Julio Saez-Rodriguez - Publications

Affiliations: 
European Bioinformatics Institute, Hinxton, England, United Kingdom 

81 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biology. 21: 36. PMID 32051003 DOI: 10.1186/s13059-020-1949-z  0.56
2020 Tajti F, Kuppe C, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Holland CH, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. A Functional Landscape of CKD Entities From Public Transcriptomic Data. Kidney International Reports. 5: 211-224. PMID 32043035 DOI: 10.1016/j.ekir.2019.11.005  0.56
2019 Kotelnikova E, Kiani NA, Messinis D, Pertsovskaya I, Pliaka V, Bernardo-Faura M, Rinas M, Vila G, Zubizarreta I, Pulido-Valdeolivas I, Sakellaropoulos T, Faigle W, Silberberg G, Masso M, Stridh P, ... ... Saez-Rodriguez J, et al. MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis. Proceedings of the National Academy of Sciences of the United States of America. PMID 31004050 DOI: 10.1073/pnas.1818347116  0.56
2018 Razzaq M, Paulevé L, Siegel A, Saez-Rodriguez J, Bourdon J, Guziolowski C. Computational discovery of dynamic cell line specific Boolean Networks from multiplex time-course data. Plos Computational Biology. 14: e1006538. PMID 30372442 DOI: 10.1371/journal.pcbi.1006538  0.48
2017 Antoranz A, Sakellaropoulos T, Saez-Rodriguez J, Alexopoulos LG. Mechanism-based biomarker discovery. Drug Discovery Today. PMID 28458042 DOI: 10.1016/j.drudis.2017.04.013  0.56
2017 Videla S, Saez-Rodriguez J, Guziolowski C, Siegel A. caspo: a toolbox for automated reasoning on the response of logical signaling networks families. Bioinformatics (Oxford, England). PMID 28065903 DOI: 10.1093/bioinformatics/btw738  0.48
2016 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, ... ... Saez-Rodriguez J, et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell. PMID 27397505 DOI: 10.1016/j.cell.2016.06.017  1
2016 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. A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. Bmc Bioinformatics. 17: 155. PMID 27059896 DOI: 10.1186/s12859-016-1008-7  1
2016 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. Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells. Oncotarget. PMID 26871292 DOI: 10.18632/oncotarget.7255  1
2015 Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, ... ... Saez-Rodriguez J, et al. DREAMTools: a Python package for scoring collaborative challenges. F1000research. 4: 1030. PMID 27134723 DOI: 10.12688/f1000research.7118.1  1
2015 Thiele S, Cerone L, Saez-Rodriguez J, Siegel A, Guziołowski C, Klamt S. Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. Bmc Bioinformatics. 16: 345. PMID 26510976 DOI: 10.1186/s12859-015-0733-7  1
2015 Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J, Draviam VM. A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions. Plos One. 10: e0139446. PMID 26452147 DOI: 10.1371/journal.pone.0139446  1
2015 Videla S, Konokotina I, Alexopoulos LG, Saez-Rodriguez J, Schaub T, Siegel A, Guziolowski C. Designing Experiments to Discriminate Families of Logic Models. Frontiers in Bioengineering and Biotechnology. 3: 131. PMID 26389116 DOI: 10.3389/fbioe.2015.00131  0.56
2015 Wilkes EH, Terfve C, Gribben JG, Saez-Rodriguez J, Cutillas PR. Empirical inference of circuitry and plasticity in a kinase signaling network. Proceedings of the National Academy of Sciences of the United States of America. 112: 7719-24. PMID 26060313 DOI: 10.1073/pnas.1423344112  1
2015 MacNamara A, Stein F, Feng S, Schultz C, Saez-Rodriguez J. A single-cell model of PIP3 dynamics using chemical dimerization. Bioorganic & Medicinal Chemistry. 23: 2868-76. PMID 26004322 DOI: 10.1016/j.bmc.2015.04.074  1
2015 Henriques D, Rocha M, Saez-Rodriguez J, Banga JR. Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Bioinformatics (Oxford, England). PMID 26002881 DOI: 10.1093/bioinformatics/btv314  1
2015 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, ... ... Saez-Rodriguez J, et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell. 161: 933-45. PMID 25957691 DOI: 10.1016/j.cell.2015.03.053  1
2015 Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP. Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 25932872 DOI: 10.1039/c4ib00294f  1
2015 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. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. Bmc Systems Biology. 9: 8. PMID 25880925 DOI: 10.1186/s12918-015-0144-4  1
