Publications

Publications

2017

Mechanism-based biomarker discovery.
Antoranz A, Sakellaropoulos T, Saez-Rodriguez J, Alexopoulos LG.
Drug discovery today Volume 22 (2017) p.1209-1215

Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.
Mateo F, Arenas EJ, Aguilar H, Serra-Musach J, de Garibay GR, Boni J, Maicas M, Du S, Iorio F, Herranz-Ors C, Islam A, Prado X, Llorente A, Petit A, Vidal A, Català I, Soler T, Venturas G, Rojo-Sebastian A, Serra H, Cuadras D, Blanco I, Lozano J, Canals F, Sieuwerts AM, de Weerd V, Look MP, Puertas S, García N, Perkins AS, Bonifaci N, Skowron M, Gómez-Baldó L, Hernández V, Martínez-Aranda A, Martínez-Iniesta M, Serrat X, Cerón J, Brunet J, Barretina MP, Gil M, Falo C, Fernández A, Morilla I, Pernas S, Plà MJ, Andreu X, Seguí MA, Ballester R, Castellà E, Nellist M, Morales S, Valls J, Velasco A, Matias-Guiu X, Figueras A, Sánchez-Mut JV, Sánchez-Céspedes M, Cordero A, Gómez-Miragaya J, Palomero L, Gómez A, Gajewski TF, Cohen EEW, Jesiotr M, Bodnar L, Quintela-Fandino M, López-Bigas N, Valdés-Mas R, Puente XS, Viñals F, Casanovas O, Graupera M, Hernández-Losa J, Ramón Y Cajal S, García-Alonso L, Saez-Rodriguez J, Esteller M, Sierra A, Martín-Martín N, Matheu A, Carracedo A, González-Suárez E, Nanjundan M, Cortés J, Lázaro C, Odero MD, Martens JWM, Moreno-Bueno G, Barcellos-Hoff MH, Villanueva A, Gomis RR, Pujana MA.
Oncogene Volume 36 (2017) p.2737-2749

Gli1+ Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target.
Schneider RK, Mullally A, Dugourd A, Peisker F, Hoogenboezem R, Van Strien PMH, Bindels EM, Heckl D, Büsche G, Fleck D, Müller-Newen G, Wongboonsin J, Ventura Ferreira M, Puelles VG, Saez-Rodriguez J, Ebert BL, Humphreys BD, Kramann R.
Cell stem cell Volume 20 (2017) p.785-800.e8

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.
Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S, Tarpey P, Alifrangis C, Bignell G, Vidal J, Young J, Stebbings L, Beal K, Stratton MR, Saez-Rodriguez J, Garnett M, Montagut C, Iorio F, McDermott U.
Genome research Volume 27 (2017) p.613-625

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.
Penas DR, Henriques D, González P, Doallo R, Saez-Rodriguez J, Banga JR.
PloS one Volume 12 (2017) p.e0182186

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.
Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J.
Metabolic engineering Volume (2017) p.

caspo: a toolbox for automated reasoning on the response of logical signaling networks families.
Videla S, Saez-Rodriguez J, Guziolowski C, Siegel A.
Bioinformatics (Oxford, England) Volume 33 (2017) p.947-950

GDSCTools for Mining Pharmacogenomic Interactions in Cancer.
Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ.
Bioinformatics (Oxford, England) Volume (2017) p.

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.
Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P.
Cell systems Volume 5 (2017) p.386-398.e4

Logic Modeling in Quantitative Systems Pharmacology.
Traynard P, Tobalina L, Eduati F, Calzone L, Saez-Rodriguez J.
CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.499-511

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
Henriques D, Villaverde AF, Rocha M, Saez-Rodriguez J, Banga JR.
PLoS computational biology Volume 13 (2017) p.e1005379

Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P.
Bioinformatics (Oxford, England) Volume 33 (2017) p.1845-1851

Transcription factor activities enhance markers of drug sensitivity in cancer.
Garcia-Alonso LM, Iorio F, Matchan A, Fonseca NA, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell GR, McDade S, Garnett MJ, Saez-Rodriguez J.
Cancer research Volume (2017) p.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.
Cell reports Volume 20 (2017) p.2201-2214

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J.
PLoS computational biology Volume 13 (2017) p.e1005297

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.
Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R.
Cell systems Volume (2017) p.

