Andrea Bagnacani

I implement computational tools for data annotation, contextualization, and reuse, providing a mean to go from data to information.

Research interest

I write computational tools for bioinformatics data analysis.

I'm a member of the de.STAIR project, which maintains and develops tools for RNA-Seq analysis within the Galaxy framework.
My work aims at creating a recommendation system for data analysis tools within Galaxy, leveraging on tool annotations and shared best practices. This is done in conjunction with the RNA Bioinformatics Center (RBC), located in Freiburg.

de.STAIR and RBC are members of the German Network for Bioinformatics Infrastructure (de.NBI), which is the German node of ELIXIR.

Within de.NBI, I provide trainings on the topics of usage, data preprocessing, and visualization using Galaxy, while in the Rostock team, I'm working on the TriplexRNA: a database of cooperative microRNAs and their mutual targets.
The database contains human and mouse RNA triplexes: a regulatory pattern composed of a siynergistic miRNA pair regulating a target mRNA, which can be used as a biological marker for disease diagnosis. Here, I'm involved in the extension and redesign of the computational pipeline used to compute and organize predicted RNA triplexes for multiple organisms.


Research Projects

GB-XMap: Assessing the risk of gut-brain cross-diseases

Investigating the gut-brain-axis

The gut–brain axis (GBA) provides a bidirectional homeostatic communication between the gastrointestinal tract and the central nervous system. The interdisciplinary collaboration is going to fully explore a first comprehensive GBA cross-disease map of genetic, expression and regulatory changes associated with ulcerative colitis and schizophrenia disease entities.



The TriplexRNA is a database of cooperating microRNAs and their mutual targets.

The database collects predicted and experimentally validated RNA triplexes, and provides an interactive interface for highligting targets of concerted RNA regulation within known disease pathways.


Academic background


ELIXIR-EXCELERATE Training the Trainers, SciLife Lab, Sweden


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


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


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


SEMS Hackathon on Model statistics, University of Rostock, Germany


16th Bioinformatics Winter School, University of Bologna, Italy


EuroPython 2013, Florence, Italy


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


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


Selected publications

The RNA workbench 2.0: next generation RNA data analysis

Fallmann J, Pavankumar V, Bagnacani A, ..., Gruening BA

Nucleic Acid Research

Community-driven data analysis training for biology

Batut B, Hiltemann S, Bagnacani A, …, Wolfien M, ..., Gruening B

Evolution of computational models in BioModels Database and the Physiome Model Repository

Scharm M, Gebhardt T, Touré V, Bagnacani A, Salehzadeh-Yazdi A, Wolkenhauer O, Waltemath D

BMC Systems Biology 12:53 (2018)

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

Möller S, ..., Bagnacani A, ..., Crusoe MR

Springer Data Science and Engineering

Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments

Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR

Journal of Biotechnology

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Gruening BA, ..., Bagnacani A, Wolfien M, ..., Wolkenhauer O, ..., Backofen R

Nucleic Acids Research

Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis

Bagnacani A, Wolfien M, Wolkenhauer O

Springer (2019), chapter in Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912.

Workflow Development for the Functional Characterization of ncRNAs

Wolfien M, Brauer DL, Bagnacani A, Wolkenhauer O

Springer (2019), chapter in Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912.

Design of the TriplexRNA: a database of cooperating microRNAs and their mutual targets

Andrea Bagnacani

MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Single miRNAs can repress the expression of many genes, however, experimental evidence suggest that their repressive effect alone is rather mild compared with that carried out by cooperating miRNAs. Although synergistic target regulation has been confirmed as a prevalent pattern in gene regulation, the mechanism behind this phenomena are little known, and it is unclear which miRNA pairs and gene targets are involved in the formation of RNA triplexes. The growing amount of data on miRNA-mediated gene expression is motivated by the role they play in cellular functions, where their presence can be correlated with cancers, and cardiovascular diseases, making them good biomarkers for diagnostic and prognostic purposes. However, existing databases relate disease associations with the duplex model: one miRNA inhibiting the expression of one or many genes, while none of them provide an exploration of the more effective regulation operated by synergistic pairs. To overcome this gap, the present work describes the design and implementation of the TriplexRNA: a database of cooperating miRNAs and their mutual targets, which we realised to enable researchers explore novel patterns in gene regulation. The database can be accessed at

Education and Work Experience

present PhD student in Systems Biology and Bioinformatics, University of Rostock, Germany
2019 Carpentry instructor Trainer

Master with honours in Bioinformatics, University of Bologna, Italy


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


Bachelor in Computer Science, University of Bologna, Italy



Teaching Experience

BioSystems Modelling and Simulation - course: "Gene expression analysis and hands-on session with the Galaxy environment"


  • Introduction to Gene expression analysis
  • Gene expression analysis with Galaxy
  • Tools for reproducible data analysis


  • Winter Semester 2019/2020
  • Summer Semester 2019
  • Winter Semester 2018/2019
  • Summer Semester 2018