Matthew Jon Yoder

2025

Radiology referrals patterns in a free clinic setting

Koso, M., Pandharipande, P., Ovestrud, I., Vickery, S., Charleton, M., Yoder, M., Takacs, N. & Shah, S., May 2025, In: Clinical Imaging. 121, 110459.

Research output: Contribution to journal › Article › peer-review

2024

The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps

Cruaud, A., Rasplus, J. Y., Zhang, J., Burks, R., Delvare, G., Fusu, L., Gumovsky, A., Huber, J. T., Janšta, P., Mitroiu, M. D., Noyes, J. S., van Noort, S., Baker, A., Böhmová, J., Baur, H., Blaimer, B. B., Brady, S. G., Bubeníková, K., Chartois, M. & Copeland, R. S. & 22 others, Dale-Skey Papilloud, N., Dal Molin, A., Dominguez, C., Gebiola, M., Guerrieri, E., Kresslein, R. L., Krogmann, L., Lemmon, E., Murray, E. A., Nidelet, S., Nieves-Aldrey, J. L., Perry, R. K., Peters, R. S., Polaszek, A., Sauné, L., Torréns, J., Triapitsyn, S., Tselikh, E. V., Yoder, M., Lemmon, A. R., Woolley, J. B. & Heraty, J. M., Feb 2024, In: Cladistics. 40, 1, p. 34-63 30 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2023

Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics

Girón, J. C., Tarasov, S., González Montaña, L. A., Matentzoglu, N., Smith, A. D., Koch, M., Boudinot, B. E., Bouchard, P., Burks, R., Vogt, L., Yoder, M., Osumi-Sutherland, D., Friedrich, F., Beutel, R. & Mikó, I., Sep 1 2023, In: Systematic biology. 72, 5, p. 1084-1100 17 p., syad025.

Research output: Contribution to journal › Article › peer-review

2022

ontoFAST: An R package for interactive and semi-automatic annotation of characters with biological ontologies

Tarasov, S., Mikó, I. & Yoder, M. J., Feb 2022, In: Methods in Ecology and Evolution. 13, 2, p. 324-329 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Self-publishing Biodiversity Data Products on the Web

Yoder, M., Pereira, J. L., Pereira, H., Dmitriev, D., Dewalt, R., Cigliano, M.-M., Paul, D. L. & Flood, J., 2022, TDWG 2022, 17-21 October 2022, Sofia, Bulgaria (Hybrid).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Open Access

2021

WCO-Lite version 1.1: An online nomenclatural catalogue of harvestmen of the world (Arachnida, Opiliones) curated in TaxonWorks

Kury, A. B., Mendes, A. C., Cardoso, L., Kury, M. S., Granado, A. A., Yoder, M. J. & Kury, I. S., Jan 15 2021, In: Zootaxa. 4908, 3, p. 447-450 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2020

Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of chalcidoid wasps

Zhang, J., Lindsey, A. R. I., Peters, R. S., Heraty, J. M., Hopper, K. R., Werren, J. H., Martinson, E. O., Woolley, J. B., Yoder, M. J. & Krogmann, L., Oct 1 2020, In: Systematic Entomology. 45, 4, p. 783-802 20 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Meeting In-Between: Moving beyond the buzz, bottlenecks, and bubble to collaboratively develop digitization tooling

Yoder, M., Sep 10 2020, TDWG 2020. Vol. 4. p. e59265 (Biodiversity Information Science and Standards).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Transforming the study of organisms: Phenomic data models and knowledge bases

Thessen, A. E., Walls, R. L., Vogt, L., Singer, J., Warren, R., Buttigieg, P. L., Balhoff, J. P., Mungall, C. J., McGuinness, D. L., Stucky, B. J., Yoder, M. J. & Haendel, M. A., Nov 24 2020, In: PLoS computational biology. 16, 11, e1008376.

Research output: Contribution to journal › Review article › peer-review

Open Access

What Can You Do with a TaxonWorks API?

