Publications
Horlacher M., Cantini G., Hesse J., Schinke P., Goedert N., Londhe S., Moyon L., Marsico A.
A Systematic Benchmark of Machine Learning Methods for Protein-RNA Interaction PredictionHorlacher M., Wagner N., Moyon L., Kuret K., Goedert N., Salvatore M., Ule J., Gagneur J., Winther O., Marsico A.
Towards In-Silico CLIP-seq: Predicting Protein-RNA Interaction via Sequence-to-Signal LearningIto-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 survivalHu Y., Rehawi G., Moyon L., Gerstner N., Ogris C., Knauer-Arloth J., Bittner F., Marsico A.*, Mueller N. S.*, * equal contributions
Network Embedding Across Multiple Tissues and Data Modalities Elucidates the Context of Host Factors Important for COVID-19 InfectionGjaltema 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 locusPacini G., Dunkel I., Mages N., Mutzel V., Timmermann B., Marsico A.*, Schulz EG*. * equal contributions
Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolutionSchulte-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 mechanismsHorlacher 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 InteractomeHerkt 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.* , * equal contributions
A MicroRNA Network Controls Legionella pneumophila Replication in Human Macrophages via LGALS8 and MX1Ntini E., Budach S., Ørom UAV., Marsico A.
Predictive modeling of long non-coding RNA chromatin (dis-)associationSchulte-Sasse R., Budach S., Hnisz D., Marsico A.
Graph Convolutional Networks Improve the Prediction of Cancer Driver GenesSousa L.*, Jonkers I.*, Syx L., Dunkel I., Chaumell J., Picard C., Foret B., Chen CJ, Lis JT*, Heard E.*, Schulz EG*, Marsico A*. * equal contributions
Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic featuresThiel D., Conrad N.D., Ntini E., Peschutter R.X., Siebert H*., Marsico A*.
Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysisNitni E., Marsico A.
Functional impacts of non-coding RNA processing on enhancer activity and target gene expressionBressin A, Schulte-Sasse R, Figini D, Urdaneta EC, Beckmann BM*, Marsico A*. * equal contributions
TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifsPiro RM, Marsico A.
Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease AssociationsNtini E, Louloupi A, Liz J, Muino JM, Marsico A, Ørom UAV.
Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatinBudach S, Marsico A.
pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networksOliveira 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 mansoniKrakau S, Richard H*, Marsico A*. * co-corresponding author
PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq dataHeller D, Krestel R, Ohler U, Vingron M, Marsico A.
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein dataBudach S, Heinig M*, Marsico A*, * co-corresponding author
Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci. GeneticsDu Bois I, *Marsico A*, Bertrams W*, Schweiger MR, Caffrey BE, Sittka-Stark A, Eberhardt M, Vera J, Vingron M, Schmeck BT. * equal contributions
Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2Huska MR, Ramisch A, Vingron M and Marsico A.
Predicting enhancers using a small subset of high confidence examples and co-trainingSousa L, Marsico A.
A statistical model for epigenetic control of miRNAsMusahl 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 transcriptionCaffrez B, Marsico A.
Computational modeling of miRNA biogenesisConrad T*, Marsico A*, Gehre M, Orom UA. * equal contributions
Microprocessor activity controls differential miRNA biogenesis In VivoMarsico 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 miRNAsPrykhozhij SV, Marsico A, Meijsing SH.
Zebrafish Expression Ontology of Gene Sets (ZEOGS): a tool to analyze enrichment of zebrafish anatomical terms in large gene setsMarsico 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 proteinsMarsico A, Scheubert K, Tuukkanen A, Henschel A, Winter C, Winnenburg R, Schroeder M.
MeMotif: a database of linear motifs in alpha-helical transmembrane proteinsMarsico 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 spectroscopyDressel F, Marsico A, Tuukkanen A, Schroeder M, Labudde D.
Understanding of SMFS barriers by means of energy profiles