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ORCIDBibTeX records: Julio Saez-Rodriguez
@article{DBLP:journals/ploscb/KennedyRUCICPHBBHBBPBBBKASCZMKSR24,
author = {Keith E. Kennedy and
Nicole Kerlero de Rosbo and
Antonio Uccelli and
Maria Cellerino and
Federico Ivaldi and
Paola Contini and
Raffaele De Palma and
Hanne F. Harbo and
Tone Berge and
Steffan D. Bos and
Einar A. H{\o}gest{\o}l and
Synne Brune{-}Ingebretsen and
Sigrid A. de Rodez Benavent and
Friedemann Paul and
Alexander U. Brandt and
Priscilla B{\"{a}}cker{-}Koduah and
Janina Behrens and
Joseph Kuchling and
Susanna Asseyer and
Michael Scheel and
Claudia Chien and
Hanna Zimmermann and
Seyedamirhosein Motamedi and
Josef Kauer{-}Bonin and
Julio Saez{-}Rodriguez and
Melanie Rinas and
Leonidas G. Alexopoulos and
Magi Andorra and
Sara Llufriu and
Albert Saiz and
Yolanda Blanco and
Eloy Martinez{-}Heras and
Elisabeth Solana and
Irene Pulido{-}Valdeolivas and
Elena H. Martinez{-}Lapiscina and
Jordi Garc{\'{\i}}a{-}Ojalvo and
Pablo Villoslada},
title = {Multiscale networks in multiple sclerosis},
journal = {PLoS Comput. Biol.},
volume = {20},
number = {2},
year = {2024},
url = {https://doi.org/10.1371/journal.pcbi.1010980},
doi = {10.1371/JOURNAL.PCBI.1010980},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KennedyRUCICPHBBHBBPBBBKASCZMKSR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2301-01682,
author = {Arezou Rahimi and
Lu{\'{\i}}s A. Vale Silva and
Maria Faelth Savitski and
Jovan Tanevski and
Julio Saez{-}Rodriguez},
title = {{DOT:} Fast Cell Type Decomposition of Spatial Omics by Optimal Transport},
journal = {CoRR},
volume = {abs/2301.01682},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2301.01682},
doi = {10.48550/ARXIV.2301.01682},
eprinttype = {arXiv},
eprint = {2301.01682},
timestamp = {Tue, 10 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2301-01682.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-01790,
author = {Annika Reinke and
Minu Tizabi and
Michael Baumgartner and
Matthias Eisenmann and
Doreen Heckmann{-}N{\"{o}}tzel and
A. Emre Kavur and
Tim R{\"{a}}dsch and
Carole H. Sudre and
Laura Aci{\'{o}}n and
Michela Antonelli and
Tal Arbel and
Spyridon Bakas and
Arriel Benis and
Matthew B. Blaschko and
Florian B{\"{u}}ttner and
M. Jorge Cardoso and
Veronika Cheplygina and
Jianxu Chen and
Evangelia Christodoulou and
Beth A. Cimini and
Gary S. Collins and
Keyvan Farahani and
Luciana Ferrer and
Adrian Galdran and
Bram van Ginneken and
Ben Glocker and
Patrick Godau and
Robert Haase and
Daniel A. Hashimoto and
Michael M. Hoffman and
Merel Huisman and
Fabian Isensee and
Pierre Jannin and
Charles E. Kahn and
Dagmar Kainmueller and
Bernhard Kainz and
Alexandros Karargyris and
Alan Karthikesalingam and
Hannes Kenngott and
Jens Kleesiek and
Florian Kofler and
Thijs Kooi and
Annette Kopp{-}Schneider and
Michal Kozubek and
Anna Kreshuk and
Tahsin M. Kur{\c{c}} and
Bennett A. Landman and
Geert Litjens and
Amin Madani and
Klaus H. Maier{-}Hein and
Anne L. Martel and
Peter Mattson and
Erik Meijering and
Bjoern H. Menze and
Karel G. M. Moons and
Henning M{\"{u}}ller and
Brennan Nichyporuk and
Felix Nickel and
Jens Petersen and
Susanne M. Rafelski and
Nasir M. Rajpoot and
Mauricio Reyes and
Michael A. Riegler and
Nicola Rieke and
Julio Saez{-}Rodriguez and
Clara I. S{\'{a}}nchez and
Shravya Shetty and
Maarten van Smeden and
Ronald M. Summers and
Abdel A. Taha and
Aleksei Tiulpin and
Sotirios A. Tsaftaris and
Ben Van Calster and
Ga{\"{e}}l Varoquaux and
Manuel Wiesenfarth and
Ziv R. Yaniv and
Paul F. J{\"{a}}ger and
Lena Maier{-}Hein},
title = {Understanding metric-related pitfalls in image analysis validation},
journal = {CoRR},
volume = {abs/2302.01790},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.01790},
doi = {10.48550/ARXIV.2302.01790},
eprinttype = {arXiv},
eprint = {2302.01790},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-01790.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2312-05296,
author = {Gustavo Stolovitzky and
Julio Saez{-}Rodriguez and
Julie Bletz and
Jacob Albrecht and
Gaia Andreoletti and
James C. Costello and
Paul C. Boutros},
title = {{AI} Competitions and Benchmarks: The life cycle of challenges and
benchmarks},
journal = {CoRR},
volume = {abs/2312.05296},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2312.05296},
doi = {10.48550/ARXIV.2312.05296},
eprinttype = {arXiv},
eprint = {2312.05296},
timestamp = {Wed, 03 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2312-05296.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Hernansaiz-Ballesteros22,
author = {Rosa D. Hernansaiz{-}Ballesteros and
Christian H. Holland and
Aur{\'{e}}lien Dugourd and
Julio Saez{-}Rodriguez},
title = {{FUNKI:} interactive functional footprint-based analysis of omics
data},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2075--2076},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac055},
doi = {10.1093/BIOINFORMATICS/BTAC055},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Hernansaiz-Ballesteros22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/eswa/GonzalezPGSBD22,
author = {Patricia Gonz{\'{a}}lez and
Roberto Prado{-}Rodriguez and
Attila G{\'{a}}bor and
Julio Saez{-}Rodriguez and
Julio R. Banga and
Ram{\'{o}}n Doallo},
title = {Parallel ant colony optimization for the training of cell signaling
networks},
journal = {Expert Syst. Appl.},
volume = {208},
pages = {118199},
year = {2022},
url = {https://doi.org/10.1016/j.eswa.2022.118199},
doi = {10.1016/J.ESWA.2022.118199},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/eswa/GonzalezPGSBD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/BarsiPVTKMHVSJS22,
author = {Szilvia Barsi and
Henrietta Papp and
Alberto Valdeolivas and
D{\'{a}}niel J. T{\'{o}}th and
Anett Kuczmog and
M{\'{o}}nika Madai and
L{\'{a}}szl{\'{o}} Hunyady and
P{\'{e}}ter V{\'{a}}rnai and
Julio Saez{-}Rodriguez and
Ferenc Jakab and
Bence Szalai},
title = {Computational drug repurposing against SARS-CoV-2 reveals plasma membrane
