List of works - Todd Vision

The origins of genomic duplications in Arabidopsis

scientific article

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

scientific article published in 2011

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

scientific article

Contrasting modes of diversification in the Aux/IAA and ARF gene families

scientific article published on 9 July 2004

Divergence in Expression between Duplicated Genes in Arabidopsis

article

The molecular ecologist's guide to expressed sequence tags

scientific article published on March 2007

Data reuse and the open data citation advantage

scientific article

A decadal view of biodiversity informatics: challenges and priorities

scientific article

Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana

scientific article published in September 2002

Identification and characterization of aluminum tolerance loci in Arabidopsis (Landsberg erecta x Columbia) by quantitative trait locus mapping. A physiologically simple but genetically complex trait

scientific article

Open Data and the Social Contract of Scientific Publishing

2010 article by Todd Vision

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

scientific article

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

scientific article (publication date: March 2011)

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature

scientific article (publication date: 20 May 2010)

Fast identification and statistical evaluation of segmental homologies in comparative maps.

scientific article

A computational system to select candidate genes for complex human traits

scientific article published on 19 January 2007

Phenex: ontological annotation of phenotypic diversity

scientific article (publication date: 5 May 2010)

The teleost anatomy ontology: anatomical representation for the genomics age

scientific article

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

scientific article (publication date: June 2012)

Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples

scientific article

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

scientific article

Data archiving is a good investment

scientific article published in May 2011

The standing pool of genomic structural variation in a natural population of Mimulus guttatus

scientific article published on January 2014

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

scientific article

Phytome: a platform for plant comparative genomics

scientific article

DataONE: Data Observation Network for Earth Preserving Data and Enabling Innovation in the Biological and Environmental Sciences

article

Fine mapping a QTL for carbon isotope composition in tomato

scientific article published on 30 April 2008

Tracking the evolution of alternatively spliced exons within the Dscam family

scientific article

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

scientific article

Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites

scientific article

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

scientific article published on 28 July 2015

Science incubators: synthesis centers and their role in the research ecosystem

scientific article

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex

scientific article

Assessing the significance of quantitative trait loci in replicable mapping populations

scientific article

Beginning to track 1000 datasets from public repositories into the published literature

Gene order in plants: a slow but sure shuffle

scientific article

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

article

Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae

scientific article

The effects of resource availability and environmental conditions on genetic rankings for carbon isotope discrimination during growth in tomato and rice

article

The location of the citation: changing practices in how publications cite original data in the Dryad Digital Repository

scientific article (publication date: 6 October 2016)

Comparison of full-text searching to metadata searching for genes in two biomedical literature cohorts

article

Journal data policies: Exploring how the understanding of editors and authors corresponds to the policies themselves

scientific article published on 25 March 2020

Pathogen-induced systemic resistance in Ipomoea purpurea

scientific article published in June 1995

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems

scientific article published on 01 January 2018

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

scientific article published on January 2016

A hierarchical model for incomplete alignments in phylogenetic inference

scientific article published on 15 January 2009

An analysis and comparison of the statistical sensitivity of semantic similarity metrics

What Factors Influence Where Researchers Deposit their Data? A Survey of Researchers Submitting to Data Repositories

article by Shea Swauger & Todd Vision published 30 January 2015 in International Journal of Digital Curation

The Teleost Taxonomy Ontology

scientific article published on 6 July 2010

List of works by Todd Vision

The origins of genomic duplications in Arabidopsis

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

Contrasting modes of diversification in the Aux/IAA and ARF gene families

Divergence in Expression between Duplicated Genes in Arabidopsis

The molecular ecologist's guide to expressed sequence tags

Data reuse and the open data citation advantage

A decadal view of biodiversity informatics: challenges and priorities

Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana

Identification and characterization of aluminum tolerance loci in Arabidopsis (Landsberg erecta x Columbia) by quantitative trait locus mapping. A physiologically simple but genetically complex trait

Open Data and the Social Contract of Scientific Publishing

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature

Fast identification and statistical evaluation of segmental homologies in comparative maps.

A computational system to select candidate genes for complex human traits

Phenex: ontological annotation of phenotypic diversity

The teleost anatomy ontology: anatomical representation for the genomics age

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

Data archiving is a good investment

The standing pool of genomic structural variation in a natural population of Mimulus guttatus

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

Phytome: a platform for plant comparative genomics

DataONE: Data Observation Network for Earth Preserving Data and Enabling Innovation in the Biological and Environmental Sciences

Fine mapping a QTL for carbon isotope composition in tomato

Tracking the evolution of alternatively spliced exons within the Dscam family

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

Science incubators: synthesis centers and their role in the research ecosystem

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex

Assessing the significance of quantitative trait loci in replicable mapping populations

Beginning to track 1000 datasets from public repositories into the published literature

Gene order in plants: a slow but sure shuffle

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae

The effects of resource availability and environmental conditions on genetic rankings for carbon isotope discrimination during growth in tomato and rice

The location of the citation: changing practices in how publications cite original data in the Dryad Digital Repository

Comparison of full-text searching to metadata searching for genes in two biomedical literature cohorts

Journal data policies: Exploring how the understanding of editors and authors corresponds to the policies themselves

Pathogen-induced systemic resistance in Ipomoea purpurea

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

A hierarchical model for incomplete alignments in phylogenetic inference

An analysis and comparison of the statistical sensitivity of semantic similarity metrics

What Factors Influence Where Researchers Deposit their Data? A Survey of Researchers Submitting to Data Repositories

The Teleost Taxonomy Ontology

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY