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Scopus Author ID: 55892870500

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Employment (2)

Northeastern University: Boston, US

2023-08 to present
Employment
Source: Self-asserted source
Benjamin M. Gyori

Harvard Medical School: Boston, US

2023-07
Employment
Source: Self-asserted source
Benjamin M. Gyori

Works (34)

Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge

Nature Methods
2024-08 | Journal article
DOI: 10.1038/s41592-024-02324-4
Contributors: Benjamin M. Gyori; Olga Vitek
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Nociceptor-immune interactomes reveal insult-specific immune signatures of pain

Nature Immunology
2024-07 | Journal article
DOI: 10.1038/s41590-024-01857-2
Contributors: Aakanksha Jain; Benjamin M. Gyori; Sara Hakim; Ashish Jain; Liang Sun; Veselina Petrova; Shamsuddin A. Bhuiyan; Shannon Zhen; Qing Wang; Riki Kawaguchi et al.
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The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources

Scientific Data
2024-05-29 | Journal article
DOI: 10.1038/s41597-024-03406-w
Contributors: Charles Tapley Hoyt; Benjamin M. Gyori
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Crossref

Automated assembly of molecular mechanisms at scale from text mining and curated databases

Molecular Systems Biology
2023-05-09 | Journal article
DOI: 10.15252/msb.202211325
Contributors: John A Bachman; Benjamin M Gyori; Peter K Sorger
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Crossref

Prediction and curation of missing biomedical identifier mappings with Biomappings

Bioinformatics
2023-04-03 | Journal article
DOI: 10.1093/bioinformatics/btad130
Contributors: Charles Tapley Hoyt; Amelia L Hoyt; Benjamin M Gyori; Peter Robinson
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Crossref

Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways

2023-02-03 | Preprint
DOI: 10.1101/2023.02.01.526526
Contributors: Aakanksha Jain; Benjamin M. Gyori; Sara Hakim; Samuel Bunga; Daniel G Taub; Mari Carmen Ruiz-Cantero; Candace Tong-Li; Nicholas Andrews; Peter K Sorger; Clifford J Woolf
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Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings

2022-12-02 | Preprint
DOI: 10.1101/2022.11.29.518386
Contributors: Charles Tapley Hoyt; Amelia L. Hoyt; Benjamin M. Gyori
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Crossref

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

2022-10-25 | Preprint
DOI: 10.1101/2022.10.24.513552
Contributors: RT Pillich; J Chen; C Churas; D Fong; T Ideker; SN Liu; BM Gyori; K Karis; K Ono; A Pico et al.
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Crossref

Automated assembly of molecular mechanisms at scale from text mining and curated databases

2022-08-31 | Preprint
DOI: 10.1101/2022.08.30.505688
Contributors: John A. Bachman; Benjamin M. Gyori; Peter K. Sorger
Source: check_circle
Crossref

Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes

eLife
2022-06-23 | Journal article
DOI: 10.7554/eLife.72879
Contributors: Laura M Doherty; Caitlin E Mills; Sarah A Boswell; Xiaoxi Liu; Charles Tapley Hoyt; Benjamin Gyori; Sara J Buhrlage; Peter K Sorger
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Crossref

Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment

Environmental Health Perspectives
2022-03 | Journal article
DOI: 10.1289/EHP9112
Contributors: Bernice Scholten; Laura Guerrero Simón; Shaji Krishnan; Roel Vermeulen; Anjoeka Pronk; Benjamin M. Gyori; John A. Bachman; Jelle Vlaanderen; Rob Stierum
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Crossref

PyBioPAX: biological pathway exchange in Python

Journal of Open Source Software
2022-03-11 | Journal article
DOI: 10.21105/joss.04136
Contributors: Benjamin M. Gyori; Charles Tapley Hoyt
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Crossref

STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs

Bioinformatics
2022-03-04 | Journal article
DOI: 10.1093/bioinformatics/btac001
Contributors: Helena Balabin; Charles Tapley Hoyt; Colin Birkenbihl; Benjamin M Gyori; John Bachman; Alpha Tom Kodamullil; Paul G Plöger; Martin Hofmann-Apitius; Daniel Domingo-Fernández; Jonathan Wren
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Crossref

Gilda: biomedical entity text normalization with machine-learned disambiguation as a service

Bioinformatics Advances
2022-01-10 | Journal article
DOI: 10.1093/bioadv/vbac034
Contributors: Benjamin M Gyori; Charles Tapley Hoyt; Albert Steppi; Cecilia Arighi
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Crossref

From knowledge to models: Automated modeling in systems and synthetic biology

Current Opinion in Systems Biology
2021-12 | Journal article
DOI: 10.1016/j.coisb.2021.100362
Contributors: Benjamin M. Gyori; John A. Bachman
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Crossref

Gilda: biomedical entity text normalization with machine-learned disambiguation as a service

2021-09-11 | Other
DOI: 10.1101/2021.09.10.459803
Contributors: Benjamin M. Gyori; Charles Tapley Hoyt; Albert Steppi
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Crossref

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

2021-08-18 | Other
DOI: 10.1101/2021.08.17.456616
Contributors: Helena Balabin; Charles Tapley Hoyt; Colin Birkenbihl; Benjamin M Gyori; John Bachman; Alpha Tom Kodamullil; Paul G Plöger; Martin Hofmann-Apitius; Daniel Domingo-Fernández
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Crossref

Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes

2021-08-09 | Other
DOI: 10.1101/2021.08.06.455458
Contributors: Laura M. Doherty; Caitlin E. Mills; Sarah A. Boswell; Xiaoxi Liu; Charles Tapley Hoyt; Benjamin M. Gyori; Sara J. Buhrlage; Peter K. Sorger
Source: check_circle
Crossref

Robustness and parameter geography in post-translational modification systems

PLOS Computational Biology
2020-05-04 | Journal article
DOI: 10.1371/journal.pcbi.1007573
Contributors: Kee-Myoung Nam; Pedro Mendes; Benjamin M. Gyori; Silviana V. Amethyst; Daniel J. Bates; Jeremy Gunawardena
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Crossref

A resource for exploring the understudied human kinome for research and therapeutic opportunities

2020-04-02 | Preprint
DOI: 10.1101/2020.04.02.022277
Contributors: Nienke Moret; Changchang Liu; Benjamin M. Gyori; John A. Bachman; Albert Steppi; Clemens Hug; Rahil Taujale; Liang-Chin Huang; Matthew E. Berginski; Shawn M. Gomez et al.
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Crossref

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

Journal of Open Source Software
2020-01-16 | Journal article
DOI: 10.21105/joss.01708
Contributors: Albert Steppi; Benjamin Gyori; John Bachman
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Crossref

Robustness and parameter geography in post-translational modification systems

2019-12-02 | Other
DOI: 10.1101/862003
Contributors: Kee-Myoung Nam; Benjamin M. Gyori; Silviana V. Amethyst; Daniel J. Bates; Jeremy Gunawardena
Source: check_circle
Crossref

Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining

2019-10-29 | Preprint
DOI: 10.1101/822668
Contributors: John A. Bachman; Peter K. Sorger; Benjamin M. Gyori
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Crossref

Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language

2019-01-31 | Other
DOI: 10.1101/536409
Contributors: Charles Tapley Hoyt; Daniel Domingo-Fernández; Rana Aldisi; Lingling Xu; Kristian Kolpeja; Sandra Spalek; Esther Wollert; John Bachman; Benjamin M. Gyori; Patrick Greene et al.
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Crossref

Re-curation and rational enrichment of knowledge graphs in Biological Expression Language

Database
2019-01-01 | Journal article
DOI: 10.1093/database/baz068
Contributors: Charles Tapley Hoyt; Daniel Domingo-Fernández; Rana Aldisi; Lingling Xu; Kristian Kolpeja; Sandra Spalek; Esther Wollert; John Bachman; Benjamin M Gyori; Patrick Greene et al.
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From word models to executable models of signaling networks using automated assembly

Molecular Systems Biology
2017-11 | Journal article
DOI: 10.15252/msb.20177651
Contributors: Benjamin M Gyori; John A Bachman; Kartik Subramanian; Jeremy L Muhlich; Lucian Galescu; Peter K Sorger
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Crossref

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

2017-11-27 | Other
DOI: 10.1101/225698
Contributors: John A Bachman; Benjamin M Gyori; Peter K Sorger
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Crossref

From word models to executable models of signaling networks using automated assembly

2017-03-23 | Preprint
DOI: 10.1101/119834
Contributors: Benjamin M Gyori; John A Bachman; Kartik Subramanian; Jeremy L Muhlich; Lucian Galescu; Peter K Sorger
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Crossref

Approximate Probabilistic Verification of Hybrid Systems

Hybrid Systems Biology
2015 | Other
DOI: 10.1007/978-3-319-26916-0_6
Contributors: Benjamin M. Gyori; Bing Liu; Soumya Paul; R. Ramanathan; P. S. Thiagarajan
Source: Self-asserted source
Benjamin M. Gyori via Crossref Metadata Search

Parallelized Parameter Estimation of Biological Pathway Models

Hybrid Systems Biology
2015 | Other
DOI: 10.1007/978-3-319-26916-0_3
Contributors: R. Ramanathan; Yan Zhang; Jun Zhou; Benjamin M. Gyori; Weng-Fai Wong; P. S. Thiagarajan
Source: Self-asserted source
Benjamin M. Gyori via Crossref Metadata Search

Simulation-guided parameter synthesis for chance-constrained optimization of control systems

2015 IEEE/ACM International Conference on Computer-Aided Design (ICCAD)
2015-11 | Conference paper
DOI: 10.1109/iccad.2015.7372572
Contributors: Yan Zhang; Sriram Sankaranarayanan; Benjamin M. Gyori
Source: Self-asserted source
Benjamin M. Gyori via Crossref Metadata Search

Hypothesis testing for Markov chain Monte Carlo

Stat Comput
2015-07-10 | Journal article
DOI: 10.1007/s11222-015-9594-1
Contributors: Benjamin M. Gyori; Daniel Paulin
Source: Self-asserted source
Benjamin M. Gyori via Crossref Metadata Search

OpenComet: An automated tool for comet assay image analysis

Redox Biology
2014 | Journal article
DOI: 10.1016/j.redox.2013.12.020
Contributors: Benjamin M. Gyori; Gireedhar Venkatachalam; P.S. Thiagarajan; David Hsu; Marie-Veronique Clement
Source: Self-asserted source
Benjamin M. Gyori via Crossref Metadata Search

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

Computational Methods in Systems Biology
2013 | Other
DOI: 10.1007/978-3-642-40708-6_10
Contributors: Sucheendra K. Palaniappan; Benjamin M. Gyori; Bing Liu; David Hsu; P. S. Thiagarajan
Source: Self-asserted source
Benjamin M. Gyori via Crossref Metadata Search
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