cholesterol depletion as key factor of antiviral drug activity},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {4},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1010021},
doi = {10.1371/JOURNAL.PCBI.1010021},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/BarsiPVTKMHVSJS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2206-01653,
author = {Lena Maier{-}Hein and
Annika Reinke and
Evangelia Christodoulou and
Ben Glocker and
Patrick Godau and
Fabian Isensee and
Jens Kleesiek and
Michal Kozubek and
Mauricio Reyes and
Michael A. Riegler and
Manuel Wiesenfarth and
Michael Baumgartner and
Matthias Eisenmann and
Doreen Heckmann{-}N{\"{o}}tzel and
A. Emre Kavur and
Tim R{\"{a}}dsch and
Minu Dietlinde Tizabi and
Laura Aci{\'{o}}n and
Michela Antonelli and
Tal Arbel and
Spyridon Bakas and
Peter Bankhead and
Arriel Benis and
M. Jorge Cardoso and
Veronika Cheplygina and
Beth A. Cimini and
Gary S. Collins and
Keyvan Farahani and
Bram van Ginneken and
Daniel A. Hashimoto and
Michael M. Hoffman and
Merel Huisman and
Pierre Jannin and
Charles E. Kahn and
Alexandros Karargyris and
Alan Karthikesalingam and
Hannes Kenngott and
Annette Kopp{-}Schneider and
Anna Kreshuk and
Tahsin M. Kur{\c{c}} and
Bennett A. Landman and
Geert Litjens and
Amin Madani and
Klaus H. Maier{-}Hein and
Anne L. Martel and
Peter Mattson and
Erik Meijering and
Bjoern H. Menze and
David Moher and
Karel G. M. Moons and
Henning M{\"{u}}ller and
Felix Nickel and
Brennan Nichyporuk and
Jens Petersen and
Nasir M. Rajpoot and
Nicola Rieke and
Julio Saez{-}Rodriguez and
Clarisa S{\'{a}}nchez Guti{\'{e}}rrez and
Shravya Shetty and
Maarten van Smeden and
Carole H. Sudre and
Ronald M. Summers and
Abdel A. Taha and
Sotirios A. Tsaftaris and
Ben Van Calster and
Ga{\"{e}}l Varoquaux and
Paul F. J{\"{a}}ger},
title = {Metrics reloaded: Pitfalls and recommendations for image analysis
validation},
journal = {CoRR},
volume = {abs/2206.01653},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2206.01653},
doi = {10.48550/ARXIV.2206.01653},
eprinttype = {arXiv},
eprint = {2206.01653},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2206-01653.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NiarakisKOMCTFT21,
author = {Anna Niarakis and
Martin Kuiper and
Marek Ostaszewski and
Rahuman S. Malik{-}Sheriff and
Cristina Casals{-}Casas and
Denis Thieffry and
Tom C. Freeman and
Paul D. Thomas and
Vasundra Tour{\'{e}} and
Vincent No{\"{e}}l and
Gautier Stoll and
Julio Saez{-}Rodriguez and
Aur{\'{e}}lien Naldi and
Eugenia Oshurko and
Ioannis Xenarios and
Sylvain Soliman and
Claudine Chaouiya and
Tom{\'{a}}s Helikar and
Laurence Calzone},
title = {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},
journal = {Briefings Bioinform.},
volume = {22},
number = {2},
pages = {1848--1859},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa046},
doi = {10.1093/BIB/BBAA046},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/NiarakisKOMCTFT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MazeinRKSOS21,
author = {Alexander Mazein and
Adrien Rougny and
Jonathan R. Karr and
Julio Saez{-}Rodriguez and
Marek Ostaszewski and
Reinhard Schneider},
title = {Reusability and composability in process description maps: {RAS-RAF-MEK-ERK}
signalling},
journal = {Briefings Bioinform.},
volume = {22},
number = {5},
year = {2021},
url = {https://doi.org/10.1093/bib/bbab103},
doi = {10.1093/BIB/BBAB103},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MazeinRKSOS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ToureVALOBCCdFG21,
author = {Vasundra Tour{\'{e}} and
Steven Vercruysse and
Marcio Luis Acencio and
Ruth C. Lovering and
Sandra E. Orchard and
Glyn Bradley and
Cristina Casals{-}Casas and
Claudine Chaouiya and
Noemi del{-}Toro and
{\AA}smund Flobak and
Pascale Gaudet and
Henning Hermjakob and
Charles Tapley Hoyt and
Luana Licata and
Astrid L{\ae}greid and
Christopher J. Mungall and
Anne Niknejad and
Simona Panni and
Livia Perfetto and
Pablo Porras and
Dexter Pratt and
Julio Saez{-}Rodriguez and
Denis Thieffry and
Paul D. Thomas and
D{\'{e}}nes T{\"{u}}rei and
Martin Kuiper},
title = {The Minimum Information about a Molecular Interaction CAusal STatement
{(MI2CAST)}},
journal = {Bioinform.},
volume = {36},
number = {24},
pages = {5712--5718},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa622},
doi = {10.1093/BIOINFORMATICS/BTAA622},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ToureVALOBCCdFG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DragerHBBCCHKNM21,
author = {Andreas Dr{\"{a}}ger and
Tom{\'{a}}s Helikar and
Matteo Barberis and
Marc R. Birtwistle and
Laurence Calzone and
Claudine Chaouiya and
Jan Hasenauer and
Jonathan R. Karr and
Anna Niarakis and
Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez and
Julio Saez{-}Rodriguez and
Juilee Thakar},
title = {SysMod: the {ISCB} community for data-driven computational modelling
and multi-scale analysis of biological systems},
journal = {Bioinform.},
volume = {37},
number = {21},
pages = {3702--3706},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab229},
doi = {10.1093/BIOINFORMATICS/BTAB229},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DragerHBBCCHKNM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Martorell-Marugan21,
author = {Jordi Martorell{-}Marugan and
Ra{\'{u}}l L{\'{o}}pez{-}Dom{\'{\i}}nguez and
Adri{\'{a}}n Garc{\'{\i}}a{-}Moreno and
Daniel Toro{-}Dom{\'{\i}}nguez and
Juan Antonio Villatoro{-}Garc{\'{\i}}a and
Guillermo Barturen and
Adoraci{\'{o}}n Mart{\'{\i}}n{-}G{\'{o}}mez and
Kevin Troul{\'{e}} and
Gonzalo G{\'{o}}mez{-}L{\'{o}}pez and
F{\'{a}}tima Al{-}Shahrour and
V{\'{\i}}ctor Gonz{\'{a}}lez{-}Rumayor and
Mar{\'{\i}}a Pe{\~{n}}a{-}Chilet and
Joaqu{\'{\i}}n Dopazo and
Julio S{\'{a}}ez{-}Rodr{\'{\i}}guez and
Marta E. Alarc{\'{o}}n{-}Riquelme and
Pedro Carmona{-}Saez},
title = {A comprehensive database for integrated analysis of omics data in
autoimmune diseases},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {343},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-04268-4},
