Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Benjamin Gyori, Ph.D.

Title
Institution
Department
Address
Phone
Fax

Bibliographic
selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Jain A, Gyori BM, Hakim S, Bunga S, Taub DG, Ruiz-Cantero MC, Tong-Li C, Andrews N, Sorger PK, Woolf CJ. Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways. bioRxiv. 2023 Feb 03. PMID: 36778477; PMCID: PMC9915698.
    Citations:    
  2. Hoyt CT, Balk M, Callahan TJ, Domingo-Fernández D, Haendel MA, Hegde HB, Himmelstein DS, Karis K, Kunze J, Lubiana T, Matentzoglu N, McMurry J, Moxon S, Mungall CJ, Rutz A, Unni DR, Willighagen E, Winston D, Gyori BM. Unifying the identification of biomedical entities with the Bioregistry. Sci Data. 2022 11 19; 9(1):714. PMID: 36402838; PMCID: PMC9675740.
    Citations: 2     Fields:    
  3. de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford). 2022 08 12; 2022. PMID: 35961013; PMCID: PMC9374478.
    Citations: 3     Fields:    Translation:Cells
  4. Doherty LM, Mills CE, Boswell SA, Liu X, Hoyt CT, Gyori B, Buhrlage SJ, Sorger PK. Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. Elife. 2022 06 23; 11. PMID: 35737447; PMCID: PMC9225015.
    Citations: 1     Fields:    Translation:HumansCells
  5. Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde HB, Hoyt AL, Hoyt CT, Jiao D, Jiménez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ. A Simple Standard for Sharing Ontological Mappings (SSSOM). Database (Oxford). 2022 05 25; 2022. PMID: 35616100; PMCID: PMC9216545.
    Citations:    Fields:    
  6. Gyori BM, Hoyt CT, Steppi A. Gilda: biomedical entity text normalization with machine-learned disambiguation as a service. Bioinform Adv. 2022; 2(1):vbac034. PMID: 36699362; PMCID: PMC9710686.
    Citations:    
  7. Gyori BM, Hoyt CT. PyBioPAX: biological pathway exchange in Python. J Open Source Softw. 2022; 7(71). PMID: 36071952; PMCID: PMC9447860.
    Citations: 1     
  8. Balabin H, Hoyt CT, Birkenbihl C, Gyori BM, Bachman J, Kodamullil AT, Plöger PG, Hofmann-Apitius M, Domingo-Fernández D. STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. Bioinformatics. 2022 03 04; 38(6):1648-1656. PMID: 34986221; PMCID: PMC8896635.
    Citations: 1     Fields:    
  9. Scholten B, Simón LG, Krishnan S, Vermeulen R, Pronk A, Gyori BM, Bachman JA, Vlaanderen J, Stierum R. Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment. Environ Health Perspect. 2022 03; 130(3):37002. PMID: 35238605; PMCID: PMC8893280.
    Citations:    Fields:    Translation:Humans
  10. Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi J, Rodchenkov I, Babur Ö, Bachman JA, Gyori BM, Demir E, Bader GD, Sander C. Author-sourced capture of pathway knowledge in computable form using Biofactoid. Elife. 2021 12 03; 10. PMID: 34860157; PMCID: PMC8683078.
    Citations: 1     Fields:    
  11. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Dec; 17(12):e10851. PMID: 34939300; PMCID: PMC8696085.
    Citations:    Fields:    
  12. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 10; 17(10):e10387. PMID: 34664389; PMCID: PMC8524328.
    Citations: 11     Fields:    Translation:HumansCells
  13. Gyori BM, Venkatachalam G, Thiagarajan PS, Hsu D, Clement MV. Corrigendum to OpenComet: An automated tool for comet assay image analysis [Redox Biol. Volume 2, 2014, Pages 457-465]. Redox Biol. 2021 Apr; 40:101876. PMID: 33558181.
    Citations:    Fields:    
  14. Ietswaart R, Gyori BM, Bachman JA, Sorger PK, Churchman LS. GeneWalk identifies relevant gene functions for a biological context using network representation learning. Genome Biol. 2021 02 02; 22(1):55. PMID: 33526072.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  15. Nam KM, Gyori BM, Amethyst SV, Bates DJ, Gunawardena J. Robustness and parameter geography in post-translational modification systems. PLoS Comput Biol. 2020 05; 16(5):e1007573. PMID: 32365103; PMCID: PMC7224580.
    Citations: 3     Fields:    Translation:Cells
  16. Steppi A, Gyori BM, Bachman JA. Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. J Open Source Softw. 2020; 5(45). PMID: 32337477; PMCID: PMC7182313.
    Citations: 1     
  17. Todorov PV, Gyori BM, Bachman JA, Sorger PK. INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinformatics. 2019 11 01; 35(21):4501-4503. PMID: 31070726.
    Citations: 4     Fields:    
  18. Hoyt CT, Domingo-Fernández D, Aldisi R, Xu L, Kolpeja K, Spalek S, Wollert E, Bachman J, Gyori BM, Greene P, Hofmann-Apitius M. Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database (Oxford). 2019 01 01; 2019. PMID: 31225582; PMCID: PMC6587072.
    Citations: 6     Fields:    
  19. Bachman JA, Gyori BM, Sorger PK. FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. BMC Bioinformatics. 2018 06 28; 19(1):248. PMID: 29954318.
    Citations: 11     Fields:    Translation:Humans
  20. Sampattavanich S, Steiert B, Kramer BA, Gyori BM, Albeck JG, Sorger PK. Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases. Cell Syst. 2018 06 27; 6(6):664-678.e9. PMID: 29886111; PMCID: PMC6322215.
    Citations: 18     Fields:    Translation:HumansCells
  21. Gyori BM, Bachman JA, Subramanian K, Muhlich JL, Galescu L, Sorger PK. From word models to executable models of signaling networks using automated assembly. Mol Syst Biol. 2017 11 24; 13(11):954. PMID: 29175850.
    Citations: 43     Fields:    Translation:HumansCells
  22. Gyori BM, Venkatachalam G, Thiagarajan PS, Hsu D, Clement MV. OpenComet: an automated tool for comet assay image analysis. Redox Biol. 2014; 2:457-65. PMID: 24624335.
    Citations: 188     Fields:    Translation:AnimalsCells
Local representatives can answer questions about the Profiles website or help with editing a profile or issues with profile data. For assistance with this profile: HMS/HSDM faculty should contact contactcatalyst.harvard.edu. For faculty or fellow appointment updates and changes, please ask your appointing department to contact HMS. For fellow personal and demographic information, contact HMS Human Resources at human_resourceshms.harvard.edu. For faculty personal and demographic information, contact HMS Office for Faculty Affairs at facappthms.harvard.edu.
Gyori's Networks
Click the
Explore
buttons for more information and interactive visualizations!
Concepts (83)
Explore
_
Co-Authors (12)
Explore
_
Similar People (60)
Explore
_
Same Department 
Explore
_
© 2023 President and Fellows of Harvard College
Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.