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Dugourd, Aurélien [Author] ; Sáez Rodríguez, Julio [Degree supervisor]

Bridging the gap between signalling and metabolism through functional and mechanistic analysis of multi-omic data

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Heidelberg: Universitätsbibliothek Heidelberg, 2022
Dugourd, Aurélien [Author] ; Sáez Rodríguez, Julio [Degree supervisor]

Bridging the gap between signalling and metabolism through functional and mechanistic analysis of multi-omic data

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Heidelberg, 06 Apr. 2022
Dugourd, Aurélien [Author]; Gjerga, Enio [Author]; Gabor, Attila [Author]; Sáez Rodríguez, Julio [Author]; Kuppe, Christoph [Author]; Sciacovelli, Marco [Author]; Emdal, Kristina B. [Author]; Vieira, Vitor [Author]; Bekker-Jensen, Dorte B. [Author]; Kranz, Jennifer [Author]; Bindels, Eric M. J. [Author]; Costa, Ana S. H. [Author]; Sousa, Abel [Author]; Beltrao, Pedro [Author]; Rocha, Miguel [Author]; Olsen, Jesper V. [Author]; Frezza, Christian [Author]; Kramann, Rafael [Author]

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses

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27 January 2021

Published in: Molecular systems biology ; 17(2021), 1, Artikel-ID e9730, Seite 1-17
Dimitrov, Daniel [Author]; Türei, Dénes [Author]; Garrido-Rodriguez, Martin [Author]; Burmedi, Paul L. [Author]; Nagai, James S. [Author]; Boys, Charlotte [Author]; Ramirez Flores, Ricardo O. [Author]; Kim, Hyojin [Author]; Szalai, Bence [Author]; Costa, Ivan G. [Author]; Valdeolivas, Alberto [Author]; Dugourd, Aurélien [Author]; Sáez Rodríguez, Julio [Author]

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

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09 June 2022

Published in: Nature Communications ; 13(2022), Artikel-ID 3224, Seite 1-13
Gegner, Hagen M. [Author]; Naake, Thomas [Author]; Dugourd, Aurélien [Author]; Müller, Torsten [Author]; Czernilofsky, Felix [Author]; Kliewer, Georg [Author]; Jäger, Evelyn [Author]; Helm, Barbara [Author]; Kunze-Rohrbach, Nina [Author]; Klingmüller, Ursula [Author]; Hopf, Carsten [Author]; Müller-Tidow, Carsten [Author]; Dietrich, Sascha [Author]; Sáez Rodríguez, Julio [Author]; Huber, Wolfgang [Author]; Hell, Rüdiger [Author]; Poschet, Gernot [Author]; Krijgsveld, Jeroen [Author]

Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis

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20 December 2022

Published in: Frontiers in molecular biosciences ; 9(2022), Artikel-ID 961448, Seite 1-13
Le Fèvre, Aurélien; Dugourd, Philippe; Chirot, Fabien

Exploring Conformational Landscapes Using Trap and Release Tandem Ion Mobility Spectrometry

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American Chemical Society (ACS), 2021

Published in: Analytical Chemistry, 93 (2021) 9, Seite 4183-4190
Stoll, Gautier; Caron, Barthélémy; Viara, Eric; Dugourd, Aurélien; Zinovyev, Andrei; Naldi, Aurélien; Kroemer, Guido; Barillot, Emmanuel; Calzone, Laurence

MaBoSS 2.0: an environment for stochastic Boolean modeling

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Oxford University Press (OUP), 2017

Published in: Bioinformatics, 33 (2017) 14, Seite 2226-2228
Sousa, Abel; Dugourd, Aurelien; Memon, Danish; Petursson, Borgthor; Petsalaki, Evangelia; Saez‐Rodriguez, Julio; Beltrao, Pedro

Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival

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Springer Science and Business Media LLC, 2023

Published in: Molecular Systems Biology, 19 (2023) 3
Hernansaiz-Ballesteros, Rosa; Holland, Christian H; Dugourd, Aurelien; Saez-Rodriguez, Julio

FUNKI: interactive functional footprint-based analysis of omics data

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Oxford University Press (OUP), 2022