2015 Naldi A, Monteiro PT, Müssel C, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C. Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics (Oxford, England). 31: 1154-9. PMID 25619997 DOI: 10.1093/bioinformatics/btv013  1
2015 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, ... ... Saez-Rodriguez J, et al. Signaling networks in MS: a systems-based approach to developing new pharmacological therapies. Multiple Sclerosis (Houndmills, Basingstoke, England). 21: 138-46. PMID 25112814 DOI: 10.1177/1352458514543339  1
2014 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. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast. Molecular Systems Biology. 10: 767. PMID 25492886 DOI: 10.15252/msb.20145112  1
2014 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, ... ... Saez-Rodriguez J, et al. A community computational challenge to predict the activity of pairs of compounds. Nature Biotechnology. 32: 1213-22. PMID 25419740 DOI: 10.1038/nbt.3052  1
2014 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. Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy. Integrative Biology : Quantitative Biosciences From Nano to Macro. 6: 1170-82. PMID 25303361 DOI: 10.1039/c4ib00086b  1
2014 Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G, Saez-Rodriguez J. Fast randomization of large genomic datasets while preserving alteration counts. Bioinformatics (Oxford, England). 30: i617-23. PMID 25161255 DOI: 10.1093/bioinformatics/btu474  1
2014 Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S. A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Bio Systems. 124: 26-38. PMID 25063553 DOI: 10.1016/j.biosystems.2014.07.002  1
2014 Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J. MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. Bmc Bioinformatics. 15: 136. PMID 24885957 DOI: 10.1186/1471-2105-15-136  1
2014 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, ... ... Saez-Rodriguez J, et al. A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology. 32: 1202-12. PMID 24880487 DOI: 10.1038/nbt.2877  1
2014 Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C. A rapidly reversible chemical dimerizer system to study lipid signaling in living cells. Angewandte Chemie (International Ed. in English). 53: 6720-3. PMID 24841150 DOI: 10.1002/anie.201402294  1
2014 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, ... ... Saez-Rodriguez J, et al. Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. Bmc Systems Biology. 8: 13. PMID 24507381 DOI: 10.1186/1752-0509-8-13  1
2014 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. PIP₃ induces the recycling of receptor tyrosine kinases. Science Signaling. 7: ra5. PMID 24425787 DOI: 10.1126/scisignal.2004532  1
2013 Gonçalves E, Saez-Rodriguez J. Cyrface: An interface from Cytoscape to R that provides a user interface to R packages. F1000research. 2: 192. PMID 24715956 DOI: 10.12688/f1000research.2-192.v1  1
2013 Iorio F, Saez-Rodriguez J, di Bernardo D. Network based elucidation of drug response: from modulators to targets. Bmc Systems Biology. 7: 139. PMID 24330611 DOI: 10.1186/1752-0509-7-139  1
2013 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, ... ... Saez-Rodriguez J, et al. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. Bmc Systems Biology. 7: 135. PMID 24321545 DOI: 10.1186/1752-0509-7-135  1
2013 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, ... ... Saez-Rodriguez J, et al. Path2Models: large-scale generation of computational models from biochemical pathway maps. Bmc Systems Biology. 7: 116. PMID 24180668 DOI: 10.1186/1752-0509-7-116  1
2013 Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J. BioServices: a common Python package to access biological Web Services programmatically. Bioinformatics (Oxford, England). 29: 3241-2. PMID 24064416 DOI: 10.1093/bioinformatics/btt547  1
2013 Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics (Oxford, England). 29: 2320-6. PMID 23853063 DOI: 10.1093/bioinformatics/btt393  1
2013 MacNamara A, Henriques D, Saez-Rodriguez J. Modeling signaling networks with different formalisms: a preview. Methods in Molecular Biology (Clifton, N.J.). 1021: 89-105. PMID 23715981 DOI: 10.1007/978-1-62703-450-0_5  1
