| deepTools2: a next generation web server for deep-sequencing data analysis F Ramírez, DP Ryan, B Grüning, V Bhardwaj, F Kilpert, AS Richter, ... Nucleic acids research 44 (W1), W160-W165, 2016 | 4074 | 2016 |
| deepTools: a flexible platform for exploring deep-sequencing data F Ramírez, F Dündar, S Diehl, BA Grüning, T Manke Nucleic acids research 42 (W1), W187-W191, 2014 | 1976 | 2014 |
| Computing topological parameters of biological networks Y Assenov, F Ramírez, SE Schelhorn, T Lengauer, M Albrecht Bioinformatics 24 (2), 282-284, 2008 | 1635 | 2008 |
| GOATOOLS: A Python library for Gene Ontology analyses DV Klopfenstein, L Zhang, BS Pedersen, F Ramírez, A Warwick Vesztrocy, ... Scientific reports 8 (1), 1-17, 2018 | 587 | 2018 |
| High-resolution TADs reveal DNA sequences underlying genome organization in flies F Ramírez, V Bhardwaj, L Arrigoni, KC Lam, BA Grüning, J Villaveces, ... Nature communications 9 (1), 189, 2018 | 543 | 2018 |
| Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment S Reiss, I Rebhan, P Backes, I Romero-Brey, H Erfle, P Matula, L Kaderali, ... Cell host & microbe 9 (1), 32-45, 2011 | 533 | 2011 |
| Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells A Bulut-Karslioglu, A Inti, F Ramirez, M Barenboim, M Onishi-Seebacher, ... Molecular cell 55 (2), 277-290, 2014 | 293 | 2014 |
| The implications of alternative splicing in the ENCODE protein complement ML Tress, PL Martelli, A Frankish, GA Reeves, JJ Wesselink, C Yeats, ... Proceedings of the National Academy of Sciences 104 (13), 5495-5500, 2007 | 245 | 2007 |
| pyGenomeTracks: reproducible plots for multivariate genomic data sets L Lopez-Delisle, L Rabbani, J Wolff, V Bhardwaj, R Backofen, B Grüning, ... Bioinformatics, 2021 | 137 | 2021 |
| Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization J Wolff, V Bhardwaj, S Nothjunge, G Richard, G Renschler, R Gilsbach, ... Nucleic acids research 46 (W1), W11-W16, 2018 | 133 | 2018 |
| The genomic landscape of the somatic linker histone subtypes H1. 1 to H1. 5 in human cells A Izzo, K Kamieniarz-Gdula, F Ramírez, N Noureen, J Kind, T Manke, ... Cell reports 3 (6), 2142-2154, 2013 | 131 | 2013 |
| Community-driven data analysis training for biology B Batut, S Hiltemann, A Bagnacani, D Baker, V Bhardwaj, C Blank, ... Cell systems 6 (6), 752-758. e1, 2018 | 129 | 2018 |
| Computational analysis of human protein interaction networks F Ramirez, A Schlicker, Y Assenov, T Lengauer, M Albrecht Proteomics 7 (15), 2541-2552, 2007 | 90 | 2007 |
| MOF-associated complexes ensure stem cell identity and Xist repression T Chelmicki, F Dündar, MJ Turley, T Khanam, T Aktas, F Ramírez, ... Elife 3, e02024, 2014 | 79 | 2014 |
| High-affinity sites form an interaction network to facilitate spreading of the MSL complex across the X chromosome in Drosophila F Ramirez, T Lingg, S Toscano, KC Lam, P Georgiev, HR Chung, ... Molecular cell 60 (1), 146-162, 2015 | 78 | 2015 |
| GOATOOLS: tools for gene ontology H Tang, D Klopfenstein, B Pedersen, P Flick, K Sato, F Ramirez, J Yunes, ... Zenodo 10 (10872), 10.1038, 2015 | 71 | 2015 |
| A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains A Salhab, K Nordström, G Gasparoni, K Kattler, P Ebert, F Ramirez, ... Genome biology 19, 1-13, 2018 | 70 | 2018 |
| Functional evaluation of domain–domain interactions and human protein interaction networks A Schlicker, C Huthmacher, F Ramírez, T Lengauer, M Albrecht Bioinformatics 23 (7), 859-865, 2007 | 50 | 2007 |
| Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling G Renschler, G Richard, CIK Valsecchi, S Toscano, L Arrigoni, F Ramírez, ... Genes & development 33 (21-22), 1591-1612, 2019 | 36 | 2019 |
| CAPRI enables comparison of evolutionarily conserved RNA interacting regions A Panhale, FM Richter, F Ramírez, M Shvedunova, T Manke, G Mittler, ... Nature communications 10 (1), 2682, 2019 | 33 | 2019 |
Thomas MankeHead of Bioinformatics and Deep-Sequencing Unit, Max Planck Institute for Immunobiology andVerified email at ie-freiburg.mpg.de
