Lista de obras - Martin Kuiper - Dominio Público Uruguay

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

artículo científico publicado en 1988

A Cell-Cycle Knowledge Integration Framework

A GO catalogue of human DNA-binding transcription factors

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2005

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

artículo científico publicado en 2005

BioGateway: a semantic systems biology tool for the life sciences

artículo científico publicado en 2009

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 ⬇️

artículo científico publicado el 1 de enero de 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

artículo científico publicado en 2018

Cell Cycle Ontology (CCO)

article

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

artículo científico publicado en 2000

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

artículo científico publicado en 2010

Combined mapping of AFLP and RFLP markers in barley

artículo científico publicado en 1995

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

artículo científico publicado el 1 de julio de 1997

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

artículo científico publicado en 2011

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

artículo científico publicado en 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

artículo científico publicado en 2015

European consortia building integrated resources for Arabidopsis functional genomics.

artículo científico publicado en 2003

Extracting expression modules from perturbational gene expression compendia

artículo científico publicado en 2008

Finding gene regulatory network candidates using the gene expression knowledge base

artículo científico publicado en 2014

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

artículo científico publicado en 2010

Gauging triple stores with actual biological data.

artículo científico publicado en 2012

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

artículo científico publicado en 2013

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

artículo científico

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

artículo científico publicado en 2016

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

artículo científico

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

Genetic analysis of variation in gene expression in Arabidopsis thaliana

artículo científico publicado en 2005

Genetic dissection of transcriptional regulation by cDNA-AFLP.

artículo científico publicado en 2006

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

artículo científico publicado en 2006

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

artículo científico publicado en 2007

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

artículo científico publicado en 1990

Initialization Dependence of Clustering Algorithms

Integration of biological networks and gene expression data using Cytoscape

artículo científico publicado en 2007

Jointly creating digital abstracts: dealing with synonymy and polysemy ⬇️

artículo científico publicado el 30 de octubre de 2012

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

artículo científico publicado en 2013

Linking PubDictionaries with UniBioDicts to support Community Curation

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

artículo científico publicado en 2001

Modeling gene and genome duplications in eukaryotes

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 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 ⬇️

artículo científico publicado el 10 de julio de 2012

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

artículo científico publicado en 2008

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

artículo científico publicado en 2010

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

artículo científico publicado en 2008

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

artículo científico publicado en 2008

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

artículo científico publicado en 2008

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

artículo científico

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.

artículo científico publicado en 2005

Semantic systems biology

article

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

artículo científico publicado en 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

artículo científico publicado en 2020

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

artículo científico publicado en 2004

Specific impact of tobamovirus infection on the Arabidopsis small RNA profile

artículo científico publicado en 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

artículo científico publicado en 2013

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

artículo científico publicado en 2010

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

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 1992

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

artículo científico publicado en 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

artículo científico publicado en 2005

The emergence of Semantic Systems Biology

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2020

UniBioDicts: Unified access to Biological Dictionaries

UniBioDicts: Unified access to biological dictionaries

artículo científico publicado en 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

artículo científico publicado en 2020

Validating clusterings of gene expression data

article

Validating module network learning algorithms using simulated data

artículo científico publicado en 2007

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

artículo científico publicado en 2004

WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary

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

artículo científico publicado en 2020

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

artículo científico

Lista de obras de Martin Kuiper

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

A Cell-Cycle Knowledge Integration Framework

A GO catalogue of human DNA-binding transcription factors

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

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

A novel reverse transcriptase activity associated with mitochondrial plasmids of neurospora

AFLP™ markers for DNA fingerprinting in cattle

Benchmarking Triple Stores with Biological Data ⬇️

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

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

BioGateway: a semantic systems biology tool for the life sciences

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

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

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

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

Cell Cycle Ontology (CCO)

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

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

Combined mapping of AFLP and RFLP markers in barley

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

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

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

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

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

European consortia building integrated resources for Arabidopsis functional genomics.

Extracting expression modules from perturbational gene expression compendia

Finding gene regulatory network candidates using the gene expression knowledge base

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

Gauging triple stores with actual biological data.

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

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

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

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

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

Genetic analysis of variation in gene expression in Arabidopsis thaliana

Genetic dissection of transcriptional regulation by cDNA-AFLP.

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

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

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

Initialization Dependence of Clustering Algorithms

Integration of biological networks and gene expression data using Cytoscape

Jointly creating digital abstracts: dealing with synonymy and polysemy ⬇️

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

Linking PubDictionaries with UniBioDicts to support Community Curation

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

Modeling gene and genome duplications in eukaryotes

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

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

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

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

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

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

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

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

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

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

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.

Semantic systems biology

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

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

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

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

Specific impact of tobamovirus infection on the Arabidopsis small RNA profile

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

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

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

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

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

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

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

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

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

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

The emergence of Semantic Systems Biology