MaBoSS 2.0: an environment for stochastic Boolean modeling by Stoll, Gautier, Caron, Barthélémy, Viara, Eric, Dugourd, Aurélien, Zinovyev, Andrei, Naldi, Aurélien, Kroemer, Guido, Barillot, Emmanuel, Calzone, Laurence

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decoupleR: ensemble of computational methods to infer biological activities from omics data by Badia-i-Mompel, Pau, Vélez Santiago, Jesús, Braunger, Jana, Geiss, Celina, Dimitrov, Daniel, Müller-Dott, Sophia, Taus, Petr, Dugourd, Aurelien, Holland, Christian H, Ramirez Flores, Ricardo O, Saez-Rodriguez, Julio

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Footprint-based functional analysis of multiomic data by Dugourd, Aurelien, Saez-Rodriguez, Julio

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Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses by Dugourd, Aurelien, Kuppe, Christoph, Sciacovelli, Marco, Gjerga, Enio, Gabor, Attila, Emdal, Kristina B., Vieira, Vitor, Bekker‐Jensen, Dorte B., Kranz, Jennifer, Bindels, Eric.M.J., Costa, Ana S.H., Sousa, Abel, Beltrao, Pedro, Rocha, Miguel, Olsen, Jesper V., Frezza, Christian, Kramann, Rafael, Saez‐Rodriguez, Julio

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Reducing lipid bilayer stress by monounsaturated fatty acids protects renal proximal tubules in diabetes by Pérez-Martí, Albert, Ramakrishnan, Suresh, Li, Jiayi, Dugourd, Aurelien, Molenaar, Martijn R, De La Motte, Luigi R, Grand, Kelli, Mansouri, Anis, Parisot, Mélanie, Lienkamp, Soeren S, Saez-Rodriguez, Julio, Simons, Matias

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Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival by Sousa, Abel, Dugourd, Aurelien, Memon, Danish, Petursson, Borgthor, Petsalaki, Evangelia, Saez‐Rodriguez, Julio, Beltrao, Pedro

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COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms by Ostaszewski, Marek, Mazein, Alexander, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Brauner, Barbara, Frishman, Goar, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Borlinghaus, Hanna, Czauderna, Tobias, Hiki, Yusuke, Yamada, Takahiro G, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Börnigen, Daniela, Conti, Marta, Rameil, Marius, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Oxford, Kristie, Kocakaya, Ebru, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Slenter, Denise, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Senff-Ribeiro, Andrea, 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, Yuryev, Anton, de Waard, Anita, Babur, Ozgun, Soliman, Sylvain, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Dugourd, Aurélien, Noël, Vincent, Calzone, Laurence, Demir, Emek, Augé, Franck, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Evelo, Chris T, Stein, Lincoln D, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, Schneider, Reinhard

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Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression by Sciacovelli, Marco, Dugourd, Aurelien, Jimenez, Lorea Valcarcel, Yang, Ming, Nikitopoulou, Efterpi, Costa, Ana S. H., Tronci, Laura, Caraffini, Veronica, Rodrigues, Paulo, Schmidt, Christina, Ryan, Dylan Gerard, Young, Timothy, Zecchini, Vincent R., Rossi, Sabrina H., Massie, Charlie, Lohoff, Caroline, Masid, Maria, Hatzimanikatis, Vassily, Kuppe, Christoph, Von Kriegsheim, Alex, Kramann, Rafael, Gnanapragasam, Vincent, Warren, Anne Y., Stewart, Grant D., Erez, Ayelet, Vanharanta, Sakari, Saez-Rodriguez, Julio, Frezza, Christian

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Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data by Dimitrov, Daniel, Türei, Dénes, Garrido-Rodriguez, Martin, Burmedi, Paul L., Nagai, James S., Boys, Charlotte, Ramirez Flores, Ricardo O., Kim, Hyojin, Szalai, Bence, Costa, Ivan G., Valdeolivas, Alberto, Dugourd, Aurélien, Saez-Rodriguez, Julio

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Increased CXCL4 expression in hematopoietic cells links inflammation and progression of bone marrow fibrosis in MPN by Gleitz, Hélène F.E., Dugourd, Aurélien J.F., Leimkühler, Nils B., Snoeren, Inge A.M., Fuchs, Stijn N.R., Menzel, Sylvia, Ziegler, Susanne, Kröger, Nicolaus, Triviai, Ioanna, Büsche, Guntram, Kreipe, Hans, Banjanin, Bella, Pritchard, Jessica E., Hoogenboezem, Remco, Bindels, Eric M., Schumacher, Neele, Rose-John, Stefan, Elf, Shannon, Saez-Rodriguez, Julio, Kramann, Rafael, Schneider, Rebekka K.

