Works by Lapp, Hilmar

Results: 40

Science Incubators: Synthesis Centers and Their Role in the Research Ecosystem.

Published in:

PLoS Biology, 2013, v. 11, n. 1, p. 1, doi. 10.1371/journal.pbio.1001468

By:

Rodrigo, Allen;
Alberts, Susan;
Cranston, Karen;
Kingsolver, Joel;
Lapp, Hilmar;
McClain, Craig;
Smith, Robin;
Vision, Todd;
Weintraub, Jory;
Wiegmann, Brian

Publication type:

Article

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

Published in:

2020

By:

Woody, Stephen K.;
Burdick, David;
Lapp, Hilmar;
Huang, Erich S.

Publication type:

Correction Notice

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

Published in:

NPJ Digital Medicine, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s41746-020-0235-5

By:

Woody, Stephen K;
Burdick, David;
Lapp, Hilmar;
Huang, Erich S.

Publication type:

Article

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

Published in:

Philosophy, Theory, & Practice in Biology, 2022, v. 14, p. 1, doi. 10.3998/ptpbio.2101

By:

Cellinese, Nico;
Conix, Stijn;
Lapp, Hilmar

Publication type:

Article

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

Published in:

2012

By:

Robbins, Robert J.;
Amaral-Zettler, Linda;
Bik, Holly;
Blum, Stan;
Edwards, James;
Field, Dawn;
Garrity, George;
Gilbert, Jack A.;
Kottmann, Renzo;
Krishtalka, Leonard;
Lapp, Hilmar;
Lawrence, Carolyn;
Morrison, Norman;
Tuama, Éamonn Ó.;
Parr, Cynthia;
Gil, Inigo San;
Schindel, David;
Schriml, Lynn;
Vieglas, David;
Wooley, John

Publication type:

Proceeding

A FAIR and modular image‐based workflow for knowledge discovery in the emerging field of imageomics.

Published in:

Methods in Ecology & Evolution, 2024, v. 15, n. 6, p. 1129, doi. 10.1111/2041-210X.14327

By:

Balk, Meghan A.;
Bradley, John;
Maruf, M.;
Altintaş, Bahadir;
Bakiş, Yasin;
Bart, Henry L.;
Breen, David;
Florian, Christopher R.;
Greenberg, Jane;
Karpatne, Anuj;
Karnani, Kevin;
Mabee, Paula;
Pepper, Joel;
Jebbia, Dom;
Tabarin, Thibault;
Wang, Xiaojun;
Lapp, Hilmar

Publication type:

Article

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

Published in:

Methods in Ecology & Evolution, 2023, v. 14, n. 10, p. 2531, doi. 10.1111/2041-210X.14210

By:

Porto, Diego S.;
Tarasov, Sergei;
Charpentier, Caleb;
Lapp, Hilmar;
Balhoff, James P.;
Vision, Todd J.;
Dahdul, Wasila M.;
Mabee, Paula M.;
Uyeda, Josef

Publication type:

Article

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

Published in:

Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 3, doi. 10.1186/2041-1480-4-34

By:

Midford, Peter E.;
Dececchi, Thomas Alex;
Balhoff, James P.;
Dahdul, Wasila M.;
Ibrahim, Nizar;
Lapp, Hilmar;
Lundberg, John G.;
Mabee, Paula M.;
Sereno, Paul C.;
Westerfield, Monte;
Vision, Todd J.;
Blackburn, David C.

Publication type:

Article

Robust DNA microarray image analysis.

Published in:

Machine Vision & Applications, 2003, v. 15, n. 1, p. 11, doi. 10.1007/s00138-002-0114-x

By:

Brändle, Norbert;
Bischof, Horst;
Lapp, Hilmar

Publication type:

Article

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

Published in:

PLoS ONE, 2016, v. 11, n. 2, p. 1, doi. 10.1371/journal.pone.0149102

By:

Druzinsky, Robert E.;
Balhoff, James P.;
Crompton, Alfred W.;
Done, James;
German, Rebecca Z.;
Haendel, Melissa A.;
Herrel, Anthony;
Herring, Susan W.;
Lapp, Hilmar;
Mabee, Paula M.;
Muller, Hans-Michael;
Mungall, Christopher J.;
Sternberg, Paul W.;
Van Auken, Kimberly;
Vinyard, Christopher J.;
Williams, Susan H.;
Wall, Christine E.

