Automatic Grid Fitting for Genetic Spot Array Images Containing Guide Spots. - Norbert Brändle; Hilmar Lapp; Horst Bischof (CAIP, 1999)

Robust Spot Fitting for Genetic Spot Array Images. - Horng-Yang Chen; Norbert Brändle; Horst Bischof; Hilmar Lapp (ICIP, 2000)

Robust Parametric and Semi-Parametric Spot Fitting for Spot Array Images. - Norbert Brändle; Horng-Yang Chen; Horst Bischof; Hilmar Lapp (ISMB, 2000)

Robust DNA microarray image analysis. - Norbert Brändle; Horst Bischof; Hilmar Lapp (Mach. Vis. Appl., 2003)

Open source tools and toolkits for bioinformatics: significance, and where are we? - Jason E. Stajich; Hilmar Lapp (Briefings Bioinform., 2006)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

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)

Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies. - James P. Balhoff; Peter E. Midford; Hilmar Lapp (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)

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. - Sook Jung; Naama Menda; Seth Redmond; Robert M. Buels; Maren Friesen; Yuri R. Bendaña; Lacey-Anne Sanderson; Hilmar Lapp; Taein Lee; Bob MacCallum; Kirstin E. Bett; Scott Cain; et al. (Database J. Biol. Databases Curation, 2011)

The PLOS Computational Biology Software Section. - Andreas Prlic; Hilmar Lapp (PLoS Comput. Biol., 2012)

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)

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. - Arlin Stoltzfus; Hilmar Lapp; Naim Matasci; Helena F. Deus; Brian Sidlauskas; Christian M. Zmasek; Gaurav Vaidya; Enrico Pontelli; Karen Cranston; Rutger A. Vos; Campbell O. Webb; Luke J. Harmon; et al. (BMC Bioinform., 2013)

Software Engineering as Instrumentation for the Long Tail of Scientific Software. - Daisie Huang; Hilmar Lapp (CoRR, 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)

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

Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1). - Daniel S. Katz; Sou-Cheng T. Choi; Hilmar Lapp; Ketan Maheshwari; Frank Löffler 001; Matthew Turk 002; Marcus D. Hanwell; Nancy Wilkins-Diehr; James Hetherington; James Howison; Shel Swenson; Gabrielle Allen; et al. (CoRR, 2014)

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)

The Bioinformatics Open Source Conference (BOSC) 2013. - Nomi L. Harris; Peter J. A. Cock; Brad A. Chapman; Jeremy Goecks; Hans-Rudolf Hotz; Hilmar Lapp (Bioinform., 2015)

Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity. - Prashanti Manda; Christopher J. Mungall; James P. Balhoff; Hilmar Lapp; Todd J. Vision (PSB, 2016)

The 2016 Bioinformatics Open Source Conference (BOSC). - Nomi L. Harris; Peter J. A. Cock; Brad Chapman; Christopher J. Fields; Karsten Hokamp; Hilmar Lapp; Monica C. Munoz-Torres; Heather Wiencko (F1000Research, 2016)

The 2015 Bioinformatics Open Source Conference (BOSC 2015). - Nomi L. Harris; Peter J. A. Cock; Hilmar Lapp; Brad Chapman; Rob Davey; Christopher J. Fields; Karsten Hokamp; Monica C. Munoz-Torres (PLoS Comput. Biol., 2016)

On the Ontological Modeling of Trees. - David Carral; Pascal Hitzler; Hilmar Lapp; Sebastian Rudolph (WOP@ISWC, 2017)

The 2017 Bioinformatics Open Source Conference (BOSC). - Nomi L. Harris; Peter J. A. Cock; Brad Chapman; Christopher J. Fields; Karsten Hokamp; Hilmar Lapp; Monica C. Munoz-Torres; Bastian Greshake Tzovaras; Heather Wiencko (F1000Research, 2017)

Community and Code: Nine Lessons from Nine NESCent Hackathons. - Arlin Stoltzfus; Michael S. Rosenberg; Hilmar Lapp; Aidan Budd; Karen Cranston; Enrico Pontelli; Shann Oliver; Rutger A. Vos (F1000Research, 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)

The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018). - Nomi L. Harris; Heather Wiencko; Brad Chapman; Peter J. A. Cock; Karsten Hokamp; Hilmar Lapp; Christopher J. Fields; Bastian Greshake Tzovaras (F1000Research, 2018)

'Computable' Phenotypes Enable Comparative and Predictive Phenomics Among Plant Species and Across Domains of Life. - Ian Braun; James P. Balhoff; Tanya Z. Berardini; Laurel Cooper; Georgios V. Gkoutos; Lisa C. Harper; Eva Huala; Pankaj Jaiswal; Toni Kazic; Hilmar Lapp; James A. Macklin; Chelsea D. Specht; et al. (Application of Semantic Technology in Biodiversity Science, 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)

Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare. - Stephen K. Woody; David Burdick; Hilmar Lapp; Erich S. Huang (npj Digit. Medicine, 2020)

Publisher Correction: Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare. - Stephen K. Woody; David Burdick; Hilmar Lapp; Erich S. Huang (npj Digit. Medicine, 2020)

Seed Patterns for Modeling Trees. - Aaron Eberhart; David Carral; Pascal Hitzler; Hilmar Lapp; Sebastian Rudolph (WOP (Book), 2021)

JPhyloRef: a tool for testing and resolving phyloreferences. - Gaurav Vaidya; Nico Cellinese; Hilmar Lapp (J. Open Source Softw., 2021)

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)

OmniMesh: Addressing Findability Challenges in Distributed Nature Data Repositories. - Arnab Nandi 001; Wei-Lun Chao; Rongjun Qin; Carl Boettiger; Hilmar Lapp; Tanya Y. Berger-Wolf (SSDBM, 2025)

Static Segmentation by Tracking: A Frustratingly Label-Efficient Approach to Fine-Grained Segmentation. - Zhenyang Feng; Zihe Wang; Saul Ibaven Bueno; Tomasz Frelek; Advikaa Ramesh; Jingyan Bai; Lemeng Wang; Zanming Huang; Jianyang Gu; Jinsu Yoo; Tai-Yu Pan; Arpita Chowdhury; et al. (CoRR, 2025)

Building Machine Learning Challenges for Anomaly Detection in Science. - Elizabeth G. Campolongo; Yuan-Tang Chou; Ekaterina Govorkova; Wahid Bhimji; Wei-Lun Chao; Chris Harris; Shih-Chieh Hsu; Hilmar Lapp; Mark S. Neubauer; Josephine M. Namayanja; Aneesh Subramanian; Philip C. Harris; et al. (CoRR, 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)

BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning. - Jianyang Gu; Samuel Stevens 001; Elizabeth G. Campolongo; Matthew J. Thompson; Net Zhang; Jiaman Wu; Andrei Kopanev; Zheda Mai; Alexander E. White; James P. Balhoff; Wasila M. Dahdul; Daniel I. Rubenstein; et al. (CoRR, 2025)