doi = {10.1186/S12859-021-04268-4},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Martorell-Marugan21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2109-05796,
author = {Rosa D. Hernansaiz{-}Ballesteros and
Christian H. Holland and
Aur{\'{e}}lien Dugourd and
Julio Saez{-}Rodriguez},
title = {{FUNKI:} Interactive functional footprint-based analysis of omics
data},
journal = {CoRR},
volume = {abs/2109.05796},
year = {2021},
url = {https://arxiv.org/abs/2109.05796},
eprinttype = {arXiv},
eprint = {2109.05796},
timestamp = {Wed, 22 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2109-05796.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CeccarelliTGS20,
author = {Francesco Ceccarelli and
D{\'{e}}nes T{\"{u}}rei and
Attila G{\'{a}}bor and
Julio Saez{-}Rodriguez},
title = {Bringing data from curated pathway resources to Cytoscape with OmniPath},
journal = {Bioinform.},
volume = {36},
number = {8},
pages = {2632--2633},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz968},
doi = {10.1093/BIOINFORMATICS/BTZ968},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CeccarelliTGS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GjergaTGKCCDMSW20,
author = {Enio Gjerga and
Panuwat Trairatphisan and
Attila G{\'{a}}bor and
Hermann Koch and
C{\'{e}}line Chevalier and
Franceco Ceccarelli and
Aur{\'{e}}lien Dugourd and
Alexander Mitsos and
Julio Saez{-}Rodriguez and
Jonathan D. Wren},
title = {Converting networks to predictive logic models from perturbation signalling
data with CellNOpt},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4523--4524},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa561},
doi = {10.1093/BIOINFORMATICS/BTAA561},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GjergaTGKCCDMSW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mia/Maier-HeinRKMAE20,
author = {Lena Maier{-}Hein and
Annika Reinke and
Michal Kozubek and
Anne L. Martel and
Tal Arbel and
Matthias Eisenmann and
Allan Hanbury and
Pierre Jannin and
Henning M{\"{u}}ller and
Sinan Onogur and
Julio Saez{-}Rodriguez and
Bram van Ginneken and
Annette Kopp{-}Schneider and
Bennett A. Landman},
title = {{BIAS:} Transparent reporting of biomedical image analysis challenges},
journal = {Medical Image Anal.},
volume = {66},
pages = {101796},
year = {2020},
url = {https://doi.org/10.1016/j.media.2020.101796},
doi = {10.1016/J.MEDIA.2020.101796},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/mia/Maier-HeinRKMAE20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tjs/GonzalezAPPSBD19,
author = {Patricia Gonz{\'{a}}lez and
Pablo Arg{\"{u}}eso{-}Alejandro and
David R. Penas and
Xo{\'{a}}n C. Pardo and
Julio Saez{-}Rodriguez and
Julio R. Banga and
Ram{\'{o}}n Doallo},
title = {Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic
optimization problems in computational systems biology},
journal = {J. Supercomput.},
volume = {75},
number = {7},
pages = {3471--3498},
year = {2019},
url = {https://doi.org/10.1007/s11227-019-02871-0},
doi = {10.1007/S11227-019-02871-0},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tjs/GonzalezAPPSBD19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1904-11223,
author = {Matteo Manica and
Ali Oskooei and
Jannis Born and
Vigneshwari Subramanian and
Julio S{\'{a}}ez{-}Rodr{\'{\i}}guez and
Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez},
title = {Towards Explainable Anticancer Compound Sensitivity Prediction via
Multimodal Attention-based Convolutional Encoders},
journal = {CoRR},
volume = {abs/1904.11223},
year = {2019},
url = {http://arxiv.org/abs/1904.11223},
eprinttype = {arXiv},
eprint = {1904.11223},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1904-11223.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1910-04071,
author = {Lena Maier{-}Hein and
Annika Reinke and
Michal Kozubek and
Anne L. Martel and
Tal Arbel and
Matthias Eisenmann and
Allan Hanbury and
Pierre Jannin and
Henning M{\"{u}}ller and
Sinan Onogur and
Julio Saez{-}Rodriguez and
Bram van Ginneken and
Annette Kopp{-}Schneider and
Bennett A. Landman},
title = {{BIAS:} Transparent reporting of biomedical image analysis challenges},
journal = {CoRR},
volume = {abs/1910.04071},
year = {2019},
url = {http://arxiv.org/abs/1910.04071},
eprinttype = {arXiv},
eprint = {1910.04071},
timestamp = {Fri, 04 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1910-04071.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CokelaerCIMLSG18,
author = {Thomas Cokelaer and
Elisabeth Chen and
Francesco Iorio and
Michael P. Menden and
Howard Lightfoot and
Julio Saez{-}Rodriguez and
Mathew Garnett},
title = {GDSCTools for mining pharmacogenomic interactions in cancer},
journal = {Bioinform.},
volume = {34},
number = {7},
pages = {1226--1228},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx744},
doi = {10.1093/BIOINFORMATICS/BTX744},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CokelaerCIMLSG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/EsfahaniSSSB18,
author = {Ali Hadizadeh Esfahani and
Angelina Sverchkova and
Julio Saez{-}Rodriguez and
Andreas Schuppert and
Marc Brehme},
title = {A systematic atlas of chaperome deregulation topologies across the
human cancer landscape},
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number = {1},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1005890},
doi = {10.1371/JOURNAL.PCBI.1005890},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/EsfahaniSSSB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RazzaqPSSBG18,
author = {Misbah Razzaq and
Lo{\"{\i}}c Paulev{\'{e}} and
Anne Siegel and
Julio Saez{-}Rodriguez and
J{\'{e}}r{\'{e}}mie Bourdon and
Carito Guziolowski},
title = {Computational discovery of dynamic cell line specific Boolean networks
from multiplex time-course data},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {10},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1006538},