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2006, v. 7, n. 3, p. 287, doi. 10.1093/bib/bbl026

By:

Stajich, Jason E.;
Lapp, Hilmar

Publication type:

Article

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.

Published in:

Molecular Biology & Evolution, 2016, v. 33, n. 1, p. 13, doi. 10.1093/molbev/msv223

By:

Edmunds, Richard C.;
Baofeng Su;
Balhoff, James P.;
Eames, B. Frank;
Dahdul, Wasila M.;
Lapp, Hilmar;
Lundberg, John G.;
Vision, Todd J.;
Dunham, Rex A.;
Mabee, Paula M.;
Westerfield, Monte

Publication type:

Article

The Bioinformatics Open Source Conference (BOSC) 2013.

Published in:

2015

By:

Harris, Nomi L.;
Cock, Peter J. A.;
Chapman, Brad A.;
Goecks, Jeremy;
Hotz, Hans-Rudolf;
Lapp, Hilmar

Publication type:

Proceeding

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

Published in:

Biodiversity Information Science & Standards, 2024, p. 1, doi. 10.3897/biss.8.115232

By:

Girón Duque, Jennifer C.;
Balk, Meghan A;
Dahdul, Wasila;
Lapp, Hilmar;
Mikó, István;
Alhajjar, Elie;
Wynd, Brenen;
Tarasov, Sergei;
Lawrence, Christopher;
Khakurel, Basanta;
Porto, Arthur;
Yan, Lin;
E Fluck, Isadora;
Porto, Diego S;
Keating, Joseph N;
Borokini, Israel T;
Seltmann, Katja Chantre;
Montanaro, Giulio;
Mabee, Paula

Publication type:

Article

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

Published in:

2018

By:

Vaidya, Gaurav;
Guanyang Zhang;
Lapp, Hilmar;
Cellinese, Nico

Publication type:

Abstract

RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in R.

Published in:

Methods in Ecology & Evolution, 2016, v. 7, n. 3, p. 352, doi. 10.1111/2041-210X.12469

By:

Boettiger, Carl;
Chamberlain, Scott;
Vos, Rutger;
Lapp, Hilmar;
Fitzjohn, Richard

Publication type:

Article

The Primate Life History Database: a unique shared ecological data resource.

Published in:

Methods in Ecology & Evolution, 2010, v. 1, n. 2, p. 199, doi. 10.1111/j.2041-210X.2010.00023.x

By:

Strier, Karen B.;
Altmann, Jeanne;
Brockman, Diane K.;
Bronikowski, Anne M.;
Cords, Marina;
Fedigan, Linda M.;
Lapp, Hilmar;
Liu, Xianhua;
Morris, William F.;
Pusey, Anne E.;
Stoinski, Tara S.;
Alberts, Susan C.

Publication type:

Article

Overview of FEED, the Feeding Experiments End-user Database.

Published in:

Integrative & Comparative Biology, 2011, v. 51, n. 2, p. 215, doi. 10.1093/icb/icr047

By:

Wall, Christine E.;
Vinyard, Christopher J.;
Williams, Susan H.;
Gapeyev, Vladimir;
Xianhua Liu;
Lapp, Hilmar;
German, Rebecca Z.

Publication type:

Article

What is an anatomy ontology?

Published in:

Anatomical Record: Advances in Integrative Anatomy & Evolutionary Biology, 2013, v. 296, n. 12, p. 1797, doi. 10.1002/ar.22805

By:

Druzinsky, Robert;
Mungall, Christopher;
Haendel, Melissa;
Lapp, Hilmar;
Mabee, Paula

Publication type:

Article

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

Published in:

Molecular Ecology Resources, 2017, v. 17, n. 1, p. 120, doi. 10.1111/1755-0998.12558

By:

Kamvar, Zhian N.;
López ‐ Uribe, Margarita M.;
Coughlan, Simone;
Grünwald, Niklaus J.;
Lapp, Hilmar;
Manel, Stéphanie

Publication type:

Article

apex: phylogenetics with multiple genes.