Yoder, M., Pereira, H., Pereira, J. L., Dmitriev, D., Ower, G. & Flood, J., Sep 10 2020, TDWG 2020. Vol. 4. p. e59170 (Biodiversity Information Science and Standards).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2019

Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

Stucky, B. J., Balhoff, J. P., Barve, N., Barve, V., Brenskelle, L., Brush, M. H., Dahlem, G. A., Gilbert, J. D. J., Kawahara, A. Y., Keller, O., Lucky, A., Mayhew, P. J., Plotkin, D., Seltmann, K. C., Talamas, E., Vaidya, G., Walls, R., Yoder, M., Zhang, G. & Guralnick, R., 2019, In: Biodiversity Data Journal. 7, p. e33303 e33303.

Research output: Contribution to journal › Article › peer-review

Open Access

Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

Tarasov, S., Miko, I., Yoder, M. & Uyeda, J., Jun 13 2019, Biodiversity Next. Vol. 3. p. e37038 (Biodiversity Information Science and Standards).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

PARAMO: A Pipeline for Reconstructing Ancestral Anatomies Using Ontologies and Stochastic Mapping

Tarasov, S., Mikó, I., Yoder, M. J. & Uyeda, J. C., Nov 1 2019, In: Insect Systematics and Diversity. 3, 6

Research output: Contribution to journal › Article › peer-review

TaxonWorks 1.0?

Yoder, M., Dmitriev, D., Pereira, J. L., Flood, J., Tucker, J., Pereira, H. & Beckman, M., Jun 26 2019, Biodiversity Next. Vol. 3. p. e37374 (Biodiversity Information Science and Standards).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2018

Current progress in the development of taxonomic and anatomical ontologies within the scope of BIOfid

Koch, M., Driller, C., Schmidt, M., Hörnschemeyer, T., Weiland, C., Miko, I., Yoder, M. & Hickler, T., May 17 2018, SPNHC + TDWG 2018. Vol. 2. p. e25585 (Biodiversity Information Science and Standards).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Revision of Trassedia (Hymenoptera: Ceraphronidae), an Evolutionary Relict with an Unusual Distribution

Mikó, I., Trietsch, C., Van De Kamp, T., Masner, L., Ulmer, J. M., Yoder, M. J., Zuber, M., Sandall, E. L., Baumbach, T. & Deans, A. R., Nov 1 2018, In: Insect Systematics and Diversity. 2, 6, 4.

Research output: Contribution to journal › Article › peer-review

Specimens, Databases, and Accession Books: Using TaxonWorks to Integrate Multiple Sources of Modern and Historical Data in the INHS Insect Collection

McElrath, T., Dmitriev, D., Yoder, M., DeWalt, R. E. & Dietrich, C., 2018, In: Biodiversity Information Science and Standards. 2, p. e25896

Research output: Contribution to journal › Article › peer-review

Taxonomy and the Production of Semantic Phenotypes

Yoder, M. J., Twidale, M. B., Thomer, A. K., Vogt, L., Franz, N. M., Guo, J., Deans, A. R. & Balhoff, J. P., Jul 2 2018, Application of Semantic Technology in Biodiversity Science. Thessen, A. E. (ed.). IOS Press, Vol. 33. p. 53-77 25 p. (Studies on the Semantic Web; vol. 33).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Open Access

TaxonWorks: A Use Case in Documenting Complex Biological Relationships

Trivellone, V., Dietrich, C. H., Dmitriev, D. & Yoder, M., 2018, In: Biodiversity Information Science and Standards. 2, e25723.

Research output: Contribution to journal › Article › peer-review

Open Access

Transforming Taxonomic Interfaces: “Arm’s length” Cooperative work and the maintenance of a long-lived classification system

Thomer, A. K., Twidale, M. B. & Yoder, M. J., Nov 2018, p. 173:1-173:23.

