Search Results - "Julio Saez‐Rodriguez"

Comprehensive evaluation of phosphoproteomic-based kinase activity inference

Sophia Müller-Dott, Eric J. Jaehnig, Khoi Pham Munchic, Wen Jiang, Tomer M. Yaron-Barir, Sara R. Savage, Martin Garrido-Rodriguez, Jared L. Johnson, Alessandro Lussana, Evangelia Petsalaki, Jonathan T. Lei, Aurelien Dugourd, Karsten Krug, Lewis C. Cantley, D. R. Mani, Bing Zhang, Julio Saez-Rodriguez

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Learning tissue representation by identification of persistent local patterns in spatial omics data

Jovan Tanevski, Loan Vulliard, Miguel A. Ibarra-Arellano, Denis Schapiro, Felix J. Hartmann, Julio Saez-Rodriguez

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Unveiling the role of sex in the metabolism of indoxyl sulfate and apixaban

Blanca Pina-Beltran, Daniel Dimitrov, Nathalie McKay, Matthieu Giot, Zbyněk Zdráhal, David Potěšil, Václav Pustka, Jorge Peinado-Izaguerri, Julio Saez-Rodriguez, Stéphane Poitevin, Stéphane Burtey

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Community assessment of methods to deconvolve cellular composition from bulk gene expression

Brian S. White, Aurélien de Reyniès, Aaron M. Newman, Joshua J. Waterfall, Andrew Lamb, Florent Petitprez, Yating Lin, Rongshan Yu, Martin E. Guerrero-Gimenez, Sergii Domanskyi, Gianni Monaco, Verena Chung, Jineta Banerjee, Daniel Derrick, Alberto Valdeolivas, Haojun Li, Xu Xiao, Shun Wang, Frank Zheng, Wenxian Yang, Carlos A. Catania, Benjamin J. Lang, Thomas J. Bertus, Carlo Piermarocchi, Francesca P. Caruso, Michele Ceccarelli, Thomas Yu, Xindi Guo, Julie Bletz, John Coller, Holden Maecker, Caroline Duault, Vida Shokoohi, Shailja Patel, Joanna E. Liliental, Stockard Simon, Tumor Deconvolution DREAM Challenge consortium, Julio Saez-Rodriguez, Laura M. Heiser, Justin Guinney, Andrew J. Gentles

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DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics

Arezou Rahimi, Luis A. Vale-Silva, Maria Fälth Savitski, Jovan Tanevski, Julio Saez-Rodriguez

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Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice

Yuvarani Masarapu, Egle Cekanaviciute, Zaneta Andrusivova, Jakub O. Westholm, Åsa Björklund, Robin Fallegger, Pau Badia-i-Mompel, Valery Boyko, Shubha Vasisht, Amanda Saravia-Butler, Samrawit Gebre, Enikő Lázár, Marta Graziano, Solène Frapard, Robert G. Hinshaw, Olaf Bergmann, Deanne M. Taylor, Douglas C. Wallace, Christer Sylvén, Konstantinos Meletis, Julio Saez-Rodriguez, Jonathan M. Galazka, Sylvain V. Costes, Stefania Giacomello

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Molecular causality in the advent of foundation models

Sebastian Lobentanzer, Pablo Rodriguez-Mier, Stefan Bauer, Julio Saez-Rodriguez

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Author Correction: Community assessment of methods to deconvolve cellular composition from bulk gene expression

Brian S. White, Aurélien de Reyniès, Aaron M. Newman, Joshua J. Waterfall, Andrew Lamb, Florent Petitprez, Yating Lin, Rongshan Yu, Martin E. Guerrero-Gimenez, Sergii Domanskyi, Gianni Monaco, Verena Chung, Jineta Banerjee, Daniel Derrick, Alberto Valdeolivas, Haojun Li, Xu Xiao, Shun Wang, Frank Zheng, Wenxian Yang, Carlos A. Catania, Benjamin J. Lang, Thomas J. Bertus, Carlo Piermarocchi, Francesca P. Caruso, Michele Ceccarelli, Thomas Yu, Xindi Guo, Julie Bletz, John Coller, Holden Maecker, Caroline Duault, Vida Shokoohi, Shailja Patel, Joanna E. Liliental, Stockard Simon, Tumor Deconvolution DREAM Challenge consortium, Julio Saez-Rodriguez, Laura M. Heiser, Justin Guinney, Andrew J. Gentles

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Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition

Mira L Burtscher, Stephan Gade, Martin Garrido-Rodriguez, Anna Rutkowska, Thilo Werner, H Christian Eberl, Massimo Petretich, Natascha Knopf, Katharina Zirngibl, Paola Grandi, Giovanna Bergamini, Marcus Bantscheff, Maria Fälth-Savitski, Julio Saez-Rodriguez

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Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics

Alberto Valdeolivas, Bettina Amberg, Nicolas Giroud, Marion Richardson, Eric J. C. Gálvez, Solveig Badillo, Alice Julien-Laferrière, Demeter Túrós, Lena Voith von Voithenberg, Isabelle Wells, Benedek Pesti, Amy A. Lo, Emilio Yángüez, Meghna Das Thakur, Michael Bscheider, Marc Sultan, Nadine Kumpesa, Björn Jacobsen, Tobias Bergauer, Julio Saez-Rodriguez, Sven Rottenberg, Petra C. Schwalie, Kerstin Hahn

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Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage

