Julio Saez-Rodriguez

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 27

Top Topics

Systems Biology

Dynamic Optimization

Top Venues

PLoS Comput. Biol.

Publications

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, Magí Andorrà, Sara Llufriu, Albert Saiz, Yolanda Blanco, Eloy Martinez-Heras, Elisabeth Solana, Irene Pulido-Valdeolivas, Elena H. Martinez-Lapiscina, Jordi García-Ojalvo, Pablo Villoslada
Multiscale networks in multiple sclerosis. PLoS Comput. Biol. 20 (2) (2024)
Gustavo Stolovitzky, Julio Saez-Rodriguez, Julie Bletz, Jacob Albrecht, Gaia Andreoletti, James C. Costello, Paul C. Boutros
AI Competitions and Benchmarks: The life cycle of challenges and benchmarks. CoRR (2023)
Annika Reinke, Minu Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Carole H. Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B. Blaschko, Florian Büttner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini, Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp-Schneider, Michal Kozubek, Anna Kreshuk, Tahsin M. Kurç, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus H. Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern H. Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M. Rafelski, Nasir M. Rajpoot, Mauricio Reyes, Michael A. Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I. Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul F. Jäger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. CoRR (2023)
Arezou Rahimi, Luís A. Vale Silva, Maria Faelth Savitski, Jovan Tanevski, Julio Saez-Rodriguez
DOT: Fast Cell Type Decomposition of Spatial Omics by Optimal Transport. CoRR (2023)
Patricia González, Roberto Prado-Rodriguez, Attila Gábor, Julio Saez-Rodriguez, Julio R. Banga, Ramón Doallo
Parallel ant colony optimization for the training of cell signaling networks. Expert Syst. Appl. 208 (2022)
Rosa D. Hernansaiz-Ballesteros, Christian H. Holland, Aurélien Dugourd, Julio Saez-Rodriguez
FUNKI: interactive functional footprint-based analysis of omics data. Bioinform. 38 (7) (2022)
Szilvia Barsi, Henrietta Papp, Alberto Valdeolivas, Dániel J. Tóth, Anett Kuczmog, Mónika Madai, László Hunyady, Péter Várnai, Julio Saez-Rodriguez, Ferenc Jakab, Bence Szalai
Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity. PLoS Comput. Biol. 18 (4) (2022)
Lena Maier-Hein, Annika Reinke, Evangelia Christodoulou, Ben Glocker, Patrick Godau, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A. Riegler, Manuel Wiesenfarth, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Minu Dietlinde Tizabi, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, M. Jorge Cardoso, Veronika Cheplygina, Beth Cimini, Gary S. Collins, Keyvan Farahani, Bram van Ginneken, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Pierre Jannin, Charles E. Kahn, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Annette Kopp-Schneider, Anna Kreshuk, Tahsin M. Kurç, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus H. Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern H. Menze, David Moher, Karel G. M. Moons, Henning Müller, Felix Nickel, Brennan Nichyporuk, Jens Petersen, Nasir Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clarisa Sánchez Gutiérrez, Shravya Shetty, Maarten van Smeden, Carole H. Sudre, Ronald M. Summers, Abdel A. Taha, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Paul F. Jäger
Metrics reloaded: Pitfalls and recommendations for image analysis validation. CoRR (2022)
Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C. Lovering, Sandra E. Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36 (24) (2021)
Alexander Mazein, Adrien Rougny, Jonathan R. Karr, Julio Saez-Rodriguez, Marek Ostaszewski, Reinhard Schneider
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. Briefings Bioinform. 22 (5) (2021)
Rosa D. Hernansaiz-Ballesteros, Christian H. Holland, Aurélien Dugourd, Julio Saez-Rodriguez
FUNKI: Interactive functional footprint-based analysis of omics data. CoRR (2021)
Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik-Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C. Freeman, Paul D. Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone
Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. Briefings Bioinform. 22 (2) (2021)
Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37 (21) (2021)
Lena Maier-Hein, Annika Reinke, Michal Kozubek, Anne L. Martel, Tal Arbel, Matthias Eisenmann, Allan Hanbury, Pierre Jannin, Henning Müller, Sinan Onogur, Julio Saez-Rodriguez, Bram van Ginneken, Annette Kopp-Schneider, Bennett A. Landman
BIAS: Transparent reporting of biomedical image analysis challenges. Medical Image Anal. 66 (2020)
Francesco Ceccarelli, Dénes Türei, Attila Gábor, Julio Saez-Rodriguez
