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; et al. (PLoS Comput. Biol., 2024)

DOT: Fast Cell Type Decomposition of Spatial Omics by Optimal Transport - Arezou Rahimi; Luís A. Vale Silva; Maria Faelth Savitski; Jovan Tanevski; Julio Saez-Rodriguez (CoRR, 2023)

Understanding metric-related pitfalls in image analysis validation - 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; et al. (CoRR, 2023)

AI Competitions and Benchmarks: The life cycle of challenges and benchmarks - Gustavo Stolovitzky; Julio Saez-Rodriguez; Julie Bletz; Jacob Albrecht; Gaia Andreoletti; James C. Costello; Paul C. Boutros (CoRR, 2023)

FUNKI: interactive functional footprint-based analysis of omics data - Rosa D. Hernansaiz-Ballesteros; Christian H. Holland; Aurélien Dugourd; Julio Saez-Rodriguez (Bioinform., 2022)

Parallel ant colony optimization for the training of cell signaling networks - Patricia González; Roberto Prado-Rodriguez; Attila Gábor; Julio Saez-Rodriguez; Julio R. Banga; Ramón Doallo (Expert Syst. Appl., 2022)

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity - Szilvia Barsi; Henrietta Papp; Alberto Valdeolivas; Dániel J. Tóth; Anett Kuczmog; Mónika Madai; László Hunyady; Péter Várnai; Julio Saez-Rodriguez; Ferenc Jakab; Bence Szalai (PLoS Comput. Biol., 2022)

Metrics reloaded: Pitfalls and recommendations for image analysis validation - 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; et al. (CoRR, 2022)

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 - 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; et al. (Briefings Bioinform., 2021)

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling - Alexander Mazein; Adrien Rougny; Jonathan R. Karr; Julio Saez-Rodriguez; Marek Ostaszewski; Reinhard Schneider (Briefings Bioinform., 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST) - 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; et al. (Bioinform., 2021)

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems - 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 (Bioinform., 2021)

A comprehensive database for integrated analysis of omics data in autoimmune diseases - 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; et al. (BMC Bioinform., 2021)

FUNKI: Interactive functional footprint-based analysis of omics data - Rosa D. Hernansaiz-Ballesteros; Christian H. Holland; Aurélien Dugourd; Julio Saez-Rodriguez (CoRR, 2021)

Bringing data from curated pathway resources to Cytoscape with OmniPath - Francesco Ceccarelli; Dénes Türei; Attila Gábor; Julio Saez-Rodriguez (Bioinform., 2020)

Converting networks to predictive logic models from perturbation signalling data with CellNOpt - Enio Gjerga; Panuwat Trairatphisan; Attila Gábor; Hermann Koch; Céline Chevalier; Franceco Ceccarelli; Aurélien Dugourd; Alexander Mitsos; Julio Saez-Rodriguez; Jonathan D. Wren (Bioinform., 2020)

BIAS: Transparent reporting of biomedical image analysis challenges - 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; et al. (Medical Image Anal., 2020)

Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology - Patricia González; Pablo Argüeso-Alejandro; David R. Penas; Xoán C. Pardo; Julio Saez-Rodriguez; Julio R. Banga; Ramón Doallo (J. Supercomput., 2019)

Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders - Matteo Manica; Ali Oskooei; Jannis Born; Vigneshwari Subramanian; Julio Sáez-Rodríguez; María Rodríguez Martínez (CoRR, 2019)

BIAS: Transparent reporting of biomedical image analysis challenges - 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; et al. (CoRR, 2019)

GDSCTools for mining pharmacogenomic interactions in cancer - Thomas Cokelaer; Elisabeth Chen; Francesco Iorio; Michael P. Menden; Howard Lightfoot; Julio Saez-Rodriguez; Mathew Garnett (Bioinform., 2018)

A systematic atlas of chaperome deregulation topologies across the human cancer landscape - Ali Hadizadeh Esfahani; Angelina Sverchkova; Julio Saez-Rodriguez; Andreas Schuppert; Marc Brehme (PLoS Comput. Biol., 2018)

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data - Misbah Razzaq; Loïc Paulevé; Anne Siegel; Julio Saez-Rodriguez; Jérémie Bourdon; Carito Guziolowski (PLoS Comput. Biol., 2018)

PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks - Ali Oskooei; Jannis Born; Matteo Manica; Vigneshwari Subramanian; Julio Sáez-Rodríguez; María Rodríguez Martínez (CoRR, 2018)

caspo: a toolbox for automated reasoning on the response of logical signaling networks families - Santiago Videla; Julio Saez-Rodriguez; Carito Guziolowski; Anne Siegel (Bioinform., 2017)

