CARO - The Common Anatomy Reference Ontology. - Melissa A. Haendel; Fabian Neuhaus; David Osumi-Sutherland; Paula M. Mabee; José L. V. Mejino Jr.; Chris Mungall; Barry Smith 001 (Anatomy Ontologies for Bioinformatics, 2008)

Employing Reasoning within the Phenoscape Knowledgebase. - James P. Balhoff; Wasila M. Dahdul; Hilmar Lapp; Peter E. Midford; Todd J. Vision; Monte Westerfield; Paula M. Mabee (ICBO, 2011)

Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes. - Wasila M. Dahdul; James P. Balhoff; Hilmar Lapp; Peter E. Midford; Todd J. Vision; Monte Westerfield; Paula M. Mabee (ICBO, 2011)

Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. - Todd J. Vision; Judith A. Blake; Hilmar Lapp; Paula M. Mabee; Monte Westerfield (LISC, 2011)

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. - Cecilia N. Arighi; Ben Carterette; K. Bretonnel Cohen; Martin Krallinger; W. John Wilbur; Petra Fey; Robert J. Dodson; Laurel Cooper; Ceri E. Van Slyke; Wasila M. Dahdul; Paula M. Mabee; Donghui Li; et al. (Database J. Biol. Databases Curation, 2013)

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. - Peter E. Midford; Thomas Dececchi; James P. Balhoff; Wasila M. Dahdul; Nizar Ibrahim; Hilmar Lapp; John G. Lundberg; Paula M. Mabee; Paul C. Sereno; Monte Westerfield; Todd J. Vision; David C. Blackburn (J. Biomed. Semant., 2013)

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. - James P. Balhoff; Wasila M. Dahdul; Thomas Dececchi; Hilmar Lapp; Paula M. Mabee; Todd J. Vision (J. Biomed. Semant., 2014)

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. - Wasila M. Dahdul; Hong Cui; Paula M. Mabee; Christopher J. Mungall; David Osumi-Sutherland; Ramona L. Walls; Melissa A. Haendel (J. Biomed. Semant., 2014)

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. - Melissa A. Haendel; James P. Balhoff; Frederic B. Bastian; David C. Blackburn; Judith A. Blake; Yvonne M. Bradford; Aurélie Comte; Wasila M. Dahdul; Thomas Dececchi; Robert E. Druzinsky; Terry F. Hayamizu; Nizar Ibrahim; et al. (J. Biomed. Semant., 2014)

Presence-absence reasoning for evolutionary phenotypes. - James P. Balhoff; T. Alexander Dececchi; Paula M. Mabee; Hilmar Lapp (CoRR, 2014)

CharaParser+EQ: Performance evaluation without gold standard. - Hong Cui; Wasila M. Dahdul; T. Alexander Dececchi; Nizar Ibrahim; Paula M. Mabee; James P. Balhoff; Hariharan Gopalakrishnan (ASIST, 2015)

Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. - Wasila M. Dahdul; T. Alexander Dececchi; Nizar Ibrahim; Hilmar Lapp; Paula M. Mabee (Database J. Biol. Databases Curation, 2015)

A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. - Pasan C. Fernando; Laura M. Jackson; Erliang Zeng; Paula M. Mabee; James P. Balhoff (BIBM, 2017)

Reasoning over Anatomical Homology in the Phenoscape KB. - Paula M. Mabee; James P. Balhoff; Wasila M. Dahdul; Hilmar Lapp; Christopher J. Mungall; Todd J. Vision (ICBO, 2018)

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. - Wasila M. Dahdul; Prashanti Manda; Hong Cui; James P. Balhoff; T. Alexander Dececchi; Nizar Ibrahim; Hilmar Lapp; Todd J. Vision; Paula M. Mabee (Database J. Biol. Databases Curation, 2018)

