Aerts S. Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Molecular Biology and Evolution. PMID 25944915 DOI: 10.1093/molbev/msv107  0.8
2015 Verfaillie A, Imrichova H, Atak ZK, Dewaele M, Rambow F, Hulselmans G, Christiaens V, Svetlichnyy D, Luciani F, Van den Mooter L, Claerhout S, Fiers M, Journe F, Ghanem GE, Herrmann C, ... ... Aerts S, et al. Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. Nature Communications. 6: 6683. PMID 25865119 DOI: 10.1038/ncomms7683  0.8
2015 Raponi S, Gianfelici V, Chiaretti S, Peragine N, Brugnoletti F, De Propris MS, Marinelli M, Hulselmans G, Aerts S, Geerdens E, Cools J, Foà R, Guarini A. CD45 antigen negativity in T-lineage ALL correlates with PTPRC mutation and sensitivity to a selective JAK inhibitor. British Journal of Haematology. PMID 25854815 DOI: 10.1111/bjh.13448  0.8
2015 Laurette P, Strub T, Koludrovic D, Keime C, Le Gras S, Seberg H, Van Otterloo E, Imrichova H, Siddaway R, Aerts S, Cornell RA, Mengus G, Davidson I. Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells. Elife. 4. PMID 25803486 DOI: 10.7554/eLife.06857  0.8
2015 Davie K, Jacobs J, Atkins M, Potier D, Christiaens V, Halder G, Aerts S. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. Plos Genetics. 11: e1004994. PMID 25679813 DOI: 10.1371/journal.pgen.1004994  0.8
2015 Oliva C, Molina-Fernandez C, Maureira M, Candia N, López E, Hassan B, Aerts S, Cánovas J, Olguín P, Sierralta J. Hindsight regulates photoreceptor axon targeting through transcriptional control of jitterbug/Filamin and multiple genes involved in axon guidance in Drosophila. Developmental Neurobiology. PMID 25652545 DOI: 10.1002/dneu.22271  0.8
2014 Potier D, Davie K, Hulselmans G, Naval Sanchez M, Haagen L, Huynh-Thu VA, Koldere D, Celik A, Geurts P, Christiaens V, Aerts S. Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. Cell Reports. 9: 2290-303. PMID 25533349 DOI: 10.1016/j.celrep.2014.11.038  0.8
2014 Hattori H, Janky R, Nietfeld W, Aerts S, Madan Babu M, Venkitaraman AR. p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response. Cell Cycle (Georgetown, Tex.). 13: 2572-86. PMID 25486198 DOI: 10.4161/15384101.2015.942209  0.8
2014 Fernandes AC, Uytterhoeven V, Kuenen S, Wang YC, Slabbaert JR, Swerts J, Kasprowicz J, Aerts S, Verstreken P. Reduced synaptic vesicle protein degradation at lysosomes curbs TBC1D24/sky-induced neurodegeneration. The Journal of Cell Biology. 207: 453-62. PMID 25422373 DOI: 10.1083/jcb.201406026  0.8
2014 Degryse S, de Bock CE, Cox L, Demeyer S, Gielen O, Mentens N, Jacobs K, Geerdens E, Gianfelici V, Hulselmans G, Fiers M, Aerts S, Meijerink JP, Tousseyn T, Cools J. JAK3 mutants transform hematopoietic cells through JAK1 activation, causing T-cell acute lymphoblastic leukemia in a mouse model. Blood. 124: 3092-100. PMID 25193870 DOI: 10.1182/blood-2014-04-566687  0.8
2014 Zhao H, Thienpont B, Yesilyurt BT, Moisse M, Reumers J, Coenegrachts L, Sagaert X, Schrauwen S, Smeets D, Matthijs G, Aerts S, Cools J, Metcalf A, Spurdle A, et al. Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks. Elife. 3: e02725. PMID 25085081 DOI: 10.7554/eLife.02725  0.8