David R. Ghasemi, Konstantin Okonechnikov, Anne Rademacher, Stephan Tirier, Kendra K. Maass, Hanna Schumacher, Piyush Joshi, Maxwell P. Gold, Julia Sundheimer, Britta Statz, Ahmet S. Rifaioglu, Katharina Bauer, Sabrina Schumacher, Michele Bortolomeazzi, Felice Giangaspero, Kati J. Ernst, Steven C. Clifford, Julio Saez-Rodriguez, David T. W. Jones, Daisuke Kawauchi, Ernest Fraenkel, Jan-Philipp Mallm, Karsten Rippe, Andrey Korshunov, Stefan M. Pfister, Kristian W. Pajtler

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Author Correction: Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage

David R. Ghasemi, Konstantin Okonechnikov, Anne Rademacher, Stephan Tirier, Kendra K. Maass, Hanna Schumacher, Piyush Joshi, Maxwell P. Gold, Julia Sundheimer, Britta Statz, Ahmet S. Rifaioglu, Katharina Bauer, Sabrina Schumacher, Michele Bortolomeazzi, Felice Giangaspero, Kati J. Ernst, Steven C. Clifford, Julio Saez-Rodriguez, David T. W. Jones, Daisuke Kawauchi, Ernest Fraenkel, Jan-Philipp Mallm, Karsten Rippe, Andrey Korshunov, Stefan M. Pfister, Kristian W. Pajtler

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A network medicine approach to study comorbidities in heart failure with preserved ejection fraction

Jan D. Lanzer, Alberto Valdeolivas, Mark Pepin, Hauke Hund, Johannes Backs, Norbert Frey, Hans-Christoph Friederich, Jobst-Hendrik Schultz, Julio Saez-Rodriguez, Rebecca T. Levinson

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Single‐cell biology: what does the future hold?

Maria Polychronidou, Jingyi Hou, M Madan Babu, Prisca Liberali, Ido Amit, Bart Deplancke, Galit Lahav, Shalev Itzkovitz, Matthias Mann, Julio Saez‐Rodriguez, Fabian Theis, Roland Eils

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Multiscale networks in multiple sclerosis

Keith E. Kennedy, Nicole Kerlero de Rosbo, Antonio Uccelli, Maria Cellerino, Federico Ivaldi, Paola Contini, Raffaele De Palma, Hanne F. Harbo, Tone Berge, Steffan D. Bos, Einar A. Høgestøl, Synne Brune-Ingebretsen, Sigrid A. de Rodez Benavent, Friedemann Paul, Alexander U. Brandt, Priscilla Bäcker-Koduah, Janina Behrens, Joseph Kuchling, Susanna Asseyer, Michael Scheel, Claudia Chien, Hanna Zimmermann, Seyedamirhosein Motamedi, Josef Kauer-Bonin, Julio Saez-Rodriguez, Melanie Rinas, Leonidas G. Alexopoulos, Magi Andorra, Sara Llufriu, Albert Saiz, Yolanda Blanco, Eloy Martinez-Heras, Elisabeth Solana, Irene Pulido-Valdeolivas, Elena H. Martinez-Lapiscina, Jordi Garcia-Ojalvo, Pablo Villoslada

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Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Anna Niarakis, Marek Ostaszewski, Alexander Mazein, Inna Kuperstein, Martina Kutmon, Marc E. Gillespie, Akira Funahashi, Marcio Luis Acencio, Ahmed Hemedan, Michael Aichem, Karsten Klein, Tobias Czauderna, Felicia Burtscher, Takahiro G. Yamada, Yusuke Hiki, Noriko F. Hiroi, Finterly Hu, Nhung Pham, Friederike Ehrhart, Egon L. Willighagen, Alberto Valdeolivas, Aurelien Dugourd, Francesco Messina, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Sylvain Soliman, Sara Sadat Aghamiri, Bhanwar Lal Puniya, Aurélien Naldi, Tomáš Helikar, Vidisha Singh, Marco Fariñas Fernández, Viviam Bermudez, Eirini Tsirvouli, Arnau Montagud, Vincent Noël, Miguel Ponce-de-Leon, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Augustin Luna, Janet Piñero, Laura I. Furlong, Irina Balaur, Adrien Rougny, Yohan Jarosz, Rupert W. Overall, Robert Phair, Livia Perfetto, Lisa Matthews, Devasahayam Arokia Balaya Rex, Marija Orlic-Milacic, Luis Cristobal Monraz Gomez, Bertrand De Meulder, Jean Marie Ravel, Bijay Jassal, Venkata Satagopam, Guanming Wu, Martin Golebiewski, Piotr Gawron, Laurence Calzone, Jacques S. Beckmann, Chris T. Evelo, Peter D’Eustachio, Falk Schreiber, Julio Saez-Rodriguez, Joaquin Dopazo, Martin Kuiper, Alfonso Valencia, Olaf Wolkenhauer, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community

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

Abel Sousa, Aurelien Dugourd, Danish Memon, Borgthor Petursson, Evangelia Petsalaki, Julio Saez‐Rodriguez, Pedro Beltrao

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Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease

Ricardo Omar Ramirez Flores, Jan David Lanzer, Daniel Dimitrov, Britta Velten, Julio Saez-Rodriguez

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Enablers and challenges of spatial omics, a melting pot of technologies

Theodore Alexandrov, Julio Saez‐Rodriguez, Sinem K Saka

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Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression

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

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