PathVisio 3: an extendable pathway analysis toolbox von Kutmon, Martina, van Iersel, Martijn P, Bohler, Anwesha, Kelder, Thomas, Nunes, Nuno, Pico, Alexander R, Evelo, Chris T

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WikiPathways: capturing the full diversity of pathway knowledge von Kutmon, Martina, Riutta, Anders, Nunes, Nuno, Hanspers, Kristina, Willighagen, Egon L, Bohler, Anwesha, Mélius, Jonathan, Waagmeester, Andra, Sinha, Sravanthi R, Miller, Ryan, Coort, Susan L, Cirillo, Elisa, Smeets, Bart, Evelo, Chris T, Pico, Alexander R

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WikiPathways: connecting communities von Martens, Marvin, Ammar, Ammar, Riutta, Anders, Waagmeester, Andra, Slenter, Denise N, Hanspers, Kristina, A. Miller, Ryan, Digles, Daniela, Lopes, Elisson N, Ehrhart, Friederike, Dupuis, Lauren J, Winckers, Laurent A, Coort, Susan L, Willighagen, Egon L, Evelo, Chris T, Pico, Alexander R, Kutmon, Martina

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WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research von Slenter, Denise N, Kutmon, Martina, Hanspers, Kristina, Riutta, Anders, Windsor, Jacob, Nunes, Nuno, Mélius, Jonathan, Cirillo, Elisa, Coort, Susan L, Digles, Daniela, Ehrhart, Friederike, Giesbertz, Pieter, Kalafati, Marianthi, Martens, Marvin, Miller, Ryan, Nishida, Kozo, Rieswijk, Linda, Waagmeester, Andra, Eijssen, Lars M T, Evelo, Chris T, Pico, Alexander R, Willighagen, Egon L

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WikiPathways 2024: next generation pathway database von Agrawal, Ayushi, Balcı, Hasan, Hanspers, Kristina, Coort, Susan L, Martens, Marvin, Slenter, Denise N, Ehrhart, Friederike, Digles, Daniela, Waagmeester, Andra, Wassink, Isabel, Abbassi-Daloii, Tooba, Lopes, Elisson N, Iyer, Aishwarya, Acosta, Javier Millán, Willighagen, Lars G, Nishida, Kozo, Riutta, Anders, Basaric, Helena, Evelo, Chris T, Willighagen, Egon L, Kutmon, Martina, Pico, Alexander R

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Ten simple rules to make your publication look better von Ehrhart, Friederike, Evelo, Chris T.

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CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis von Kutmon, Martina, Kelder, Thomas, Mandaviya, Pooja, Evelo, Chris T A, Coort, Susan L

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The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching von Willighagen, Egon L., Mayfield, John W., Alvarsson, Jonathan, Berg, Arvid, Carlsson, Lars, Jeliazkova, Nina, Kuhn, Stefan, Pluskal, Tomáš, Rojas-Chertó, Miquel, Spjuth, Ola, Torrance, Gilleain, Evelo, Chris T., Guha, Rajarshi, Steinbeck, Christoph

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GO-Elite: a flexible solution for pathway and ontology over-representation von ZAMBON, Alexander C, GAJ, Stan, HO, Isaac, HANSPERS, Kristina, VRANIZAN, Karen, EVELO, Chris T, CONKLIN, Bruce R, PICO, Alexander R, SALOMONIS, Nathan

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Comparison of metabolic states using genome-scale metabolic models von Sarathy, Chaitra, Breuer, Marian, Kutmon, Martina, Adriaens, Michiel E., Evelo, Chris T., Arts, Ilja C. W.

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A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants von Cirillo, Elisa, Parnell, Laurence D, Evelo, Chris T

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User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org von Eijssen, Lars M T, Jaillard, Magali, Adriaens, Michiel E, Gaj, Stan, de Groot, Philip J, Müller, Michael, Evelo, Chris T

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From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results von Cirillo, Elisa, Kutmon, Martina, Gonzalez Hernandez, Manuel, Hooimeijer, Tom, Adriaens, Michiel E, Eijssen, Lars M T, Parnell, Laurence D, Coort, Susan L, Evelo, Chris T

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Exploring pathway interactions to detect molecular mechanisms of disease: 22q11.2 deletion syndrome von Shin, Woosub, Kutmon, Martina, Mina, Eleni, van Amelsvoort, Therese, Evelo, Chris T, Ehrhart, Friederike

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Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions von Miller, Ryan A, Kutmon, Martina, Bohler, Anwesha, Waagmeester, Andra, Evelo, Chris T, Willighagen, Egon L

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The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services von van Iersel, Martijn P, Pico, Alexander R, Kelder, Thomas, Gao, Jianjiong, Ho, Isaac, Hanspers, Kristina, Conklin, Bruce R, Evelo, Chris T

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Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients von Pham, Nhung, Hu, Finterly, Evelo, Chris T., Kutmon, Martina

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Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes von Ehrhart, Friederike, Coort, Susan L M, Cirillo, Elisa, Smeets, Eric, Evelo, Chris T, Curfs, Leopold M G

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COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms von Ostaszewski, Marek, Mazein, Alexander, Gillespie, Marc E., Kuperstein, Inna, Niarakis, Anna, Hermjakob, Henning, Pico, Alexander R., Willighagen, Egon L., Evelo, Chris T., Hasenauer, Jan, Schreiber, Falk, Dräger, Andreas, Demir, Emek, Wolkenhauer, Olaf, Furlong, Laura I., Barillot, Emmanuel, Dopazo, Joaquin, Orta-Resendiz, Aurelio, Messina, Francesco, Valencia, Alfonso, Funahashi, Akira, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, Schneider, Reinhard

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A novel insight into neurological disorders through HDAC6 protein–protein interactions von Bahram Sangani, Nasim, Koetsier, Jarno, Mélius, Jonathan, Kutmon, Martina, Ehrhart, Friederike, Evelo, Chris T., Curfs, Leopold M. G., Reutelingsperger, Chris P., Eijssen, Lars M. T.

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