Benjamin M. Gyori

According to our database, Benjamin M. Gyori authored at least 23 papers between 2013 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Prediction and curation of missing biomedical identifier mappings with Biomappings.

Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori

Bioinform., April, 2023

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.

Rudolf T. Pillich, Jing Chen, Christopher Churas, Dylan Fong, Benjamin M. Gyori, Trey Ideker, Klas Karis, Sophie N. Liu, Keiichiro Ono, Alexander R. Pico, Dexter Pratt

Bioinform., March, 2023

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, Huanyu Li, James A. McLaughlin, Cássia Trojahn, Nicole A. Vasilevsky, Christopher J. Mungall

Proceedings of the 18th International Workshop on Ontology Matching co-located with the 22nd International Semantic Web Conference (ISWC 2023), 2023

2022

PyBioPAX: biological pathway exchange in Python.

Benjamin M. Gyori, Charles Tapley Hoyt

J. Open Source Softw., 2022

A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs.

Charles Tapley Hoyt, Max Berrendorf, Mikhail Galkin, Volker Tresp, Benjamin M. Gyori

CoRR, 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

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 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

Database J. Biol. Databases Curation, 2022

A roadmap for the functional annotation of protein families: a community perspective.

Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu

Database J. Biol. Databases Curation, 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

Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022

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, Tyler Derr, Benjamin M. Gyori

Proceedings of the KDD '22: The 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Washington, DC, USA, August 14, 2022

2020

Robustness and parameter geography in post-translational modification systems.

Kee-Myoung Nam, Benjamin M. Gyori, Silviana V. Amethyst, Daniel J. Bates, Jeremy Gunawardena

PLoS Comput. Biol., 2020

Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature.

Albert Steppi, Benjamin M. Gyori, John A. Bachman

J. Open Source Softw., 2020

2019

Statistical Model Checking-Based Analysis of Biological Networks.

Bing Liu, Benjamin M. Gyori, P. S. Thiagarajan

Proceedings of the Automated Reasoning for Systems Biology and Medicine, 2019

INDRA-IPM: interactive pathway modeling using natural language with automated assembly.

Petar V. Todorov, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger

Bioinform., 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, Martin Hofmann-Apitius

Database J. Biol. Databases Curation, 2019

Eidos, INDRA, & Delphi: From Free Text to Executable Causal Models.

Rebecca Sharp, Adarsh Pyarelal, Benjamin M. Gyori, Keith Alcock, Egoitz Laparra, Marco Antonio Valenzuela-Escárcega, Ajay Nagesh, Vikas Yadav, John A. Bachman, Zheng Tang, Heather C. Lent, Fan Luo, Mithun Paul, Steven Bethard, Kobus Barnard, Clayton T. Morrison, Mihai Surdeanu

Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2019

2018

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

John A. Bachman, Benjamin M. Gyori, Peter K. Sorger

BMC Bioinform., 2018

2016

Hypothesis testing for Markov chain Monte Carlo.

Benjamin M. Gyori, Daniel Paulin

Stat. Comput., 2016

2015

Simulation-Guided Parameter Synthesis for Chance-Constrained Optimization of Control Systems.

Yan Zhang, Sriram Sankaranarayanan, Benjamin M. Gyori

Proceedings of the IEEE/ACM International Conference on Computer-Aided Design, 2015

Parallelized Parameter Estimation of Biological Pathway Models.

R. Ramanathan, Yan Zhang, Jun Zhou, Benjamin M. Gyori, Weng-Fai Wong, P. S. Thiagarajan

Proceedings of the Hybrid Systems Biology - Fourth International Workshop, 2015

Approximate Probabilistic Verification of Hybrid Systems.

Benjamin M. Gyori, Bing Liu, Soumya Paul, R. Ramanathan, P. S. Thiagarajan

Proceedings of the Hybrid Systems Biology - Fourth International Workshop, 2015

2014

Probabilistic verification of partially observable dynamical systems.

Benjamin M. Gyori, Daniel Paulin, Sucheendra K. Palaniappan

CoRR, 2014

2013

Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models.

Sucheendra K. Palaniappan, Benjamin M. Gyori, Bing Liu, David Hsu, P. S. Thiagarajan

Proceedings of the Computational Methods in Systems Biology, 2013