Bringing data from curated pathway resources to Cytoscape with OmniPath. Bioinform. 36 (8) (2020)
Enio Gjerga, Panuwat Trairatphisan, Attila Gábor, Hermann Koch, Céline Chevalier, Franceco Ceccarelli, Aurélien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez, Jonathan D. Wren
Converting networks to predictive logic models from perturbation signalling data with CellNOpt. Bioinform. 36 (16) (2020)
Lena Maier-Hein, Annika Reinke, Michal Kozubek, Anne L. Martel, Tal Arbel, Matthias Eisenmann, Allan Hanbury, Pierre Jannin, Henning Müller, Sinan Onogur, Julio Saez-Rodriguez, Bram van Ginneken, Annette Kopp-Schneider, Bennett A. Landman
BIAS: Transparent reporting of biomedical image analysis challenges. CoRR (2019)
Patricia González, Pablo Argüeso-Alejandro, David R. Penas, Xoán C. Pardo, Julio Saez-Rodriguez, Julio R. Banga, Ramón Doallo
Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology. J. Supercomput. 75 (7) (2019)
Thomas Cokelaer, Elisabeth Chen, Francesco Iorio, Michael P. Menden, Howard Lightfoot, Julio Saez-Rodriguez, Mathew Garnett
GDSCTools for mining pharmacogenomic interactions in cancer. Bioinform. 34 (7) (2018)
Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, Carito Guziolowski
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PLoS Comput. Biol. 14 (10) (2018)
Ali Hadizadeh Esfahani, Angelina Sverchkova, Julio Saez-Rodriguez, Andreas Schuppert, Marc Brehme
A systematic atlas of chaperome deregulation topologies across the human cancer landscape. PLoS Comput. Biol. 14 (1) (2018)
Santiago Videla, Julio Saez-Rodriguez, Carito Guziolowski, Anne Siegel
caspo: a toolbox for automated reasoning on the response of logical signaling networks families. Bioinform. 33 (6) (2017)
Emanuel J. V. Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão, Julio Saez-Rodriguez
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PLoS Comput. Biol. 13 (1) (2017)
David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PLoS Comput. Biol. 13 (2) (2017)
Claudia Hernandez-Armenta, David Ochoa, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Pedro Beltrão
Benchmarking substrate-based kinase activity inference using phosphoproteomic data. Bioinform. 33 (12) (2017)
Rob Patro, Raquel Norel, Robert J. Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Lustrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky, Carl Kingsford
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. BMC Bioinform. 17 (2016)
Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman, Julio Saez-Rodriguez
Efficient randomization of biological networks while preserving functional characterization of individual nodes. BMC Bioinform. 17 (2016)
David Henriques, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Bioinform. 31 (18) (2015)
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. 31 (7) (2015)
Sven Thiele, Luca Cerone, Julio Saez-Rodriguez, Anne Siegel, Carito Guziolowski, Steffen Klamt
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinform. 16 (2015)
Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, Julio R. Banga
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Syst. Biol. 9 (2015)
Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Mehmet Gönen, Steven M. Hill, Bruce R. Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Saez-Rodriguez
DREAMTools: a Python package for scoring collaborative challenges. F1000Research 4 (2015)
Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Martin Gebser, Jacques Nicolas, Julio Saez-Rodriguez, Torsten Schaub, Anne Siegel
Learning Boolean logic models of signaling networks with ASP. Theor. Comput. Sci. 599 (2015)
Andrea Gobbi, Francesco Iorio, Kevin J. Dawson, David C. Wedge, David Tamborero, Ludmil B. Alexandrov, Núria López-Bigas, Mathew Garnett, Giuseppe Jurman, Julio Saez-Rodriguez
Fast randomization of large genomic datasets while preserving alteration counts. Bioinform. 30 (17) (2014)
Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, Julio R. Banga
BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology. CoRR (2014)
Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst. Biol. 8 (2014)
Thomas Cokelaer, Julio Saez-Rodriguez
Using Python to Dive into Signalling Data with CellNOpt and BioServices. CoRR (2014)
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R. Banga, Julio Saez-Rodriguez
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinform. 15 (2014)
Anke Ryll, Joachim Bucher, Anne Bonin, Sophia Bongard, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Jens Niklas, Steffen Klamt
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosyst. 124 (2014)
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinform. 30 (13) (2014)
