Charles Tapley Hoyt

Publication Activity (10 Years)

Years Active: 2017-2023
Publications (10 Years): 47

Top Topics

Biomedical Text

Graph Embedding

Top Venues

Database J. Biol. Databases Curation

Publications

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, Huanyu Li, James A. McLaughlin, Cássia Trojahn, Nicole A. Vasilevsky, Christopher J. Mungall
A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling. OM@ISWC (2023)
Sara Mohammad Taheri, Vartika Tewari, Rohan Kapre, Ehsan Rahiminasab, Karen Sachs, Charles Tapley Hoyt, Jeremy Zucker, Olga Vitek
Optimal adjustment sets for causal query estimation in partially observed biomolecular networks. Bioinform. 39 (Supplement-1) (2023)
Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori
Prediction and curation of missing biomedical identifier mappings with Biomappings. Bioinform. 39 (4) (2023)
Charles Tapley Hoyt, Barbara Zdrazil, Rajarshi Guha, Nina Jeliazkova, Karina Martínez-Mayorga, Eva Nittinger
Improving reproducibility and reusability in the Journal of Cheminformatics. J. Cheminformatics 15 (1) (2023)
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, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook E. Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
An Open-Source Knowledge Graph Ecosystem for the Life Sciences. CoRR (2023)
Benedek Rozemberczki, Charles Tapley Hoyt, Anna Gogleva, Piotr Grabowski, Klas Karis, Andrej Lamov, Andriy Nikolov, Sebastian Nilsson, Michaël Ughetto, Yu Wang, Tyler Derr, Benjamin M. Gyori
ChemicalX: A Deep Learning Library for Drug Pair Scoring. CoRR (2022)
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, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. CoRR (2022)
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 Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022 (2022) (2022)
Benedek Rozemberczki, Charles Tapley Hoyt, Anna Gogleva, Piotr Grabowski, Klas Karis, Andrej Lamov, Andriy Nikolov, Sebastian Nilsson, Michaël Ughetto, Yu Wang, Tyler Derr, Benjamin M. Gyori
ChemicalX: A Deep Learning Library for Drug Pair Scoring. KDD (2022)
Mikhail Galkin, Max Berrendorf, Charles Tapley Hoyt
An Open Challenge for Inductive Link Prediction on Knowledge Graphs. CoRR (2022)
Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue, Mikhail Galkin, Sahand Sharifzadeh, Asja Fischer, Volker Tresp, Jens Lehmann
Bringing Light Into the Dark: A Large-Scale Evaluation of Knowledge Graph Embedding Models Under a Unified Framework. IEEE Trans. Pattern Anal. Mach. Intell. 44 (12) (2022)
Ozlem Muslu, Charles Tapley Hoyt, Mauricio Lacerda, Martin Hofmann-Apitius, Holger Fröhlich
GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Nicolas Matentzoglu, Joe E. Flack, John Graybeal, Nomi L. Harris, Harshad B. Hegde, Charles Tapley Hoyt, Hyeongsik Kim, Sabrina Toro, Nicole A. Vasilevsky, Christopher J. Mungall
A simple standard for ontological mappings 2022: updates of data model and outlook. OM@ISWC (2022)
Helena Balabin, Charles Tapley Hoyt, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs. SWAT4HCLS (2022)
Charles Tapley Hoyt, Max Berrendorf, Mikhail Galkin, Volker Tresp, Benjamin M. Gyori
A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs. CoRR (2022)
Benjamin M. Gyori, Charles Tapley Hoyt
PyBioPAX: biological pathway exchange in Python. J. Open Source Softw. 7 (71) (2022)
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, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database J. Biol. Databases Curation 2022 (2022) (2022)
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
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. Bioinform. 38 (6) (2022)
Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Andreas Bender, Charles Tapley Hoyt, William L. Hamilton
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective. Briefings Bioinform. 23 (6) (2022)
Jeremy Zucker, Kaushal Paneri, Sara Mohammad Taheri, Somya Bhargava, Pallavi Kolambkar, Craig Bakker, Jeremy Teuton, Charles Tapley Hoyt, Kristie Oxford, Robert Osazuwa Ness, Olga Vitek
Leveraging Structured Biological Knowledge for Counterfactual Inference: a Case Study of Viral Pathogenesis. CoRR (2021)
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 Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR (2021)
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, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36 (24) (2021)
Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
The role of metadata in reproducible computational research. Patterns 2 (9) (2021)
Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue, Sahand Sharifzadeh, Volker Tresp, Jens Lehmann
