A Case Study on the Parametric Occurrence of Multiple Steady States. - Russell J. Bradford; James H. Davenport; Matthew England 001; Hassan Errami; Vladimir P. Gerdt; Dima Grigoriev; Charles Tapley Hoyt; Marek Kosta; Ovidiu Radulescu; Thomas Sturm 001; Andreas Weber 004 (ISSAC, 2017)

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities. - Charles Tapley Hoyt; Daniel Domingo-Fernández; Nora Balzer; Anka Güldenpfennig; Martin Hofmann-Apitius (Database J. Biol. Databases Curation, 2018)

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. - Charles Tapley Hoyt; Daniel Domingo-Fernández; Martin Hofmann-Apitius (Database J. Biol. Databases Curation, 2018)

BEL2ABM: agent-based simulation of static models in Biological Expression Language. - Michaela Gündel; Charles Tapley Hoyt; Martin Hofmann-Apitius (Bioinform., 2018)

PyBEL: a computational framework for Biological Expression Language. - Charles Tapley Hoyt; Andrej Konotopez; Christian Ebeling (Bioinform., 2018)

RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Rational Kernels. - Eduardo Brito; Bogdan Georgiev; Daniel Domingo-Fernández; Charles Tapley Hoyt; Christian Bauckhage (LWDA, 2019)

Predicting Missing Links Using PyKEEN. - Mehdi Ali; Charles Tapley Hoyt; Daniel Domingo-Fernández; Jens Lehmann 001 (ISWC (Satellites), 2019)

The KEEN Universe - An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability. - Mehdi Ali; Hajira Jabeen; Charles Tapley Hoyt; Jens Lehmann 001 (ISWC (2), 2019)

Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. - Charles Tapley Hoyt; Daniel Domingo-Fernández; Rana Aldisi; Lingling Xu; Kristian Kolpeja; Sandra Spalek; Esther Wollert; John A. Bachman; Benjamin M. Gyori; Patrick Greene 001; Martin Hofmann-Apitius (Database J. Biol. Databases Curation, 2019)

BioKEEN: a library for learning and evaluating biological knowledge graph embeddings. - Mehdi Ali; Charles Tapley Hoyt; Daniel Domingo-Fernández; Jens Lehmann 001; Hajira Jabeen (Bioinform., 2019)

PathMe: merging and exploring mechanistic pathway knowledge. - Daniel Domingo-Fernández; Sarah Mubeen; Josep Marín-Llaó; Charles Tapley Hoyt; Martin Hofmann-Apitius (BMC Bioinform., 2019)

Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. - Reagon Karki; Alpha Tom Kodamullil; Charles Tapley Hoyt; Martin Hofmann-Apitius (BMC Bioinform., 2019)

Generation and Applications of Knowledge Graphs in Systems and Networks Biology - Charles Tapley Hoyt (2019)

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. - Mohammad Asif Emon; Daniel Domingo-Fernández; Charles Tapley Hoyt; Martin Hofmann-Apitius (BMC Bioinform., 2020)

The role of metadata in reproducible computational research. - Jeremy Leipzig; Daniel Nüst; Charles Tapley Hoyt; Stian Soiland-Reyes; Karthik Ram; Jane Greenberg (CoRR, 2020)

Identifying the parametric occurrence of multiple steady states for some biological networks. - Russell J. Bradford; James H. Davenport; Matthew England 001; Hassan Errami; Vladimir P. Gerdt; Dima Grigoriev; Charles Tapley Hoyt; Marek Kosta; Ovidiu Radulescu; Thomas Sturm 001; Andreas Weber 004 (J. Symb. Comput., 2020)

CLEP: a hybrid data- and knowledge-driven framework for generating patient representations. - Vinay Srinivas Bharadhwaj; Mehdi Ali; Colin Birkenbihl; Sarah Mubeen; Jens Lehmann 001; Martin Hofmann-Apitius; Charles Tapley Hoyt; Daniel Domingo-Fernández (Bioinform., 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - Vasundra Touré; Steven Vercruysse; Marcio Luis Acencio; Ruth C. Lovering; Sandra E. Orchard; Glyn Bradley; Cristina Casals-Casas; Claudine Chaouiya; Noemi del-Toro; Åsmund Flobak; Pascale Gaudet; Henning Hermjakob; et al. (Bioinform., 2021)