2013 Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J. Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. Plos One. 8: e61318. PMID 23646105 DOI: 10.1371/journal.pone.0061318  1
2013 Casado P, Alcolea MP, Iorio F, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR. Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors. Genome Biology. 14: R37. PMID 23628362 DOI: 10.1186/gb-2013-14-4-r37  1
2013 Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J. Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular Biosystems. 9: 1576-83. PMID 23525368 DOI: 10.1039/c3mb25489e  1
2013 Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31: 126-34. PMID 23354101 DOI: 10.1038/nbt.2486  1
2013 Gonçalves E, van Iersel M, Saez-Rodriguez J. CySBGN: a Cytoscape plug-in to integrate SBGN maps. Bmc Bioinformatics. 14: 17. PMID 23324051 DOI: 10.1186/1471-2105-14-17  1
2013 Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J. DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinformatics (Oxford, England). 29: 132-4. PMID 23129297 DOI: 10.1093/bioinformatics/bts656  1
2013 Morris MK, Melas I, Saez-Rodriguez J. Construction of cell type-specific logic models of signaling networks using CellNOpt. Methods in Molecular Biology (Clifton, N.J.). 930: 179-214. PMID 23086842 DOI: 10.1007/978-1-62703-059-5_8  1
2013 Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J. Transcriptional data: a new gateway to drug repositioning? Drug Discovery Today. 18: 350-7. PMID 22897878 DOI: 10.1016/j.drudis.2012.07.014  1
2012 Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, Alexopoulos LG. Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways. Plos One. 7: e50085. PMID 23226239 DOI: 10.1371/journal.pone.0050085  1
2012 Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris MK, van Iersel M, Lauffenburger DA, Saez-Rodriguez J. CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. Bmc Systems Biology. 6: 133. PMID 23079107 DOI: 10.1186/1752-0509-6-133  1
2012 Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G. Mapping the human phosphatome on growth pathways. Molecular Systems Biology. 8: 603. PMID 22893001 DOI: 10.1038/msb.2012.36  1
2012 MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J. State-time spectrum of signal transduction logic models. Physical Biology. 9: 045003. PMID 22871648 DOI: 10.1088/1478-3975/9/4/045003  1
2012 Serra-Musach J, Aguilar H, Iorio F, Comellas F, Berenguer A, Brunet J, Saez-Rodriguez J, Pujana MA. Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network. Integrative Biology : Quantitative Biosciences From Nano to Macro. 4: 1038-48. PMID 22806580 DOI: 10.1039/c2ib20052j  1
2012 Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J. Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics (Oxford, England). 28: 2311-7. PMID 22734019 DOI: 10.1093/bioinformatics/bts363  1
2012 Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK. Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. Bmc Systems Biology. 6: 29. PMID 22548703 DOI: 10.1186/1752-0509-6-29  1
2012 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, ... ... Saez-Rodriguez J, et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 483: 570-5. PMID 22460902 DOI: 10.1038/nature11005  1
2012 Terfve C, Saez-Rodriguez J. Modeling signaling networks using high-throughput phospho-proteomics. Advances in Experimental Medicine and Biology. 736: 19-57. PMID 22161321 DOI: 10.1007/978-1-4419-7210-1_2  1
2011 Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G. Crowdsourcing network inference: the DREAM predictive signaling network challenge. Science Signaling. 4: mr7. PMID 21900204 DOI: 10.1126/scisignal.2002212  1
2011 Saez-Rodriguez J, Alexopoulos LG, Zhang M, Morris MK, Lauffenburger DA, Sorger PK. Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Research. 71: 5400-11. PMID 21742771 DOI: 10.1158/0008-5472.CAN-10-4453  1
2011 Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. Plos Computational Biology. 7: e1001099. PMID 21408212 DOI: 10.1371/journal.pcbi.1001099  1
2011 Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G. Setting the standards for signal transduction research. Science Signaling. 4: pe10. PMID 21325202 DOI: 10.1126/scisignal.2001844  1
2010 Alexopoulos LG, Melas IN, Chairakaki AD, Saez-Rodriguez J, Mitsos A. Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2010: 6717-20. PMID 21096084 DOI: 10.1109/IEMBS.2010.5626246  1
