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List of works by Hilmar Lapp

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

scientific article (publication date: June 2012)

A <scp>FAIR</scp> and modular image‐based workflow for knowledge discovery in the emerging field of imageomics

scientific article published on 22 April 2024

A Logical Model of Homology for Comparative Biology

scientific article published on 01 March 2020

A gene atlas of the mouse and human protein-encoding transcriptomes

scientific article

A logical model of homology for comparative biology

scientific article published on 26 March 2019

A unified anatomy ontology of the vertebrate skeletal system

scientific article (publication date: 2012)

All the Clades in the World: Building a Semantically-Rich and Testable Ontology of Phylogenetic Clade Definitions

scholarly article by Gaurav Vaidya et al published 21 May 2018 in Biodiversity Information Science and Standards

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

Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare

scientific article published on 28 February 2020

Applications of a rat multiple tissue gene expression data set.

scientific article published in April 2004

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

scientific article published on 10 March 2022

Automatic Grid Fitting for Genetic Spot Array Images Containing Guide Spots

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

scientific article (publication date: 5 February 2014)

Community and Code: Nine Lessons from Nine NESCent Hackathons

Data Carpentry: Workshops to Increase Data Literacy for Researchers

article by Tracy K. Teal et al published 18 March 2015 in International Journal of Digital Curation

Data and animal management software for large-scale phenotype screening

scientific article

Developing educational resources for population genetics in R: an open and collaborative approach

scientific article

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

scientific article published on 04 August 2023

Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.

scientific article published on 28 March 2018

Enabling Machines to Integrate Biodiversity Data with Evolutionary Knowledge

scientific article published in 2020

Erratum: Publisher Correction: Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare

scientific article published on 09 April 2020

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

scientific article (publication date: 20 May 2010)

Exploring trafficking GTPase function by mRNA expression profiling: use of the SymAtlas web-application and the Membrome datasets

scientific article published in January 2005

Finding our way through phenotypes

scientific article

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

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

JPhyloRef: a tool for testing and resolving phyloreferences

scientific article published on 14 August 2021

Large-scale profiling of Rab GTPase trafficking networks: the membrome

scientific article

Liberating Our Beautiful Trees: A Call to Arms

Linking big: the continuing promise of evolutionary synthesis

scientific article published on 6 November 2009

Meeting Report for the Phenoscape TraitFest 2023 with Comments on Organising Interdisciplinary Meetings

scientific article published in 2024

Meeting Report: BioSharing at ISMB 2010

scientific article (publication date: 4 December 2010)

Molecular classification of human carcinomas by use of gene expression signatures.

scientific article

Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy

scientific article

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

scientific article

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

scientific article (publication date: July 2012)

Open source tools and toolkits for bioinformatics: significance, and where are we?

scientific article

Organizing our knowledge of biodiversity

article

Overview of FEED, the feeding experiments end-user database

scientific article

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: 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

Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts

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

scientific article (publication date: 13 May 2013)

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.

scientific article

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

Robust DNA microarray image analysis

article

Robust parametric and semi-parametric spot fitting for spot array images

scientific article published on 01 January 2000

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

scientific article

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

article

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

scientific article

The 2016 Bioinformatics Open Source Conference (BOSC)

scientific article

The 2017 Bioinformatics Open Source Conference (BOSC).

scientific article published on 19 October 2017

The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018)

scientific article published on 17 August 2018

The Bioinformatics Open Source Conference (BOSC) 2013

scientific article

The Bioinformatics Open Source Conference (BOSC) 2013

The Bioperl toolkit: Perl modules for the life sciences

scientific article

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

scientific article

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

scientific article (publication date: 21 August 2010)

The PLOS Computational Biology Software Section

scientific article (publication date: 29 November 2012)

The Primate Life History Database: A unique shared ecological data resource

scientific article

The teleost anatomy ontology: anatomical representation for the genomics age

scientific article

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

scientific article

Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies

scientific article

Towards an integrated ecosystem of R packages for the analysis of population genetic data

scientific article

TreeBASE2: Rise of the Machines

article

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

scientific article published on 28 July 2015

What is an anatomy ontology?

scientific article

apex: phylogenetics with multiple genes

scientific article published on 15 July 2016

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

scientific article published in 2023

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