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List of works by Martin Kuiper

A 3' splice site mutation in a nuclear gene encoding a mitochondrial ribosomal protein in Neurospora crassa.

scientific article

A Cell-Cycle Knowledge Integration Framework

A GO catalogue of human DNA-binding transcription factors

scientific article published on 28 October 2020

A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines

scientific article published on 09 October 2020

A foundation for reference models for drug combinations with an application to Loewe's reference model

scientific article published on 15 October 2020

A novel reverse transcriptase activity associated with mitochondrial plasmids of neurospora

scientific article published on 01 November 1988

AFLP™ markers for DNA fingerprinting in cattle

article

Benchmarking Triple Stores with Biological Data ⬇️

Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis

scientific article published in February 2005

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

scientific article (publication date: 15 August 2005)

BioGateway: a semantic systems biology tool for the life sciences

scientific article

Biological knowledge management: the emerging role of the Semantic Web technologies

scientific article published on 19 May 2009

Building a High-Density Genetic Map Using the AFLP− Technology ⬇️

scientific article published on January 1, 1998

CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator

article by Vasundra Touré et al published 6 February 2021 in Database

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

scientific article published on 6 August 2018

Cell Cycle Ontology (CCO)

article

Chromosomal regions involved in hybrid performance and heterosis: their AFLP®-based identification and practical use in prediction models

scientific article published on 01 September 2000

Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes

scientific article

Combined mapping of AFLP and RFLP markers in barley

scientific article published on 01 November 1995

Comparison of Flowering Time Genes in Brassica rapa, B. napus and Arabidopsis thaliana ⬇️

scientific article published on July 1, 1997

Contributions of the EMERALD project to assessing and improving microarray data quality

scientific article

DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data

scientific article (publication date: April 2010)

Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population

article

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

scientific article

European consortia building integrated resources for Arabidopsis functional genomics.

scientific article published in October 2003

Extracting expression modules from perturbational gene expression compendia

scientific article published on 10 April 2008

Finding gene regulatory network candidates using the gene expression knowledge base

scientific article

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

scientific article

Gauging triple stores with actual biological data.

scientific article

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort

scientific article published on 27 August 2013

Gene expression trends and protein features effectively complement each other in gene function prediction

scientific article published on 02 December 2008

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

scientific article

Genes2GO: A web application for querying gene sets for specific GO terms

scientific article published on 15 June 2016

Genetic Affinities Within the Herring Gull Larus argentatus Assemblage Revealed by AFLP Genotyping

Genetic analysis of variation in gene expression in Arabidopsis thaliana

scientific article

Genetic dissection of transcriptional regulation by cDNA-AFLP.

scientific article

Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme

scientific article published on 2 August 2006

Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme.

scientific article published on 23 January 2007

Identification of the reverse transcriptase encoded by the Mauriceville and Varkud mitochondrial plasmids of Neurospora.

scientific article

Initialization Dependence of Clustering Algorithms

Integration of biological networks and gene expression data using Cytoscape

scientific article (publication date: 2007)

Jointly creating digital abstracts: dealing with synonymy and polysemy ⬇️

scientific article published on October 30, 2012

Label-free quantitative proteomic analysis of systemic responses to local wounding and virus infection in Arabidopsis thaliana

scientific article published on 2 May 2013

Linking PubDictionaries with UniBioDicts to support Community Curation

Mapping of a QTL for serum HDL cholesterol in the rabbit using AFLP technology

scientific article

Modeling gene and genome duplications in eukaryotes

scientific article

Molecular cloning of pea mRNAs encoding a shoot-specific polypeptide and light-induced polypeptides

scientific article published in November 1983

Network Building with Cytoscape App Queries to the BioGateway 3.0 Triple Store ⬇️

Network Building with the Cytoscape BioGateway App Explained in Five Use Cases

scientific article published on 01 December 2020

Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine

scientific article published on 06 July 2020

OLSVis: an animated, interactive visual browser for bio-ontologies ⬇️

scientific article published on July 10, 2012

ONTO-PERL: an API for supporting the development and analysis of bio-ontologies

scientific article

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

scientific article

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology

scientific article published in 2008

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes.

scientific article

Reasoning with bio-ontologies: using relational closure rules to enable practical querying

scientific article published on 05 April 2011

Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles

Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004.

scientific article published on June 2005

Semantic systems biology

article

Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription

scientific article published on 6 July 2015

Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

scientific article published on 21 April 2020

Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures

scientific article published on 28 May 2020

Simulating genetic networks made easy: network construction with simple building blocks

scientific article

Specific impact of tobamovirus infection on the Arabidopsis small RNA profile

scientific article published in 2011

Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction

scientific article published on 28 July 2020

Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project ⬇️

TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors

scientific article

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

scientific article

Technologies and Best Practices for Building Bio-Ontologies

The Arabidopsis leaf as a model system for investigating the role of cell cycle regulation in organ growth

scientific article

The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process

scientific article published on 29 May 2009

The Cell Cycle Ontology: an application ontology supporting the study of cell cycle control

article published in 2009

The Cytoscape BioGateway App: explorative network building from the BioGateway triple store

scientific article published on 09 November 2019

The Mauriceville plasmid of Neurospora crassa: characterization of a novel reverse transcriptase that begins cDNA synthesis at the 3' end of template RNA.

scientific article published in November 1992

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

scientific article published on 30 June 2020

The RDF foundry

The cyclin-dependent kinase inhibitor KRP2 controls the onset of the endoreduplication cycle during Arabidopsis leaf development through inhibition of mitotic CDKA;1 kinase complexes

scientific article published on 29 April 2005

The emergence of Semantic Systems Biology

scientific article

The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms

scientific article

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling

scientific article published on 30 December 2020

UniBioDicts: Unified access to Biological Dictionaries

UniBioDicts: Unified access to biological dictionaries

scientific article published on 26 December 2020

Use of AFLP Markers for Gene Mapping and QTL Detection in the Rat

article

VSM-box: General-purpose Interface for Biocuration and Knowledge Representation

scientific article

Validating clusterings of gene expression data

article

Validating module network learning algorithms using simulated data

scientific article

Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications

scientific article published on October 2004

WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary

emba: R package for analysis and visualization of biomarkers in boolean model ensembles

scientific article published on 26 September 2020

orthAgogue: an agile tool for the rapid prediction of orthology relations

scientific article published on 09 October 2013

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