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Benjamin M. Gyori
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2020 – today
- 2023
- [j12]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) - [j11]Charles Tapley Hoyt
Prediction and curation of missing biomedical identifier mappings with Biomappings. Bioinform. 39(4) (2023) - [c8]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
A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling. OM@ISWC 2023: 73-78 - 2022
- [j10]Valérie de Crécy-Lagard
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022(2022) (2022) - [j9]Nicolas Matentzoglu
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022(2022) (2022) - [j8]Helena Balabin
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. Bioinform. 38(6): 1648-1656 (2022) - [j7]Benjamin M. Gyori
PyBioPAX: biological pathway exchange in Python. J. Open Source Softw. 7(71): 4136 (2022) - [c7]Benedek Rozemberczki, Charles Tapley Hoyt, Anna Gogleva, Piotr Grabowski, Klas Karis, Andrej Lamov, Andriy Nikolov, Sebastian Nilsson, Michaël Ughetto, Yu Wang, Tyler Derr
ChemicalX: A Deep Learning Library for Drug Pair Scoring. KDD 2022: 3819-3828 - [c6]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: 103-107 - [i5]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 abs/2202.05240 (2022) - [i4]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 abs/2203.07544 (2022) - 2021
- [i3]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 abs/2112.07051 (2021) - 2020
- [j6]Albert Steppi
Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. J. Open Source Softw. 5(45): 1708 (2020) - [j5]Kee-Myoung Nam
Robustness and parameter geography in post-translational modification systems. PLoS Comput. Biol. 16(5) (2020)
2010 – 2019
- 2019
- [j4]Charles Tapley Hoyt
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database J. Biol. Databases Curation 2019: baz068 (2019) - [j3]Petar V. Todorov
INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinform. 35(21): 4501-4503 (2019) - [c5]Rebecca Sharp, Adarsh Pyarelal, Benjamin M. Gyori, Keith Alcock
Eidos, INDRA, & Delphi: From Free Text to Executable Causal Models. NAACL-HLT (Demonstrations) 2019: 42-47 - [p1]Bing Liu
Statistical Model Checking-Based Analysis of Biological Networks. Automated Reasoning for Systems Biology and Medicine 2019: 63-92 - 2018
- [j2]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): 248:1-248:14 (2018) - 2016
- [j1]Benjamin M. Gyori
Hypothesis testing for Markov chain Monte Carlo. Stat. Comput. 26(6): 1281-1292 (2016) - 2015
- [c4]R. Ramanathan, Yan Zhang, Jun Zhou, Benjamin M. Gyori
Parallelized Parameter Estimation of Biological Pathway Models. HSB 2015: 37-57 - [c3]Benjamin M. Gyori
Approximate Probabilistic Verification of Hybrid Systems. HSB 2015: 96-116 - [c2]Yan Zhang, Sriram Sankaranarayanan, Benjamin M. Gyori
Simulation-Guided Parameter Synthesis for Chance-Constrained Optimization of Control Systems. ICCAD 2015: 208-215 - 2014
- [i2]Benjamin M. Gyori, Daniel Paulin, Sucheendra K. Palaniappan:
Probabilistic verification of partially observable dynamical systems. CoRR abs/1411.0976 (2014) - [i1]Benjamin M. Gyori, Bing Liu, Soumya Paul, R. Ramanathan, P. S. Thiagarajan:
Approximate probabilistic verification of hybrid systems. CoRR abs/1412.6953 (2014) - 2013
- [c1]Sucheendra K. Palaniappan
Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models. CMSB 2013: 120-134
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