| Bioconda: sustainable and comprehensive software distribution for the life sciences B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ... Nature methods 15 (7), 475, 2018 | 1212 | 2018 |
| A pan-cancer analysis of synonymous mutations Y Sharma, M Miladi, S Dukare, K Boulay, M Caudron-Herger, M Groß, ... Nature communications 10 (1), 2569, 2019 | 211 | 2019 |
| Freiburg RNA tools: a central online resource for RNA-focused research and teaching M Raden, SM Ali, OS Alkhnbashi, A Busch, F Costa, JA Davis, ... Nucleic acids research 46 (W1), W25-W29, 2018 | 148 | 2018 |
| SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics S Will, C Otto, M Miladi, M Möhl, R Backofen Bioinformatics 31 (15), 2489-2496, 2015 | 64 | 2015 |
| NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy W de Koning, M Miladi, S Hiltemann, A Heikema, JP Hays, S Flemming, ... GigaScience 9 (10), giaa105, 2020 | 46 | 2020 |
| RNAscClust : clustering RNA sequences using structure conservation and graph based motifs M Miladi, A Junge, F Costa, SE Seemann, JH Havgaard, J Gorodkin, ... Bioinformatics 33 (14), 2089-2096, 2017 | 33 | 2017 |
| Codonbert: Large language models for mrna design and optimization S Li, S Moayedpour, R Li, M Bailey, S Riahi, L Kogler-Anele, M Miladi, ... bioRxiv, 2023.09. 09.556981, 2023 | 32* | 2023 |
| MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration T Wallach, ZJ Mossmann, M Szczepek, M Wetzel, R Machado, M Raden, ... Molecular Neurodegeneration 16 (1), 80, 2021 | 29 | 2021 |
| MutaRNA: analysis and visualization of mutation-induced changes in RNA structure M Miladi, M Raden, S Diederichs, R Backofen Nucleic acids research 48 (W1), W287-W291, 2020 | 27 | 2020 |
| Ready-to-use public infrastructure for global SARS-CoV-2 monitoring W Maier, S Bray, M van den Beek, D Bouvier, N Coraor, M Miladi, B Singh, ... Nature Biotechnology 39 (10), 1178-1179, 2021 | 26 | 2021 |
| Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring W Maier, S Bray, M van den Beek, D Bouvier, N Coraor, M Miladi, B Singh, ... bioRxiv, 2021 | 18 | 2021 |
| The landscape of SARS-CoV-2 RNA modifications M Miladi, J Fuchs, W Maier, S Weigang, ND Pedrosa, L Weiss, A Lother, ... Biorxiv, 2020.07. 18.204362, 2020 | 18 | 2020 |
| GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering M Miladi, E Sokhoyan, T Houwaart, S Heyne, F Costa, B Grüning, ... GigaScience 8 (12), giz150, 2019 | 18 | 2019 |
| Integration of accessibility data from structure probing into RNA-RNA interaction prediction M Miladi, S Montaseri, R Backofen, M Raden Bioinformatics, 2018 | 17 | 2018 |
| ShaKer: RNA SHAPE prediction using graph kernel S Mautner, S Montaseri, M Miladi, M Raden, F Costa, R Backofen Bioinformatics, 2019 | 12 | 2019 |
| Structure-aware machine learning identifies microRNAs operating as Toll-like receptor 7/8 ligands M Raden, T Wallach, M Miladi, Y Zhai, C Krüger, ZJ Mossmann, ... RNA biology 18 (sup1), 268-277, 2021 | 10 | 2021 |
| Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq T Schwarzl, S Sahadevan, B Lang, M Miladi, R Backofen, W Huber, ... Nucleic Acids Research 52 (1), e1-e1, 2024 | 8 | 2024 |
| A pan-cancer analysis of synonymous mutations. Nat Commun 10: 2569 Y Sharma, M Miladi, S Dukare, K Boulay, M Caudron-Herger, M Groß, ... | 7 | 2019 |
| CodonBERT large language model for mRNA vaccines S Li, S Moayedpour, R Li, M Bailey, S Riahi, L Kogler-Anele, M Miladi, ... Genome research 34 (7), 1027-1035, 2024 | 6 | 2024 |
| A pan-cancer analysis of synonymous mutations. Nat Commun. 2019; 10 (1): 2569 Y Sharma, M Miladi, S Dukare, K Boulay, M Caudron-Herger, M Gross | 5 | |
Rolf BackofenProfessor für Bioinformatik, Universität FreiburgVerified email at informatik.uni-freiburg.de