Benchmarking substrate-based kinase activity inference using phosphoproteomic data - Claudia Hernandez-Armenta; David Ochoa; Emanuel J. V. Gonçalves; Julio Saez-Rodriguez; Pedro Beltrão (Bioinform., 2017)

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast - Emanuel J. V. Gonçalves; Zrinka Raguz Nakic; Mattia Zampieri; Omar Wagih; David Ochoa; Uwe Sauer; Pedro Beltrão; Julio Saez-Rodriguez (PLoS Comput. Biol., 2017)

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models - David Henriques; Alejandro Fernández Villaverde; Miguel Rocha; Julio Saez-Rodriguez; Julio R. Banga (PLoS Comput. Biol., 2017)

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin - 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; et al. (BMC Bioinform., 2016)

Efficient randomization of biological networks while preserving functional characterization of individual nodes - Francesco Iorio; Marti Bernardo-Faura; Andrea Gobbi; Thomas Cokelaer; Giuseppe Jurman; Julio Saez-Rodriguez (BMC Bioinform., 2016)

Cooperative development of logical modelling standards and tools with CoLoMoTo - Aurélien Naldi; Pedro T. Monteiro; Christoph Müssel; Hans A. Kestler; Denis Thieffry; Ioannis Xenarios; Julio Saez-Rodriguez; Tomás Helikar; Claudine Chaouiya (Bioinform., 2015)

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach - David Henriques; Miguel Rocha; Julio Saez-Rodriguez; Julio R. Banga (Bioinform., 2015)

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies - Sven Thiele; Luca Cerone; Julio Saez-Rodriguez; Anne Siegel; Carito Guziolowski; Steffen Klamt (BMC Bioinform., 2015)

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology - 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; et al. (BMC Syst. Biol., 2015)

Learning Boolean logic models of signaling networks with ASP - Santiago Videla; Carito Guziolowski; Federica Eduati; Sven Thiele; Martin Gebser; Jacques Nicolas; Julio Saez-Rodriguez; Torsten Schaub; Anne Siegel (Theor. Comput. Sci., 2015)

DREAMTools: a Python package for scoring collaborative challenges - 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; et al. (F1000Research, 2015)

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming - Carito Guziolowski; Santiago Videla; Federica Eduati; Sven Thiele; Thomas Cokelaer; Anne Siegel; Julio Saez-Rodriguez (Bioinform., 2014)

Fast randomization of large genomic datasets while preserving alteration counts - 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 (Bioinform., 2014)

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models - Anke Ryll; Joachim Bucher; Anne Bonin; Sophia Bongard; Emanuel J. V. Gonçalves; Julio Saez-Rodriguez; Jens Niklas; Steffen Klamt (Biosyst., 2014)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics - Jose A. Egea; David Henriques; Thomas Cokelaer; Alejandro Fernández Villaverde; Aidan MacNamara; Diana-Patricia Danciu; Julio R. Banga; Julio Saez-Rodriguez (BMC Bioinform., 2014)

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach - 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; et al. (BMC Syst. Biol., 2014)

8th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2014, 4-6 June, 2014, Salamanca, Spain - Julio Saez-Rodriguez; Miguel P. Rocha; Florentino Fdez-Riverola; Juan F. De Paz Santana (Springer, 2014)

BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology - 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; et al. (CoRR, 2014)

Using Python to Dive into Signalling Data with CellNOpt and BioServices - Thomas Cokelaer; Julio Saez-Rodriguez (CoRR, 2014)

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data - Clare Pacini; Francesco Iorio; Emanuel J. V. Gonçalves; Murat Iskar; Thomas Klabunde; Peer Bork; Julio Saez-Rodriguez (Bioinform., 2013)

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming - Carito Guziolowski; Santiago Videla; Federica Eduati; Sven Thiele; Thomas Cokelaer; Anne Siegel; Julio Saez-Rodriguez (Bioinform., 2013)

BioServices: a common Python package to access biological Web Services programmatically - Thomas Cokelaer; Dennis Pultz; Lea M. Harder; Jordi Serra-Musach; Julio Saez-Rodriguez (Bioinform., 2013)

CySBGN: A Cytoscape plug-in to integrate SBGN maps - Emanuel J. V. Gonçalves; Martijn P. van Iersel; Julio Saez-Rodriguez (BMC Bioinform., 2013)

Path2Models: large-scale generation of computational models from biochemical pathway maps - 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; et al. (BMC Syst. Biol., 2013)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools - 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; et al. (BMC Syst. Biol., 2013)

