YAP drives growth by controlling transcriptional pause release from dynamic enhancers GG Galli, M Carrara, WC Yuan, C Valdes-Quezada, B Gurung, ... Molecular cell 60 (2), 328-337, 2015 | 274 | 2015 |
Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping PJP De Vree, E De Wit, M Yilmaz, M Van De Heijning, P Klous, ... Nature biotechnology 32 (10), 1019-1025, 2014 | 273 | 2014 |
Enhancer hubs and loop collisions identified from single-allele topologies A Allahyar, C Vermeulen, BAM Bouwman, PHL Krijger, MJAM Verstegen, ... Nature genetics 50 (8), 1151-1160, 2018 | 212 | 2018 |
Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA N Léveillé, CA Melo, K Rooijers, A Díaz-Lagares, SA Melo, G Korkmaz, ... Nature communications 6 (1), 6520, 2015 | 180 | 2015 |
4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis PHL Krijger, G Geeven, V Bianchi, CRE Hilvering, W de Laat Methods 170, 17-32, 2020 | 137 | 2020 |
Epigenomic annotation of gene regulatory alterations during evolution of the primate brain MW Vermunt, SC Tan, B Castelijns, G Geeven, P Reinink, E De Bruijn, ... Nature neuroscience 19 (3), 494-503, 2016 | 122* | 2016 |
Sensitive monogenic noninvasive prenatal diagnosis by targeted haplotyping C Vermeulen, G Geeven, E de Wit, MJAM Verstegen, RPM Jansen, ... The American Journal of Human Genetics 101 (3), 326-339, 2017 | 102 | 2017 |
Cause and consequence of tethering a SubTAD to different nuclear compartments PJ Wijchers, PHL Krijger, G Geeven, Y Zhu, A Denker, MJAM Verstegen, ... Molecular cell 61 (3), 461-473, 2016 | 100 | 2016 |
Characterization and dynamics of pericentromere-associated domains in mice PJ Wijchers, G Geeven, M Eyres, AJ Bergsma, M Janssen, M Verstegen, ... Genome research 25 (7), 958-969, 2015 | 91 | 2015 |
Large-scale identification of coregulated enhancer networks in the adult human brain MW Vermunt, P Reinink, J Korving, E de Bruijn, PM Creyghton, O Basak, ... Cell reports 9 (2), 767-779, 2014 | 80 | 2014 |
peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data G Geeven, H Teunissen, W de Laat, E de Wit Nucleic acids research 46 (15), e91-e91, 2018 | 71 | 2018 |
Local compartment changes and regulatory landscape alterations in histone H1-depleted cells G Geeven, Y Zhu, BJ Kim, BA Bartholdy, SM Yang, TS Macfarlan, ... Genome biology 16, 1-15, 2015 | 59 | 2015 |
Identification of context-specific gene regulatory networks with GEMULA—gene expression modeling using LAsso G Geeven, RE van Kesteren, AB Smit, MCM de Gunst Bioinformatics 28 (2), 214-221, 2012 | 43 | 2012 |
Enhancers reside in a unique epigenetic environment during early zebrafish development LJT Kaaij, M Mokry, M Zhou, M Musheev, G Geeven, ASJ Melquiond, ... Genome biology 17, 1-15, 2016 | 41 | 2016 |
Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients B Castelijns, ML Baak, IS Timpanaro, CRM Wiggers, MW Vermunt, ... Nature communications 11 (1), 301, 2020 | 38 | 2020 |
A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response CA Melo, N Léveillé, K Rooijers, PJ Wijchers, G Geeven, A Tal, SA Melo, ... Oncogene 35 (33), 4399-4406, 2016 | 28 | 2016 |
Deletion/Substitution/Addition (DSA) model selection algorithm applied to the study of archaeological settlement patterning R Fernandes, G Geeven, S Soetens, V Klontza-Jaklova Journal of Archaeological Science 38 (9), 2293-2300, 2011 | 28 | 2011 |
Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies C Vermeulen, A Allahyar, BAM Bouwman, PHL Krijger, MJAM Verstegen, ... Nature Protocols 15 (2), 364-397, 2020 | 26 | 2020 |
LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data G Geeven, HD MacGillavry, R Eggers, MM Sassen, J Verhaagen, AB Smit, ... Nucleic acids research 39 (13), 5313-5327, 2011 | 26 | 2011 |
Epigenetic analyses of human left atrial tissue identifies gene networks underlying atrial fibrillation AW Hall, M Chaffin, C Roselli, H Lin, SA Lubitz, V Bianchi, G Geeven, ... Circulation: Genomic and Precision Medicine 13 (6), e003085, 2020 | 19 | 2020 |