SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
+49 381 498-7571
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.
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.
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.
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. We provide easy access to comprehensive analysis of RNA-Seq experiments as a service. To do so, we leverage on the Galaxy framework, and organise dedicated workshops, training programs, and screencasts to make Life Scientists familiar with computational approaches to biological problems.
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.
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
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
Cell Systems 2018
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
Design of the TriplexRNA: a database of cooperating microRNAs and their mutual targets
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 https://triplexrna.org.
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
|October 2019||Trainer @ "Galaxy for linking bisulfite sequencing with RNA sequencing", Freiburg|
|September 2019||Trainer @ "RNA-Seq data analysis with Galaxy for clinical applications - GMDS 2019", Dortmund|
|March 2019||Trainer @ "Galaxy for linking bisulfite sequencing with RNA sequencing", Rostock|
|September 2018||Trainer @ "RNA-Seq data analysis with Galaxy for clinical applications - GMDS 2018", Osnabrück|
|June 2018||Trainer @ "A primer for RNA-Seq Processing, Interpreting and Visualization", Jena|
|March 2018||Trainer @ "Introduction to RNA-Seq data analysis with Galaxy", Kiel|
|October 2017||Trainer @ "A Primer for RNA-Seq Processing, Interpretation and Visualization", Freiburg|
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