Published in:

Molecular Ecology Resources, 2017, v. 17, n. 1, p. 19, doi. 10.1111/1755-0998.12567

By:

Jombart, Thibaut;
Archer, Frederick;
Schliep, Klaus;
Kamvar, Zhian;
Harris, Rebecca;
Paradis, Emmanuel;
Goudet, Jérome;
Lapp, Hilmar

Publication type:

Article

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

Published in:

Molecular Ecology Resources, 2017, v. 17, n. 1, p. 1, doi. 10.1111/1755-0998.12636

By:

Paradis, Emmanuel;
Gosselin, Thierry;
Grünwald, Niklaus J.;
Jombart, Thibaut;
Manel, Stéphanie;
Lapp, Hilmar

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-158

By:

Stoltzfus, Arlin;
Lapp, Hilmar;
Matasci, Naim;
Deus, Helena;
Sidlauskas, Brian;
Zmasek, Christian M.;
Vaidya, Gaurav;
Pontelli, Enrico;
Cranston, Karen;
Vos, Rutger;
Webb, Campbell O.;
Harmon, Luke J.;
Pirrung, Megan;
O'Meara, Brian;
Pennell, Matthew W.;
Mirarab, Siavash;
Rosenberg, Michael S;
Balhoff, James P.;
Bik, Holly M.;
Heath, Tracy A.

Publication type:

Article

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Published in:

2016

By:

Harris, Nomi L.;
Cock, Peter J. A.;
Lapp, Hilmar;
Chapman, Brad;
Davey, Rob;
Fields, Christopher;
Hokamp, Karsten;
Munoz-Torres, Monica

Publication type:

Proceeding

The PLOS Computational Biology Software Section.

Published in:

2012

By:

Prlić, Andreas;
Lapp, Hilmar

Publication type:

Editorial

A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx).

Published in:

PeerJ, 2022, p. 1, doi. 10.7717/peerj.12618

By:

Vaidya, Gaurav;
Cellinese, Nico;
Lapp, Hilmar

Publication type:

Article

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

Published in:

Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay110

By:

Dahdul, Wasila;
Manda, Prashanti;
Cui, Hong;
Balhoff, James P;
Dececchi, T Alexander;
Ibrahim, Nizar;
Lapp, Hilmar;
Vision, Todd;
Mabee, Paula M

Publication type:

Article

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

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav040

By:

Dahdul, Wasila;
Dececchi, T. Alexander;
Ibrahim, Nizar;
Lapp, Hilmar;
Mabee, Paula

Publication type:

Article

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

Published in:

Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar051

By:

Jung, Sook;
Menda, Naama;
Redmond, Seth;
Buels, Robert M.;
Friesen, Maren;
Bendana, Yuri;
Sanderson, Lacey-Anne;
Lapp, Hilmar;
Lee, Taein;
MacCallum, Bob;
Bett, Kirstin E.;
Cain, Scott;
Clements, Dave;
Mueller, Lukas A.;
Main, Dorrie

Publication type:

Article

A Unified Anatomy Ontology of the Vertebrate Skeletal System.

Published in:

PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0051070

By:

Dahdul, Wasila M.;
Balhoff, James P.;
Blackburn, David C.;
Diehl, Alexander D.;
Haendel, Melissa A.;
Hall, Brian K.;
Lapp, Hilmar;
Lundberg, John G.;
Mungall, Christopher J.;
Ringwald, Martin;
Segerdell, Erik;
Van Slyke, Ceri E.;
Vickaryous, Matthew K.;
Westerfield, Monte;
Mabee, Paula M.

Publication type:

Article

Evolutionary Characters, Phenotypes and Ontologies : Curating Data from the Systematic Biology Literature.

