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2020 – today
- 2025
[c16]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, Paula M. Mabee, Hilmar Lapp, Anuj Karpatne:
What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits. ICLR 2025- [c15]Arnab Nandi
, Wei-Lun Chao, Rongjun Qin, Carl Boettiger, Hilmar Lapp, Tanya Y. Berger-Wolf:
OmniMesh: Addressing Findability Challenges in Distributed Nature Data Repositories. SSDBM 2025: 20:1-20:6 - [i17]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, Michelle Ramirez, Elizabeth G. Campolongo, Matthew J. Thompson, Christopher G. Lawrence, Sydne Record, Neil Rosser, Anuj Karpatne, Daniel I. Rubenstein, Hilmar Lapp, Charles V. Stewart, Tanya Y. Berger-Wolf, Yu Su, Wei-Lun Chao:
Static Segmentation by Tracking: A Frustratingly Label-Efficient Approach to Fine-Grained Segmentation. CoRR abs/2501.06749 (2025) - [i16]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, Advaith Anand, David Edward Carlyn, Subhankar Ghosh, Christopher G. Lawrence, Eric A. Moreno, Ryan Raikman, Jiaman Wu, Ziheng Zhang, Bayu Adhi, Mohammad Ahmadi Gharehtoragh, Saúl Alonso-Monsalve, Marta Babicz, Furqan Baig, Namrata Banerji, William Bardon, Tyler Barna, Tanya Y. Berger-Wolf, Adji Bousso Dieng, Micah Brachman, Quentin Buat, David C. Y. Hui, Phuong Cao, Franco Cerino, Yi-Chun Chang, Shivaji Chaulagain, An-Kai Chen, Deming Chen, Eric Chen, Chia-Jui Chou, Zih-Chen Ciou, Miles Cochran-Branson, Artur Cordeiro Oudot Choi, Michael Coughlin, Matteo Cremonesi, Maria Dadarlat, Peter Darch, Malina Desai, Daniel Diaz, Steven Dillmann, Javier Duarte, Isla Duporge, Urbas Ekka, Saba Entezari Heravi, Hao Fang, Rian Flynn, Geoffrey Fox, Emily Freed, Hang Gao, Jing Gao, Julia Gonski, Matthew J. Graham, Abolfazl Hashemi, Scott Hauck, James Hazelden, Joshua Henry Peterson, Duc Hoang, Wei Hu, Mirco Hünnefeld, David Hyde, Vandana P. Janeja, Nattapon Jaroenchai, Haoyi Jia, Yunfan Kang, Maksim Kholiavchenko, Elham E Khoda, Sangin Kim, Aditya Kumar, Bo-Cheng Lai, Trung Le, Chi-Wei Lee, JangHyeon Lee, Shaocheng Lee, Suzan van der Lee, Charles Lewis, Haitong Li, Haoyang Li, Henry Liao, Mia Liu, Xiaolin Liu, Xiulong Liu, Vladimir Loncar, Fangzheng Lyu, Ilya Makarov, Abhishikth Mallampalli Chen-Yu Mao, Alexander Michels, Alexander Migala, Farouk Mokhtar, Mathieu Morlighem:
Building Machine Learning Challenges for Anomaly Detection in Science. CoRR abs/2503.02112 (2025) - [i15]Alyson East, Elizabeth G. Campolongo, Luke Meyers, S. M. Rayeed, Samuel Stevens, Iuliia Zarubiieva, Isadora E. Fluck, Jennifer C. Girón, Maximiliane Jousse, Scott C. Lowe, Kayla I Perry, Isabelle Betancourt, Noah Charney, Evan Donoso, Nathan Fox, Kim J. Landsbergen, Ekaterina Nepovinnykh, Michelle Ramirez, Parkash Singh, Khum Thapa-Magar, Matthew J. Thompson, Evan Waite, Tanya Y. Berger-Wolf, Hilmar Lapp, Paula M. Mabee, Graham Taylor, Sydne Record:
Optimizing Image Capture for Computer Vision-Powered Taxonomic Identification and Trait Recognition of Biodiversity Specimens. CoRR abs/2505.17317 (2025) - [i14]Jianyang Gu, Samuel Stevens, 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, Hilmar Lapp, Tanya Y. Berger-Wolf, Wei-Lun Chao, Yu Su:
BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning. CoRR abs/2505.23883 (2025) - 2024
- [c14]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, Charles V. Stewart, Tanya Y. Berger-Wolf, Anuj Karpatne:
Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution. ECCV (89) 2024: 137-153 - [c13]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, Josef C. Uyeda, Hilmar Lapp, Henry L. Bart Jr., Paula M. Mabee, Yu Su, Wei-Lun Chao, Charles V. Stewart, Tanya Y. Berger-Wolf, Wasila M. Dahdul, Anuj Karpatne:
VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images. NeurIPS 2024 - [i13]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, Wei-Lun Chao, Paula M. Mabee, Henry L. Bart Jr., Wasila M. Dahdul, Anuj Karpatne:
