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List of works by Todd Vision

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

scientific article (publication date: June 2012)

A Logical Model of Homology for Comparative Biology

scientific article published on 01 March 2020

A computational system to select candidate genes for complex human traits

scientific article published on 19 January 2007

A decadal view of biodiversity informatics: challenges and priorities

scientific article

A hierarchical model for incomplete alignments in phylogenetic inference

scientific article published on 15 January 2009

A logical model of homology for comparative biology

scientific article published on 26 March 2019

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

An international showcase of bioinformatics research

scientific article

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

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

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

scientific article

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies

scientific article published on 10 March 2022

Assessing the significance of quantitative trait loci in replicable mapping populations

scientific article

Avoiding "conflicts of interest": a computational approach to scheduling parallel conference tracks and its human evaluation

scientific article

Avoiding "conflicts of interest'': A computational approach to scheduling parallel conference tracks and its human evaluation

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

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

article

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

scientific article

Complete plastome sequences of two species from the Galápagos Islands

scientific article published on 30 August 2018

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

scientific article published on 9 July 2004

Data archiving is a good investment

scientific article published in May 2011

Data citation in the wild

article

Data reuse and the open data citation advantage ⬇️

scientific article

Data reuse and the open data citation advantage

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

article

Divergence in Expression between Duplicated Genes in Arabidopsis

article

Do Synthesis Centers Synthesize? A Semantic Analysis of Diversity and Performance

Do synthesis centers synthesize? A semantic analysis of topical diversity in research

scientific article published on 01 January 2021

Evaluating data citation and sharing policies in the environmental sciences

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

Fine mapping a QTL for carbon isotope composition in tomato.

scientific article published on 30 April 2008

Gene order in plants: a slow but sure shuffle

scientific article

Genetic architecture influences when and how hybridization contributes to colonization

scientific article published on 08 April 2020

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

scientific article (publication date: March 2011)

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

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

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

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

scientific article

Inferring species trees from gene duplication episodes

article

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

scientific article

Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity

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

scientific article published on 25 March 2020

Linking Evolution, Ecology, and Health: TriCEM

article

Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles

ODIN: the ORCID and DataCite interoperability network

article published in International Journal of Knowledge and Learning, 2014

Open Data and the Social Contract of Scientific Publishing

2010 article by Todd Vision

Open data for evolutionary synthesis: an introduction to the NESCent collection

scientific article

Pathogen-induced systemic resistance in Ipomoea purpurea.

scientific article published in June 1995

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

scientific article published in September 2002

Phenex: ontological annotation of phenotypic diversity

scientific article (publication date: 5 May 2010)

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

scientific article

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets

scientific article published on 14 August 2009

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology

scholarly article published 13 June 2018

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology

article

Phytome: a platform for plant comparative genomics

scientific article

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

scientific article

Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae

scientific article

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

scientific article

Taxonomic assessment of blade-forming <i>Ulva</i> species (Ulvales, Chlorophyta) in the Galápagos Archipelago, Ecuador using DNA sequencing

scientific article published on 19 February 2024

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

article

The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem

scientific article published in 2010

The Teleost Taxonomy Ontology

scientific article published on 6 July 2010

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

article

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

scientific article published in 2011

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)

The molecular ecologist's guide to expressed sequence tags

scientific article published on March 2007

The origins of genomic duplications in Arabidopsis.

scientific article

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

scientific article published on January 2014

The teleost anatomy ontology: anatomical representation for the genomics age

scientific article

The two faces of secondary contact on islands: Introgressive hybridization between endemics and reproductive interference between endemics and introduced species

scientific article published on 7 December 2023

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

scientific article

Tracking the evolution of alternatively spliced exons within the Dscam family

scientific article

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

scientific article

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

scientific article published on 28 July 2015

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

rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits

scientific article published in 2023

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