Published in: Bioinformatics, 38 (2022) 7, Seite 2075-2076
Gjerga, Enio; Dugourd, Aurelien; Tobalina, Luis; Sousa, Abel; Saez-Rodriguez, Julio

PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data

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American Chemical Society (ACS), 2021

Published in: Journal of Proteome Research, 20 (2021) 4, Seite 2138-2144
Verlingue, Loic; Dugourd, Aurélien; Stoll, Gautier; Barillot, Emmanuel; Calzone, Laurence; Londoño‐Vallejo, Arturo

A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion

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Wiley, 2016

Published in: Aging Cell, 15 (2016) 6, Seite 1018-1026
Gjerga, Enio; Trairatphisan, Panuwat; Gabor, Attila; Koch, Hermann; Chevalier, Celine; Ceccarelli, Franceco; Dugourd, Aurelien; Mitsos, Alexander; Saez-Rodriguez, Julio

Converting networks to predictive logic models from perturbation signalling data with CellNOpt

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Oxford University Press (OUP), 2020

Published in: Bioinformatics, 36 (2020) 16, Seite 4523-4524
Salovska, Barbora; Gao, Erli; Müller‐Dott, Sophia; Li, Wenxue; Cordon, Carlos Chacon; Wang, Shisheng; Dugourd, Aurelien; Rosenberger, George; Saez‐Rodriguez, Julio; Liu, Yansheng

Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities

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Wiley, 2023

Published in: Clinical and Translational Medicine, 13 (2023) 2
Petkevicius, Kasparas; Bidault, Guillaume; Virtue, Sam; Newland, Stephen A.; Dale, Martin; Dugourd, Aurelien; Saez-Rodriguez, Julio; Mallat, Ziad; Vidal-Puig, Antonio

Macrophage beta2-adrenergic receptor is dispensable for the adipose tissue inflammation and function

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Elsevier BV, 2021

Published in: Molecular Metabolism, 48 (2021), Seite 101220
Petkevicius, Kasparas; Bidault, Guillaume; Virtue, Sam; Jenkins, Benjamin; Dierendonck, Xanthe A. M. H.; Dugourd, Aurelien; Saez‐Rodriguez, Julio; Stienstra, Rinke; Koulman, Albert; Vidal‐Puig, Antonio

Norepinephrine promotes triglyceride storage in macrophages via beta2‐adrenergic receptor activation

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Wiley, 2021

Published in: The FASEB Journal, 35 (2021) 2
Lone, Anna Mari; Giansanti, Piero; Jørgensen, Marthe Jøntvedt; Gjerga, Enio; Dugourd, Aurelien; Scholten, Arjen; Saez‐Rodriguez, Julio; Heck, Albert; Tasken, Kjetil

Prostaglandin E2 signaling networks in T cells revealed through a systems approach

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Wiley, 2019

Published in: The FASEB Journal, 33 (2019) S1
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

NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction

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Elsevier BV, 2018

Published in: Molecular Cell, 69 (2018) 4, Seite 581-593.e7
Gleitz, Hélène; Snoeren, Inge; Fuchs, Stijn; Nagai, James; Dugourd, Aurélien; Boys, Charlotte; Klöker, Vanessa; Pritchard, Jessica; Bindels, Eric; Te Boekhorst, Peter André Willem; Crysandt, Martina; Saez-Rodriguez, Julio; Vogl, Thomas; Kramann, Rafael; Costa, Ivan; Schneider, Rebekka

S205: INHIBITING THE ALARMIN-DRIVEN HEMATOPOIESIS-STROMAL CELLS CROSSTALK IN PRIMARY MYELOFIBROSIS AMELIORATES BONE MARROW FIBROSIS

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Wiley, 2023

Published in: HemaSphere, 7 (2023) S3, Seite e36177f7
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

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

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Springer Science and Business Media LLC, 2022

Published in: Nature Communications, 13 (2022) 1
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

decoupleR: ensemble of computational methods to infer biological activities from omics data

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Oxford University Press (OUP), 2022

Published in: Bioinformatics Advances, 2 (2022) 1

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