| An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57, 2012 | 13903 | 2012 |
| Landscape of transcription in human cells S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann, A Mortazavi, ... Nature 489 (7414), 101-108, 2012 | 5502 | 2012 |
| The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression T Derrien, R Johnson, G Bussotti, A Tanzer, S Djebali, H Tilgner, ... Genome research 22 (9), 1775-1789, 2012 | 5296 | 2012 |
| An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Overall coordination (data analysis coordination ... Nature 489 (7414), 57-74, 2012 | 3076 | 2012 |
| A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS Biol 9 (4), e1001046, 2011 | 1445 | 2011 |
| Genome analysis of the platypus reveals unique signatures of evolution Nature 453 (7192), 175-183, 2008 | 772 | 2008 |
| Whole-genome fingerprint of the DNA methylome during human B cell differentiation M Kulis, A Merkel, S Heath, AC Queirós, RP Schuyler, G Castellano, ... Nature genetics 47 (7), 746-756, 2015 | 313 | 2015 |
| The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia R Beekman, V Chapaprieta, N Russiñol, R Vilarrasa-Blasi, ... Nature medicine 24 (6), 868-880, 2018 | 186 | 2018 |
| Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers X Agirre, G Castellano, M Pascual, S Heath, M Kulis, V Segura, ... Genome research 25 (4), 478-487, 2015 | 158 | 2015 |
| Decoding the DNA methylome of mantle cell lymphoma in the light of the entire B cell lineage AC Queiros, R Beekman, R Vilarrasa-Blasi, M Duran-Ferrer, G Clot, ... Cancer cell 30 (5), 806-821, 2016 | 141 | 2016 |
| Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time J Feichtinger, I Hernández, C Fischer, M Hanscho, N Auer, M Hackl, ... Biotechnology and bioengineering 113 (10), 2241-2253, 2016 | 140 | 2016 |
| Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types S Ecker, L Chen, V Pancaldi, FO Bagger, JM Fernández, ... Genome biology 18, 1-17, 2017 | 116 | 2017 |
| Dynamics of transcription regulation in human bone marrow myeloid differentiation to mature blood neutrophils L Grassi, F Pourfarzad, S Ullrich, A Merkel, F Were, ... Cell reports 24 (10), 2784-2794, 2018 | 112 | 2018 |
| Detecting short tandem repeats from genome data: opening the software black box A Merkel, N Gemmell Briefings in bioinformatics 9 (5), 355-366, 2008 | 89 | 2008 |
| Systemic inflammation in preclinical ulcerative colitis D Bergemalm, E Andersson, J Hultdin, C Eriksson, ST Rush, R Kalla, ... Gastroenterology 161 (5), 1526-1539. e9, 2021 | 71 | 2021 |
| Distinct trends of DNA methylation patterning in the innate and adaptive immune systems RP Schuyler, A Merkel, E Raineri, L Altucci, E Vellenga, JHA Martens, ... Cell reports 17 (8), 2101-2111, 2016 | 66 | 2016 |
| gemBS: high throughput processing for DNA methylation data from bisulfite sequencing A Merkel, M Fernández-Callejo, E Casals, S Marco-Sola, R Schuyler, ... Bioinformatics 35 (5), 737-742, 2019 | 51 | 2019 |
| Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture I Hernandez, H Dhiman, G Klanert, V Jadhav, N Auer, M Hanscho, ... Biotechnology and Bioengineering 116 (3), 677-692, 2019 | 43 | 2019 |
| Grape RNA-Seq analysis pipeline environment DG Knowles, M Röder, A Merkel, R Guigó Bioinformatics 29 (5), 614-621, 2013 | 39 | 2013 |
| Chromatin-based classification of genetically heterogeneous AMLs into two distinct subtypes with diverse stemness phenotypes G Yi, ATJ Wierenga, F Petraglia, P Narang, EM Janssen-Megens, ... Cell reports 26 (4), 1059-1069. e6, 2019 | 38 | 2019 |