2010 Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK. Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Molecular & Cellular Proteomics : McP. 9: 1849-65. PMID 20460255 DOI: 10.1074/mcp.M110.000406  1
2010 Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA. Logic-based models for the analysis of cell signaling networks. Biochemistry. 49: 3216-24. PMID 20225868 DOI: 10.1021/bi902202q  1
2010 Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. Plos One. 5: e9202. PMID 20186320 DOI: 10.1371/journal.pone.0009202  1
2009 Mitsos A, Melas IN, Siminelakis P, Chairakaki AD, Saez-Rodriguez J, Alexopoulos LG. Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data. Plos Computational Biology. 5: e1000591. PMID 19997482 DOI: 10.1371/journal.pcbi.1000591  1
2009 Cosgrove BD, Alexopoulos LG, Saez-Rodriguez J, Griffith LG, Lauffenburger DA. A multipathway phosphoproteomic signaling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 5452-5. PMID 19964679 DOI: 10.1109/IEMBS.2009.5334019  1
2009 Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology. 5: 331. PMID 19953085 DOI: 10.1038/msb.2009.87  1
2009 Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis FJ. Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. Bmc Systems Biology. 3: 98. PMID 19785753 DOI: 10.1186/1752-0509-3-98  1
2009 Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S. The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. Plos Computational Biology. 5: e1000438. PMID 19662154 DOI: 10.1371/journal.pcbi.1000438  1
2009 Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. Plos Computational Biology. 5: e1000340. PMID 19343194 DOI: 10.1371/journal.pcbi.1000340  1
2008 Saez-Rodriguez J, Gayer S, Ginkel M, Gilles ED. Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. Bioinformatics (Oxford, England). 24: i213-9. PMID 18689828 DOI: 10.1093/bioinformatics/btn289  1
2008 Wang X, Simeoni L, Lindquist JA, Saez-Rodriguez J, Ambach A, Gilles ED, Kliche S, Schraven B. Dynamics of proximal signaling events after TCR/CD8-mediated induction of proliferation or apoptosis in mature CD8+ T cells. Journal of Immunology (Baltimore, Md. : 1950). 180: 6703-12. PMID 18453590  1
2008 Saez-Rodriguez J, Hammerle-Fickinger A, Dalal O, Klamt S, Gilles ED, Conradi C. Multistability of signal transduction motifs. Iet Systems Biology. 2: 80-93. PMID 18397119 DOI: 10.1049/iet-syb:20070012  1
2008 Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, Lauffenburger DA, Sorger PK. Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics (Oxford, England). 24: 840-7. PMID 18218655 DOI: 10.1093/bioinformatics/btn018  1
2007 Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus UU, Weismantel R, Gilles ED, Klamt S, Schraven B. A logical model provides insights into T cell receptor signaling. Plos Computational Biology. 3: e163. PMID 17722974 DOI: 10.1371/journal.pcbi.0030163  1
2007 Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with CellNetAnalyzer. Bmc Systems Biology. 1: 2. PMID 17408509 DOI: 10.1186/1752-0509-1-2  1
2007 Kremling A, Saez-Rodriguez J. Systems biology--an engineering perspective. Journal of Biotechnology. 129: 329-51. PMID 17400319 DOI: 10.1016/j.jbiotec.2007.02.009  1
2006 Saez-Rodriguez J, Mirschel S, Hemenway R, Klamt S, Gilles ED, Ginkel M. Visual setup of logical models of signaling and regulatory networks with ProMoT. Bmc Bioinformatics. 7: 506. PMID 17109765 DOI: 10.1186/1471-2105-7-506  1
2006 Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED. A methodology for the structural and functional analysis of signaling and regulatory networks. Bmc Bioinformatics. 7: 56. PMID 16464248 DOI: 10.1186/1471-2105-7-56  1
2006 Conzelmann H, Saez-Rodriguez J, Sauter T, Kholodenko BN, Gilles ED. A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. Bmc Bioinformatics. 7: 34. PMID 16430778 DOI: 10.1186/1471-2105-7-34  1
2005 Conradi C, Saez-Rodriguez J, Gilles ED, Raisch J. Using chemical reaction network theory to discard a kinetic mechanism hypothesis. Systems Biology. 152: 243-8. PMID 16986266 DOI: 10.1049/ip-syb:20050045  1
2004 Conzelmann H, Saez-Rodriguez J, Sauter T, Bullinger E, Allgöwer F, Gilles ED. Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling. Systems Biology. 1: 159-69. PMID 17052126 DOI: 10.1049/sb:20045011  1
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