Research output: Contribution to conference › Paper › peer-review

Wet collections accession: a workflow based on a large stonefly (Insecta, Plecoptera) donation

DeWalt, R. E., Yoder, M., Snyder, E. A., Dmitriev, D. & Ower, G. D., 2018, In: Biodiversity Data Journal. 6, e30256.

Research output: Contribution to journal › Article › peer-review

2017

Design and use of NOMEN, an ontology defining the rules of biological nomenclature

Yoder, M., Dmitriev, D., Pereira, J. L. & Cigliano, M. M., 2017, Proceedings of TDWG. Vol. 1. p. e20284

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Sustainability in Biodiversity Software Development: More financing or better practices?

Yoder, M., Twidale, M. & Thomer, A., 2017, Proceedings of TDWG. Vol. 1. p. e20283

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

The first organ-based ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions

Wirkner, C. S., Göpel, T., Runge, J., Keiler, J., Klussmann-Fricke, B. J., Huckstorf, K., Scholz, S., Mikó, I., Yoder, M. J. & Richter, S., Sep 1 2017, In: Systematic biology. 66, 5, p. 754-768 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2016

Co-designing scientific software: Hackathons for participatory interface design

Thomer, A. K., Twidale, M. B., Guo, J. & Yoder, M. J., May 7 2016, CHI EA 2016: #chi4good - Extended Abstracts, 34th Annual CHI Conference on Human Factors in Computing Systems. Association for Computing Machinery, p. 3219-3226 8 p. (Conference on Human Factors in Computing Systems - Proceedings; vol. 07-12-May-2016).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

From catalogs to phenotypes: The evolution and current status of TaxonWorks with emphasis on its utility for entomologists

Yoder, M. J., 2016.

Research output: Contribution to conference › Other › peer-review

Malagasy Conostigmus (Hymenoptera: Ceraphronoidea) and the secret of scutes

Mikó, I., Trietsch, C., Sandall, E. L., Yoder, M. J., Hines, H. & Deans, A. R., 2016, In: PeerJ. 2016, 12, e2682.

Research output: Contribution to journal › Article › peer-review

Open Access

Progress on Digitization of the Kenneth Wilson Stewart Plecoptera Collections at the Illinois Natural History Survey

Dewalt, R. E., Dmitriev, D. & Yoder, M., 2016, In: Perla. 34, p. 49-69

Research output: Contribution to journal › Article › peer-review

Taxonomic Work as Information Work: Design for Semantic Refactoring

Thomer, A. K., Twidale, M., Guo, J. & Yoder, M. J., 2016. 5 p.

Research output: Contribution to conference › Paper › peer-review

2015

Finding Our Way through Phenotypes

Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., Burleigh, J. G., Chanet, B., Cooper, L. D., Courtot, M., Csösz, S., Cui, H., Dahdul, W., Das, S., Dececchi, T. A., Dettai, A., Diogo, R. & Druzinsky, R. E. & 54 others, Dumontier, M., Franz, N. M., Friedrich, F., Gkoutos, G. V., Haendel, M., Harmon, L. J., Hayamizu, T. F., He, Y., Hines, H. M., Ibrahim, N., Jackson, L. M., Jaiswal, P., James-Zorn, C., Köhler, S., Lecointre, G., Lapp, H., Lawrence, C. J., Le Novère, N., Lundberg, J. G., Macklin, J., Mast, A. R., Midford, P. E., Mikó, I., Mungall, C. J., Oellrich, A., Osumi-Sutherland, D., Parkinson, H., Ramírez, M. J., Richter, S., Robinson, P. N., Ruttenberg, A., Schulz, K. S., Segerdell, E., Seltmann, K. C., Sharkey, M. J., Smith, A. D., Smith, B., Specht, C. D., Squires, R. B., Thacker, R. W., Thessen, A., Fernandez-Triana, J., Vihinen, M., Vize, P. D., Vogt, L., Wall, C. E., Walls, R. L., Westerfeld, M., Wharton, R. A., Wirkner, C. S., Woolley, J. B., Yoder, M. J., Zorn, A. M. & Mabee, P., 2015, In: PLoS biology. 13, 1

Research output: Contribution to journal › Article › peer-review

2014

Folding wings like a cockroach: A review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania)

Mikó, I., Copeland, R. S., Balhoff, J. P., Yoder, M. J. & Deans, A. R., May 2 2014, In: PloS one. 9, 5, e94056.

