Benjamin M Gyori (Benjamin Gyori)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 24

Top Topics

Postoperative Pain

Top Venues

Nature immunology

Scientific data

Molecular systems biology

This page only lists publications with an associated author ORCID identifier.

Publications

Aakanksha Jain, Benjamin M Gyori, Sara Hakim, Ashish Jain, Liang Sun, Veselina Petrova, Shamsuddin A Bhuiyan, Shannon Zhen, Qing Wang, Riki Kawaguchi, Samuel Bunga, Daniel G Taub, M Carmen Ruiz-Cantero, Candace Tong-Li, Nicholas Andrews, Masakazu Kotoda, William Renthal, Peter Karl Sorger, Clifford J Woolf
Nociceptor-immune interactomes reveal insult-specific immune signatures of pain. Nature immunology 25 (7) (2024)
Aakanksha Jain, Benjamin M Gyori, Sara Hakim, Ashish Jain, Liang Sun, Veselina Petrova, Shamsuddin A Bhuiyan, Shannon Zhen, Qing Wang, Riki Kawaguchi, Samuel Bunga, Daniel G Taub, M Carmen Ruiz-Cantero, Candace Tong-Li, Nicholas Andrews, Masakazu Kotoda, William Renthal, Peter Karl Sorger, Clifford J Woolf
Nociceptor-immune interactomes reveal insult-specific immune signatures of pain. Nature immunology 25 (7) (2024)
Aakanksha Jain, Benjamin M Gyori, Sara Hakim, Ashish Jain, Liang Sun, Veselina Petrova, Shamsuddin A Bhuiyan, Shannon Zhen, Qing Wang, Riki Kawaguchi, Samuel Bunga, Daniel G Taub, M Carmen Ruiz-Cantero, Candace Tong-Li, Nicholas Andrews, Masakazu Kotoda, William Renthal, Peter Karl Sorger, Clifford J Woolf
Nociceptor-immune interactomes reveal insult-specific immune signatures of pain. Nature immunology 25 (7) (2024)
Charles Tapley Hoyt, Benjamin M Gyori
The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources. Scientific data 11 (1) (2024)
Benjamin M Gyori, Olga Vitek
Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge. Nature methods 21 (8) (2024)
Aakanksha Jain, Benjamin M Gyori, Sara Hakim, Ashish Jain, Liang Sun, Veselina Petrova, Shamsuddin A Bhuiyan, Shannon Zhen, Qing Wang, Riki Kawaguchi, Samuel Bunga, Daniel G Taub, M Carmen Ruiz-Cantero, Candace Tong-Li, Nicholas Andrews, Masakazu Kotoda, William Renthal, Peter Karl Sorger, Clifford J Woolf
Nociceptor-immune interactomes reveal insult-specific immune signatures of pain. Nature immunology 25 (7) (2024)
Aakanksha Jain, Benjamin M Gyori, Sara Hakim, Ashish Jain, Liang Sun, Veselina Petrova, Shamsuddin A Bhuiyan, Shannon Zhen, Qing Wang, Riki Kawaguchi, Samuel Bunga, Daniel G Taub, M Carmen Ruiz-Cantero, Candace Tong-Li, Nicholas Andrews, Masakazu Kotoda, William Renthal, Peter Karl Sorger, Clifford J Woolf
Nociceptor-immune interactomes reveal insult-specific immune signatures of pain. Nature immunology (2024)
Benjamin M Gyori, Olga Vitek
Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge. Nature methods 21 (8) (2024)
Charles Tapley Hoyt, Benjamin M Gyori
The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources. Scientific data 11 (1) (2024)
Aakanksha Jain, Benjamin M Gyori, Sara Hakim, Samuel Bunga, Daniel G Taub, Mari Carmen Ruiz-Cantero, Candace Tong-Li, Nicholas Andrews, Peter Karl Sorger, Clifford J Woolf
Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways. bioRxiv : the preprint server for biology (2023)
John A Bachman, Benjamin M Gyori, Peter Karl Sorger
Automated assembly of molecular mechanisms at scale from text mining and curated databases. Molecular systems biology (2023)
Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar, Vincent J Carey, Pornpimol Charoentong, Katharina Danhauser, Tunca Doğan, Johann Dreo, Ian Dunham, Elias Farr, Adrià Fernandez-Torras, Benjamin M Gyori, Michael Hartung, Charles Tapley Hoyt, Christoph Klein, Tamas Korcsmaros, Andreas Maier, Matthias Mann, David Ochoa, Elena Pareja-Lorente, Ferdinand Popp, Martin Preusse, Niklas Probul, Benno Schwikowski, Bünyamin Sen, Maximillian T Strauss, Denes Turei, Erva Ulusoy, Dagmar Waltemath, Judith A H Wodke, Julio Saez-Rodriguez
