Krakau S, Richard H, Marsico A. PureCLIP: Capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data. bioRxiv 146704; doi: https://doi.org/10.1101/146704

Heller D, Kreste R, Ohler U, Vingron M and Marsico A. ssHMM: Extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data. Under revision, Bioarxiv version: http://biorxiv.org/content/early/2016/10/11/076034   now accepted in Nucleic Acids Research !!

Yang X and Marsico A. In silico promoter recognition from deepCAGE data, Methods Mol Biol 2017. 1468:171-99

Barros de Andrade E Sousa L and Marsico A: A statistical model for epigenetic control of miRNAs. PeerJ PrePrints, GCB 2016

Huska M, Ramisch A, Vingron M and Marsico A: Predicting enhancers using a small subset of high confidence examples and co-trainin.  PeerJ PrePrints, GCB 2016

Caffrey B and Marsico A: Computational modeling of microRNA Biogenesis, book chapter in Mathematical Models in Biology: Bringing mathematics to life, Springer 2016, DOI 10.1007/978-3-319-23497-7_6.

Budach S, Heinig M, Marsico A Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci. Genetics 2016. Jun 3. pii: genetics.116.187153. [Epub ahead of print]

Dubois I*, Marsico A*, Bertram W*, Schweiger M, Caffrey B, Sittka-Stark A, Eberhardt M, Vera J, Vingron M, Schmeck B. Genome-wide chromatin profiling of Legionella pneumophila-infected human macrophages reveals activation of the pro-bacterial host factor TNFAIP2. J Infect Dis 2016. 214(3):454-63. doi: 10.1093/infdis/jiw171, Epub 2016 Apr 29.

Annalisa Marsico: Statistical models of non-coding RNA-mediated gene regulation. PeerJ PrePrints, GCB 2015

Musahl AF, 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 Jan 12. doi: 10.1038/onc.2014.424. [Epub ahead of print]. PMID: 25579178.

Conrad T*, Marsico A*, Gehre M, Orom UA: Microprocessor activity controls differential miRNA biogenesis in Vivo. Cell Reports 2014 Oct 23;9(2):542-54.doi: 10.1016/j.celrep.2014.09.007. Epub 2014 Oct 9. PubMed PMID: 25310978.

Marsico A, Huska MR, Lasserre J, Hu H, Vucicevic D, Musahl A, Orom UA, Vingron, M. PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol. 2013 Aug 16;14(8):R84.PubMed PMID: 23958307.

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. doi: 10.1089/zeb.2012.0865. Epub 2013 May 8. PubMed PMID: 23656298; PubMed Central PMCID: PMC3760060.

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. doi: 10.1186/1471-2105-11-204. PubMed PMID: 20420672; PubMed Central PMCID: PMC2876129.

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. doi:10.1093/nar/gkp1042. Epub 2009 Nov 12. PubMed PMID: 19910368; PubMed Central PMCID: PMC2808916.

Annalisa Marsico, Kerstin Vanselow, Jing Wang, Dirk Labudde: 2D Visualisation of SMFS Data on Membrane Proteins. ER (Tutorials, Posters, Panels & Industrial Contributions) 2007

Dirk Labudde, Annalisa Marsico, K. Tanuj Sapra, Michael Schroeder: Pattern Recognition of Single-Molecule Force Spectroscopy Data. ER Workshops 2007: 3-13

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. PubMed PMID: 17237097.

Frank Dressel, Annalisa Marsico, Anne Tuukkanen, Michael Schroeder, Dirk Labudde: Understanding of SMFS Barriers by Means of Energy Profiles. Proceedings of the German Conference on Bioinformatics 2007: 90-99.

Annalisa Marsico, K. Tanuj Sapra, Daniel J. Muller, Michael Schroeder, Dirk Labudde: A Structure-Based Analysis of Single Molecule Force Spectroscopy (SMFS) Data for Bacteriorhodopsin and Four Mutants. CompLife 2006 (Lecture Notes in Computer Science): 162-172. 

 

 
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