Publications

2015

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR.
BMC Syst Biol Volume 9 (2015) p.8

Signaling networks in MS: a systems-based approach to developing new pharmacological therapies.
Kotelnikova E, Bernardo-Faura M, Silberberg G, Kiani NA, Messinis D, Melas IN, Artigas L, Schwartz E, Mazo I, Masso M, Alexopoulos LG, Mas JM, Olsson T, Tegner J, Martin R, Zamora A, Paul F, Saez-Rodriguez J, Villoslada P.
Mult Scler Volume 21 (2015) p.138-146

Cooperative development of logical modelling standards and tools with CoLoMoTo.
Naldi A, Monteiro PT, Müssel C, Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C.
Bioinformatics Volume 31 (2015) p.1154-1159

2014

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.
Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C.
Angew Chem Int Ed Engl Volume 53 (2014) p.6720-6723

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S.
Biosystems Volume 124 (2014) p.26-38

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Dream Six and Seven Parameter Estimation Consortium, Sauro HM, Stolovitzky G, Saez-Rodriguez J.
BMC Syst Biol Volume 8 (2014) p.13

A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.
Nat Biotechnol Volume 32 (2014) p.1202-1212

Fast randomization of large genomic datasets while preserving alteration counts.
Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G, Saez-Rodriguez J.
Bioinformatics Volume 30 (2014) p.i617-23

Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy.
Weiss MS, Peñalver Bernabé B, Shin S, Asztalos S, Dubbury SJ, Mui MD, Bellis AD, Bluver D, Tonetti DA, Saez-Rodriguez J, Broadbelt LJ, Jeruss JS, Shea LD.
Integr Biol (Camb) Volume 6 (2014) p.1170-1182

Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery.
Schubert M, Iorio F.
Pharmacogenomics Volume 15 (2014) p.1943-1946

A community computational challenge to predict the activity of pairs of compounds.
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community.
Nat Biotechnol Volume 32 (2014) p.1213-1222

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J.
BMC Bioinformatics Volume 15 (2014) p.136

PIP₃ induces the recycling of receptor tyrosine kinases.
Laketa V, Zarbakhsh S, Traynor-Kaplan A, Macnamara A, Subramanian D, Putyrski M, Mueller R, Nadler A, Mentel M, Saez-Rodriguez J, Pepperkok R, Schultz C.
Sci Signal Volume 7 (2014) p.ra5

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R.
Mol Syst Biol Volume 10 (2014) p.767

2013

Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.
BMC Syst Biol Volume 7 (2013) p.116

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.
Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J.
PLoS One Volume 8 (2013) p.e61318

Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors.
Casado P, Alcolea MP, Iorio F, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR.
Genome Biol Volume 14 (2013) p.r37

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.
Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J.
Mol Biosyst Volume 9 (2013) p.1576-1583

Network based elucidation of drug response: from modulators to targets.
Iorio F, Saez-Rodriguez J, di Bernardo D.
BMC Syst Biol Volume 7 (2013) p.139

Construction of cell type-specific logic models of signaling networks using CellNOpt.
Morris MK, Melas I, Saez-Rodriguez J.
Methods Mol Biol Volume 930 (2013) p.179-214

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Gonçalves E, Saez-Rodriguez J.
F1000Res Volume 2 (2013) p.192

Modeling signaling networks with different formalisms: a preview.
MacNamara A, Henriques D, Saez-Rodriguez J.
Methods Mol Biol Volume 1021 (2013) p.89-105

BioServices: a common Python package to access biological Web Services programmatically.
Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J.
Bioinformatics Volume 29 (2013) p.3241-3242

Critical assessment of automated flow cytometry data analysis techniques.
Aghaeepour N, Finak G, FlowCAP Consortium, DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.
Nat Methods Volume 10 (2013) p.228-238

Evaluation of methods for modeling transcription factor sequence specificity.
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.
Nat Biotechnol Volume 31 (2013) p.126-134

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J.
Bioinformatics Volume 29 (2013) p.2320-2326

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.
BMC Syst Biol Volume 7 (2013) p.135

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J.
Bioinformatics Volume 29 (2013) p.132-134

CySBGN: a Cytoscape plug-in to integrate SBGN maps.
Gonçalves E, van Iersel M, Saez-Rodriguez J.
BMC Bioinformatics Volume 14 (2013) p.17

Transcriptional data: a new gateway to drug repositioning?
Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J.
Drug Discov Today Volume 18 (2013) p.350-357

2012

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.
BMC Syst Biol Volume 6 (2012) p.29

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.
Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, Alexopoulos LG.
PLoS One Volume 7 (2012) p.e50085

Systematic identification of genomic markers of drug sensitivity in cancer cells.
Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O'Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH.
Nature Volume 483 (2012) p.570-575

Modeling signaling networks using high-throughput phospho-proteomics.
Terfve C, Saez-Rodriguez J.
Adv Exp Med Biol Volume 736 (2012) p.19-57

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.
Melas IN, Mitsos A, Messinis DE, Weiss TS, Rodriguez JS, Alexopoulos LG.
Mol Biosyst Volume 8 (2012) p.1571-1584

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris MK, van Iersel M, Lauffenburger DA, Saez-Rodriguez J.
BMC Syst Biol Volume 6 (2012) p.133

Integrating literature-constrained and data-driven inference of signalling networks.
Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J.
Bioinformatics Volume 28 (2012) p.2311-2317

Revisiting the training of logic models of protein signaling networks with ASP
Videla S, Guziolowski C, Eduati F, Thiele S, Grabe N, Saez-Rodriguez J, Siegel A.
Volume (2012) p.342-361

Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network.
Serra-Musach J, Aguilar H, Iorio F, Comellas F, Berenguer A, Brunet J, Saez-Rodriguez J, Pujana MA.
Integr Biol (Camb) Volume 4 (2012) p.1038-1048

State-time spectrum of signal transduction logic models.
MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J.
Phys Biol Volume 9 (2012) p.045003

Mapping the human phosphatome on growth pathways.
Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G.
Mol Syst Biol Volume 8 (2012) p.603

2011

Crowdsourcing network inference: the DREAM predictive signaling network challenge.
Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.
Sci Signal Volume 4 (2011) p.mr7

Retroactivity as a Criterion to Define Modules in Signaling Networks
Saez-Rodriguez J, Conzelmann H, Ederer M, Gilles ED.
Volume (2011) p.139-159

Setting the standards for signal transduction research.
Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G.
Sci Signal Volume 4 (2011) p.pe10

Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.
Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA.
PLoS Comput Biol Volume 7 (2011) p.e1001099