2014 Janky R, Verfaillie A, Imrichová H, Van de Sande B, Standaert L, Christiaens V, Hulselmans G, Herten K, Naval Sanchez M, Potier D, Svetlichnyy D, Kalender Atak Z, Fiers M, Marine JC, Aerts S. iRegulon: from a gene list to a gene regulatory network using large motif and track collections. Plos Computational Biology. 10: e1003731. PMID 25058159 DOI: 10.1371/journal.pcbi.1003731  0.8
2014 Potier D, Seyres D, Guichard C, Iche-Torres M, Aerts S, Herrmann C, Perrin L. Identification of cis-regulatory modules encoding temporal dynamics during development. Bmc Genomics. 15: 534. PMID 24972496 DOI: 10.1186/1471-2164-15-534  0.8
2014 Neville MC, Nojima T, Ashley E, Parker DJ, Walker J, Southall T, Van de Sande B, Marques AC, Fischer B, Brand AH, Russell S, Ritchie MG, Aerts S, Goodwin SF. Male-specific fruitless isoforms target neurodevelopmental genes to specify a sexually dimorphic nervous system. Current Biology : Cb. 24: 229-41. PMID 24440396 DOI: 10.1016/j.cub.2013.11.035  0.8
2013 Atak ZK, Gianfelici V, Hulselmans G, De Keersmaecker K, Devasia AG, Geerdens E, Mentens N, Chiaretti S, Durinck K, Uyttebroeck A, Vandenberghe P, Wlodarska I, Cloos J, Foà R, Speleman F, ... ... Aerts S, et al. Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. Plos Genetics. 9: e1003997. PMID 24367274 DOI: 10.1371/journal.pgen.1003997  0.8
2013 Lau P, Bossers K, Janky R, Salta E, Frigerio CS, Barbash S, Rothman R, Sierksma AS, Thathiah A, Greenberg D, Papadopoulou AS, Achsel T, Ayoubi T, Soreq H, Verhaagen J, ... ... Aerts S, et al. Alteration of the microRNA network during the progression of Alzheimer's disease. Embo Molecular Medicine. 5: 1613-34. PMID 24014289 DOI: 10.1002/emmm.201201974  0.8
2013 Menoret D, Santolini M, Fernandes I, Spokony R, Zanet J, Gonzalez I, Latapie Y, Ferrer P, Rouault H, White KP, Besse P, Hakim V, Aerts S, Payre F, Plaza S. Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization. Genome Biology. 14: R86. PMID 23972280 DOI: 10.1186/gb-2013-14-8-r86  0.8
2013 Aerts S, Cools J. Cancer: Mutations close in on gene regulation. Nature. 499: 35-6. PMID 23823789 DOI: 10.1038/499035a  0.8
2013 Vanden Broeck L, Naval-Sánchez M, Adachi Y, Diaper D, Dourlen P, Chapuis J, Kleinberger G, Gistelinck M, Van Broeckhoven C, Lambert JC, Hirth F, Aerts S, Callaerts P, Dermaut B. TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila. Cell Reports. 3: 160-72. PMID 23333275 DOI: 10.1016/j.celrep.2012.12.014  0.8
2013 van den Berghe V, Stappers E, Vandesande B, Dimidschstein J, Kroes R, Francis A, Conidi A, Lesage F, Dries R, Cazzola S, Berx G, Kessaris N, Vanderhaeghen P, van Ijcken W, Grosveld FG, ... ... Aerts S, et al. Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1. Neuron. 77: 70-82. PMID 23312517 DOI: 10.1016/j.neuron.2012.11.009  0.8
2013 De Keersmaecker K, Atak ZK, Li N, Vicente C, Patchett S, Girardi T, Gianfelici V, Geerdens E, Clappier E, Porcu M, Lahortiga I, Lucà R, Yan J, Hulselmans G, Vranckx H, ... ... Aerts S, et al. Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia. Nature Genetics. 45: 186-90. PMID 23263491 DOI: 10.1038/ng.2508  0.8
2013 Naval-Sánchez M, Potier D, Haagen L, Sánchez M, Munck S, Van de Sande B, Casares F, Christiaens V, Aerts S. Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions. Genome Research. 23: 74-88. PMID 23070853 DOI: 10.1101/gr.140426.112  0.8