Research output: Contribution to journal › Review article › peer-review

Open Access

Monograph of the afrotropical species of Scelio Latreille (hymenoptera, platygastridae), egg parasitoids of acridid grasshoppers (Orthoptera, Acrididae)

Yoder, M. J., Valerio, A. A., Polaszek, A., van Noort, S., Masner, L. & Johnson, N. F., 2014, In: ZooKeys. 380, SPEC. ISSUE, p. 1-188 188 p.

Research output: Contribution to journal › Article › peer-review

2013

A phylogenetic analysis of the megadiverse Chalcidoidea (Hymenoptera)

Heraty, J. M., Burks, R. A., Cruaud, A., Gibson, G. A. P., Liljeblad, J., Munro, J., Rasplus, J. Y., Delvare, G., Janšta, P., Gumovsky, A., Huber, J., Woolley, J. B., Krogmann, L., Heydon, S., Polaszek, A., Schmidt, S., Darling, D. C., Gates, M. W., Mottern, J. & Murray, E. & 7 others, Dal Molin, A., Triapitsyn, S., Baur, H., Pinto, J. D., van Noort, S., George, J. & Yoder, M., Oct 2013, In: Cladistics. 29, 5, p. 466-542 77 p.

Research output: Contribution to journal › Article › peer-review

Open Access

A semantic model for species description applied to the ensign wasps (Hymenoptera: Evaniidae) of new caledonia

Balhoff, J. P., Mikó, I., Yoder, M. J., Mullins, P. L. & Deans, A. R., Sep 2013, In: Systematic biology. 62, 5, p. 639-659 21 p.

Research output: Contribution to journal › Article › peer-review

Male terminalia of Ceraphronoidea: Morphological diversity in an otherwise monotonous taxon

Mikó, I., Masner, L., Johannes, E., Yoder, M. J. & Deans, A. R., Dec 17 2013, In: Insect Systematics and Evolution. 44, 3-4, p. 261-347 87 p.

Research output: Contribution to journal › Article › peer-review

Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment

Bertone, M. A., Mikó, I., Yoder, M. J., Seltmann, K. C., Balhoff, J. P. & Deans, A. R., 2013, In: Database. 2013, bas057.

Research output: Contribution to journal › Article › peer-review

Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology

Seltmann, K. C., Pénzes, Z., Yoder, M. J., Bertone, M. A. & Deans, A. R., Feb 18 2013, In: PloS one. 8, 2, e55674.

Research output: Contribution to journal › Article › peer-review

2012

A hymenopterists' guide to the Hymenoptera Anatomy Ontology: Utility, clarification, and future directions

Seltmann, K. C., Yoder, M. J., Mikó, I., Forshage, M., Bertone, M. A., Agosti, D., Austin, A. D., Balhoff, J. P., Borowiec, M. L., Brady, S. G., Broad, G. R., XBrothers, G. R., Burks, R. A., Buffington, M. L., Campbell, H. M., Dew, K. J., Ernst, A. F., Fernández-Triana, J. L., Gates, M. W. & Gibson, G. A. P. & 18 others, Jennings, J. T., Johnson, N. F., Karlsson, D., Kawada, R., Krogmann, L., Kula, R. R., Mullins, P. L., Ohl, M., Rasmussen, C., Ronquist, F., Schulmeister, S., Sharkey, M. J., Talamas, E., Tucker, E., Vilhelmsen, L., Ward, P. S., Wharton, R. A. & Deans, A. R., 2012, In: Journal of Hymenoptera Research. 27, 1, p. 67-88 22 p.

