Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Andrea Bagnacani

Image: Andrea Bagnacani

Current Projects

Identification and functional analysis of microRNAs involved in malignant melanoma progression (MicroRna)
Cancer
MicroRNAs (miRNAs) are endogenous, small, non-coding ~22 nt RNA molecules that have emerged as a major class of regulatory genes for diverse range of biological functions. In our preliminary studies, we were able to demonstrate that primary melanoma show a distinct miRNA expression pattern compared with benign melanocytic nevi. The aim of the present project is to identify and functionally characterize miRNAs that might play a role during further melanoma progression (metastasis).
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Structured Analysis and Integration of RNA-Seq Experiments - de.STAIR
RNA sequencing (RNA-Seq) has become a widely used tool to study quantitative and qualitative aspects of the transcriptome. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. Our aim is to enable a comprehensive analysis of RNA-Seq experiments as a service. To enable maximum usefulness, interconnectivity, and accessibility for the developed approaches and services, we will provide dedicated workshops, training programs and screen casts for bioinformaticians and other life scientists and, ultimately, lower the barriers to RNA-Seq data analysis as a whole.
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Research Interest

I'm interested in providing useful tools to researchers.

I'm a member of the de.STAIR partner project within the de.NBI RNA Bioinformatics Center (RBC), which maintains and develops tools for RNA-Seq analysis within the Galaxy platform.

I'm currently working on extending the TriplexRNA dataset with new functionalities.
The dataset contains predicted human and mouse target genes whose expression is regulated by cooperative miRNA pairs forming miRNA triplexes.
The dataset contains graphic representations of their secondary structures, their Gibbs-free energies (i.e. triplex-free energies) and their predicted equilibrium concentrations.

 

 

Academic Background

present - PhD student in Systems Biology and Bioinformatics, University of Rostock, Germany

 

2017 Galaxy workshop on HTS data analysis, University of Freiburg, Germany

2016 Workshop on Computational Life Sciences, Bayer Pharma AG Berlin, Germany

2016 Master with honours in Bioinformatics, University of Bologna, Italy

2016 IDaMo Summer School on the Integration of Data and Models in Medicine

2016 SEMS Hackathon on Model statistics, University of Rostock, Germany

2015 16th Bioinformatics Winter School, University of Bologna, Italy

2014 Contribution to the Semantic Lancet Project, University of Bologna, Italy

2014 Bachelor in Computer Science, University of Bologna, Italy

2013 EuroPython 2013, Florence, Italy

2011 XML Summer School, St. Edmund Hall, Oxford, UK

2011 Workshop on markup and its semantics, University of Bologna, Italy

Publications

Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR
Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments

Journal of Biotechnology
doi.org/10.1016/j.jbiotec.2017.06.1203

Gruening BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Nucleic Acids Research

doi.org/10.1093/nar/gkx409

Contact Details

Dept. of Systems Biology and Bioinformatics,
Ulmenstrasse 69 (building 3, 3rd floor)
18057 Rostock, Germany
Room 401

phone: +49 381 498-7684
mail: andrea.bagnacani(at)uni-rostock.de

Collaborators & Partners

de.NBI
German Network for Bioinformatics Infrastructure
Federal Ministry for Education and Research (BMBF)
Dr. Dr. Steve Hoffmann
Interdisciplinary Center for Bioinformatics
University of Leipzig,
Leipzig, Germany
Prof. Dr. Wolfgang Hess
Dept. for Biology III
Albert-Ludwigs-University Freiburg,
Freiburg, Germany