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timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/RazzaqPSSBG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/corr/abs-1811-06802,
author = {Ali Oskooei and
Jannis Born and
Matteo Manica and
Vigneshwari Subramanian and
Julio S{\'{a}}ez{-}Rodr{\'{\i}}guez and
Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez},
title = {PaccMann: Prediction of anticancer compound sensitivity with multi-modal
attention-based neural networks},
journal = {CoRR},
volume = {abs/1811.06802},
year = {2018},
url = {http://arxiv.org/abs/1811.06802},
eprinttype = {arXiv},
eprint = {1811.06802},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1811-06802.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VidelaSGS17,
author = {Santiago Videla and
Julio Saez{-}Rodriguez and
Carito Guziolowski and
Anne Siegel},
title = {caspo: a toolbox for automated reasoning on the response of logical
signaling networks families},
journal = {Bioinform.},
volume = {33},
number = {6},
pages = {947--950},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw738},
doi = {10.1093/BIOINFORMATICS/BTW738},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VidelaSGS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Hernandez-Armenta17,
author = {Claudia Hernandez{-}Armenta and
David Ochoa and
Emanuel J. V. Gon{\c{c}}alves and
Julio Saez{-}Rodriguez and
Pedro Beltr{\~{a}}o},
title = {Benchmarking substrate-based kinase activity inference using phosphoproteomic
data},
journal = {Bioinform.},
volume = {33},
number = {12},
pages = {1845--1851},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx082},
doi = {10.1093/BIOINFORMATICS/BTX082},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Hernandez-Armenta17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/GoncalvesNZWOSB17,
author = {Emanuel J. V. Gon{\c{c}}alves and
Zrinka Raguz Nakic and
Mattia Zampieri and
Omar Wagih and
David Ochoa and
Uwe Sauer and
Pedro Beltr{\~{a}}o and
Julio Saez{-}Rodriguez},
title = {Systematic Analysis of Transcriptional and Post-transcriptional Regulation
of Metabolism in Yeast},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {1},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005297},
doi = {10.1371/JOURNAL.PCBI.1005297},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/GoncalvesNZWOSB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HenriquesVRSB17,
author = {David Henriques and
Alejandro Fern{\'{a}}ndez Villaverde and
Miguel Rocha and
Julio Saez{-}Rodriguez and
Julio R. Banga},
title = {Data-driven reverse engineering of signaling pathways using ensembles
of dynamic models},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {2},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005379},
doi = {10.1371/JOURNAL.PCBI.1005379},
timestamp = {Wed, 12 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/HenriquesVRSB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PatroNPSLSZLBTB16,
author = {Rob Patro and
Raquel Norel and
Robert J. Prill and
Julio Saez{-}Rodriguez and
Peter Lorenz and
Felix Steinbeck and
Bjoern Ziems and
Mitja Lustrek and
Nicola Barbarini and
Alessandra Tiengo and
Riccardo Bellazzi and
Hans{-}J{\"{u}}rgen Thiesen and
Gustavo Stolovitzky and
Carl Kingsford},
title = {A computational method for designing diverse linear epitopes including
citrullinated peptides with desired binding affinities to intravenous
immunoglobulin},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {155},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1008-7},
doi = {10.1186/S12859-016-1008-7},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PatroNPSLSZLBTB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/IorioBGCJS16,
author = {Francesco Iorio and
Marti Bernardo{-}Faura and
Andrea Gobbi and
Thomas Cokelaer and
Giuseppe Jurman and
Julio Saez{-}Rodriguez},
title = {Efficient randomization of biological networks while preserving functional
characterization of individual nodes},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {542:1--542:14},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1402-1},
doi = {10.1186/S12859-016-1402-1},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/IorioBGCJS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NaldiMMKTXSHC15,
author = {Aur{\'{e}}lien Naldi and
Pedro T. Monteiro and
Christoph M{\"{u}}ssel and
Hans A. Kestler and
Denis Thieffry and
Ioannis Xenarios and
Julio Saez{-}Rodriguez and
Tom{\'{a}}s Helikar and
Claudine Chaouiya},
title = {Cooperative development of logical modelling standards and tools with
CoLoMoTo},
journal = {Bioinform.},
volume = {31},
number = {7},
pages = {1154--1159},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv013},
doi = {10.1093/BIOINFORMATICS/BTV013},
timestamp = {Thu, 04 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NaldiMMKTXSHC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HenriquesRSB15,
author = {David Henriques and
Miguel Rocha and
Julio Saez{-}Rodriguez and
Julio R. Banga},
title = {Reverse engineering of logic-based differential equation models using
a mixed-integer dynamic optimization approach},
journal = {Bioinform.},
volume = {31},
number = {18},
pages = {2999--3007},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv314},
doi = {10.1093/BIOINFORMATICS/BTV314},
timestamp = {Wed, 12 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HenriquesRSB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ThieleCSSGK15,
author = {Sven Thiele and
Luca Cerone and
Julio Saez{-}Rodriguez and
Anne Siegel and
Carito Guziolowski and
Steffen Klamt},
title = {Extended notions of sign consistency to relate experimental data to
signaling and regulatory network topologies},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {345:1--345:13},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0733-7},
doi = {10.1186/S12859-015-0733-7},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ThieleCSSGK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/VillaverdeHSB0C15,
author = {Alejandro Fern{\'{a}}ndez Villaverde and
