Julio Saez-Rodriguez

Julio Saez-Rodriguez

Group Leader - Saez-Rodriguez research group

I studied Chemical Engineering at the University of Oviedo in Spain and the University of Stuttgart in Germany (1996-2001), and did my PhD at the Max-Planck-Institute for Dynamics of Complex Technical Systems in Magdeburg (2002-2007), under the supervision of E. D. Gilles. After that I was a postdoctoral fellow at Harvard Medical School and M.I.T, with Peter Sorger and Doug Lauffenburger. I am a group leader at EMBL-EBI since July 2010, with a joint appointment in the EMBL Genome Biology Unit in Heidelberg; I am also a senior fellow at Wolfson College (Cambridge). I am generally interested in computational methods and tools to study information transfer within signalling networks, and application to disease-related questions. 

ORCID iD: 0000-0002-8552-8976

Tel:+ 44 (0) 1223 494 564 / Fax:+ 44 (0) 1223 494 468

http://sites.google.com/site/saezrodriguez/ (personal homepage)

Research

Find out about research activity in the Saez-Rodriguez research group

Publications

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
DOI: 10.1002/anie.201402294

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 (2014) p.
DOI: 10.1038/nbt.2877

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
DOI: 10.1186/1471-2105-15-136

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, Sauro HM, Stolovitzky G, Saez-Rodriguez J.
BMC Syst Biol Volume 8 (2014) p.13
DOI: 10.1186/1752-0509-8-13

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
DOI: 10.1126/scisignal.2004532

2013

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
DOI: 10.1039/c3mb25489e

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
DOI: 10.1016/j.drudis.2012.07.014

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
DOI: 10.1038/nmeth.2365

CySBGN: a Cytoscape plug-in to integrate SBGN maps.
Gonçalves E, van Iersel M, Saez-Rodriguez J.
BMC Bioinformatics Volume 14 (2013) p.17
DOI: 10.1186/1471-2105-14-17

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
DOI: 10.1186/1752-0509-7-116

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
DOI: 10.1186/1752-0509-7-135

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
DOI: 10.1093/bioinformatics/btt547

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
DOI: 10.1038/nbt.2486

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
DOI: 10.1186/1752-0509-7-139

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
DOI: 10.1007/978-1-62703-059-5_8

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
DOI: 10.1093/bioinformatics/bts656

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
DOI: 10.1186/gb-2013-14-4-r37

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
DOI: 10.12688/f1000research.2-192.v1

Modeling signaling networks with different formalisms: a preview.
MacNamara A, Henriques D, Saez-Rodriguez J.
Methods Mol Biol Volume 1021 (2013) p.89-105
DOI: 10.1007/978-1-62703-450-0_5

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
DOI: 10.1371/journal.pone.0061318

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
DOI: 10.1093/bioinformatics/btt393

2012

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
DOI: 10.1093/bioinformatics/bts363

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
DOI: 10.1186/1752-0509-6-29

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
DOI: 10.1039/c2ib20052j

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
DOI: 10.1038/msb.2012.36

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
DOI: 10.1007/978-3-642-33636-2_20

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
DOI: 10.1038/nature11005

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
DOI: 10.1039/c2mb05482e

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
DOI: 10.1371/journal.pone.0050085

Modeling signaling networks using high-throughput phospho-proteomics.
Terfve C, Saez-Rodriguez J.
Adv Exp Med Biol Volume 736 (2012) p.19-57
DOI: 10.1007/978-1-4419-7210-1_2

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
DOI: 10.1088/1478-3975/9/4/045003

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
DOI: 10.1186/1752-0509-6-133

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
DOI: 10.1126/scisignal.2002212

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
DOI: 10.1371/journal.pcbi.1001099

Retroactivity as a Criterion to Define Modules in Signaling Networks
Saez-Rodriguez J, Conzelmann H, Ederer M, Gilles ED.
Volume (2011) p.139-159
DOI: 10.1007/978-1-4419-6766-4_7

Setting the standards for signal transduction research.
Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G.
Sci Signal Volume 4 (2011) p.pe10
DOI: 10.1126/scisignal.2001844

2010

Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges.
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.
PLoS ONE Volume 5 (2010) p.

Towards a rigorous assessment of systems biology models: the DREAM3 challenges.
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.
PLoS One Volume 5 (2010) p.e9202
DOI: 10.1371/journal.pone.0009202

Logic-based models for the analysis of cell signaling networks.
Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA.
Biochemistry Volume 49 (2010) p.3216-3224
DOI: 10.1021/bi902202q

2009

Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling.
Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA.
PLoS Comput Biol Volume 5 (2009) p.e1000340
DOI: 10.1371/journal.pcbi.1000340

Cellular Regulatory Networks
Joughin BA, Cheung E, Karuturi RKM, Saez-Rodriguez J, Lauffenburger DA, Liu ET.
Volume (2009) p.57-108
DOI: 10.1016/b978-0-12-372550-9.00004-3

