Computational RNA Biology

  • Gjaltema RAF, Schwämmle T., Kautz P., Robson M., Schöpflin R., Lustig LR, Brandenburg L., Dunkel I., Vechiatto C., Ntini E., Mutzel V., Schmiedel V., Marsico A., Mundlos S., Schulz EG. Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Molecular Cell 82 (1), 190-208. e17. 2022.
  • Ito-Kureha T., Leoni C., Borland K., Bataclan M., Metzger R., Ammann G., Krug A., Marsico A., Kellner S., Canzar S., Feske S., Monticelli S., König J., Heissmeyer V. N6-adenosine methylation of mRNAs requires Wtap expression and controls T cell receptor signaling and survival. Preprint from Research Square, 16 Nov 2021. 
  • Pacini G., Dunkel I., Mages N., Mutzel V., Timmermann B., Marsico A.*, Schulz EG*. Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolution. Nature Communications 12 (1), 1-17. 2021. * equal contributions
  • Schulte-Sasse R., Budach S., Hnisz D., Marsico A. Integration of multiomics data with graph convolutional networks to identify new cancer genes and their associated molecular mechanisms. Nature Machine Intelligence 3 (6), 513-526. 2021. 
  • Horlacher M., Oleshko S., Hu Y., Ghanbari M., Elorduy Vergara E., Mueller N., Ohler U., Moyon L., Marsico A. Computational Mapping of the Human-SARS-CoV-2 Protein-RNA Interactome. Biorxiv. 2021.
  • Herkt CE, Caffrey BE, Surmann K, Blankenburg S., Gesell Salazar M., Jung AL, Herbel SM, Hoffmann K., Schulte LN, Chen W, Sittka-Stark A., Völker U., Vingron M., Marsico A.*, Bertrams W.*, Schmeck B.* A MicroRNA Network Controls Legionella pneumophila Replication in Human Macrophages via LGALS8 and MX1. Mbio 11 (2), e03155-19. 2020. * equal contributions
  • Ntini E., Budach S., Ørom UAV., Marsico APredictive modeling of long non-coding RNA chromatin (dis-)association. Biorxiv, 2020.12. 15.422063.  
  • Schulte-Sasse R., Budach S., Hnisz D., Marsico A. Graph Convolutional networks improve the prediction of cancer driver genes. International Conference on Artificial Neural Networks, 658-668. 2019. 
  • Sousa L.*, Jonkers I.*, Syx L., Dunkel I., Chaumell J., Picard C., Foret B., Chen CJ,  Lis JT*, Heard E.*, Schulz EG*, Marsico A*. Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Genome research. 2019. * equal contributions
  • Thiel D., Conrad N.D., Ntini E., Peschutter R.X., Siebert H*., Marsico A*. Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis. BMC bioinformatics 20 (1), 1-16. 2019.
  • Nitni E., Marsico A. Functional impacts of non-coding RNA processing on enhancer activity and target gene expression. Journal of molecular cell biology 11 (10), 868-879. 2019. 
  • Bressin A, Schulte-Sasse R, Figini D, Urdaneta EC, Beckmann BM*, Marsico A*. TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs. Nucleic Acids Research 47 (9), 4406-4417. 2019. * equal contributions
  • Piro RM, Marsico A. Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations. Methods Mol Biol. 2019;1912:301-321. 
  • Ntini E, Louloupi A, Liz J, Muino JM, Marsico A, Ørom UAV. Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin. Nat Commun. 2018 Apr 24;9(1):1636.
  • Budach S, Marsico A. pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks. Bioinformatics. 2018 Sep 1;34(17):3035-3037.
  • Oliveira VF, Moares LAG, Mota EA, Jannotti-Passos LK, Coelho PMZ, Mattos ACA, Couto FFB, Caffrey BE, Marsico A, Guerra-Sá R. Identification of 170 New Long Noncoding RNAs in Schistosoma mansoni. Biomed Res Int. 2018 Jul 11;2018:1264697.
  • Krakau S, Richard H*, Marsico A*. PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data. Genome Biol. 2017 Dec 28;18(1):240. *co-corresponding author
  • Heller D, Krestel R, Ohler U, Vingron M, Marsico A. ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data. Nucleic Acids Res. 2017 Nov 2;45(19):11004-11018.
  • Yang X, Marsico A. In Silico Promoter Recognition from deepCAGE Data. Methods Mol Biol. 2017;1468:171-99.
  • Budach S, Heinig M*, Marsico A*. Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci. Genetics. 2016 Aug;203(4):1629-40. * co-corresponding author
  • Du Bois I, *Marsico A*, Bertrams W*, Schweiger MR, Caffrey BE, Sittka-Stark A, Eberhardt M, Vera J, Vingron M, Schmeck BT. Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2. J Infect Dis. 2016 Aug 1;214(3):454-63. * equal contributions
  • Huska MR, Ramisch A, Vingron M and Marsico A. Predicting enhancers using a small subset of high confidence examples and co-training. Proceedings of the German Conference on Bioinformatics, 2016.
  • Sousa L, Marsico A. A statistical model for epigenetic control of miRNAs. Proceedings of the German Conference on Bioinformatics, 2016.
  • Musahl AS, Huang X, Rusakiewicz S, Ntini E, Marsico A, Kroemer G, Kepp O, Orom UA. A long non-coding RNA links calreticulin-mediated immunogenic cell removal to RB1 transcription. Oncogene. 2015 Sep 24;34(39):5046-54.
  • Caffrez B, Marsico A. Computational modeling of miRNA biogenesis. Book chapter in ‚Mathematical models in biology’.
  • Conrad T*, Marsico A*, Gehre M, Orom UA. Microprocessor activity controls differential miRNA biogenesis In Vivo. Cell Rep. 2014 Oct 23;9(2):542-54. * Equal contributions
  • Marsico A, Huska MR, Lasserre J, Hu H, Vucicevic D, Musahl A, Orom U, Vingron M. PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol. 2013 Aug 16;14(8):
  • Prykhozhij SV, Marsico A, Meijsing SH. Zebrafish Expression Ontology of Gene Sets (ZEOGS): a tool to analyze enrichment of zebrafish anatomical terms in large gene sets. Zebrafish. 2013 Sep;10(3):303-15.
  • Marsico A, Henschel A, Winter C, Tuukkanen A, Vassilev B, Scheubert K, Schroeder M. Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. BMC Bioinformatics 2010 Apr 26;11:204.
  • Marsico A, Scheubert K, Tuukkanen A, Henschel A, Winter C, Winnenburg R, Schroeder M. MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. Nucleic Acids Res. 2010 Jan;38(Database issue):D181-9.
  • Marsico A, Labudde D, Sapra T, Muller DJ, Schroeder M. A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy. Bioinformatics. 2007 Jan 15;23(2):e231-6.
  • Dressel F, Marsico A, Tuukkanen A, Schroeder M, Labudde D. Understanding of SMFS barriers by means of energy profiles. Proceedings of the German Conference on Bioinformatics, 2007.