Network based elucidation of drug response: from modulators to targets - Francesco Iorio; Julio Saez-Rodriguez; Diego di Bernardo (BMC Syst. Biol., 2013)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics - Jose A. Egea; David Henriques; Thomas Cokelaer; Alejandro Fernández Villaverde; Julio R. Banga; Julio Saez-Rodriguez (CoRR, 2013)

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages - Emanuel J. V. Gonçalves; Julio Saez-Rodriguez (F1000Research, 2013)

Integrating literature-constrained and data-driven inference of signalling networks - Federica Eduati; Javier De Las Rivas; Barbara Di Camillo; Gianna Toffolo; Julio Saez-Rodriguez (Bioinform., 2012)

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks - Daniel C. Kirouac; Julio Saez-Rodriguez; Jennifer Swantek; John M. Burke; Douglas A. Lauffenburger; Peter K. Sorger (BMC Syst. Biol., 2012)

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms - 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 (BMC Syst. Biol., 2012)

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP - Santiago Videla; Carito Guziolowski; Federica Eduati; Sven Thiele; Niels Grabe; Julio Saez-Rodriguez; Anne Siegel (Computational Methods in Systems Biology - 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings, 2012)

Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming - Santiago Videla; Carito Guziolowski; Federica Eduati; Sven Thiele; Niels Grabe; Julio Saez-Rodriguez; Anne Siegel (CoRR, 2012)

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties - Michael P. Menden; Francesco Iorio; Mathew Garnett; Ultan McDermott; Cyril Benes; Pedro J. Ballester; Julio Saez-Rodriguez (CoRR, 2012)

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli - Melody K. Morris; Julio Saez-Rodriguez; David C. Clarke; Peter K. Sorger; Douglas A. Lauffenburger (PLoS Comput. Biol., 2011)

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling - Dominik M. Wittmann; Jan Krumsiek; Julio Saez-Rodriguez; Douglas A. Lauffenburger; Steffen Klamt; Fabian J. Theis (BMC Syst. Biol., 2009)

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling - Bree B. Aldridge; Julio Saez-Rodriguez; Jeremy Muhlich; Peter K. Sorger; Douglas A. Lauffenburger (PLoS Comput. Biol., 2009)

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data - Regina Samaga; Julio Saez-Rodriguez; Leonidas G. Alexopoulos; Peter K. Sorger; Steffen Klamt (PLoS Comput. Biol., 2009)

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data - Alexander Mitsos; Ioannis N. Melas; Paraskeuas Siminelakis; Aikaterini D. Chairakaki; Julio Saez-Rodriguez; Leonidas G. Alexopoulos (PLoS Comput. Biol., 2009)

Flexible informatics for linking experimental data to mathematical models via DataRail - Julio Saez-Rodriguez; Arthur Goldsipe; Jeremy Muhlich; Leonidas G. Alexopoulos; Bjorn Millard; Douglas A. Lauffenburger; Peter K. Sorger (Bioinform., 2008)

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules - Julio Saez-Rodriguez; Stefan Gayer; Martin Ginkel; Ernst Dieter Gilles (ECCB'08 Proceedings, Seventh European Conference on Computational Biology, 22-26 September 2008, Cagliari, Italy, 2008)

Structural and functional analysis of cellular networks with CellNetAnalyzer - Steffen Klamt; Julio Saez-Rodriguez; Ernst Dieter Gilles (BMC Syst. Biol., 2007)

A Logical Model Provides Insights into T Cell Receptor Signaling - 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 (PLoS Comput. Biol., 2007)

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks - Holger Conzelmann; Julio Saez-Rodriguez; Thomas Sauter; Boris N. Kholodenko; Ernst Dieter Gilles (BMC Bioinform., 2006)

A methodology for the structural and functional analysis of signaling and regulatory networks - Steffen Klamt; Julio Saez-Rodriguez; Jonathan A. Lindquist; Luca Simeoni; Ernst Dieter Gilles (BMC Bioinform., 2006)

Visual setup of logical models of signaling and regulatory networks with ProMoT - Julio Saez-Rodriguez; Sebastian Mirschel; Rebecca Hemenway; Steffen Klamt; Ernst Dieter Gilles; Martin Ginkel (BMC Bioinform., 2006)

Dissecting the puzzle of life: modularization of signal transduction networks - Julio Saez-Rodriguez; Andreas Kremling; Ernst Dieter Gilles (Comput. Chem. Eng., 2005)

Topological Analysis and Visualisation of large Signalling Networks: The TGF-beta Signal Transductionin Eukaryotic Systems - Knut Behrendt; Andreas Politzer; Julio Saez-Rodriguez; Matthias Reuss; Klaus Mauch (Computer science and biology: Proceedings of the German Conference on Bioinformatics, GCB 2001, October 7-10, 2001, Braunschweig, Germany, 2001)