PyBioPAX: biological pathway exchange in Python

por Gyori, Benjamin M., Hoyt, Charles Tapley
Publicado 2022

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

por Steppi, Albert, Gyori, Benjamin M., Bachman, John A.
Publicado 2020

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

por Gyori, Benjamin M, Hoyt, Charles Tapley, Steppi, Albert
Publicado 2022

Prediction and curation of missing biomedical identifier mappings with Biomappings

por Hoyt, Charles Tapley, Hoyt, Amelia L, Gyori, Benjamin M
Publicado 2023

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

por Bachman, John A, Gyori, Benjamin M, Sorger, Peter K
Publicado 2023

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

por Bachman, John A., Gyori, Benjamin M., Sorger, Peter K.
Publicado 2018

OpenComet: An automated tool for comet assay image analysis

por Gyori, Benjamin M., Venkatachalam, Gireedhar, Thiagarajan, P.S., Hsu, David, Clement, Marie-Veronique
Publicado 2014

INDRA-IPM: interactive pathway modeling using natural language with automated assembly

por Todorov, Petar V, Gyori, Benjamin M, Bachman, John A, Sorger, Peter K
Publicado 2019

Robustness and parameter geography in post-translational modification systems

por Nam, Kee-Myoung, Gyori, Benjamin M., Amethyst, Silviana V., Bates, Daniel J., Gunawardena, Jeremy
Publicado 2020

GeneWalk identifies relevant gene functions for a biological context using network representation learning

por Ietswaart, Robert, Gyori, Benjamin M., Bachman, John A., Sorger, Peter K., Churchman, L. Stirling
Publicado 2021

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

por Gyori, Benjamin M, Bachman, John A, Subramanian, Kartik, Muhlich, Jeremy L, Galescu, Lucian, Sorger, Peter K
Publicado 2017

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

por Scholten, Bernice, Simón, Laura Guerrero, Krishnan, Shaji, Vermeulen, Roel, Pronk, Anjoeka, Gyori, Benjamin M., Bachman, John A., Vlaanderen, Jelle, Stierum, Rob
Publicado 2022

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

por Pillich, Rudolf T, Chen, Jing, Churas, Christopher, Fong, Dylan, Gyori, Benjamin M, Ideker, Trey, Karis, Klas, Liu, Sophie N, Ono, Keiichiro, Pico, Alexander, Pratt, Dexter
Publicado 2023

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

por Balabin, Helena, Hoyt, Charles Tapley, Birkenbihl, Colin, Gyori, Benjamin M, Bachman, John, Kodamullil, Alpha Tom, Plöger, Paul G, Hofmann-Apitius, Martin, Domingo-Fernández, Daniel
Publicado 2022

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

por Hoyt, Charles Tapley, Domingo-Fernández, Daniel, Aldisi, Rana, Xu, Lingling, Kolpeja, Kristian, Spalek, Sandra, Wollert, Esther, Bachman, John, Gyori, Benjamin M, Greene, Patrick, Hofmann-Apitius, Martin
Publicado 2019

Author-sourced capture of pathway knowledge in computable form using Biofactoid

por Wong, Jeffrey V, Franz, Max, Siper, Metin Can, Fong, Dylan, Durupinar, Funda, Dallago, Christian, Luna, Augustin, Giorgi, John, Rodchenkov, Igor, Babur, Özgün, Bachman, John A, Gyori, Benjamin M, Demir, Emek, Bader, Gary D, Sander, Chris
Publicado 2021

Unifying the identification of biomedical entities with the Bioregistry

por Hoyt, Charles Tapley, Balk, Meghan, Callahan, Tiffany J., Domingo-Fernández, Daniel, Haendel, Melissa A., Hegde, Harshad B., Himmelstein, Daniel S., Karis, Klas, Kunze, John, Lubiana, Tiago, Matentzoglu, Nicolas, McMurry, Julie, Moxon, Sierra, Mungall, Christopher J., Rutz, Adriano, Unni, Deepak R., Willighagen, Egon, Winston, Donald, Gyori, Benjamin M.
Publicado 2022

A Simple Standard for Sharing Ontological Mappings (SSSOM)

por Matentzoglu, Nicolas, Balhoff, James P, Bello, Susan M, Bizon, Chris, Brush, Matthew, Callahan, Tiffany J, Chute, Christopher G, Duncan, William D, Evelo, Chris T, Gabriel, Davera, Graybeal, John, Gray, Alasdair, Gyori, Benjamin M, Haendel, Melissa, Harmse, Henriette, Harris, Nomi L, Harrow, Ian, Hegde, Harshad B, Hoyt, Amelia L, Hoyt, Charles T, Jiao, Dazhi, Jiménez-Ruiz, Ernesto, Jupp, Simon, Kim, Hyeongsik, Koehler, Sebastian, Liener, Thomas, Long, Qinqin, Malone, James, McLaughlin, James A, McMurry, Julie A, Moxon, Sierra, Munoz-Torres, Monica C, Osumi-Sutherland, David, Overton, James A, Peters, Bjoern, Putman, Tim, Queralt-Rosinach, Núria, Shefchek, Kent, Solbrig, Harold, Thessen, Anne, Tudorache, Tania, Vasilevsky, Nicole, Wagner, Alex H, Mungall, Christopher J
Publicado 2022

A roadmap for the functional annotation of protein families: a community perspective

por de Crécy-lagard, Valérie, Amorin de Hegedus, Rocio, Arighi, Cecilia, Babor, Jill, Bateman, Alex, Blaby, Ian, Blaby-Haas, Crysten, Bridge, Alan J, Burley, Stephen K, Cleveland, Stacey, Colwell, Lucy J, Conesa, Ana, Dallago, Christian, Danchin, Antoine, de Waard, Anita, Deutschbauer, Adam, Dias, Raquel, Ding, Yousong, Fang, Gang, Friedberg, Iddo, Gerlt, John, Goldford, Joshua, Gorelik, Mark, Gyori, Benjamin M, Henry, Christopher, Hutinet, Geoffrey, Jaroch, Marshall, Karp, Peter D, Kondratova, Liudmyla, Lu, Zhiyong, Marchler-Bauer, Aron, Martin, Maria-Jesus, McWhite, Claire, Moghe, Gaurav D, Monaghan, Paul, Morgat, Anne, Mungall, Christopher J, Natale, Darren A, Nelson, William C, O’Donoghue, Seán, Orengo, Christine, O’Toole, Katherine H, Radivojac, Predrag, Reed, Colbie, Roberts, Richard J, Rodionov, Dmitri, Rodionova, Irina A, Rudolf, Jeffrey D, Saleh, Lana, Sheynkman, Gloria, Thibaud-Nissen, Francoise, Thomas, Paul D, Uetz, Peter, Vallenet, David, Carter, Erica Watson, Weigele, Peter R, Wood, Valerie, Wood-Charlson, Elisha M, Xu, Jin
Publicado 2022

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

por Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard
Publicado 2021