geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. - Matthew W. Pennell; Jonathan M. Eastman; Graham J. Slater; Joseph W. Brown; Josef C. Uyeda; Richard G. FitzJohn; Michael E. Alfaro; Luke J. Harmon (Bioinform., 2014)

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)

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)

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)

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)