Automated assembly of molecular mechanisms at scale from text mining and curated databases von Bachman, John A, Gyori, Benjamin M, Sorger, Peter K

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OpenComet: an automated tool for comet assay image analysis von Gyori, Benjamin M, Venkatachalam, Gireedhar, Thiagarajan, P S, Hsu, David, Clement, Marie-Veronique

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GeneWalk identifies relevant gene functions for a biological context using network representation learning von Ietswaart, Robert, Gyori, Benjamin M., Bachman, John A., Sorger, Peter K., Churchman, L. Stirling

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From word models to executable models of signaling networks using automated assembly von Gyori, Benjamin M, Bachman, John A, Subramanian, Kartik, Muhlich, Jeremy L, Galescu, Lucian, Sorger, Peter K

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FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining von Bachman, John A, Gyori, Benjamin M, Sorger, Peter K

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The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources von Hoyt, Charles Tapley, Gyori, Benjamin M.

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Robustness and parameter geography in post-translational modification systems von Nam, Kee-Myoung, Gyori, Benjamin M., Amethyst, Silviana, Bates, Daniel J., Gunawardena, Jeremy

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Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge von Gyori, Benjamin M., Vitek, Olga

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

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Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases von Sampattavanich, Somponnat, Steiert, Bernhard, Kramer, Bernhard A., Gyori, Benjamin M., Albeck, John G., Sorger, Peter K.

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Unifying the identification of biomedical entities with the Bioregistry von 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.

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Prediction and curation of missing biomedical identifier mappings with Biomappings von Hoyt, Charles Tapley, Hoyt, Amelia L, Gyori, Benjamin M

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Eliater: a Python package for estimating outcomes of perturbations in biomolecular networks von Mohammad-Taheri, Sara, Navada, Pruthvi Prakash, Hoyt, Charles Tapley, Zucker, Jeremy, Sachs, Karen, Gyori, Benjamin M, Vitek, Olga

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

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INDRA-IPM: interactive pathway modeling using natural language with automated assembly von Todorov, Petar V, Gyori, Benjamin M, Bachman, John A, Sorger, Peter K

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STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs von Balabin, Helena, Hoyt, Charles Tapley, Birkenbihl, Colin, Gyori, Benjamin M, Bachman, John, Kodamullil, Alpha Tom, Plöger, Paul G, Hofmann-Apitius, Martin, Domingo-Fernández, Daniel

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Democratizing knowledge representation with BioCypher von Lobentanzer, Sebastian, Aloy, Patrick, Baumbach, Jan, Bohar, Balazs, Carey, Vincent J., Charoentong, Pornpimol, Danhauser, Katharina, Doğan, Tunca, Dreo, Johann, Dunham, Ian, Farr, Elias, Fernandez-Torras, Adrià, Gyori, Benjamin M., Hartung, Michael, Hoyt, Charles Tapley, Klein, Christoph, Korcsmaros, Tamas, Maier, Andreas, Mann, Matthias, Ochoa, David, Pareja-Lorente, Elena, Popp, Ferdinand, Preusse, Martin, Probul, Niklas, Schwikowski, Benno, Sen, Bünyamin, Strauss, Maximilian T., Turei, Denes, Ulusoy, Erva, Waltemath, Dagmar, Wodke, Judith A. H., Saez-Rodriguez, Julio

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Nociceptor-immune interactomes reveal insult-specific immune signatures of pain von Jain, Aakanksha, Gyori, Benjamin M., Hakim, Sara, Jain, Ashish, Sun, Liang, Petrova, Veselina, Bhuiyan, Shamsuddin A., Zhen, Shannon, Wang, Qing, Kawaguchi, Riki, Bunga, Samuel, Taub, Daniel G., Ruiz-Cantero, M. Carmen, Tong-Li, Candace, Andrews, Nicholas, Kotoda, Masakazu, Renthal, William, Sorger, Peter K., Woolf, Clifford J.

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Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment von Scholten, Bernice, Simón, Laura Guerrero, Krishnan, Shaji, Vermeulen, Roel, Pronk, Anjoeka, Gyori, Benjamin M, Bachman, John A, Vlaanderen, Jelle, Stierum, Rob

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PyBioPAX: biological pathway exchange in Python von Gyori, Benjamin M., Hoyt, Charles Tapley

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