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data.
Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S.
PLoS Comput Biol Volume 5 (2009) p.e1000438
DOI: 10.1371/journal.pcbi.1000438

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction.
Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK.
Mol Syst Biol Volume 5 (2009) p.331
DOI: 10.1038/msb.2009.87

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.
Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis FJ.
BMC Syst Biol Volume 3 (2009) p.98
DOI: 10.1186/1752-0509-3-98

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.
Mitsos A, Melas IN, Siminelakis P, Chairakaki AD, Saez-Rodriguez J, Alexopoulos LG.
PLoS Comput Biol Volume 5 (2009) p.e1000591
DOI: 10.1371/journal.pcbi.1000591

2008

Flexible informatics for linking experimental data to mathematical models via DataRail.
Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, Lauffenburger DA, Sorger PK.
Bioinformatics Volume 24 (2008) p.840-847
DOI: 10.1093/bioinformatics/btn018

Dynamics of proximal signaling events after TCR/CD8-mediated induction of proliferation or apoptosis in mature CD8+ T cells.
Wang X, Simeoni L, Lindquist JA, Saez-Rodriguez J, Ambach A, Gilles ED, Kliche S, Schraven B.
J Immunol Volume 180 (2008) p.6703-6712
DOI: 10.4049/jimmunol.180.10.6703

Multistability of signal transduction motifs.
Saez-Rodriguez J, Hammerle-Fickinger A, Dalal O, Klamt S, Gilles ED, Conradi C.
IET Syst Biol Volume 2 (2008) p.80-93
DOI: 10.1049/iet-syb:20070012

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.
Saez-Rodriguez J, Gayer S, Ginkel M, Gilles ED.
Bioinformatics Volume 24 (2008) p.i213-9
DOI: 10.1093/bioinformatics/btn289

High-throughput protein-based technologies and computational models for drug development, efficacy, and toxicity
Alexopoulos LG, Saez-Rodriguez J, Espelin CW.
Volume (2008) p.29-52
DOI: 10.1002/9780470431818.ch2

2007

Modular analysis of signal transduction networks
Saez-Rodriguez J.
Volume (2007) p.

Systems biology--an engineering perspective.
Kremling A, Saez-Rodriguez J.
J Biotechnol Volume 129 (2007) p.329-351
DOI: 10.1016/j.jbiotec.2007.02.009

A logical model provides insights into T cell receptor signaling.
Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus UU, Weismantel R, Gilles ED, Klamt S, Schraven B.
PLoS Comput Biol Volume 3 (2007) p.e163
DOI: 10.1371/journal.pcbi.0030163

Structural and functional analysis of cellular networks with CellNetAnalyzer.
Klamt S, Saez-Rodriguez J, Gilles ED.
BMC Syst Biol Volume 1 (2007) p.2
DOI: 10.1186/1752-0509-1-2

2006

A methodology for the structural and functional analysis of signaling and regulatory networks.
Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED.
BMC Bioinformatics Volume 7 (2006) p.56
DOI: 10.1186/1471-2105-7-56

Chemical Reaction Network Theory: a tool for systems biology
Conradi C, Saez-Rodriguez J, Gilles ED, Raisch J.
Volume (2006) p.n/a

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks.
Conzelmann H, Saez-Rodriguez J, Sauter T, Kholodenko BN, Gilles ED.
BMC Bioinformatics Volume 7 (2006) p.34
DOI: 10.1186/1471-2105-7-34

Visual setup of logical models of signaling and regulatory networks with ProMoT.
Saez-Rodriguez J, Mirschel S, Hemenway R, Klamt S, Gilles ED, Ginkel M.
BMC Bioinformatics Volume 7 (2006) p.506
DOI: 10.1186/1471-2105-7-506

2005

Using chemical reaction network theory to discard a kinetic mechanism hypothesis.
Conradi C, Saez-Rodriguez J, Gilles ED, Raisch J.
Syst Biol (Stevenage) Volume 152 (2005) p.243-248
DOI: 10.1049/ip-syb:20050045

Dissecting the puzzle of life: modularization of signal transduction networks
Saez-Rodriguez J, Kremling A, Gilles ED.
Comput Chem Eng Volume 29 (2005) p.619-629
DOI: 10.1016/j.compchemeng.2004.08.035

Domain-oriented and modular approaches to the reduction of mathematical models of signaling networks
Saez-Rodriguez J, Conzelmann H, Sauter T, Kholodenko BN, Gilles ED.
Volume (2005) p.13-20

Using chemical reaction network theory to discard a kinetic mechanism hypothesis
Conradi C, Saez-Rodriguez J, Gilles ED, Raisch J.
Volume (2005) p.325-328

2004

Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling.
Conzelmann H, Saez-Rodriguez J, Sauter T, Bullinger E, Allgöwer F, Gilles ED.
Syst Biol (Stevenage) Volume 1 (2004) p.159-169
DOI: 10.1049/sb:20045011