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinform. 29 (18) (2013)
Thomas Cokelaer, Dennis Pultz, Lea M. Harder, Jordi Serra-Musach, Julio Saez-Rodriguez
BioServices: a common Python package to access biological Web Services programmatically. Bioinform. 29 (24) (2013)
Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7 (2013)
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7 (2013)
Clare Pacini, Francesco Iorio, Emanuel J. V. Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinform. 29 (1) (2013)
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Julio R. Banga, Julio Saez-Rodriguez
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. CoRR (2013)
Francesco Iorio, Julio Saez-Rodriguez, Diego di Bernardo
Network based elucidation of drug response: from modulators to targets. BMC Syst. Biol. 7 (2013)
Emanuel J. V. Gonçalves, Martijn P. van Iersel, Julio Saez-Rodriguez
CySBGN: A Cytoscape plug-in to integrate SBGN maps. BMC Bioinform. 14 (2013)
Emanuel J. V. Gonçalves, Julio Saez-Rodriguez
packages. F1000Research 2 (2013)
Daniel C. Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M. Burke, Douglas A. Lauffenburger, Peter K. Sorger
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst. Biol. 6 (2012)
Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel
Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming CoRR (2012)
Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel J. V. Gonçalves, Melody K. Morris, Martijn P. van Iersel, Douglas A. Lauffenburger, Julio Saez-Rodriguez
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst. Biol. 6 (2012)
Federica Eduati, Javier De Las Rivas, Barbara Di Camillo, Gianna Toffolo, Julio Saez-Rodriguez
Integrating literature-constrained and data-driven inference of signalling networks. Bioinform. 28 (18) (2012)
Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel
Revisiting the Training of Logic Models of Protein Signaling Networks with ASP. CMSB (2012)
Michael P. Menden, Francesco Iorio, Mathew Garnett, Ultan McDermott, Cyril Benes, Pedro J. Ballester, Julio Saez-Rodriguez
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties CoRR (2012)
Melody K. Morris, Julio Saez-Rodriguez, David C. Clarke, Peter K. Sorger, Douglas A. Lauffenburger
Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. PLoS Comput. Biol. 7 (3) (2011)
Regina Samaga, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, Steffen Klamt
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. PLoS Comput. Biol. 5 (8) (2009)
Bree B. Aldridge, Julio Saez-Rodriguez, Jeremy Muhlich, Peter K. Sorger, Douglas A. Lauffenburger
Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. PLoS Comput. Biol. 5 (4) (2009)
Alexander Mitsos, Ioannis N. Melas, Paraskeuas Siminelakis, Aikaterini D. Chairakaki, Julio Saez-Rodriguez, Leonidas G. Alexopoulos
Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data. PLoS Comput. Biol. 5 (12) (2009)
Dominik M. Wittmann, Jan Krumsiek, Julio Saez-Rodriguez, Douglas A. Lauffenburger, Steffen Klamt, Fabian J. Theis
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst. Biol. 3 (2009)
Julio Saez-Rodriguez, Stefan Gayer, Martin Ginkel, Ernst Dieter Gilles
Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. ECCB (2008)
Julio Saez-Rodriguez, Arthur Goldsipe, Jeremy Muhlich, Leonidas G. Alexopoulos, Bjorn Millard, Douglas A. Lauffenburger, Peter K. Sorger
. Bioinform. 24 (6) (2008)
Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1 (2007)
Julio Saez-Rodriguez, Luca Simeoni, Jonathan A. Lindquist, Rebecca Hemenway, Ursula Bommhardt, Boerge Arndt, Utz-Uwe Haus, Robert Weismantel, Ernst Dieter Gilles, Steffen Klamt, Burkhart Schraven
A Logical Model Provides Insights into T Cell Receptor Signaling. PLoS Comput. Biol. 3 (8) (2007)
Steffen Klamt, Julio Saez-Rodriguez, Jonathan A. Lindquist, Luca Simeoni, Ernst Dieter Gilles
A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinform. 7 (2006)
Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst Dieter Gilles, Martin Ginkel
Visual setup of logical models of signaling and regulatory networks with ProMoT. BMC Bioinform. 7 (2006)
Holger Conzelmann, Julio Saez-Rodriguez, Thomas Sauter, Boris N. Kholodenko, Ernst Dieter Gilles
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. BMC Bioinform. 7 (2006)
Julio Saez-Rodriguez, Andreas Kremling, Ernst Dieter Gilles
Dissecting the puzzle of life: modularization of signal transduction networks. Comput. Chem. Eng. 29 (3) (2005)
Knut Behrendt, Andreas Politzer, Julio Saez-Rodriguez, Matthias Reuss, Klaus Mauch
Topological Analysis and Visualisation of large Signalling Networks: The TGF-beta Signal Transductionin Eukaryotic Systems. German Conference on Bioinformatics (2001)