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publications.bib
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<!DOCTYPE html>
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<title>Galaxy Europe</title>
<meta name="description" content="The European Galaxy Instance">
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# Publications
@Article{Gruning_Rasche_Rebolledo-Jaramillo-Jupyt_and_Galax-2017,
author = {Gruning, Bjorn A. and Rasche, Eric and Rebolledo-Jaramillo,
Boris and Eberhard, Carl and Houwaart, Torsten and Chilton,
John and Coraor, Nate and Backofen, Rolf and Taylor, James
and Nekrutenko, Anton},
title = {Jupyter and {Galaxy}: {Easing} entry barriers into complex
data analyses for biomedical researchers},
journal = {PLoS Comput Biol},
year = {2017},
volume = {13},
number = {5},
pages = {e1005425},
user = {backofen},
pmid = {28542180},
doi = {10.1371/journal.pcbi.1005425},
issn = {1553-734X},
issn = {1553-7358},
abstract = {What does it take to convert a heap of sequencing data into
a publishable result? First, common tools are employed to
reduce primary data (sequencing reads) to a form suitable
for further analyses (i.e., the list of variable sites). The
subsequent exploratory stage is much more ad hoc and
requires the development of custom scripts and pipelines,
making it problematic for biomedical researchers. Here, we
describe a hybrid platform combining common analysis
pathways with the ability to explore data interactively. It
aims to fully encompass and simplify the "raw
data-to-publication" pathway and make it reproducible.}
}
@Article{Backofen_Engelhardt_Erxleben-RNA_Tools_servi-2017,
author = {Backofen, Rolf and Engelhardt, Jan and Erxleben, Anika and
Fallmann, Jorg and Gruning, Bjorn and Ohler, Uwe and
Rajewsky, Nikolaus and Stadler, Peter F.},
title = {RNA-bioinformatics: {Tools}, services and databases for
the analysis of {RNA}-based regulation},
journal = {J Biotechnol},
year = {2017},
volume = {},
number = {},
pages = {},
user = {backofen},
pmid = {28554830},
doi = {10.1016/j.jbiotec.2017.05.019},
issn = {1873-4863},
issn = {0168-1656},
abstract = {The importance of RNA-based regulation is becoming more and
more evident. Genome-wide sequencing efforts have shown that
the majority of the DNA in eukaryotic genomes is
transcribed. Advanced high-throughput techniques like CLIP
for the genome-wide detection of RNA-protein interactions
have shown that post-transcriptional regulation by
RNA-binding proteins matches the complexity of
transcriptional regulation. The need for a specialized and
integrated analysis of RNA-based data has led to the
foundation of the RNA Bioinformatics Center (RBC) within the
German Network of Bioinformatics Infrastructure (de.NBI).
This paper describes the tools, services and databases
provided by the RBC, and shows example applications.
Furthermore, we have setup an RNA workbench within the
Galaxy framework. For an easy dissemination, we offer a
virtualized version of Galaxy (via Galaxy Docker) enabling
other groups to use our RNA workbench in a very simple way.}
}
@Article{Gruning_Fallmann_Yusuf-The_RNA_workb-NAR2017,
author = {Gruning, Bjorn A. and Fallmann, Jorg and Yusuf, Dilmurat
and Will, Sebastian and Erxleben, Anika and Eggenhofer,
Florian and Houwaart, Torsten and Batut, Berenice and Videm,
Pavankumar and Bagnacani, Andrea and Wolfien, Markus and
Lott, Steffen C. and Hoogstrate, Youri and Hess, Wolfgang R.
and Wolkenhauer, Olaf and Hoffmann, Steve and Akalin, Altuna
and Ohler, Uwe and Stadler, Peter F. and Backofen, Rolf},
title = {The {RNA} workbench: best practices for {RNA} and
high-throughput sequencing bioinformatics in {Galaxy}},
journal = NAR,
year = {2017},
volume = {},
number = {},
pages = {},
user = {backofen},
pmid = {28582575},
doi = {10.1093/nar/gkx409},
issn = {1362-4962},
issn = {0305-1048},
abstract = {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
taken into account. Thus, it is increasingly important but
not yet standard to combine RNA-centric data and analysis
tools with other types of experimental data such as RNA-seq
or ChIP-seq. Here, we present the RNA workbench, a
comprehensive set of analysis tools and consolidated
workflows that enable the researcher to combine these two
worlds. Based on the Galaxy framework the workbench
guarantees simple access, easy extension, flexible adaption
to personal and security needs, and sophisticated analyses
that are independent of command-line knowledge. Currently,
it includes more than 50 bioinformatics tools that are
dedicated to different research areas of RNA biology
including RNA structure analysis, RNA alignment, RNA
annotation, RNA-protein interaction, ribosome profiling,
RNA-seq analysis and RNA target prediction. The workbench is
developed and maintained by experts in RNA bioinformatics
and the Galaxy framework. Together with the growing
community evolving around this workbench, we are committed
to keep the workbench up-to-date for future standards and
needs, providing researchers with a reliable and robust
framework for RNA data analysis. AVAILABILITY: The RNA
workbench is available at
https://github.com/bgruening/galaxy-rna-workbench.}
}
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<p>The Freiburg Galaxy Team is part of the <a href="http://www.bioinf.uni-freiburg.de/">Bionformatics Group Freiburg</a>, headed by the Prof. Dr. Rolf Backofen. The team is supported by <a href="https://www.denbi.de/">de.NBI</a> and <a href="https://www.elixir-europe.org/">ELIXIR</a></p>
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