Democratizing knowledge representation with BioCypher. Nature biotechnology (2023)
Michael A Gargano, Nicolas A Matentzoglu, Ben Coleman, Eunice B Addo-Lartey, Anna V Anagnostopoulos, Joel Anderton, Paul Avillach, Anita M Bagley, Eduard Bakštein, James P Balhoff, Gareth Baynam, Susan M Bello, Michael Berk, Holli Bertram, Somer L Bishop, Hannah Blau, David F Bodenstein, Pablo Botas, Kaan Boztug, Jolana Čady, Tiffany J Callahan, Rhiannon Cameron, Seth J Carbon, Francisco Castellanos, J Harry Caufield, Lauren E Chan, Christopher G Chute, Jaime Cruz-Rojo, Noemi Dahan-Oliel, Jon Robert Davids, Maud De Dieuleveult, Vinicius de Souza, Bert B A de Vries, Esther de Vries, J Raymond DePaulo, Beata Derfalvi, Ferdinand Dhombres, Claudia Diaz-Byrd, Alexander J M Dingemans, Bruno Donadille, Michael Henri Duyzend, Reem Elfeky, Shahim Essaid, Carolina Fabrizzi, Giovanna Fico, Helen V Firth, Yun Freudenberg-Hua, Janice M Fullerton, Davera L Gabriel, Kimberley C Gilmour, Jessica L Giordano, Fernando S Goes, Rachel Gore Moses, Ian Green, Matthias Griese, Tudor Groza, Weihong Gu, Julia Pazmandi, Benjamin M Gyori, Ada Hamosh, Marc Hanauer, Kateřina Hanušová, Yongqun Oliver He, Harshad Hegde, Ingo Helbig, Kateřina Řehořová, Charles Tapley Hoyt, Shangzhi Huang, Eric Hurwitz, Julius O B Jacobsen, Xiaofeng Jiang, Lisa Joseph, Kamyar Keramatian, Bryan King, Katrin Knoflach, David A Koolen, Megan L Kraus, Carlo Kroll, Maaike A A Kusters, Markus S Ladewig, David Lagorce, Meng-Chuan Lai, Pablo Lapunzina, Bryan Laraway, David Lewis-Smith, Xiarong Li, Caterina Lucano, Marzieh Majd, Mary L Marazita, Victor Martínez-González, Toby H McHenry, Melvin G McInnis, Julie A McMurry, Michaela Zelinová, Caitlin E Millett, Philip B Mitchell, Veronika Moslerová, Kenji Narutomi, Shahrzad Nematollahi, Julián Nevado, Andrew A Nierenberg, Nikola Novák Čajbiková, Michael C Neale, Soichi Ogishima, Daniel Olson, Abigail Ortiz, Harry Pachajoa, Guiomar Perez de Nanclares, Amy T Peters, Timothy Putman, Christina K Rapp, Ana Rath, Justin T Reese, Lauren Rekerle, Angharad M Roberts, Suzy Roy, Stephan J Sanders, Catharina Schuetz, Eva C Schulte, Thomas G Schulze, Martin Schwarz, Katie Scott, Dominik Seelow, Berthold Seitz, Yiping Shen, Morgan N Similuk, Eric S Simon, Balwinder Singh, Damian Smedley, Cynthia L Smith, Jake T Smolinsky, Sarah H Sperry, Elizabeth Stafford, Ray Stefancsik, Robin Steinhaus, Rebecca Strawbridge, Jagadish Chandrabose Sundaramurthi, Polina Talapova, Jair Antonio Tenorio Castaño, Pavel Tesner, Rhys Huw Thomas, Audrey Thurm, Marek Turnovec, Marielle E van Gijn, Nicole A Vasilevsky, Markéta Vlčková, Anita Walden, Kai Wang, Ronald J Wapner, James Simon Ware, Addo A Wiafe, Samuel A Wiafe, Lisa D Wiggins, Andrew E Williams, Chen Wu, Margot Julia Wyrwoll, Hui Xiong, Nefize Yalin, Yasunori Yamamoto, Lakshmi N Yatham, Anastasia K Yocum, Allan H Young, Zafer Yüksel, Peter P Zandi, Andreas Zankl, Ignacio Zarante, Miroslav Zvolský, Sabrina Toro, Leigh C Carmody, Nomi L Harris, Monica C Munoz-Torres, Daniel Danis, Christopher John Mungall, Sebastian Koehler, Melissa A Haendel, Peter Nick Robinson
The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic acids research (2023)
Benjamin M Gyori, Charles Tapley Hoyt, Albert Steppi
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service. Bioinformatics advances 2 (1) (2022)
Benjamin M Gyori, Charles Tapley Hoyt, Albert Steppi
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service. Bioinformatics advances 2 (1) (2022)
Bernice Scholten, Laura Guerrero Simón, Shaji Krishnan, Roel C H Vermeulen, Anjoeka Pronk, Benjamin M Gyori, John A Bachman, Jelle Vlaanderen, Rob Stierum
Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment. Environmental health perspectives 130 (3) (2022)