Fish-Vista: A Multi-Purpose Dataset for Understanding & Identification of Traits from Images. CoRR abs/2407.08027 (2024) - [i12]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, Charles V. Stewart, Tanya Y. Berger-Wolf, Anuj Karpatne:
Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution. CoRR abs/2408.00160 (2024) - [i11]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, Josef C. Uyeda, Hilmar Lapp, Henry L. Bart Jr., Paula M. Mabee, Yu Su, Wei-Lun Chao, Charles V. Stewart, Tanya Y. Berger-Wolf, Wasila M. Dahdul, Anuj Karpatne:
VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images. CoRR abs/2408.16176 (2024) - [i10]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, Anuj Karpatne:
What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits. CoRR abs/2409.02335 (2024) - 2023
- [c12]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, David Carlyn, Wei-Lun Chao, Charles V. Stewart, Daniel I. Rubenstein, Tanya Y. Berger-Wolf, Anuj Karpatne:
Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks. KDD 2023: 3966-3978 - [i9]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, David Carlyn, Wei-Lun Chao, Charles V. Stewart, Daniel I. Rubenstein, Tanya Y. Berger-Wolf, Anuj Karpatne:
Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks. CoRR abs/2306.03228 (2023) - 2021
- [j15]Gaurav Vaidya, Nico Cellinese, Hilmar Lapp:
JPhyloRef: a tool for testing and resolving phyloreferences. J. Open Source Softw. 6(64): 3374 (2021) - [c11]Aaron Eberhart, David Carral, Pascal Hitzler, Hilmar Lapp, Sebastian Rudolph:
Seed Patterns for Modeling Trees. WOP (Book) 2021: 48-67 - 2020
- [j14]Stephen K. Woody, David Burdick, Hilmar Lapp, Erich S. Huang:
Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare. npj Digit. Medicine 3 (2020) - [j13]Stephen K. Woody, David Burdick, Hilmar Lapp, Erich S. Huang:
Publisher Correction: Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare. npj Digit. Medicine 3 (2020)
2010 – 2019
- 2018
- [j12]Wasila M. Dahdul, Prashanti Manda, Hong Cui, James P. Balhoff, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Todd J. Vision, Paula M. Mabee:
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. Database J. Biol. Databases Curation 2018: bay110 (2018) - [c10]Paula M. Mabee, James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Christopher J. Mungall, Todd J. Vision:
Reasoning over Anatomical Homology in the Phenoscape KB. ICBO 2018 - [p2]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, Todd J. Vision, Ramona L. Walls, Carolyn J. Lawrence-Dill:
'Computable' Phenotypes Enable Comparative and Predictive Phenomics Among Plant Species and Across Domains of Life. Application of Semantic Technology in Biodiversity Science 2018: 187-205 - [p1]Paula M. Mabee, Wasila M. Dahdul, James P. Balhoff, Hilmar Lapp, Prashanti Manda, Josef C. Uyeda, Todd J. Vision, Monte Westerfield:
Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. Application of Semantic Technology in Biodiversity Science 2018: 207-224 - [i8]Nomi L. Harris, Heather Wiencko, Brad Chapman, Peter J. A. Cock, Karsten Hokamp, Hilmar Lapp, Christopher J. Fields, Bastian Greshake Tzovaras:
The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018). F1000Research 7: 1309 (2018) - 2017
- [c9]David Carral, Pascal Hitzler, Hilmar Lapp, Sebastian Rudolph:
On the Ontological Modeling of Trees. WOP@ISWC 2017 - [i7]David Carral, Pascal Hitzler, Hilmar Lapp, Sebastian Rudolph:
On the Ontological Modeling of Trees. CoRR abs/1710.05096 (2017) - [i6]Arlin Stoltzfus, Michael S. Rosenberg, Hilmar Lapp, Aidan Budd, Karen Cranston, Enrico Pontelli, Shann Oliver, Rutger A. Vos:
Community and Code: Nine Lessons from Nine NESCent Hackathons. F1000Research 6: 786- (2017) - [i5]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:
The 2017 Bioinformatics Open Source Conference (BOSC). F1000Research 6: 1858- (2017) - 2016
- [j11]Nomi L. Harris, Peter J. A. Cock, Hilmar Lapp, Brad Chapman, Rob Davey, Christopher J. Fields, Karsten Hokamp, Monica C. Munoz-Torres:
The 2015 Bioinformatics Open Source Conference (BOSC 2015). PLoS Comput. Biol. 12(2) (2016) - [c8]Prashanti Manda, Christopher J. Mungall, James P. Balhoff, Hilmar Lapp, Todd J. Vision:
Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity. PSB 2016: 132-143 - [i4]Nomi L. Harris, Peter J. A. Cock, Brad Chapman, Christopher J. Fields, Karsten Hokamp, Hilmar Lapp, Monica C. Munoz-Torres, Heather Wiencko:
The 2016 Bioinformatics Open Source Conference (BOSC). F1000Research 5: 2464 (2016) - 2015
- [j10]Wasila M. Dahdul, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Paula M. Mabee:
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. Database J. Biol. Databases Curation 2015 (2015) - [j9]Nomi L. Harris, Peter J. A. Cock, Brad A. Chapman, Jeremy Goecks, Hans-Rudolf Hotz, Hilmar Lapp:
The Bioinformatics Open Source Conference (BOSC) 2013. Bioinform. 31(2): 299-300 (2015) - 2014
- [j8]James P. Balhoff, Wasila M. Dahdul, Thomas Dececchi, Hilmar Lapp, Paula M. Mabee, Todd J. Vision:
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. J. Biomed. Semant. 5: 45 (2014) - [i3]Daniel S. Katz, Sou-Cheng T. Choi, Hilmar Lapp, Ketan Maheshwari, Frank Löffler, Matthew Turk, Marcus D. Hanwell, Nancy Wilkins-Diehr, James Hetherington, James Howison, Shel Swenson, Gabrielle Allen, Anne C. Elster, G. Bruce Berriman, Colin C. Venters:
Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1). CoRR abs/1404.7414 (2014) - [i2]James P. Balhoff, T. Alexander Dececchi, Paula M. Mabee, Hilmar Lapp:
Presence-absence reasoning for evolutionary phenotypes. CoRR abs/1410.3862 (2014) - 2013
- [j7]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:
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. J. Biomed. Semant. 4: 34 (2013) - [j6]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, Meg Pirrung, Brian C. O'Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenberg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E. Alfaro, Aaron Steele, Greg Jordan:
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinform. 14: 158 (2013) - [i1]Daisie Huang, Hilmar Lapp:
Software Engineering as Instrumentation for the Long Tail of Scientific Software. CoRR abs/1309.1806 (2013) - 2012
- [j5]Andreas Prlic, Hilmar Lapp:
The PLOS Computational Biology Software Section. PLoS Comput. Biol. 8(11) (2012) - 2011
- [j4]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, Dave Clements, Lukas A. Mueller, Dorrie Main:
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. Database J. Biol. Databases Curation 2011 (2011) - [c7]James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee:
Employing Reasoning within the Phenoscape Knowledgebase. ICBO 2011 - [c6]James P. Balhoff, Peter E. Midford, Hilmar Lapp:
Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies. ICBO 2011 - [c5]Wasila M. Dahdul, James P. Balhoff, Hilmar Lapp, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee:
Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes. ICBO 2011 - [c4]Todd J. Vision, Judith A. Blake, Hilmar Lapp, Paula M. Mabee, Monte Westerfield:
Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. LISC 2011 - 2010
- [j3]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, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi:
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1: 8 (2010)
2000 – 2009
- 2006
- [j2]Jason E. Stajich, Hilmar Lapp:
Open source tools and toolkits for bioinformatics: significance, and where are we? Briefings Bioinform. 7(3): 287-296 (2006) - 2003
- [j1]Norbert Brändle, Horst Bischof, Hilmar Lapp:
Robust DNA microarray image analysis. Mach. Vis. Appl. 15(1): 11-28 (2003) - 2000
- [c3]Horng-Yang Chen, Norbert Brändle, Horst Bischof, Hilmar Lapp:
Robust Spot Fitting for Genetic Spot Array Images. ICIP 2000: 412-415 - [c2]Norbert Brändle, Horng-Yang Chen, Horst Bischof, Hilmar Lapp:
Robust Parametric and Semi-Parametric Spot Fitting for Spot Array Images. ISMB 2000: 46-56
1990 – 1999
- 1999
- [c1]Norbert Brändle, Hilmar Lapp, Horst Bischof:
Automatic Grid Fitting for Genetic Spot Array Images Containing Guide Spots. CAIP 1999: 357-366
Coauthor Index
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