Ben C Stöver

Ben C Stöver
University of Münster | WWU · Institute for Evolution and Biodiversity

Dr. rer. nat.

About

18
Publications
7,914
Reads
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1,391
Citations
Citations since 2016
8 Research Items
1101 Citations
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Introduction
I'm a bioinformatician and biologist. My major research interests are improving automated multiple sequence alignment for phylogenetic purposes and automated identification of taxa using computer vision methods. Besides that I spend a lot of time developing bioinformatical libraries helping other bioinformaticians and applications helping other biologists. More on me: http://bioinfweb.info/People/Stoever
Additional affiliations
January 2019 - present
University of Münster
Position
  • Scientific staff
Description
  • Scientific assistant (Postdoc), teaching bachelor and master courses, IT administration
February 2011 - December 2018
University of Münster
Position
  • Scientific staff
Description
  • Scientific assistant during PhD, teaching bachelor and master courses, IT administration
April 2008 - March 2010
University of Bonn
Position
  • Research Assistant
Description
  • Development of different phylogenetic software (e.g. the phylogenetic tree editor TreeGraph 2)
Education
October 2011 - December 2018
University of Münster
Field of study
  • Biology
October 2003 - March 2010
University of Bonn
Field of study
  • Biology

Publications

Publications (18)
Article
Full-text available
Background: Today a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata representation. Although most currently available software only supports the classical formats with a limited metadata model, it would be...
Poster
Full-text available
Phylogenetics, phylogenomics and related fields have become data-intensive due to increasingly cheaper high-throughput sequencing technologies, the digitization of large biological collections or data contributions from citizen science. An increasing number of computationally accessible methods for analyses that produce derived data, like phylogene...
Conference Paper
Full-text available
Specimens form the falsifiable evidence used in plant systematics. Derivatives of specimens (including the specimen as the organism in the field) such as tissue and DNA samples play an increasing role in research. The EDIT Platform for Cybertaxonomy is a specialist's tool that allows to document and sustainably store all data that are used in the t...
Article
Aims Taxon identification is an important step in many plant ecological studies. Its efficiency and reproducibility might greatly benefit from partly automating this task. Image-based identification systems exist, but mostly rely on hand-crafted algorithms to extract sets of features chosen a priori to identify species of selected taxa. In conseque...
Poster
Full-text available
In philosophy ontology is defined as the study of the nature and relations of being. Information sciences apply this concept to create naming conventions describing types, properties and interrelationships of certain entities. Ontologies aim to limit complexity and organize information. In phylogenetics they allow scientists to provide semantic inf...
Poster
Full-text available
TreeGraph 2 is a user friendly tree editor with the main focus on processing, visualizing and comparing phylogenetic trees carrying numerous annotations. Here, new features added since its initial publication in 2010 are presented. The ability to import and visualize probabilities for ancestral character states (e.g. by pie charts attached to inter...
Conference Paper
Collection and maintenance of biodiversity data is in need for automation. We present first results of an automated and model-free approach to the species identification from herbarium specimens kept in herbaria worldwide. Methodologically, our approach relies on standard methods for the detection and description of so-called interest points and th...
Poster
Full-text available
Today a variety of alignment and tree file formats exist, some of which well-established but limited in their data model, others more recently proposed offer advanced future-orientated features for metadata representation. Most phylogenetic and other bioinformatic software currently only supports one or few different formats, while supporting many...
Article
Full-text available
Unlabelled: We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of...
Poster
Full-text available
TreeGraph 2 is a user friendly and widely used tree editor with the main focus on processing, visualizing and comparing phylogenetic trees carrying numerous annotations. Since its initial publication a number of features have been added. The ability to import and visualize probabilities for ancestral character states (as reconstructed by software p...
Poster
Full-text available
http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=100872
Poster
Full-text available
http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=100873
Poster
Full-text available
Several applications currently developed in our group and by cooperators deal with multiple sequence alignments (MSA) or associated raw and meta data, and allow the user to view and edit these in a graphical user interface. Instead of implementing independent solutions for these different tasks, we decided to develop LibrAlign, a Java library provi...
Poster
Full-text available
With a growing number of alternative algorithms for automated multiple sequence alignment (MSA) and different strategies for manual alignment corrections it becomes more and more relevant to visualize the differences between alternative MSAs of the same data set. This allows the researcher to decide which alternative alignments to take into account...
Poster
Full-text available
Several applications currently developed in our group and by our cooperators deal with multiple sequence alignments (MSA) or associated raw and meta data, and allow the user to view and edit it in a graphical user interface (GUI). Instead of implementing independent solutions for these different tasks, we decided to create a library containing powe...
Poster
Full-text available
http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=94531
Poster
See also: http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Theses/Detail?id=0
Article
Full-text available
Today it is common to apply multiple potentially conflicting data sources to a given phylogenetic problem. At the same time, several different inference techniques are routinely employed instead of relying on just one. In view of both trends it is becoming increasingly important to be able to efficiently compare different sets of statistical values...

Network

Cited By

Projects

Projects (6)
Project
PhyDE 2 is a complete rewrite of the Phylogenetic Data Editor. The first version of PhyDE is in use since 2005 and PhyDE 2 is planned to fully replace it in the future. http://bioinfweb.info/PhyDE2/ https://github.com/bioinfweb/PhyDE2 http://twitter.com/bioinfweb Legal notice: http://bioinfweb.info/PhyDE2/About Privacy Policy: http://bioinfweb.info/Privacy
Project
AlignmentComparator is able to visually compare and annotate differences between alternative multiple sequence alignments (MSAs) of the same data set. This allows the researcher to decide which alternative alignments to take into account as the bases of e.g. a phylogenetic study or numerous other tasks. Manual alignment corrections can be visualized or a bioinformatician can determine the effect of changes made to a MSA algorithm. http://bioinfweb.info/AlignmentComparator/ https://github.com/bioinfweb/AlignmentComparator http://twitter.com/bioinfweb Legal notice: http://bioinfweb.info/AlignmentComparator/About Privacy Policy: http://bioinfweb.info/Privacy
Project
JPhyloIO is Java library for reading and writing phylogenetic (alignment and tree) file formats. It's aim is to allow developers of bioinformatical applications access to various formats using a single interface, while being independent of the concrete application data model. The library supports event based I/O of NeXML, Nexus, PhyloXML, FASTA, Newick, Phylip, Extended Phylip, MEGA, PDE and XTG, including all metadata modeled by these formats. This project keeps you up to date on the development of JPhyloIO, new releases and publications. The documentation, including full JavaDocs and multiple example applications showing how to use JPhyloIO are available here: http://bioinfweb.info/JPhyloIO/Documentation. If you have further questions, don't hesitate to ask one in this project. The project is open source under GNU LGPL. Suggestions and contributions (e.g. via GitHub) are always welcome. http://bioinfweb.info/JPhyloIO/ https://twitter.com/bioinfweb https://github.com/bioinfweb/JPhyloIO Legal notice: http://bioinfweb.info/JPhyloIO/About Privacy Policy: http://bioinfweb.info/Privacy