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Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis by Gegner, Hagen M, Naake, Thomas, Dugourd, Aurélien, Müller, Torsten, Czernilofsky, Felix, Kliewer, Georg, Jäger, Evelyn, Helm, Barbara, Kunze-Rohrbach, Nina, Klingmüller, Ursula, Hopf, Carsten, Müller-Tidow, Carsten, Dietrich, Sascha, Saez-Rodriguez, Julio, Huber, Wolfgang, Hell, Rüdiger, Poschet, Gernot, Krijgsveld, Jeroen

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Macrophage beta2-adrenergic receptor is dispensable for the adipose tissue inflammation and function by Petkevicius, Kasparas, Bidault, Guillaume, Virtue, Sam, Newland, Stephen A., Dale, Martin, Dugourd, Aurelien, Saez-Rodriguez, Julio, Mallat, Ziad, Vidal-Puig, Antonio

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Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities by Salovska, Barbora, Gao, Erli, Müller‐Dott, Sophia, Li, Wenxue, Cordon, Carlos Chacon, Wang, Shisheng, Dugourd, Aurelien, Rosenberger, George, Saez‐Rodriguez, Julio, Liu, Yansheng

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Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer by Berndt, Nikolaus, Egners, Antje, Mastrobuoni, Guido, Vvedenskaya, Olga, Fragoulis, Athanassios, Dugourd, Aurélien, Bulik, Sascha, Pietzke, Matthias, Bielow, Chris, van Gassel, Rob, Damink, Steven W. Olde, Erdem, Merve, Saez-Rodriguez, Julio, Holzhütter, Hermann-Georg, Kempa, Stefan, Cramer, Thorsten

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NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction by Gaude, Edoardo, Schmidt, Christina, Gammage, Payam A., Dugourd, Aurelien, Blacker, Thomas, Chew, Sew Peak, Saez-Rodriguez, Julio, O’Neill, John S., Szabadkai, Gyorgy, Minczuk, Michal, Frezza, Christian

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Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ by Cappelletti, Valentina, Hauser, Thomas, Piazza, Ilaria, Pepelnjak, Monika, Malinovska, Liliana, Fuhrer, Tobias, Li, Yaozong, Dörig, Christian, Boersema, Paul, Gillet, Ludovic, Grossbach, Jan, Dugourd, Aurelien, Saez-Rodriguez, Julio, Beyer, Andreas, Zamboni, Nicola, Caflisch, Amedeo, de Souza, Natalie, Picotti, Paola

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The Global Phosphorylation Landscape of SARS-CoV-2 Infection by Bouhaddou, Mehdi, Memon, Danish, Meyer, Bjoern, White, Kris M., Rezelj, Veronica V., Correa Marrero, Miguel, Polacco, Benjamin J., Melnyk, James E., Ulferts, Svenja, Kaake, Robyn M., Batra, Jyoti, Richards, Alicia L., Stevenson, Erica, Gordon, David E., Rojc, Ajda, Obernier, Kirsten, Fabius, Jacqueline M., Soucheray, Margaret, Miorin, Lisa, Moreno, Elena, Koh, Cassandra, Tran, Quang Dinh, Hardy, Alexandra, Robinot, Rémy, Vallet, Thomas, Nilsson-Payant, Benjamin E., Hernandez-Armenta, Claudia, Dunham, Alistair, Weigang, Sebastian, Knerr, Julian, Modak, Maya, Quintero, Diego, Zhou, Yuan, Dugourd, Aurelien, Valdeolivas, Alberto, Patil, Trupti, Li, Qiongyu, Hüttenhain, Ruth, Cakir, Merve, Muralidharan, Monita, Kim, Minkyu, Jang, Gwendolyn, Tutuncuoglu, Beril, Hiatt, Joseph, Guo, Jeffrey Z., Xu, Jiewei, Bouhaddou, Sophia, Mathy, Christopher J.P., Gaulton, Anna, Manners, Emma J., Félix, Eloy, Shi, Ying, Goff, Marisa, Lim, Jean K., McBride, Timothy, O’Neal, Michael C., Cai, Yiming, Chang, Jason C.J., Broadhurst, David J., Klippsten, Saker, De wit, Emmie, Leach, Andrew R., Kortemme, Tanja, Shoichet, Brian, Ott, Melanie, Saez-Rodriguez, Julio, tenOever, Benjamin R., Mullins, R. Dyche, Fischer, Elizabeth R., Kochs, Georg, Grosse, Robert, García-Sastre, Adolfo, Vignuzzi, Marco, Johnson, Jeffery R., Shokat, Kevan M., Swaney, Danielle L., Beltrao, Pedro, Krogan, Nevan J.

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MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions by Farr, Elias, Dimitrov, Daniel, Schmidt, Christina, Turei, Denes, Lobentanzer, Sebastian, Dugourd, Aurelien, Saez-Rodriguez, Julio

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PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data by Gjerga, Enio, Dugourd, Aurelien, Tobalina, Luis, Sousa, Abel, Saez-Rodriguez, Julio

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FUNKI: interactive functional footprint-based analysis of omics data by Hernansaiz-Ballesteros, Rosa, Holland, Christian H, Dugourd, Aurelien, Saez-Rodriguez, Julio

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