[PDF][PDF] Community-driven data analysis training for biology

B Batut, S Hiltemann, A Bagnacani, D Baker… - Cell systems, 2018 - cell.com
The primary problem with the explosion of biomedical datasets is not the data, not computational
resources, and not the required storage space, but the general lack of trained and …

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

…, B Batut, P Videm, A Bagnacani… - Nucleic acids …, 2017 - academic.oup.com
RNA-based regulation has become a major research topic in molecular biology. The analysis
of epigenetic and expression data is therefore incomplete if RNA-based regulation is not …

[HTML][HTML] Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis

…, S Soiland-Reyes, F Klötzl, A Bagnacani… - Data Science and …, 2017 - Springer
Abstract Information integration and workflow technologies for data analysis have always
been major fields of investigation in bioinformatics. A range of popular workflow suites are …

The semantic lancet project: a linked open dataset for scholarly publishing

A Bagnacani, P Ciancarini, A Di Iorio… - … : EKAW 2014 Satellite …, 2015 - Springer
In this poster we introduce the Semantic Lancet Project, whose goal is to make available rich
data about scholarly publications and to provide users with sophisticated services on top of …

Workflow development for the functional characterization of ncRNAs

M Wolfien, DL Brauer, A Bagnacani… - Computational Biology of …, 2019 - Springer
During the last decade, ncRNAs have been investigated intensively and revealed their
regulatory role in various biological processes. Worldwide research efforts have identified …

The RNA workbench 2.0: next generation RNA data analysis

J Fallmann, P Videm, A Bagnacani, B Batut… - Nucleic acids …, 2019 - academic.oup.com
RNA has become one of the major research topics in molecular biology. As a central player
in key processes regulating gene expression, RNA is in the focus of many efforts to decipher …

[HTML][HTML] Customized workflow development and data modularization concepts for RNA-sequencing and metatranscriptome experiments

SC Lott, M Wolfien, K Riege, A Bagnacani… - Journal of …, 2017 - Elsevier
RNA-Sequencing (RNA-Seq) has become a widely used approach to study quantitative and
qualitative aspects of transcriptome data. The variety of RNA-Seq protocols, experimental …

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

M Scharm, T Gebhardt, V Touré, A Bagnacani… - BMC Systems …, 2018 - Springer
Background A useful model is one that is being (re)used. The development of a successful
model does not finish with its publication. During reuse, models are being modified, ie …

Tools for understanding miRNA–mRNA interactions for reproducible RNA analysis

A Bagnacani, M Wolfien, O Wolkenhauer - Computational Biology of Non …, 2019 - Springer
MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level.
The use of RNA data in gene expression analysis has become increasingly important to …

Knowledge Management of Scholarly Products: Semantic Lancet Project

…, AG Nuzzolese, A Bagnacani… - European …, 2015 - search.proquest.com
There is an ever increasing interest in publishing Linked Open Datasets about scientific
papers. The current landscape is very fragmented: some projects focus on bibliographic data, …