Research output: Contribution to journal › Article › peer-review

Nearly complete rRNA genes from 371 Animalia: Updated structure-based alignment and detailed phylogenetic analysis

Mallatt, J., Craig, C. W. & Yoder, M. J., Sep 2012, In: Molecular Phylogenetics and Evolution. 64, 3, p. 603-617 15 p.

Research output: Contribution to journal › Article › peer-review

On dorsal prothoracic appendages in treehoppers (Hemiptera: Membracidae) and the nature of morphological evidence

Mikó, I., Friedrich, F., Yoder, M. J., Hines, H. M., Deitz, L. L., Bertone, M. A., Seltmann, K. C., Wallace, M. S. & Deans, A. R., Jan 17 2012, In: PloS one. 7, 1, e30137.

Research output: Contribution to journal › Article › peer-review

Time to change how we describe biodiversity

Deans, A. R., Yoder, M. J. & Balhoff, J. P., Feb 2012, In: Trends in Ecology and Evolution. 27, 2, p. 78-84 7 p.

Research output: Contribution to journal › Review article › peer-review

2011

Multi-species anatomy ontology development requires a pluralist approach to label-class mapping

Mikó, I., Yoder, M. J., Bertone, M. A., Seltmann, K. C. & Deans, A. R., 2011, In: CEUR Workshop Proceedings. 833, p. 422-424 3 p.

Research output: Contribution to journal › Conference article › peer-review

2010

A gross anatomy ontology for hymenoptera

Yoder, M. J., Mikó, I., Seltmann, K. C., Bertone, M. A. & Deans, A. R., 2010, In: PloS one. 5, 12, e15991.

Research output: Contribution to journal › Article › peer-review

Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction

Mallatt, J., Craig, C. W. & Yoder, M. J., Apr 2010, In: Molecular Phylogenetics and Evolution. 55, 1, p. 1-17 17 p.

Research output: Contribution to journal › Article › peer-review

2009

Identity and synonymy of Dicroscelio Kieffer and description of Axea, a new genus from tropical Africa and Asia (Hymenoptera: Platygastroidea: Platygastridae)

Yoder, M. J., Valerio, A. A., Masner, L. & Johnson, N. F., Feb 5 2009, In: Zootaxa. 2003, p. 1-45 45 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Revision of Scelio pulchripennis - group species (Hymenoptera, Platygastroidea, Platygastridae)

Yoder, M. J., Valerio, A. A., Polaszek, A., Masner, L. & Johnson, N. F., 2009, In: ZooKeys. 20, SPEC. ISSUE 2, p. 53-118 66 p.

Research output: Contribution to journal › Article › peer-review

2008

A monograph of the genus Westwoodia (Hymenoptera: Ichneumonidae)

Wharton, R. A., Roeder, K. & Yoder, M. J., Aug 22 2008, In: Zootaxa. 1855, p. 1-40 40 p.

Research output: Contribution to journal › Article › peer-review

2007

Mannomicrus (Hymenoptera: Diapriidae), a new genus of myrmecophilic diapriid, with a digital version of Masner and García's (2002) key to New World Diapriinae and an illustration of digital description and key markup using an ontology

Yoder, M., Apr 2 2007, In: Zootaxa. 1439, p. 47-55 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2006

An evaluation of ensign wasp classification (Hymenoptera: Evaniidae) based on molecular data and insights from ribosomal RNA secondary structure

Deans, A. R., Gillespie, J. J. & Yoder, M. J., Jul 2006, In: Systematic Entomology. 31, 3, p. 517-528 12 p.

Research output: Contribution to journal › Article › peer-review

Relationships of Exodontiella, a non-alysiine, exodont member of the family Braconidae (Insecta, Hymenoptera)

Wharton, R. A., Yoder, M. J., Gillespie, J. J., Patton, J. C. & Honeycutt, R. L., Jul 2006, In: Zoologica Scripta. 35, 4, p. 323-340 18 p.

Research output: Contribution to journal › Article › peer-review

Matthew Jon Yoder

Research output

Search results