Benjamin M. Gyori

Publication Activity (10 Years)

Years Active: 2013-2023
Publications (10 Years): 22

Top Topics

Protein Families

Markov Chain Monte Carlo

Medical Literature

Top Venues

Database J. Biol. Databases Curation

J. Open Source Softw.

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)
Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori
Prediction and curation of missing biomedical identifier mappings with Biomappings. Bioinform. 39 (4) (2023)
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
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinform. 39 (3) (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, 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)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan 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 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
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022 (2022) (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)
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)
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)
Albert Steppi, Benjamin M. Gyori, John A. Bachman
Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. J. Open Source Softw. 5 (45) (2020)
Kee-Myoung Nam, Benjamin M. Gyori, Silviana V. Amethyst, Daniel J. Bates, Jeremy Gunawardena
Robustness and parameter geography in post-translational modification systems. PLoS Comput. Biol. 16 (5) (2020)
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)
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
Eidos, INDRA, & Delphi: From Free Text to Executable Causal Models. NAACL-HLT (Demonstrations) (2019)
Petar V. Todorov, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger
INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinform. 35 (21) (2019)
John A. Bachman, Benjamin M. Gyori, Peter K. Sorger
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. BMC Bioinform. 19 (1) (2018)
Benjamin M. Gyori, Daniel Paulin
Hypothesis testing for Markov chain Monte Carlo. Stat. Comput. 26 (6) (2016)
Yan Zhang, Sriram Sankaranarayanan, Benjamin M. Gyori
Simulation-Guided Parameter Synthesis for Chance-Constrained Optimization of Control Systems. ICCAD (2015)
R. Ramanathan, Yan Zhang, Jun Zhou, Benjamin M. Gyori, Weng-Fai Wong, P. S. Thiagarajan
Parallelized Parameter Estimation of Biological Pathway Models. HSB (2015)
Benjamin M. Gyori, Bing Liu, Soumya Paul, R. Ramanathan, P. S. Thiagarajan
Approximate Probabilistic Verification of Hybrid Systems. HSB (2015)
Benjamin M. Gyori, Daniel Paulin, Sucheendra K. Palaniappan
Probabilistic verification of partially observable dynamical systems. CoRR (2014)
Benjamin M. Gyori, Bing Liu, Soumya Paul, R. Ramanathan, P. S. Thiagarajan
Approximate probabilistic verification of hybrid systems. CoRR (2014)
Sucheendra K. Palaniappan, Benjamin M. Gyori, Bing Liu, David Hsu, P. S. Thiagarajan
Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models. CMSB (2013)