David Henriques and
Kieran Smallbone and
Sophia Bongard and
Joachim Schmid and
Damjan Cicin{-}Sain and
Anton Crombach and
Julio Saez{-}Rodriguez and
Klaus Mauch and
Eva Balsa{-}Canto and
Pedro Mendes and
Johannes Jaeger and
Julio R. Banga},
title = {BioPreDyn-bench: a suite of benchmark problems for dynamic modelling
in systems biology},
journal = {{BMC} Syst. Biol.},
volume = {9},
pages = {8},
year = {2015},
url = {https://doi.org/10.1186/s12918-015-0144-4},
doi = {10.1186/S12918-015-0144-4},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/VillaverdeHSB0C15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/VidelaGETGNSSS15,
author = {Santiago Videla and
Carito Guziolowski and
Federica Eduati and
Sven Thiele and
Martin Gebser and
Jacques Nicolas and
Julio Saez{-}Rodriguez and
Torsten Schaub and
Anne Siegel},
title = {Learning Boolean logic models of signaling networks with {ASP}},
journal = {Theor. Comput. Sci.},
volume = {599},
pages = {79--101},
year = {2015},
url = {https://doi.org/10.1016/j.tcs.2014.06.022},
doi = {10.1016/J.TCS.2014.06.022},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/VidelaGETGNSSS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/CokelaerBBBBNEGHHKKMMNPPW15,
author = {Thomas Cokelaer and
Mukesh Bansal and
Christopher Bare and
Erhan Bilal and
Brian M. Bot and
Elias Chaibub Neto and
Federica Eduati and
Mehmet G{\"{o}}nen and
Steven M. Hill and
Bruce R. Hoff and
Jonathan R. Karr and
Robert K{\"{u}}ffner and
Michael P. Menden and
Pablo Meyer and
Raquel Norel and
Abhishek Pratap and
Robert J. Prill and
Matthew T. Weirauch and
James C. Costello and
Gustavo Stolovitzky and
Julio Saez{-}Rodriguez},
title = {DREAMTools: a Python package for scoring collaborative challenges},
journal = {F1000Research},
volume = {4},
pages = {1030},
year = {2015},
url = {https://doi.org/10.12688/f1000research.7118.1},
doi = {10.12688/F1000RESEARCH.7118.1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/CokelaerBBBBNEGHHKKMMNPPW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuziolowskiVETCSS14,
author = {Carito Guziolowski and
Santiago Videla and
Federica Eduati and
Sven Thiele and
Thomas Cokelaer and
Anne Siegel and
Julio Saez{-}Rodriguez},
title = {Exhaustively characterizing feasible logic models of a signaling network
using Answer Set Programming},
journal = {Bioinform.},
volume = {30},
number = {13},
pages = {1942},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu357},
doi = {10.1093/BIOINFORMATICS/BTU357},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuziolowskiVETCSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GobbiIDWTALGJS14,
author = {Andrea Gobbi and
Francesco Iorio and
Kevin J. Dawson and
David C. Wedge and
David Tamborero and
Ludmil B. Alexandrov and
N{\'{u}}ria L{\'{o}}pez{-}Bigas and
Mathew Garnett and
Giuseppe Jurman and
Julio Saez{-}Rodriguez},
title = {Fast randomization of large genomic datasets while preserving alteration
counts},
journal = {Bioinform.},
volume = {30},
number = {17},
pages = {617--623},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu474},
doi = {10.1093/BIOINFORMATICS/BTU474},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GobbiIDWTALGJS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/RyllBBBGSNK14,
author = {Anke Ryll and
Joachim Bucher and
Anne Bonin and
Sophia Bongard and
Emanuel J. V. Gon{\c{c}}alves and
Julio Saez{-}Rodriguez and
Jens Niklas and
Steffen Klamt},
title = {A model integration approach linking signalling and gene-regulatory
logic with kinetic metabolic models},
journal = {Biosyst.},
volume = {124},
pages = {26--38},
year = {2014},
url = {https://doi.org/10.1016/j.biosystems.2014.07.002},
doi = {10.1016/J.BIOSYSTEMS.2014.07.002},
timestamp = {Mon, 07 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biosystems/RyllBBBGSNK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EgeaHCVMDBS14,
author = {Jose A. Egea and
David Henriques and
Thomas Cokelaer and
Alejandro Fern{\'{a}}ndez Villaverde and
Aidan MacNamara and
Diana{-}Patricia Danciu and
Julio R. Banga and
Julio Saez{-}Rodriguez},
title = {{MEIGO:} an open-source software suite based on metaheuristics for
global optimization in systems biology and bioinformatics},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {136},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-136},
doi = {10.1186/1471-2105-15-136},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/EgeaHCVMDBS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/MeyerCCKLTLBKRSTBSSS14,
author = {Pablo Meyer and
Thomas Cokelaer and
Deepak Chandran and
Kyung Hyuk Kim and
Po{-}Ru Loh and
George Tucker and
Mark Lipson and
Bonnie Berger and
Clemens Kreutz and
Andreas Raue and
Bernhard Steiert and
Jens Timmer and
Erhan Bilal and
Herbert M. Sauro and
Gustavo Stolovitzky and
Julio Saez{-}Rodriguez},
title = {Network topology and parameter estimation: from experimental design
methods to gene regulatory network kinetics using a community based
approach},
journal = {{BMC} Syst. Biol.},
volume = {8},
pages = {13},
year = {2014},
url = {https://doi.org/10.1186/1752-0509-8-13},
doi = {10.1186/1752-0509-8-13},
timestamp = {Fri, 01 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/MeyerCCKLTLBKRSTBSSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/pacbb/2014,
editor = {Julio Saez{-}Rodriguez and
Miguel P. Rocha and
Florentino Fdez{-}Riverola and
Juan F. De Paz Santana},
title = {8th International Conference on Practical Applications of Computational
Biology {\&} Bioinformatics, {PACBB} 2014, 4-6 June, 2014, Salamanca,
Spain},
series = {Advances in Intelligent Systems and Computing},
volume = {294},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-07581-5},
doi = {10.1007/978-3-319-07581-5},
isbn = {978-3-319-07580-8},
timestamp = {Wed, 12 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/pacbb/2014.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/VillaverdeHSB0CCSMBMJB14,
author = {Alejandro Fern{\'{a}}ndez Villaverde and
David Henriques and
