2023 Biorxiv DOI:10.1101/2023.02.14.528560

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 Prediction

2022 Biorxiv DOI:10.1101/2022.09.16.508290

Horlacher 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 Learning

2022 Nature Immunology DOI: 10.1038/s41590-022-01268-1

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

2022 Front Genet DOI:10.3389/fgene.2022.909714

Hu 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 Infection

2022 Molecular Cell DOI: 10.1016/j.molcel.2021.11.023

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

2021 Nature Communications DOI:10.1038/s41467-021-23643-6

Pacini 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 resolution

2021 Nature Machine Intelligence DOI:10.1038/s42256-021-00325-y

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

2021 accepted in NAR genomics and Bioinformatics DOI:10.1101/2021.12.22.472458

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

2020 mBio DOI: 10.1128/mBio.03155-19

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.* , * equal contributions

A MicroRNA Network Controls Legionella pneumophila Replication in Human Macrophages via LGALS8 and MX1

2020 Biorxiv DOI:10.1101/2020.12.15.422063

Ntini E., Budach S., Ørom UAV., Marsico A.

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

Schulte-Sasse R., Budach S., Hnisz D., Marsico A.

Graph Convolutional Networks Improve the Prediction of Cancer Driver Genes

2019 Genome research DOI:10.1101/gr.245027.118

Sousa 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 features

2019 BMC bioinformatics DOI: 10.1186/s12859-019-2900-8

Thiel D., Conrad N.D., Ntini E., Peschutter R.X., Siebert H*., Marsico A*.

Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis

2019 Journal of molecular cell biology DOI: 10.1093/jmcb/mjz047

Nitni E., Marsico A.

Functional impacts of non-coding RNA processing on enhancer activity and target gene expression

2019 Nucleic Acids Research DOI: 10.1093/nar/gkz203

Bressin 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 motifs

2019 Methods Mol Biol. DOI: 10.1007/978-1-4939-8982-9_12

Piro RM, Marsico A.

Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations

2018 Nature communications DOI: 10.1038/s41467-018-04100-3

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

2018 Bioinformatics DOI: 10.1093/bioinformatics/bty222

Budach S, Marsico A.

pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks

2018 Biomed Res Int. DOI: 10.1155/2018/1264697

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

2017 Genome Biol. 10.1186/s13059-017-1364-2

Krakau S, Richard H*, Marsico A*. * co-corresponding author

PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data

2017 Nucleic Acids Res. DOI: 10.1093/nar/gkx756

Heller D, Krestel R, Ohler U, Vingron M, Marsico A.

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

Yang X, Marsico A.

In Silico Promoter Recognition from deepCAGE Data

2016 Genetics DOI: 10.1534/genetics.116.187153

Budach S, Heinig M*, Marsico A*, * co-corresponding author

Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci. Genetics

2016 J Infect Dis. DOI: 10.1093/infdis/jiw171

Du 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 TNFAIP2

2016 Proceedings of the German Conference on Bioinformatics DOI:10.7287/PEERJ.PREPRINTS.2407V1

Huska MR, Ramisch A, Vingron M and Marsico A.

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

Sousa L, Marsico A.

A statistical model for epigenetic control of miRNAs

2015 Oncogene

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

Book chapter in ‚Mathematical models in biology’

Caffrez B, Marsico A.

Computational modeling of miRNA biogenesis

2014 Cell Reports DOI: 10.1016/j.celrep.2014.09.007

Conrad T*, Marsico A*, Gehre M, Orom UA. * equal contributions

Microprocessor activity controls differential miRNA biogenesis In Vivo

2013 Genome Biol. DOI:10.1186/gb-2013-14-8-r84

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

2013 Zebrafish DOI: 10.1089/zeb.2012.0865

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

2010 BMC Bioinformatics DOI:10.1186/1471-2105-11-204

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

2010 Nucleic Acids Res. DOI:10.1093/nar/gkp1042

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

2007 Bioinformatics DOI:10.1093/bioinformatics/btl293

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

2007 Proceedings of the German Conference on Bioinformatics

Dressel F, Marsico A, Tuukkanen A, Schroeder M, Labudde D.

Understanding of SMFS barriers by means of energy profiles