| Data-driven hypothesis weighting increases detection power in genome-scale multiple testing N Ignatiadis, B Klaus, JB Zaugg, W Huber Nature methods 13 (7), 577-580, 2016 | 634 | 2016 |
| Extensive variation in chromatin states across humans M Kasowski, S Kyriazopoulou-Panagiotopoulou, F Grubert, JB Zaugg, ... Science 342 (6159), 750-752, 2013 | 413 | 2013 |
| Genetic control of chromatin states in humans involves local and distal chromosomal interactions F Grubert, JB Zaugg, M Kasowski, O Ursu, DV Spacek, AR Martin, ... Cell 162 (5), 1051-1065, 2015 | 384 | 2015 |
| Bacterial adaptation through distributed sensing of metabolic fluxes O Kotte, JB Zaugg, M Heinemann Molecular systems biology 6 (1), 355, 2010 | 323 | 2010 |
| Gene loops enhance transcriptional directionality SM Tan-Wong, JB Zaugg, J Camblong, Z Xu, DW Zhang, HE Mischo, ... Science 338 (6107), 671-675, 2012 | 294 | 2012 |
| Integrative single-cell RNA-seq and ATAC-seq analysis of human developmental hematopoiesis AM Ranzoni, A Tangherloni, I Berest, SG Riva, B Myers, PM Strzelecka, ... Cell stem cell 28 (3), 472-487. e7, 2021 | 270 | 2021 |
| Co-expression networks reveal the tissue-specific regulation of transcription and splicing A Saha, Y Kim, ADH Gewirtz, B Jo, C Gao, IC McDowell, BE Engelhardt, ... Genome research 27 (11), 1843-1858, 2017 | 182 | 2017 |
| Landscape of cohesin-mediated chromatin loops in the human genome F Grubert, R Srivas, DV Spacek, M Kasowski, M Ruiz-Velasco, ... Nature 583 (7818), 737-743, 2020 | 161 | 2020 |
| Transcription factors: Bridge between cell signaling and gene regulation P Weidemüller, M Kholmatov, E Petsalaki, JB Zaugg Proteomics 21 (23-24), 2000034, 2021 | 160 | 2021 |
| Enhancers in disease: molecular basis and emerging treatment strategies A Claringbould, JB Zaugg Trends in molecular medicine 27 (11), 1060-1073, 2021 | 140 | 2021 |
| Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTF I Berest, C Arnold, A Reyes-Palomares, G Palla, KD Rasmussen, H Giles, ... Cell reports 29 (10), 3147-3159. e12, 2019 | 119 | 2019 |
| CTCF-mediated chromatin loops between promoter and gene body regulate alternative splicing across individuals M Ruiz-Velasco, M Kumar, MC Lai, P Bhat, AB Solis-Pinson, A Reyes, ... Cell systems 5 (6), 628-637. e6, 2017 | 104 | 2017 |
| TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells KD Rasmussen, I Berest, S Keβler, K Nishimura, L Simón-Carrasco, ... Genome research 29 (4), 564-575, 2019 | 90 | 2019 |
| Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline ML Hennrich, N Romanov, P Horn, S Jaeger, V Eckstein, V Steeples, F Ye, ... Nature communications 9 (1), 4004, 2018 | 88 | 2018 |
| Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions IL Ibarra, NM Hollmann, B Klaus, S Augsten, B Velten, J Hennig, ... Nature communications 11 (1), 124, 2020 | 78 | 2020 |
| Convolutional networks for supervised mining of molecular patterns within cellular context I de Teresa-Trueba, SK Goetz, A Mattausch, F Stojanovska, CE Zimmerli, ... Nature Methods 20 (2), 284-294, 2023 | 76 | 2023 |
| Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension A Reyes-Palomares, M Gu, F Grubert, I Berest, S Sa, M Kasowski, ... Nature communications 11 (1), 1673, 2020 | 71 | 2020 |
| Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis F Yang, J Wang, BL Pierce, LS Chen, F Aguet, KG Ardlie, BB Cummings, ... Genome research 27 (11), 1859-1871, 2017 | 71 | 2017 |
| A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast JB Zaugg, NM Luscombe Genome research 22 (1), 84-94, 2012 | 66 | 2012 |
| Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast M Castelnuovo, JB Zaugg, E Guffanti, A Maffioletti, J Camblong, Z Xu, ... Nucleic acids research 42 (7), 4348-4362, 2014 | 63 | 2014 |
