Publications
See selected2023 Biorxiv DOI:10.1101/2023.02.14.528560
A Systematic Benchmark of Machine Learning Methods for Protein-RNA Interaction Prediction
2022 Biorxiv DOI:10.1101/2022.09.16.508290
Towards In-Silico CLIP-seq: Predicting Protein-RNA Interaction via Sequence-to-Signal Learning
2022 Nature Immunology DOI: 10.1038/s41590-022-01268-1
2022 Front Genet DOI:10.3389/fgene.2022.909714
2022 Molecular Cell DOI: 10.1016/j.molcel.2021.11.023
2021 Nature Communications DOI:10.1038/s41467-021-23643-6
2021 Nature Machine Intelligence DOI:10.1038/s42256-021-00325-y
2021 accepted in NAR genomics and Bioinformatics DOI:10.1101/2021.12.22.472458
Computational Mapping of the Human-SARS-CoV-2 Protein-RNA Interactome
2020 mBio DOI: 10.1128/mBio.03155-19
2020 Biorxiv DOI:10.1101/2020.12.15.422063
Predictive modeling of long non-coding RNA chromatin (dis-)association
2019 International Conference on Artificial Neural Networks DOI:10.1007/978-3-030-30493-5_60
Graph Convolutional Networks Improve the Prediction of Cancer Driver Genes
2019 Genome research DOI:10.1101/gr.245027.118
2019 BMC bioinformatics DOI: 10.1186/s12859-019-2900-8
Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis
2019 Journal of molecular cell biology DOI: 10.1093/jmcb/mjz047
Functional impacts of non-coding RNA processing on enhancer activity and target gene expression
2019 Nucleic Acids Research DOI: 10.1093/nar/gkz203
TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs
2019 Methods Mol Biol. DOI: 10.1007/978-1-4939-8982-9_12
Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations
2018 Nature communications DOI: 10.1038/s41467-018-04100-3
Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin
2018 Bioinformatics DOI: 10.1093/bioinformatics/bty222
2018 Biomed Res Int. DOI: 10.1155/2018/1264697
Identification of 170 New Long Noncoding RNAs in Schistosoma mansoni
2017 Genome Biol. 10.1186/s13059-017-1364-2
2017 Nucleic Acids Res. DOI: 10.1093/nar/gkx756
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data
2017 Methods Mol Biol. DOI: 10.1007/978-1-4939-4035-6_13
2016 Genetics DOI: 10.1534/genetics.116.187153
2016 J Infect Dis. DOI: 10.1093/infdis/jiw171
2016 Proceedings of the German Conference on Bioinformatics DOI:10.7287/PEERJ.PREPRINTS.2407V1
Predicting enhancers using a small subset of high confidence examples and co-training
2016 Proceedings of the German Conference on Bioinformatics DOI:10.7287/peerj.preprints.2423v1
2015 Oncogene
A long non-coding RNA links calreticulin-mediated immunogenic cell removal to RB1 transcription
Book chapter in ‚Mathematical models in biology’
2014 Cell Reports DOI: 10.1016/j.celrep.2014.09.007
Microprocessor activity controls differential miRNA biogenesis In Vivo
2013 Genome Biol. DOI:10.1186/gb-2013-14-8-r84
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs
2013 Zebrafish DOI: 10.1089/zeb.2012.0865
2010 BMC Bioinformatics DOI:10.1186/1471-2105-11-204
2010 Nucleic Acids Res. DOI:10.1093/nar/gkp1042
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins
2007 Bioinformatics DOI:10.1093/bioinformatics/btl293
2007 Proceedings of the German Conference on Bioinformatics