PyKEEN 1.0: A Python Library for Training and Evaluating Knowledge Graph Embeddings. J. Mach. Learn. Res. 22 (2021)
Moritz Wolter, Felix Blanke, Charles Tapley Hoyt, Jochen Garcke
Wavelet-Packet Powered Deepfake Image Detection. CoRR (2021)
Vinay Srinivas Bharadhwaj, Mehdi Ali, Colin Birkenbihl, Sarah Mubeen, Jens Lehmann, Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández
CLEP: a hybrid data- and knowledge-driven framework for generating patient representations. Bioinform. 37 (19) (2021)
Jeremy Zucker, Kaushal Paneri, Sara Mohammad Taheri, Somya Bhargava, Pallavi Kolambkar, Craig Bakker, Jeremy Teuton, Charles Tapley Hoyt, Kristie Oxford, Robert Osazuwa Ness, Olga Vitek
Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis. IEEE Trans. Big Data 7 (1) (2021)
Russell J. Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir P. Gerdt, Dima Grigoriev, Charles Tapley Hoyt, Marek Kosta, Ovidiu Radulescu, Thomas Sturm, Andreas Weber
Identifying the parametric occurrence of multiple steady states for some biological networks. J. Symb. Comput. 98 (2020)
Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Stian Soiland-Reyes, Karthik Ram, Jane Greenberg
The role of metadata in reproducible computational research. CoRR (2020)
Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue, Mikhail Galkin, Sahand Sharifzadeh, Asja Fischer, Volker Tresp, Jens Lehmann
Bringing Light Into the Dark: A Large-scale Evaluation of Knowledge Graph Embedding Models Under a Unified Framework. CoRR (2020)
Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue, Sahand Sharifzadeh, Volker Tresp, Jens Lehmann
PyKEEN 1.0: A Python Library for Training and Evaluating Knowledge Graph Embeddings. CoRR (2020)
Mehdi Ali, Hajira Jabeen, Charles Tapley Hoyt, Jens Lehmann
The KEEN Universe: An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability. CoRR (2020)
Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt, Martin Hofmann-Apitius
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. BMC Bioinform. 21 (1) (2020)
Eduardo Brito, Bogdan Georgiev, Daniel Domingo-Fernández, Charles Tapley Hoyt, Christian Bauckhage
RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Rational Kernels. LWDA (2019)
Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt, Martin Hofmann-Apitius
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. BMC Bioinform. 20 (1) (2019)
Russell J. Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir P. Gerdt, Dima Grigoriev, Charles Tapley Hoyt, Marek Kosta, Ovidiu Radulescu, Thomas Sturm, Andreas Weber
Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks. CoRR (2019)
Charles Tapley Hoyt, Daniel Domingo-Fernández, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John A. Bachman, Benjamin M. Gyori, Patrick Greene, Martin Hofmann-Apitius
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database J. Biol. Databases Curation 2019 (2019)
Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann, Hajira Jabeen
BioKEEN: a library for learning and evaluating biological knowledge graph embeddings. Bioinform. 35 (18) (2019)
Mehdi Ali, Hajira Jabeen, Charles Tapley Hoyt, Jens Lehmann
The KEEN Universe - An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability. ISWC (2) (2019)
Mehdi Ali, Charles Tapley Hoyt, Daniel Domingo-Fernández, Jens Lehmann
Predicting Missing Links Using PyKEEN. ISWC (Satellites) (2019)
Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius
PathMe: merging and exploring mechanistic pathway knowledge. BMC Bioinform. 20 (1) (2019)
Michaela Gündel, Charles Tapley Hoyt, Martin Hofmann-Apitius
BEL2ABM: agent-based simulation of static models in Biological Expression Language. Bioinform. 34 (13) (2018)
Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database J. Biol. Databases Curation 2018 (2018)
Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig, Martin Hofmann-Apitius
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities. Database J. Biol. Databases Curation 2018 (2018)
Charles Tapley Hoyt, Andrej Konotopez, Christian Ebeling
PyBEL: a computational framework for Biological Expression Language. Bioinform. 34 (4) (2018)
Russell J. Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir P. Gerdt, Dima Grigoriev, Charles Tapley Hoyt, Marek Kosta, Ovidiu Radulescu, Thomas Sturm, Andreas Weber
A Case Study on the Parametric Occurrence of Multiple Steady States. ISSAC (2017)
Russell J. Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir P. Gerdt, Dima Grigoriev, Charles Tapley Hoyt, Marek Kosta, Ovidiu Radulescu, Thomas Sturm, Andreas Weber
A Case Study on the Parametric Occurrence of Multiple Steady States. CoRR (2017)