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.
Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R.
Journal of proteome research Volume 16 (2017) p.831-841

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA.
Cell systems Volume 5 (2017) p.485-497.e3

Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.
Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J.
Cancer research Volume 77 (2017) p.3364-3375

2016

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.
Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Ohnishi S, Cooper J, Patel M, McKerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, McDermott U, Saez-Rodriguez J, Huntly BJP, Iorio F, Pina C, Vassiliou GS, Yusa K.
Cell reports Volume 17 (2016) p.1193-1205

Inferring causal molecular networks: empirical assessment through a community-based effort.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.
Nature methods Volume 13 (2016) p.310-318

Crowdsourcing biomedical research: leveraging communities as innovation engines.
Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G.
Nature reviews. Genetics Volume 17 (2016) p.470-486

Logical Modeling and Dynamical Analysis of Cellular Networks.
Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.
Frontiers in genetics Volume 7 (2016) p.94

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C.
BMC bioinformatics Volume 17 (2016) p.155

Looking beyond the cancer cell for effective drug combinations.
Dry JR, Yang M, Saez-Rodriguez J.
Genome medicine Volume 8 (2016) p.125

OmniPath: guidelines and gateway for literature-curated signaling pathway resources.
Türei D, Korcsmáros T, Saez-Rodriguez J.
Nature methods Volume 13 (2016) p.966-967

A Landscape of Pharmacogenomic Interactions in Cancer.
Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ.
Cell Volume 166 (2016) p.740-754

Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A.
Rohwer N, Bindel F, Grimm C, Lin SJ, Wappler J, Klinger B, Blüthgen N, Du Bois I, Schmeck B, Lehrach H, de Graauw M, Goncalves E, Saez-Rodriguez J, Tan P, Grabsch HI, Prigione A, Kempa S, Cramer T.
Oncotarget Volume 7 (2016) p.6693-6710

Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.
Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa AS, Gaude E, Drubbel AV, Theobald SJ, Abbo SR, Tran MG, Rajeeve V, Cardaci S, Foster S, Yun H, Cutillas P, Warren A, Gnanapragasam V, Gottlieb E, Franze K, Huntly B, Maher ER, Maxwell PH, Saez-Rodriguez J, Frezza C.
Nature Volume 537 (2016) p.544-547

Efficient randomization of biological networks while preserving functional characterization of individual nodes.
Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J.
BMC Bioinformatics Volume 17 (2016) p.542

The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling.
Chiapparino A, Maeda K, Turei D, Saez-Rodriguez J, Gavin AC.
Progress in lipid research Volume 61 (2016) p.30-39

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.
Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T.
Drug discovery today Volume 21 (2016) p.1063-1075

Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.
Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D, Braicu I, Sehouli J, Saez-Rodriguez J, Cutillas PR, Balkwill FR.
Oncotarget Volume 7 (2016) p.15648-15661

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 systems biology Volume 9 (2015) p.8

Prospective derivation of a living organoid biobank of colorectal cancer patients.
van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H.
Cell Volume 161 (2015) p.933-945

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.
Multiple sclerosis (Houndmills, Basingstoke, England) Volume 21 (2015) p.138-146

DREAMTools: a Python package for scoring collaborative challenges.
Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J.
F1000Research Volume 4 (2015) p.1030

Modeling Signaling Networks to Advance New Cancer Therapies.
Saez-Rodriguez J, MacNamara A, Cook S.
Annual review of biomedical engineering Volume 17 (2015) p.143-163

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
Thiele S, Cerone L, Saez-Rodriguez J, Siegel A, Guziołowski C, Klamt S.
BMC bioinformatics Volume 16 (2015) p.345

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Henriques D, Rocha M, Saez-Rodriguez J, Banga JR.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2999-3007

A single-cell model of PIP3 dynamics using chemical dimerization.
MacNamara A, Stein F, Feng S, Schultz C, Saez-Rodriguez J.
Bioorganic & medicinal chemistry Volume 23 (2015) p.2868-2876

