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Julio Saez-Rodriguez
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2020 – today
- 2024
- [j54]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) - 2023
- [i15]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 abs/2301.01682 (2023) - [i14]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 abs/2302.01790 (2023) - [i13]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 abs/2312.05296 (2023) - 2022
- [j53]Rosa D. Hernansaiz-Ballesteros
, Christian H. Holland
, Aurélien Dugourd, Julio Saez-Rodriguez
:
FUNKI: interactive functional footprint-based analysis of omics data. Bioinform. 38(7): 2075-2076 (2022) - [j52]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: 118199 (2022) - [j51]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) - [i12]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 A. 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 M. 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 abs/2206.01653 (2022) - 2021
- [j50]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): 1848-1859 (2021) - [j49]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) - [j48]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): 5712-5718 (2021) - [j47]Andreas Dräger
, Tomás Helikar, Matteo Barberis
, Marc R. 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): 3702-3706 (2021) - [j46]Jordi Martorell-Marugan
, Raúl López-Domínguez
, Adrián García-Moreno
, Daniel Toro-Domínguez
, Juan Antonio Villatoro-García, Guillermo Barturen
, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez-López
, Fátima Al-Shahrour, Víctor González-Rumayor, María Peña-Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez
, Marta E. Alarcón-Riquelme, Pedro Carmona-Saez
:
A comprehensive database for integrated analysis of omics data in autoimmune diseases. BMC Bioinform. 22(1): 343 (2021) - [i11]Rosa D. Hernansaiz-Ballesteros, Christian H. Holland, Aurélien Dugourd, Julio Saez-Rodriguez:
FUNKI: Interactive functional footprint-based analysis of omics data. CoRR abs/2109.05796 (2021) - 2020
- [j45]Francesco Ceccarelli
, Dénes Türei, Attila Gábor
, Julio Saez-Rodriguez
:
Bringing data from curated pathway resources to Cytoscape with OmniPath. Bioinform. 36(8): 2632-2633 (2020) - [j44]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): 4523-4524 (2020) - [j43]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: 101796 (2020)
2010 – 2019
- 2019
- [j42]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): 3471-3498 (2019) - [i10]Matteo Manica, Ali Oskooei, Jannis Born
, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
:
Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders. CoRR abs/1904.11223 (2019) - [i9]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 abs/1910.04071 (2019) - 2018
- [j41]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): 1226-1228 (2018) - [j40]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) - [j39]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) - [i8]Ali Oskooei, Jannis Born
, Matteo Manica, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
:
PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks. CoRR abs/1811.06802 (2018) - 2017
- [j38]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): 947-950 (2017) - [j37]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): 1845-1851 (2017) - [j36]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) - [j35]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) - 2016
- [j34]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: 155 (2016) - [j33]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: 542:1-542:14 (2016) - 2015
- [j32]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): 1154-1159 (2015) - [j31]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): 2999-3007 (2015) - [j30]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: 345:1-345:13 (2015) - [j29]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: 8 (2015) - [j28]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: 79-101 (2015) - [i7]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: 1030 (2015) - 2014
- [j27]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): 1942 (2014) - [j26]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): 617-623 (2014) - [j25]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: 26-38 (2014) - [j24]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: 136 (2014) - [j23]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: 13 (2014) - [e1]Julio Saez-Rodriguez, Miguel P. Rocha
, Florentino Fdez-Riverola
, Juan F. De Paz Santana
:
8th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2014, 4-6 June, 2014, Salamanca, Spain. Advances in Intelligent Systems and Computing 294, Springer 2014, ISBN 978-3-319-07580-8 [contents] - [i6]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 abs/1407.5856 (2014) - [i5]Thomas Cokelaer, Julio Saez-Rodriguez:
Using Python to Dive into Signalling Data with CellNOpt and BioServices. CoRR abs/1412.6386 (2014) - 2013
- [j22]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): 132-134 (2013) - [j21]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): 2320-2326 (2013) - [j20]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): 3241-3242 (2013) - [j19]Emanuel J. V. Gonçalves
, Martijn P. van Iersel
, Julio Saez-Rodriguez
:
CySBGN: A Cytoscape plug-in to integrate SBGN maps. BMC Bioinform. 14: 17 (2013) - [j18]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: 116 (2013) - [j17]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: 135 (2013) - [j16]Francesco Iorio
, Julio Saez-Rodriguez
, Diego di Bernardo
:
Network based elucidation of drug response: from modulators to targets. BMC Syst. Biol. 7: 139 (2013) - [i4]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 abs/1311.5735 (2013) - [i3]Emanuel J. V. Gonçalves
, Julio Saez-Rodriguez
:
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages. F1000Research 2: 192 (2013) - 2012
- [j15]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): 2311-2317 (2012) - [j14]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: 29 (2012) - [j13]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: 133 (2012) - [c3]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: 342-361 - [i2]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 abs/1210.0690 (2012) - [i1]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 abs/1212.0504 (2012) - 2011
- [j12]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)
2000 – 2009
- 2009
- [j11]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: 98 (2009) - [j10]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) - [j9]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) - [j8]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) - 2008
- [j7]Julio Saez-Rodriguez
, Arthur Goldsipe, Jeremy Muhlich
, Leonidas G. Alexopoulos
, Bjorn Millard, Douglas A. Lauffenburger, Peter K. Sorger
:
Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinform. 24(6): 840-847 (2008) - [c2]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: 213-219 - 2007
- [j6]Steffen Klamt
, Julio Saez-Rodriguez
, Ernst Dieter Gilles:
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1: 2 (2007) - [j5]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) - 2006
- [j4]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: 34 (2006) - [j3]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: 56 (2006) - [j2]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: 506 (2006) - 2005
- [j1]Julio Saez-Rodriguez
, Andreas Kremling, Ernst Dieter Gilles:
Dissecting the puzzle of life: modularization of signal transduction networks. Comput. Chem. Eng. 29(3): 619-629 (2005) - 2001
- [c1]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: 143-144
Coauthor Index
![](https://dblp.dagstuhl.de/img/cog.dark.24x24.png)
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