Published in:

PLoS ONE, 2010, v. 5, n. 5, p. 1, doi. 10.1371/journal.pone.0010708

By:

Dahdul, Wasila M.;
Balhoff, James P.;
Engeman, Jeffrey;
Grande, Terry;
Hilton, Eric J.;
Kothari, Cartik;
Lapp, Hilmar;
Lundberg, John G.;
Midford, Peter E.;
Vision, Todd J.;
Westerfield, Monte;
Mabee, Paula M.

Publication type:

Article

Phenex: Ontological Annotation of Phenotypic Diversity.

Published in:

PLoS ONE, 2010, v. 5, n. 5, p. 1, doi. 10.1371/journal.pone.0010500

By:

Balhoff, James P.;
Dahdul, Wasila M.;
Kothari, Cartik R.;
Lapp, Hilmar;
Lundberg, John G.;
Mabee, Paula;
Midford, Peter E.;
Westerfield, Monte;
Vision, Todd J.

Publication type:

Article

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

Published in:

Systematic Biology, 2022, v. 71, n. 6, p. 1290, doi. 10.1093/sysbio/syac022

By:

Porto, Diego S;
Dahdul, Wasila M;
Lapp, Hilmar;
Balhoff, James P;
Vision, Todd J;
Mabee, Paula M;
Uyeda, Josef

Publication type:

Article

A Logical Model of Homology for Comparative Biology.

Published in:

Systematic Biology, 2020, v. 69, n. 2, p. 345, doi. 10.1093/sysbio/syz067

By:

Mabee, Paula M;
Balhoff, James P;
Dahdul, Wasila M;
Lapp, Hilmar;
Mungall, Christopher J;
Vision, Todd J

Publication type:

Article

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

Published in:

Systematic Biology, 2015, v. 64, n. 6, p. 936, doi. 10.1093/sysbio/syv031

By:

DECECCHI, T. ALEXANDER;
MABEE, PAULA M.;
BALHOFF, JAMES P.;
LAPP, HILMAR

Publication type:

Article

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata.

Published in:

Systematic Biology, 2012, v. 61, n. 4, p. 675, doi. 10.1093/sysbio/sys025

By:

Vos, Rutger A.;
Balhoff, James P.;
Caravas, Jason A.;
Holder, Mark T.;
Lapp, Hilmar;
Maddison, Wayne P.;
Midford, Peter E.;
Priyam, Anurag;
Sukumaran, Jeet;
Xia, Xuhua;
Stoltzfus, Arlin

Publication type:

Article

The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age.

Published in:

Systematic Biology, 2010, v. 59, n. 4, p. 369, doi. 10.1093/sysbio/syq013

By:

DAHDUL, WASILA M.;
LUNDBERG, JOHN G.;
MIDFORD, PETER E.;
BALHOFF, JAMES P.;
LAPP, HILMAR;
VISION, TODD J.;
HAENDEL, MELISSA A.;
WESTERFIELD, MONTE;
MABEE, PAULA M.

Publication type:

Article

Data and animal management software for large-scale phenotype screening.

Published in:

Mammalian Genome, 2006, v. 17, n. 4, p. 288, doi. 10.1007/s00335-005-0145-5

By:

Ching, Keith A.;
Cooke, Michael P.;
Tarantino, Lisa M.;
Lapp, Hilmar

Publication type:

Article

LINKING BIG: THE CONTINUING PROMISE OF EVOLUTIONARY SYNTHESIS.

Published in:

Evolution, 2010, v. 64, n. 4, p. 871, doi. 10.1111/j.1558-5646.2009.00892.x

By:

Sidlauskas, Brian;
Ganapathy, Ganeshkumar;
Hazkani-Covo, Einat;
Jenkins, Kristin P.;
Lapp, Hilmar;
McCall, Lauren W.;
Price, Samantha;
Scherle, Ryan;
Spaeth, Paula A.;
Kidd, David M.

Publication type:

Article

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.

Published in:

Genesis: The Journal of Genetics & Development, 2015, v. 53, n. 8, p. 561, doi. 10.1002/dvg.22878

By:

Manda, Prashanti;
Balhoff, James P.;
Lapp, Hilmar;
Mabee, Paula;
Vision, Todd J.

Publication type:

Article