Wavelet-Packet Powered Deepfake Image Detection. - Moritz Wolter; Felix Blanke; Charles Tapley Hoyt; Jochen Garcke (CoRR, 2021)

PyKEEN 1.0: A Python Library for Training and Evaluating Knowledge Graph Embeddings. - Mehdi Ali; Max Berrendorf; Charles Tapley Hoyt; Laurent Vermue; Sahand Sharifzadeh; Volker Tresp; Jens Lehmann 001 (J. Mach. Learn. Res., 2021)

The role of metadata in reproducible computational research. - Jeremy Leipzig; Daniel Nüst; Charles Tapley Hoyt; Karthik Ram; Jane Greenberg (Patterns, 2021)

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis. - Jeremy Zucker; Kaushal Paneri; Sara Mohammad Taheri; Somya Bhargava; Pallavi Kolambkar; Craig Bakker; Jeremy Teuton; Charles Tapley Hoyt; Kristie L. Oxford; Robert Osazuwa Ness; Olga Vitek (IEEE Trans. Big Data, 2021)

ChemicalX: A Deep Learning Library for Drug Pair Scoring. - Benedek Rozemberczki; Charles Tapley Hoyt; Anna Gogleva; Piotr Grabowski; Klas Karis; Andrej Lamov; Andriy Nikolov; Sebastian Nilsson; Michaël Ughetto; Yu Wang 160; Tyler Derr; Benjamin M. Gyori (KDD, 2022)

A simple standard for ontological mappings 2022: updates of data model and outlook. - Nicolas Matentzoglu; Joe E. Flack; John B. Graybeal; Nomi L. Harris; Harshad B. Hegde; Charles Tapley Hoyt; Hyeongsik Kim 001; Sabrina Toro; Nicole A. Vasilevsky; Christopher J. Mungall (OM@ISWC, 2022)

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs. - Helena Balabin; Charles Tapley Hoyt; Benjamin M. Gyori; John A. Bachman; Alpha Tom Kodamullil; Martin Hofmann-Apitius; Daniel Domingo-Fernández (SWAT4HCLS, 2022)

A review of biomedical datasets relating to drug discovery: a knowledge graph perspective. - Stephen Bonner; Ian P. Barrett; Cheng Ye 002; Rowan Swiers; Ola Engkvist; Andreas Bender 002; Charles Tapley Hoyt; William L. Hamilton (Briefings Bioinform., 2022)

A Simple Standard for Sharing Ontological Mappings (SSSOM). - Nicolas Matentzoglu; James P. Balhoff; Susan M. Bello; Chris Bizon; Matthew H. Brush; Tiffany J. Callahan; Christopher G. Chute; William D. Duncan; Chris T. A. Evelo; Davera Gabriel; John B. Graybeal; Alasdair J. G. Gray; et al. (Database J. Biol. Databases Curation, 2022)

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (Database J. Biol. Databases Curation, 2022)

STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. - Helena Balabin; Charles Tapley Hoyt; Colin Birkenbihl; Benjamin M. Gyori; John A. Bachman; Alpha Tom Kodamullil; Paul G. Plöger; Martin Hofmann-Apitius; Daniel Domingo-Fernández (Bioinform., 2022)

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways. - Sara Mohammad Taheri; Jeremy Zucker; Charles Tapley Hoyt; Karen Sachs; Vartika Tewari; Robert Osazuwa Ness; Olga Vitek (Bioinform., 2022)

An Open Challenge for Inductive Link Prediction on Knowledge Graphs. - Mikhail Galkin 001; Max Berrendorf; Charles Tapley Hoyt (CoRR, 2022)

A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs. - Charles Tapley Hoyt; Max Berrendorf; Mikhail Galkin 001; Volker Tresp; Benjamin M. Gyori (CoRR, 2022)

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (CoRR, 2022)

PyBioPAX: biological pathway exchange in Python. - Benjamin M. Gyori; Charles Tapley Hoyt (J. Open Source Softw., 2022)

Bringing Light Into the Dark: A Large-Scale Evaluation of Knowledge Graph Embedding Models Under a Unified Framework. - Mehdi Ali; Max Berrendorf; Charles Tapley Hoyt; Laurent Vermue; Mikhail Galkin 001; Sahand Sharifzadeh; Asja Fischer; Volker Tresp; Jens Lehmann 001 (IEEE Trans. Pattern Anal. Mach. Intell., 2022)

GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning. - Ozlem Muslu; Charles Tapley Hoyt; Mauricio Lacerda; Martin Hofmann-Apitius; Holger Fröhlich (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Benchmark Datasets for Inductive Entity Alignment. - Daniel Obraczka; Max Berrendorf; Charles Tapley Hoyt; Michael Galkin; Erhard Rahm (Zenodo, 2022)

Benchmark Datasets for Inductive Entity Alignment. - Daniel Obraczka; Max Berrendorf; Charles Tapley Hoyt; Michael Galkin; Erhard Rahm (Zenodo, 2022)

A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling. - Nicolas Matentzoglu; Ian Braun; Anita R. Caron; Damien Goutte-Gattat; Benjamin M. Gyori; Nomi L. Harris; Emily Hartley; Harshad B. Hegde; Sven Hertling; Charles Tapley Hoyt; Hyeongsik Kim 001; Huanyu Li 001; et al. (OM@ISWC, 2023)

Optimal adjustment sets for causal query estimation in partially observed biomolecular networks. - Sara Mohammad Taheri; Vartika Tewari; Rohan Kapre; Ehsan Rahiminasab; Karen Sachs; Charles Tapley Hoyt; Jeremy Zucker; Olga Vitek (Bioinform., 2023)

An Open-Source Knowledge Graph Ecosystem for the Life Sciences. - Tiffany J. Callahan; Ignacio J. Tripodi; Adrianne L. Stefanski; Luca Cappelletti; Sanya Bathla Taneja; Jordan M. Wyrwa; Elena Casiraghi; Nicolas A. Matentzoglu; Justin T. Reese; Jonathan C. Silverstein; Charles Tapley Hoyt; Richard D. Boyce; et al. (CoRR, 2023)

Prediction and curation of missing biomedical identifier mappings with Biomappings. - Charles Tapley Hoyt; Amelia L. Hoyt; Benjamin M. Gyori (Bioinform., 2023)

Improving reproducibility and reusability in the Journal of Cheminformatics. - Charles Tapley Hoyt; Barbara Zdrazil; Rajarshi Guha; Nina Jeliazkova; Karina Martínez-Mayorga; Eva Nittinger (J. Cheminformatics, 2023)

ptwt - The PyTorch Wavelet Toolbox. - Moritz Wolter; Felix Blanke; Jochen Garcke; Charles Tapley Hoyt (J. Mach. Learn. Res., 2024)

CLEP. - Vinay Srinivas Bharadhwaj; Mehdi Ali; Colin Birkenbihl; Sarah Mubeen; Jens Lehmann 001; Martin Hofmann-Apitius; Charles Tapley Hoyt; Daniel Domingo-Fernández (Zenodo, 2024)

CLEP. - Vinay Srinivas Bharadhwaj; Mehdi Ali; Colin Birkenbihl; Sarah Mubeen; Jens Lehmann 001; Martin Hofmann-Apitius; Charles Tapley Hoyt; Daniel Domingo-Fernández (Zenodo, 2024)

CLEP. - Vinay Srinivas Bharadhwaj; Mehdi Ali; Colin Birkenbihl; Sarah Mubeen; Jens Lehmann 001; Martin Hofmann-Apitius; Charles Tapley Hoyt; Daniel Domingo-Fernández (Zenodo, 2025)

The Cell Ontology in the age of single-cell omics. - Shawn Zheng Kai Tan; Aleix Puig-Barbe; Damien Goutte-Gattat; Caroline Eastwood; Brian D. Aevermann; Alida Avola; James P. Balhoff; Ismail Ugur Bayindir; Jasmine Belfiore; Anita R. Caron; David S. Fischer; Nancy George; et al. (CoRR, 2025)

Causal identification with Y0. - Charles Tapley Hoyt; Craig Bakker; Richard J. Callahan; Joseph Cottam; August George; Benjamin M. Gyori; Haley M. Hummel; Nathaniel Merrill; Sara Mohammad Taheri; Pruthvi Prakash Navada; Marc-Antoine Parent; Adam Rupe; et al. (CoRR, 2025)