Kieran Smallbone and
Sophia Bongard and
Joachim Schmid and
Damjan Cicin{-}Sain and
Anton Crombach and
Julio Saez{-}Rodriguez and
Klaus Mauch and
Eva Balsa{-}Canto and
Pedro Mendes and
Johannes Jaeger and
Julio R. Banga},
title = {BioPreDyn-bench: benchmark problems for kinetic modelling in systems
biology},
journal = {CoRR},
volume = {abs/1407.5856},
year = {2014},
url = {http://arxiv.org/abs/1407.5856},
eprinttype = {arXiv},
eprint = {1407.5856},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/VillaverdeHSB0CCSMBMJB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/CokelaerS14,
author = {Thomas Cokelaer and
Julio Saez{-}Rodriguez},
title = {Using Python to Dive into Signalling Data with CellNOpt and BioServices},
journal = {CoRR},
volume = {abs/1412.6386},
year = {2014},
url = {http://arxiv.org/abs/1412.6386},
eprinttype = {arXiv},
eprint = {1412.6386},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/CokelaerS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PaciniIGIKBS13,
author = {Clare Pacini and
Francesco Iorio and
Emanuel J. V. Gon{\c{c}}alves and
Murat Iskar and
Thomas Klabunde and
Peer Bork and
Julio Saez{-}Rodriguez},
title = {DvD: An R/Cytoscape pipeline for drug repurposing using public repositories
of gene expression data},
journal = {Bioinform.},
volume = {29},
number = {1},
pages = {132--134},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/bts656},
doi = {10.1093/BIOINFORMATICS/BTS656},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PaciniIGIKBS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuziolowskiVETCSS13,
author = {Carito Guziolowski and
Santiago Videla and
Federica Eduati and
Sven Thiele and
Thomas Cokelaer and
Anne Siegel and
Julio Saez{-}Rodriguez},
title = {Exhaustively characterizing feasible logic models of a signaling network
using Answer Set Programming},
journal = {Bioinform.},
volume = {29},
number = {18},
pages = {2320--2326},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt393},
doi = {10.1093/BIOINFORMATICS/BTT393},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuziolowskiVETCSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CokelaerPHSS13,
author = {Thomas Cokelaer and
Dennis Pultz and
Lea M. Harder and
Jordi Serra{-}Musach and
Julio Saez{-}Rodriguez},
title = {BioServices: a common Python package to access biological Web Services
programmatically},
journal = {Bioinform.},
volume = {29},
number = {24},
pages = {3241--3242},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt547},
doi = {10.1093/BIOINFORMATICS/BTT547},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CokelaerPHSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GoncalvesIS13,
author = {Emanuel J. V. Gon{\c{c}}alves and
Martijn P. van Iersel and
Julio Saez{-}Rodriguez},
title = {CySBGN: {A} Cytoscape plug-in to integrate {SBGN} maps},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {17},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-17},
doi = {10.1186/1471-2105-14-17},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GoncalvesIS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/BuchelRSWCKMSGGIKRWHHK0MZCSSLDN13,
author = {Finja B{\"{u}}chel and
Nicolas Rodriguez and
Neil Swainston and
Clemens Wrzodek and
Tobias Czauderna and
Roland Keller and
Florian Mittag and
Michael Schubert and
Mihai Glont and
Martin Golebiewski and
Martijn P. van Iersel and
Sarah M. Keating and
Matthias Rall and
Michael Wybrow and
Henning Hermjakob and
Michael Hucka and
Douglas B. Kell and
Wolfgang M{\"{u}}ller and
Pedro Mendes and
Andreas Zell and
Claudine Chaouiya and
Julio Saez{-}Rodriguez and
Falk Schreiber and
Camille Laibe and
Andreas Dr{\"{a}}ger and
Nicolas Le Nov{\`{e}}re},
title = {Path2Models: large-scale generation of computational models from biochemical
pathway maps},
journal = {{BMC} Syst. Biol.},
volume = {7},
pages = {116},
year = {2013},
url = {https://doi.org/10.1186/1752-0509-7-116},
doi = {10.1186/1752-0509-7-116},
timestamp = {Thu, 03 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/BuchelRSWCKMSGGIKRWHHK0MZCSSLDN13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ChaouiyaBKNIRDBCKWGDPMKXJHKTNSH13,
author = {Claudine Chaouiya and
Duncan B{\'{e}}renguier and
Sarah M. Keating and
Aur{\'{e}}lien Naldi and
Martijn P. van Iersel and
Nicolas Rodriguez and
Andreas Dr{\"{a}}ger and
Finja B{\"{u}}chel and
Thomas Cokelaer and
Bryan M. Kowal and
Benjamin Wicks and
Emanuel J. V. Gon{\c{c}}alves and
Julien Dorier and
Michel Page and
Pedro T. Monteiro and
Axel von Kamp and
Ioannis Xenarios and
Hidde de Jong and
Michael Hucka and
Steffen Klamt and
Denis Thieffry and
Nicolas Le Nov{\`{e}}re and
Julio Saez{-}Rodriguez and
Tom{\'{a}}s Helikar},
title = {{SBML} qualitative models: a model representation format and infrastructure
to foster interactions between qualitative modelling formalisms and
tools},
journal = {{BMC} Syst. Biol.},
volume = {7},
pages = {135},
year = {2013},
url = {https://doi.org/10.1186/1752-0509-7-135},
doi = {10.1186/1752-0509-7-135},
timestamp = {Thu, 03 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/ChaouiyaBKNIRDBCKWGDPMKXJHKTNSH13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/IorioSB13,
author = {Francesco Iorio and
Julio Saez{-}Rodriguez and
Diego di Bernardo},
title = {Network based elucidation of drug response: from modulators to targets},
journal = {{BMC} Syst. Biol.},
volume = {7},
pages = {139},
year = {2013},
url = {https://doi.org/10.1186/1752-0509-7-139},
doi = {10.1186/1752-0509-7-139},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/IorioSB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/EgeaHCVBS13,
author = {Jose A. Egea and
David Henriques and
Thomas Cokelaer and
Alejandro Fern{\'{a}}ndez Villaverde and
Julio R. Banga and
Julio Saez{-}Rodriguez},
title = {{MEIGO:} an open-source software suite based on metaheuristics for
global optimization in systems biology and bioinformatics},
journal = {CoRR},
volume = {abs/1311.5735},
year = {2013},
url = {http://arxiv.org/abs/1311.5735},