Laura M Doherty, Caitlin E Mills, Sarah A Boswell, Xiaoxi Liu, Charles Tapley Hoyt, Benjamin M Gyori, Sara J Buhrlage, Peter Karl Sorger
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. eLife 11 (2022)
Charles Tapley Hoyt, Meghan A Balk, Tiffany J Callahan, Daniel Domingo-Fernández, Melissa A Haendel, Harshad B Hegde, Daniel Scott Himmelstein, Klas Karis, John Kunze, Tiago Lubiana, Nicolas Matentzoglu, Julie McMurry, Sierra Moxon, Christopher J Mungall, Adriano Rutz, Deepak R Unni, Egon L Wilighagen, Donald Winston, Benjamin M Gyori
Unifying the identification of biomedical entities with the Bioregistry. Scientific data 9 (1) (2022)
Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T A Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa A Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, 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 Putman, Núria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne E Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H Wagner, Christopher John Mungall
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database : the journal of biological databases and curation 2022 (2022)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia Noemi Arighi, Jill Babor, Alex Bateman, Ian K 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 Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria-Jesus Martin, Claire McWhite, Gaurav D Moghe, Paul Monaghan, Anne Morgat, Christopher John Mungall, Darren A Natale, William C Nelson, Seán O'Donoghue, Christine Orengo, Katherine H O'Toole, Predrag Radivojac, Colbie Reed, Richard J Roberts, Dmitri Rodionov, Irina A Rodionova, Jeffrey D Rudolf, Lana Saleh, Gloria M Sheynkman, Francoise Thibaud-Nissen, Paul D Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter R Weigele, Valerie Wood, Elisha M Wood-Charlson, Jin Xu
A roadmap for the functional annotation of protein families: a community perspective. Database : the journal of biological databases and curation 2022 (2022)
Jeffrey V Wong, Max Franz, Metin Can Siper, Dylan Fong, Funda Durupinar, Christian Dallago, Augustin Luna, John M Giorgi, Igor Rodchenkov, Ozgun Babur, John A Bachman, Benjamin M Gyori, Emek Demir, Gary D Baider, Chris Sander
Author-sourced capture of pathway knowledge in computable form using Biofactoid. eLife 10 (2021)
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert D Phair, Aurelio Orta Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce-de-Leon, Akira Funahashi, Yusuke Hiki, Noriko F Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy D Zucker, Kristie L Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan L M Coort, Lars M T Eijssen, Friederike Ehrhart, Devasahayam Arokiar Balaya Rex, Denise N Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Mohamed Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata P Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Dénes Türei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Tomas Helikar, Bhanwar Lal Puniya, Dezső Módos, Agatha Treveil, Márton Ölbei, Bertrand de Meulder, Stephane Ballereau, Aurélien J F Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Wilighagen, Alexander R Pico, Chris T A Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquín Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, null null
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular systems biology 17 (10) (2021)
Kee-Myoung Nam, Benjamin M Gyori, Silviana V Amethyst, Daniel J Bates, Jeremy Gunawardena
Robustness and parameter geography in post-translational modification systems. PLoS computational biology 16 (5) (2020)
Benjamin M Gyori, John A Bachman, Kartik Subramanian, Jeremy L Muhlich, Lucian Galescu, Peter Karl Sorger
From word models to executable models of signaling networks using automated assembly. Molecular systems biology 13 (11) (2017)