List of works - Rutger Vos

A Web Service for Assessing Insect Abundances for Meadow Birds by Image Analysis

scholarly article published 11 June 2019

A roadmap for global synthesis of the plant tree of life

scientific article published on 30 March 2018

A tale of two 'opens': intersections between Free and Open Source Software and Open Scholarship ⬇️

report published in 2020

Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach

scientific article

Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles

scientific article

Availability of insects as feed for meadow bird chicks assessed across years by batched image analysis of sticky traps

scholarly article published in 2019

BIO::Phylo-phyloinformatic analysis using perl

scientific article

BioHackathon 2015: Semantics of data for life sciences and reproducible research

scientific article published on 24 February 2020

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

scientific article (publication date: 5 February 2014)

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

scientific article

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

scientific article

Community engagement: The ‘last mile’ challenge for European research e-infrastructures

scientific article

Differentiation between wild and domesticated Ungulates based on ecological niches

Emerging semantics to link phenotype and environment

scientific article

Enriched biodiversity data as a resource and service

scientific article

Evolution of embryonic developmental period in the marine bird families Alcidae and Spheniscidae: roles for nutrition and predation?

scientific article

Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification

article

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

scientific article published on 3 September 2014

Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system

scientific article

Incorporation of an invasive plant into a native insect herbivore food web ⬇️

scientific article

Integrating and visualizing primary data from prospective and legacy taxonomic literature

scientific article published in 2015

Modelling the niches of wild and domesticated Ungulate species using deep learning

scholarly article published 22 August 2019

Multiproxy diet analysis of the last meal of an early Holocene Yakutian bison

article by BAS VAN GEEL et al published April 2014 in Journal of Quaternary Science

Multiproxy study of the last meal of a mid-Holocene Oyogos Yar horse, Sakha Republic, Russia ⬇️

scholarly article by Barbara Gravendeel et al published 17 July 2014 in The Holocene

NeXML: rich, extensible, and verifiable representation of comparative data and metadata

scientific article (publication date: July 2012)

Ontogeny and Anatomy of the Dimorphic Pitchers of Nepenthes rafflesiana Jack

scientific article published on 18 November 2020

Phylogenetic analysis of niche divergence reveals distinct evolutionary histories and climate change implications for tropical carnivorous pitcher plants

article

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

scientific article (publication date: 13 May 2013)

Publishing re-usable phylogenetic trees, in theory and practice

scholarly article by Arlin Stoltzfus et al published 22 June 2011 in Nature Precedings

RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in r

scholarly article by Carl Boettiger et al published 19 October 2015 in Methods in Ecology and Evolution

Reconstructing Divergence Times for Supertrees

Scalariform-to-simple transition in vessel perforation plates triggered by differences in climate during the evolution of Adoxaceae

scientific article

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

scientific article (publication date: 22 October 2012)

Species Distribution Modelling Using Deep Learning

scholarly article by Rutger Vos et al published 30 July 2019 in Biodiversity Information Science and Standards

Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera

scientific article (publication date: November 2016)

Symbiont switching and trophic mode shifts in Orchidaceae

scientific article published on 01 May 2021

Ten simple rules for managing high-throughput nucleotide sequencing data

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

scientific article

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

scientific article (publication date: 11 February 2013)

The Bio::Phylo libraries for phylogenetic data analysis, version 2.0

scholarly article published 30 October 2017

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

scientific article (publication date: 21 August 2010)

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data

scientific article

The delayed rise of present-day mammals

scientific article

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

scientific article

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

scientific article

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

scientific article

TreeBASE2: Rise of the Machines

article

TreeBASEdmp: A Toolkit for Phyloinformatic Research

Unifying European Biodiversity Informatics (BioUnify)

scientific article published on 15 January 2016

WGS2NCBI - Toolkit for preparing genomes for submission to NCBI

outsider: Install and run programs, outside of R, inside of R

scientific article published on 23 January 2020

phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R.

scientific article published on 5 June 2018

List of works by Rutger Vos

A Web Service for Assessing Insect Abundances for Meadow Birds by Image Analysis

A roadmap for global synthesis of the plant tree of life

A tale of two 'opens': intersections between Free and Open Source Software and Open Scholarship ⬇️

Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach

Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles

Availability of insects as feed for meadow bird chicks assessed across years by batched image analysis of sticky traps

BIO::Phylo-phyloinformatic analysis using perl

BioHackathon 2015: Semantics of data for life sciences and reproducible research

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

Community engagement: The ‘last mile’ challenge for European research e-infrastructures

Differentiation between wild and domesticated Ungulates based on ecological niches

Emerging semantics to link phenotype and environment

Enriched biodiversity data as a resource and service

Evolution of embryonic developmental period in the marine bird families Alcidae and Spheniscidae: roles for nutrition and predation?

Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system

Incorporation of an invasive plant into a native insect herbivore food web ⬇️

Integrating and visualizing primary data from prospective and legacy taxonomic literature

Modelling the niches of wild and domesticated Ungulate species using deep learning

Multiproxy diet analysis of the last meal of an early Holocene Yakutian bison

Multiproxy study of the last meal of a mid-Holocene Oyogos Yar horse, Sakha Republic, Russia ⬇️

NeXML: rich, extensible, and verifiable representation of comparative data and metadata

Ontogeny and Anatomy of the Dimorphic Pitchers of Nepenthes rafflesiana Jack

Phylogenetic analysis of niche divergence reveals distinct evolutionary histories and climate change implications for tropical carnivorous pitcher plants

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Publishing re-usable phylogenetic trees, in theory and practice

RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in r

Reconstructing Divergence Times for Supertrees

Scalariform-to-simple transition in vessel perforation plates triggered by differences in climate during the evolution of Adoxaceae

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Species Distribution Modelling Using Deep Learning

Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera

Symbiont switching and trophic mode shifts in Orchidaceae

Ten simple rules for managing high-throughput nucleotide sequencing data

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

The Bio::Phylo libraries for phylogenetic data analysis, version 2.0

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data

The delayed rise of present-day mammals

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

TreeBASE2: Rise of the Machines

TreeBASEdmp: A Toolkit for Phyloinformatic Research

Unifying European Biodiversity Informatics (BioUnify)

WGS2NCBI - Toolkit for preparing genomes for submission to NCBI

outsider: Install and run programs, outside of R, inside of R

phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R.

restez: Create and Query a Local Copy of GenBank in R