eprinttype = {arXiv},
eprint = {1311.5735},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/EgeaHCVBS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/GoncalvesS13,
author = {Emanuel J. V. Gon{\c{c}}alves and
Julio Saez{-}Rodriguez},
title = {\emph{Cyrface}: An interface from \emph{Cytoscape} to \emph{R }that
provides a user interface to \emph{R} packages},
journal = {F1000Research},
volume = {2},
pages = {192},
year = {2013},
url = {https://doi.org/10.12688/f1000research.2-192.v1},
doi = {10.12688/F1000RESEARCH.2-192.V1},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/GoncalvesS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EduatiRCTS12,
author = {Federica Eduati and
Javier De Las Rivas and
Barbara Di Camillo and
Gianna Toffolo and
Julio Saez{-}Rodriguez},
title = {Integrating literature-constrained and data-driven inference of signalling
networks},
journal = {Bioinform.},
volume = {28},
number = {18},
pages = {2311--2317},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts363},
doi = {10.1093/BIOINFORMATICS/BTS363},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/EduatiRCTS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/KirouacSSBLS12,
author = {Daniel C. Kirouac and
Julio Saez{-}Rodriguez and
Jennifer Swantek and
John M. Burke and
Douglas A. Lauffenburger and
Peter K. Sorger},
title = {Creating and analyzing pathway and protein interaction compendia for
modelling signal transduction networks},
journal = {{BMC} Syst. Biol.},
volume = {6},
pages = {29},
year = {2012},
url = {https://doi.org/10.1186/1752-0509-6-29},
doi = {10.1186/1752-0509-6-29},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/KirouacSSBLS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/TerfveCHMGMILS12,
author = {Camille Terfve and
Thomas Cokelaer and
David Henriques and
Aidan MacNamara and
Emanuel J. V. Gon{\c{c}}alves and
Melody K. Morris and
Martijn P. van Iersel and
Douglas A. Lauffenburger and
Julio Saez{-}Rodriguez},
title = {CellNOptR: a flexible toolkit to train protein signaling networks
to data using multiple logic formalisms},
journal = {{BMC} Syst. Biol.},
volume = {6},
pages = {133},
year = {2012},
url = {https://doi.org/10.1186/1752-0509-6-133},
doi = {10.1186/1752-0509-6-133},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/TerfveCHMGMILS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/VidelaGETGSS12,
author = {Santiago Videla and
Carito Guziolowski and
Federica Eduati and
Sven Thiele and
Niels Grabe and
Julio Saez{-}Rodriguez and
Anne Siegel},
editor = {David R. Gilbert and
Monika Heiner},
title = {Revisiting the Training of Logic Models of Protein Signaling Networks
with {ASP}},
booktitle = {Computational Methods in Systems Biology - 10th International Conference,
{CMSB} 2012, London, UK, October 3-5, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7605},
pages = {342--361},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33636-2\_20},
doi = {10.1007/978-3-642-33636-2\_20},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cmsb/VidelaGETGSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1210-0690,
author = {Santiago Videla and
Carito Guziolowski and
Federica Eduati and
Sven Thiele and
Niels Grabe and
Julio Saez{-}Rodriguez and
Anne Siegel},
title = {Revisiting the Training of Logic Models of Protein Signaling Networks
with a Formal Approach based on Answer Set Programming},
journal = {CoRR},
volume = {abs/1210.0690},
year = {2012},
url = {http://arxiv.org/abs/1210.0690},
eprinttype = {arXiv},
eprint = {1210.0690},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1210-0690.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1212-0504,
author = {Michael P. Menden and
Francesco Iorio and
Mathew Garnett and
Ultan McDermott and
Cyril Benes and
Pedro J. Ballester and
Julio Saez{-}Rodriguez},
title = {Machine learning prediction of cancer cell sensitivity to drugs based
on genomic and chemical properties},
journal = {CoRR},
volume = {abs/1212.0504},
year = {2012},
url = {http://arxiv.org/abs/1212.0504},
eprinttype = {arXiv},
eprint = {1212.0504},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1212-0504.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MorrisSCSL11,
author = {Melody K. Morris and
Julio Saez{-}Rodriguez and
David C. Clarke and
Peter K. Sorger and
Douglas A. Lauffenburger},
title = {Training Signaling Pathway Maps to Biochemical Data with Constrained
Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory
Stimuli},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {3},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1001099},
doi = {10.1371/JOURNAL.PCBI.1001099},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/MorrisSCSL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/WittmannKSLKT09,
author = {Dominik M. Wittmann and
Jan Krumsiek and
Julio Saez{-}Rodriguez and
Douglas A. Lauffenburger and
Steffen Klamt and
Fabian J. Theis},
title = {Transforming Boolean models to continuous models: methodology and
application to T-cell receptor signaling},
journal = {{BMC} Syst. Biol.},
volume = {3},
pages = {98},
year = {2009},
url = {https://doi.org/10.1186/1752-0509-3-98},
doi = {10.1186/1752-0509-3-98},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/WittmannKSLKT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/AldridgeSMSL09,
author = {Bree B. Aldridge and
Julio Saez{-}Rodriguez and
Jeremy Muhlich and
Peter K. Sorger and
Douglas A. Lauffenburger},
title = {Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced
Signaling},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {4},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000340},
doi = {10.1371/JOURNAL.PCBI.1000340},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/AldridgeSMSL09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/SamagaSASK09,
author = {Regina Samaga and
Julio Saez{-}Rodriguez and
Leonidas G. Alexopoulos and
Peter K. Sorger and
Steffen Klamt},
title = {The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis
of High-Throughput Data},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {8},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000438},
doi = {10.1371/JOURNAL.PCBI.1000438},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/SamagaSASK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MitsosMSCSA09,
author = {Alexander Mitsos and
Ioannis N. Melas and
Paraskeuas Siminelakis and
Aikaterini D. Chairakaki and
Julio Saez{-}Rodriguez and
Leonidas G. Alexopoulos},
title = {Identifying Drug Effects via Pathway Alterations using an Integer
Linear Programming Optimization Formulation on Phosphoproteomic Data},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {12},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000591},
doi = {10.1371/JOURNAL.PCBI.1000591},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/MitsosMSCSA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Saez-RodriguezGMAMLS08,
author = {Julio Saez{-}Rodriguez and
Arthur Goldsipe and
Jeremy Muhlich and
Leonidas G. Alexopoulos and
Bjorn Millard and
Douglas A. Lauffenburger and
Peter K. Sorger},
title = {Flexible informatics for linking experimental data to mathematical
models via \emph{DataRail}},
journal = {Bioinform.},
volume = {24},
number = {6},
pages = {840--847},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn018},
doi = {10.1093/BIOINFORMATICS/BTN018},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Saez-RodriguezGMAMLS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/Saez-RodriguezGGG08,
author = {Julio Saez{-}Rodriguez and
Stefan Gayer and
Martin Ginkel and
Ernst Dieter Gilles},
title = {Automatic decomposition of kinetic models of signaling networks minimizing
the retroactivity among modules},
booktitle = {ECCB'08 Proceedings, Seventh European Conference on Computational
Biology, 22-26 September 2008, Cagliari, Italy},
pages = {213--219},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn289},
doi = {10.1093/BIOINFORMATICS/BTN289},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/Saez-RodriguezGGG08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/KlamtSG07,
author = {Steffen Klamt and
Julio Saez{-}Rodriguez and
Ernst Dieter Gilles},
title = {Structural and functional analysis of cellular networks with CellNetAnalyzer},
journal = {{BMC} Syst. Biol.},
volume = {1},
pages = {2},
year = {2007},
url = {https://doi.org/10.1186/1752-0509-1-2},
doi = {10.1186/1752-0509-1-2},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/KlamtSG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/Saez-RodriguezSLHBAHWGKS07,
author = {Julio Saez{-}Rodriguez and
Luca Simeoni and
Jonathan A. Lindquist and
Rebecca Hemenway and
Ursula Bommhardt and
Boerge Arndt and
Utz{-}Uwe Haus and
Robert Weismantel and
Ernst Dieter Gilles and
Steffen Klamt and
Burkhart Schraven},
title = {A Logical Model Provides Insights into {T} Cell Receptor Signaling},
journal = {PLoS Comput. Biol.},
volume = {3},
number = {8},
year = {2007},
url = {https://doi.org/10.1371/journal.pcbi.0030163},
doi = {10.1371/JOURNAL.PCBI.0030163},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/Saez-RodriguezSLHBAHWGKS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ConzelmannSSKG06,
author = {Holger Conzelmann and
Julio Saez{-}Rodriguez and
Thomas Sauter and
Boris N. Kholodenko and
Ernst Dieter Gilles},
title = {A domain-oriented approach to the reduction of combinatorial complexity
in signal transduction networks},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {34},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-34},
doi = {10.1186/1471-2105-7-34},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ConzelmannSSKG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KlamtSLSG06,
author = {Steffen Klamt and
Julio Saez{-}Rodriguez and
Jonathan A. Lindquist and
Luca Simeoni and
Ernst Dieter Gilles},
title = {A methodology for the structural and functional analysis of signaling
and regulatory networks},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {56},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-56},
doi = {10.1186/1471-2105-7-56},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KlamtSLSG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Saez-RodriguezMHKGG06,
author = {Julio Saez{-}Rodriguez and
Sebastian Mirschel and
Rebecca Hemenway and
Steffen Klamt and
Ernst Dieter Gilles and
Martin Ginkel},
title = {Visual setup of logical models of signaling and regulatory networks
with ProMoT},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {506},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-506},
doi = {10.1186/1471-2105-7-506},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Saez-RodriguezMHKGG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cce/Saez-RodriguezKG05,
author = {Julio Saez{-}Rodriguez and
Andreas Kremling and
Ernst Dieter Gilles},
title = {Dissecting the puzzle of life: modularization of signal transduction
networks},
journal = {Comput. Chem. Eng.},
volume = {29},
number = {3},
pages = {619--629},
year = {2005},
url = {https://doi.org/10.1016/j.compchemeng.2004.08.035},
doi = {10.1016/J.COMPCHEMENG.2004.08.035},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cce/Saez-RodriguezKG05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/BehrendtPSRM01,
author = {Knut Behrendt and
Andreas Politzer and
Julio Saez{-}Rodriguez and
Matthias Reuss and
Klaus Mauch},
editor = {Edgar Wingender},
title = {Topological Analysis and Visualisation of large Signalling Networks:
The TGF-beta Signal Transductionin Eukaryotic Systems},
booktitle = {Computer science and biology: Proceedings of the German Conference
on Bioinformatics, {GCB} 2001, October 7-10, 2001, Braunschweig, Germany},
pages = {143--144},
publisher = {German Research Center for Biotechnology},
year = {2001},
timestamp = {Tue, 15 Mar 2005 13:06:29 +0100},
biburl = {https://dblp.org/rec/conf/gcb/BehrendtPSRM01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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