Cytoscape Automation: empowering workflow-based network analysis von Otasek, David, Morris, John H, Bouças, Jorge, Pico, Alexander R, Demchak, Barry

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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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Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage von Wamstad, Joseph A, Alexander, Jeffrey M, Truty, Rebecca M, Shrikumar, Avanti, Li, Fugen, Eilertson, Kirsten E, Ding, Huiming, Wylie, John N, Pico, Alexander R, Capra, John A, Erwin, Genevieve, Kattman, Steven J, Keller, Gordon M, Srivastava, Deepak, Levine, Stuart S, Pollard, Katherine S, Holloway, Alisha K, Boyer, Laurie A, Bruneau, Benoit G

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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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WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics von Elizarraras, John M, Liao, Yuxing, Shi, Zhiao, Zhu, Qian, Pico, Alexander R, Zhang, Bing

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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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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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Using published pathway figures in enrichment analysis and machine learning von Shin, Min-Gyoung, Pico, Alexander R

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Pathway information extracted from 25 years of pathway figures von Hanspers, Kristina, Riutta, Anders, Summer-Kutmon, Martina, Pico, Alexander R.

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Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions von Morris, John H, Knudsen, Giselle M, Verschueren, Erik, Johnson, Jeffrey R, Cimermancic, Peter, Greninger, Alexander L, Pico, Alexander R

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Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation von Mendiola, Andrew S., Ryu, Jae Kyu, Bardehle, Sophia, Meyer-Franke, Anke, Ang, Kenny Kean-Hooi, Wilson, Chris, Baeten, Kim M., Hanspers, Kristina, Merlini, Mario, Thomas, Sean, Petersen, Mark A., Williams, Alexander, Thomas, Reuben, Rafalski, Victoria A., Meza-Acevedo, Rosa, Tognatta, Reshmi, Yan, Zhaoqi, Pfaff, Samuel J., Machado, Michael R., Bedard, Catherine, Rios Coronado, Pamela E., Jiang, Xiqian, Wang, Jin, Pleiss, Michael A., Green, Ari J., Zamvil, Scott S., Pico, Alexander R., Bruneau, Benoit G., Arkin, Michelle R., Akassoglou, Katerina

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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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WikiPathways: pathway editing for the people von Pico, Alexander R, Kelder, Thomas, van Iersel, Martijn P, Hanspers, Kristina, Conklin, Bruce R, Evelo, Chris

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Fibrin-targeting immunotherapy protects against neuroinflammation and neurodegeneration von Ryu, Jae Kyu, Rafalski, Victoria A., Meyer-Franke, Anke, Adams, Ryan A., Poda, Suresh B., Rios Coronado, Pamela E., Pedersen, Lars Østergaard, Menon, Veena, Baeten, Kim M., Sikorski, Shoana L., Bedard, Catherine, Hanspers, Kristina, Bardehle, Sophia, Mendiola, Andrew S., Davalos, Dimitrios, Machado, Michael R., Chan, Justin P., Plastira, Ioanna, Petersen, Mark A., Pfaff, Samuel J., Ang, Kenny K., Hallenbeck, Kenneth K., Syme, Catriona, Hakozaki, Hiroyuki, Ellisman, Mark H., Swanson, Raymond A., Zamvil, Scott S., Arkin, Michelle R., Zorn, Stevin H., Pico, Alexander R., Mucke, Lennart, Freedman, Stephen B., Stavenhagen, Jeffrey B., Nelson, Robert B., Akassoglou, Katerina

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Metabolic Architecture of Acute Exercise Response in Middle-Aged Adults in the Community von Nayor, Matthew, Shah, Ravi V., Miller, Patricia E., Blodgett, Jasmine B., Tanguay, Melissa, Pico, Alexander R., Murthy, Venkatesh L., Malhotra, Rajeev, Houstis, Nicholas E., Deik, Amy, Pierce, Kerry A., Bullock, Kevin, Dailey, Lucas, Velagaleti, Raghava S., Moore, Stephanie A., Ho, Jennifer E., Baggish, Aaron L., Clish, Clary B., Larson, Martin G., Vasan, Ramachandran S., Lewis, Gregory D.

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RCy3: Network biology using Cytoscape from within R [version 1; peer review: 2 approved] von Gustavsen, Julia A, Pai, Shraddha, Isserlin, Ruth, Demchak, Barry, Pico, Alexander R

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Presenting and exploring biological pathways with PathVisio von van Iersel, Martijn P, Kelder, Thomas, Pico, Alexander R, Hanspers, Kristina, Coort, Susan, Conklin, Bruce R, Evelo, Chris

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Wikidata as a knowledge graph for the life sciences von Waagmeester, Andra, Stupp, Gregory, Burgstaller-Muehlbacher, Sebastian, Good, Benjamin M, Griffith, Malachi, Griffith, Obi L, Hanspers, Kristina, Hermjakob, Henning, Hudson, Toby S, Hybiske, Kevin, Keating, Sarah M, Manske, Magnus, Mayers, Michael, Mietchen, Daniel, Mitraka, Elvira, Pico, Alexander R, Putman, Timothy, Riutta, Anders, Queralt-Rosinach, Nuria, Schriml, Lynn M, Shafee, Thomas, Slenter, Denise, Stephan, Ralf, Thornton, Katherine, Tsueng, Ginger, Tu, Roger, Ul-Hasan, Sabah, Willighagen, Egon, Wu, Chunlei, Su, Andrew I

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GenMAPP 2: new features and resources for pathway analysis von Salomonis, Nathan, Hanspers, Kristina, Zambon, Alexander C, Vranizan, Karen, Lawlor, Steven C, Dahlquist, Kam D, Doniger, Scott W, Stuart, Josh, Conklin, Bruce R, Pico, Alexander R

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