2012 Youssef KK, Lapouge G, Bouvrée K, Rorive S, Brohée S, Appelstein O, Larsimont JC, Sukumaran V, Van de Sande B, Pucci D, Dekoninck S, Berthe JV, Aerts S, Salmon I, del Marmol V, et al. Adult interfollicular tumour-initiating cells are reprogrammed into an embryonic hair follicle progenitor-like fate during basal cell carcinoma initiation. Nature Cell Biology. 14: 1282-94. PMID 23178882 DOI: 10.1038/ncb2628  0.8
2012 Herrmann C, Van de Sande B, Potier D, Aerts S. i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. Nucleic Acids Research. 40: e114. PMID 22718975 DOI: 10.1093/nar/gks543  0.8
2012 Kalender Atak Z, De Keersmaecker K, Gianfelici V, Geerdens E, Vandepoel R, Pauwels D, Porcu M, Lahortiga I, Brys V, Dirks WG, Quentmeier H, Cloos J, Cuppens H, Uyttebroeck A, Vandenberghe P, ... ... Aerts S, et al. High accuracy mutation detection in leukemia on a selected panel of cancer genes. Plos One. 7: e38463. PMID 22675565 DOI: 10.1371/journal.pone.0038463  0.8
2012 Aerts S. Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets. Current Topics in Developmental Biology. 98: 121-45. PMID 22305161 DOI: 10.1016/B978-0-12-386499-4.00005-7  0.8
2012 Spans L, Atak ZK, Van Nieuwerburgh F, Deforce D, Lerut E, Aerts S, Claessens F. Variations in the exome of the LNCaP prostate cancer cell line. The Prostate. 72: 1317-27. PMID 22213130 DOI: 10.1002/pros.22480  0.8
2012 Potier D, Atak ZK, Sanchez MN, Herrmann C, Aerts S. Using cisTargetX to predict transcriptional targets and networks in Drosophila. Methods in Molecular Biology (Clifton, N.J.). 786: 291-314. PMID 21938634 DOI: 10.1007/978-1-61779-292-2_18  0.8
2011 Kleppe M, Tousseyn T, Geissinger E, Kalender Atak Z, Aerts S, Rosenwald A, Wlodarska I, Cools J. Mutation analysis of the tyrosine phosphatase PTPN2 in Hodgkin's lymphoma and T-cell non-Hodgkin's lymphoma. Haematologica. 96: 1723-7. PMID 21791476 DOI: 10.3324/haematol.2011.041921  0.8
2011 Aerts S, Hassan B. Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation. Fly. 5: 221-3. PMID 21471735  0.8
2011 Aerts S, Hassan BA. Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation Fly. 5: 1-3.  0.8
2010 Aerts S, Quan XJ, Claeys A, Naval Sanchez M, Tate P, Yan J, Hassan BA. Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. Plos Biology. 8: e1000435. PMID 20668662 DOI: 10.1371/journal.pbio.1000435  0.8
2009 Bossuyt W, De Geest N, Aerts S, Leenaerts I, Marynen P, Hassan BA. The atonal proneural transcription factor links differentiation and tumor formation in Drosophila. Plos Biology. 7: e40. PMID 19243220 DOI: 10.1371/journal.pbio.1000040  0.8
2009 Aerts S, Vilain S, Hu S, Tranchevent LC, Barriot R, Yan J, Moreau Y, Hassan BA, Quan XJ. Integrating computational biology and forward genetics in Drosophila. Plos Genetics. 5: e1000351. PMID 19165344 DOI: 10.1371/journal.pgen.1000351  0.8
2008 Aerts S, Butland S. Sequencing the regulatory genome. Genome Biology. 9: 313. PMID 18598374 DOI: 10.1186/gb-2008-9-6-313  0.8
2008 Tranchevent LC, Barriot R, Yu S, Van Vooren S, Van Loo P, Coessens B, De Moor B, Aerts S, Moreau Y. ENDEAVOUR update: a web resource for gene prioritization in multiple species. Nucleic Acids Research. 36: W377-84. PMID 18508807 DOI: 10.1093/nar/gkn325  0.8
2008 Van Loo P, Aerts S, Thienpont B, De Moor B, Moreau Y, Marynen P. ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Genome Biology. 9: R66. PMID 18394174 DOI: 10.1186/gb-2008-9-4-r66  0.8