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. - Paula M. Mabee; Wasila M. Dahdul; James P. Balhoff; Hilmar Lapp; Prashanti Manda; Josef C. Uyeda; Todd J. Vision; Monte Westerfield (Application of Semantic Technology in Biodiversity Science, 2018)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

Biodiversity Image Quality Metadata Augments Convolutional Neural Network Classification of Fish Species. - Jeremy Leipzig; Yasin Bakis; Xiaojun Wang; Mohannad Elhamod; Kelly Diamond; Wasila M. Dahdul; Anuj Karpatne; A. Murat Maga; Paula M. Mabee; Henry L. Bart Jr.; Jane Greenberg (MTSR, 2020)

Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. - Pasan C. Fernando; Paula M. Mabee; Erliang Zeng (BMC Bioinform., 2020)

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks. - Mohannad Elhamod; Mridul Khurana; Harish Babu Manogaran; Josef C. Uyeda; Meghan A. Balk; Wasila M. Dahdul; Yasin Bakis; Henry L. Bart Jr.; Paula M. Mabee; Hilmar Lapp; James P. Balhoff; Caleb Charpentier; et al. (KDD, 2023)

Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution. - Mridul Khurana; Arka Daw; M. Maruf; Josef C. Uyeda; Wasila M. Dahdul; Caleb Charpentier; Yasin Bakis; Henry L. Bart Jr.; Paula M. Mabee; Hilmar Lapp; James P. Balhoff; Wei-Lun Chao; et al. (ECCV (89), 2024)

VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images. - M. Maruf; Arka Daw; Kazi Sajeed Mehrab; Harish Babu Manogaran; Abhilash Neog; Medha Sawhney; Mridul Khurana; James P. Balhoff; Yasin Bakis; Bahadir Altintas; Matthew J. Thompson; Elizabeth G. Campolongo; et al. (NeurIPS, 2024)

Fish-Vista: A Multi-Purpose Dataset for Understanding & Identification of Traits from Images. - Kazi Sajeed Mehrab; M. Maruf; Arka Daw; Harish Babu Manogaran; Abhilash Neog; Mridul Khurana; Bahadir Altintas; Yasin Bakis; Elizabeth G. Campolongo; Matthew J. Thompson; Xiaojun Wang; Hilmar Lapp; et al. (CoRR, 2024)

What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits. - Harish Babu Manogaran; M. Maruf; Arka Daw; Kazi Sajeed Mehrab; Caleb Charpentier; Josef C. Uyeda; Wasila M. Dahdul; Matthew J. Thompson; Elizabeth G. Campolongo; Kaiya Provost; Paula M. Mabee; Hilmar Lapp; et al. (CoRR, 2024)

Fish-Vista: A Multi-Purpose Dataset for Understanding & Identification of Traits from Images. - Kazi Sajeed Mehrab; M. Maruf; Arka Daw; Abhilash Neog; Harish Babu Manogaran; Mridul Khurana; Zhenyang Feng; Bahadir Altintas; Yasin Bakis; Elizabeth G. Campolongo; Matthew J. Thompson; Xiaojun Wang; et al. (CVPR, 2025)

What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits. - Harish Babu Manogaran; M. Maruf; Arka Daw; Kazi Sajeed Mehrab; Caleb Patrick Charpentier; Josef C. Uyeda; Wasila M. Dahdul; Matthew J. Thompson; Elizabeth G. Campolongo; Kaiya L. Provost; Wei-Lun Chao; Tanya Y. Berger-Wolf; et al. (ICLR, 2025)

Optimizing Image Capture for Computer Vision-Powered Taxonomic Identification and Trait Recognition of Biodiversity Specimens. - Alyson East; Elizabeth G. Campolongo; Luke Meyers; S. M. Rayeed; Samuel Stevens 001; Iuliia Zarubiieva; Isadora E. Fluck; Jennifer C. Girón; Maximiliane Jousse; Scott C. Lowe; Kayla I Perry; Isabelle Betancourt; et al. (CoRR, 2025)