Pharmacogenomic agreement between two cancer cell line data sets.
Cancer Cell Line Encyclopedia Consortium, Genomics of Drug Sensitivity in Cancer Consortium.
Nature Volume 528 (2015) p.84-87

Empirical inference of circuitry and plasticity in a kinase signaling network.
Wilkes EH, Terfve C, Gribben JG, Saez-Rodriguez J, Cutillas PR.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.7719-7724

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.
Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP.
Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.904-920

Integrative approaches for signalling and metabolic networks.
Hatzimanikatis V, Saez-Rodriguez J.
Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.844-845

Designing Experiments to Discriminate Families of Logic Models.
Videla S, Konokotina I, Alexopoulos LG, Saez-Rodriguez J, Schaub T, Siegel A, Guziolowski C.
Frontiers in Bioengineering and Biotechnology Volume 3 (2015) p.131

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.
Terfve CD, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J.
Nature communications Volume 6 (2015) p.8033

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 (Oxford, England) Volume 31 (2015) p.1154-1159

Prediction of human population responses to toxic compounds by a collaborative competition.
Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O, NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.
Nature biotechnology Volume 33 (2015) p.933-940

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.
Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J, Draviam VM.
PloS one Volume 10 (2015) p.e0139446

2014

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 systems biology Volume 8 (2014) p.13

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.
Molecular Systems Biology Volume 10 (2014) p.767

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.
Science signaling Volume 7 (2014) p.ra5

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.
Integrative biology : quantitative biosciences from nano to macro Volume 6 (2014) p.1170-1182

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

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.
Angewandte Chemie (International ed. in English) 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.
Bio Systems Volume 124 (2014) p.26-38

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.
Nature biotechnology 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 (Oxford, England) Volume 30 (2014) p.i617-23

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.
Nature biotechnology Volume 32 (2014) p.1213-1222

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

2013

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

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 systems biology Volume 7 (2013) p.135

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

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

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

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, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR.
Genome biology 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.
Molecular bioSystems Volume 9 (2013) p.1576-1583

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 (Oxford, England) Volume 29 (2013) p.2320-2326

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

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.
Nature methods Volume 10 (2013) p.228-238

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 systems biology Volume 7 (2013) p.116

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Gonçalves E, Mirlach F, Saez-Rodriguez J.
F1000Research Volume 2 (2013) p.192

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

Network based elucidation of drug response: from modulators to targets.
Iorio F, Saez-Rodriguez J, di Bernardo D.
BMC systems biology 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 in molecular biology (Clifton, N.J.) Volume 930 (2013) p.179-214

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.
Nature biotechnology Volume 31 (2013) p.126-134

2012

Modeling signaling networks using high-throughput phospho-proteomics.
Terfve C, Saez-Rodriguez J.
Advances in experimental medicine and biology 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.
Molecular bioSystems Volume 8 (2012) p.1571-1584

State-time spectrum of signal transduction logic models.
MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J.
Physical biology Volume 9 (2012) p.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 systems biology 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 (Oxford, England) Volume 28 (2012) p.2311-2317

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.
Integrative biology : quantitative biosciences from nano to macro Volume 4 (2012) p.1038-1048

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.
Molecular systems biology Volume 8 (2012) p.603

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 systems biology 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

2011

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

Setting the standards for signal transduction research.
Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G.
Science signaling 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 Computational Biology Volume 7 (2011) p.e1001099

Unknown year

Perturbation-response genes reveal signaling footprints in cancer gene expression
Schubert M, Klinger B, Kluenemann M, Garnett MJ, Bluethgen N, Saez-Rodriguez J.
Volume (0) p.

Dissecting the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich
Iorio F, Garcia-Alonso L, Brammeld J, Martincorena I, Wille DR, McDermott U, Saez-Rodriguez J.
Volume (0) p.

A Systematic Atlas of Chaperome Deregulation Topologies Across the Human Cancer Landscape
Hadizadeh Esfahani A, Sverchkova A, Saez-Rodriguez J, Schuppert A, Brehme M.
Volume (0) p.