2008 Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM. Text-mining assisted regulatory annotation. Genome Biology. 9: R31. PMID 18271954 DOI: 10.1186/gb-2008-9-2-r31  0.8
2008 Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. 36: D107-13. PMID 18006570 DOI: 10.1093/nar/gkm967  0.8
2007 Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Aerts S, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/nature06340  0.8
2007 Aerts S, van Helden J, Sand O, Hassan BA. Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. Plos One. 2: e1115. PMID 17973026 DOI: 10.1371/journal.pone.0001115  0.8
2006 Dabrowski M, Aerts S, Kaminska B. 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. 7: 367. PMID 16884529 DOI: 10.1186/1471-2105-7-367  0.8
2006 Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nature Biotechnology. 24: 537-44. PMID 16680138 DOI: 10.1038/nbt1203  0.8
2006 Dabrowski M, Adach A, Aerts S, Moreau Y, Kaminska B. Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro. Journal of Neurochemistry. 97: 87-91. PMID 16635255 DOI: 10.1111/j.1471-4159.2005.03537.x  0.8
2005 Aerts S, Van Loo P, Thijs G, Mayer H, de Martin R, Moreau Y, De Moor B. TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Research. 33: W393-6. PMID 15980497 DOI: 10.1093/nar/gki354  0.8
2004 Aerts S, Thijs G, Dabrowski M, Moreau Y, De Moor B. Comprehensive analysis of the base composition around the transcription start site in Metazoa. Bmc Genomics. 5: 34. PMID 15171795 DOI: 10.1186/1471-2164-5-34  0.8
2004 Aerts S, Van Loo P, Moreau Y, De Moor B. A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes. Bioinformatics (Oxford, England). 20: 1974-6. PMID 15044242 DOI: 10.1093/bioinformatics/bth179  0.8
2004 Denys H, Jadidizadeh A, Amini Nik S, Van Dam K, Aerts S, Alman BA, Cassiman JJ, Tejpar S. Identification of IGFBP-6 as a significantly downregulated gene by beta-catenin in desmoid tumors. Oncogene. 23: 654-64. PMID 14737101 DOI: 10.1038/sj.onc.1207160  0.8
2003 Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M. Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends in Genetics : Tig. 19: 570-7. PMID 14550631 DOI: 10.1016/j.tig.2003.08.006  0.8
2003 Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B. Computational detection of cis -regulatory modules. Bioinformatics (Oxford, England). 19: ii5-14. PMID 14534164 DOI: 10.1093/bioinformatics/btg1052  0.8
2003 Coessens B, Thijs G, Aerts S, Marchal K, De Smet F, Engelen K, Glenisson P, Moreau Y, Mathys J, De Moor B. INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Research. 31: 3468-70. PMID 12824346 DOI: 10.1093/nar/gkg615  0.8
2003 Dabrowski M, Aerts S, Van Hummelen P, Craessaerts K, De Moor B, Annaert W, Moreau Y, De Strooper B. Gene profiling of hippocampal neuronal culture. Journal of Neurochemistry. 85: 1279-88. PMID 12753086 DOI: 10.1046/j.1471-4159.2003.01753.x  0.8
2003 Aerts S, Thijs G, Coessens B, Staes M, Moreau Y, De Moor B. Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Research. 31: 1753-64. PMID 12626717 DOI: 10.1093/nar/gkg268  0.8
2002 Aerts S, Antal P, Timmerman D, De Moor B, Moreau Y. Web-based data collection for uterine adnexal tumors: A case study Proceedings of the Ieee Symposium On Computer-Based Medical Systems. 282-287.  0.8
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