| Year |
Citation |
Score |
| 2023 |
Wijaya LS, Gabor A, Pot IE, van de Have L, Saez-Rodriguez J, Stevens JL, Le Dévédec SE, Callegaro G, van de Water B. A Network-based Transcriptomic Landscape of HepG2 cells Uncovering Causal Gene-Cytotoxicity Interactions Underlying Drug-Induced Liver Injury. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 38015832 DOI: 10.1093/toxsci/kfad121 |
0.303 |
|
| 2022 |
Kay EJ, Paterson K, Riera-Domingo C, Sumpton D, Däbritz JHM, Tardito S, Boldrini C, Hernandez-Fernaud JR, Athineos D, Dhayade S, Stepanova E, Gjerga E, Neilson LJ, Lilla S, Hedley A, ... ... Saez-Rodriguez J, et al. Author Correction: Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix. Nature Metabolism. PMID 35927357 DOI: 10.1038/s42255-022-00632-7 |
0.72 |
|
| 2022 |
Garrido-Rodriguez M, Zirngibl K, Ivanova O, Lobentanzer S, Saez-Rodriguez J. Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks. Molecular Systems Biology. 18: e11036. PMID 35880747 DOI: 10.15252/msb.202211036 |
0.413 |
|
| 2022 |
Kay EJ, Paterson K, Riero-Domingo C, Sumpton D, Däbritz JHM, Tardito S, Boldrini C, Hernandez-Fernaud JR, Athineos D, Dhayade S, Stepanova E, Gjerga E, Neilson LJ, Lilla S, Hedley A, ... ... Saez-Rodriguez J, et al. Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix. Nature Metabolism. 4: 693-710. PMID 35760868 DOI: 10.1038/s42255-022-00582-0 |
0.732 |
|
| 2022 |
Hernansaiz-Ballesteros R, Holland CH, Dugourd A, Saez-Rodriguez J. FUNKI: Interactive functional footprint-based analysis of omics data. Bioinformatics (Oxford, England). PMID 35134857 DOI: 10.1093/bioinformatics/btac055 |
0.305 |
|
| 2021 |
Gabor A, Tognetti M, Driessen A, Tanevski J, Guo B, Cao W, Shen H, Yu T, Chung V, Bodenmiller B, Saez-Rodriguez J. Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd. Molecular Systems Biology. 17: e10402. PMID 34661974 DOI: 10.15252/msb.202110402 |
0.312 |
|
| 2021 |
Lone AM, Giansanti P, Jørgensen MJ, Gjerga E, Dugourd A, Scholten A, Saez-Rodriguez J, Heck AJR, Taskén K. Systems approach reveals distinct and shared signaling networks of the four PGE receptors in T cells. Science Signaling. 14: eabc8579. PMID 34609894 DOI: 10.1126/scisignal.abc8579 |
0.778 |
|
| 2021 |
Trairatphisan P, de Souza TM, Kleinjans J, Jennen D, Saez-Rodriguez J. Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury. Toxicology Letters. PMID 34229068 DOI: 10.1016/j.toxlet.2021.06.020 |
0.341 |
|
| 2021 |
Meyer P, Saez-Rodriguez J. Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges. Cell Systems. 12: 636-653. PMID 34139170 DOI: 10.1016/j.cels.2021.05.015 |
0.322 |
|
| 2021 |
Tognetti M, Gabor A, Yang M, Cappelletti V, Windhager J, Rueda OM, Charmpi K, Esmaeilishirazifard E, Bruna A, de Souza N, Caldas C, Beyer A, Picotti P, Saez-Rodriguez J, Bodenmiller B. Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Systems. PMID 33932331 DOI: 10.1016/j.cels.2021.04.002 |
0.322 |
|
| 2021 |
Mazein A, Rougny A, Karr JR, Saez-Rodriguez J, Ostaszewski M, Schneider R. Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. Briefings in Bioinformatics. PMID 33834185 DOI: 10.1093/bib/bbab103 |
0.334 |
|
| 2021 |
Gjerga E, Dugourd A, Tobalina L, Sousa A, Saez-Rodriguez J. PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data. Journal of Proteome Research. PMID 33682416 DOI: 10.1021/acs.jproteome.0c00958 |
0.803 |
|
| 2021 |
Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Gabor A, Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ, Costa ASH, Sousa A, Beltrao P, Rocha M, Olsen JV, ... ... Saez-Rodriguez J, et al. Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses. Molecular Systems Biology. 17: e9730. PMID 33502086 DOI: 10.15252/msb.20209730 |
0.789 |
|
| 2020 |
Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stępniak P, Warchoł M, ... ... Saez-Rodriguez J, et al. Crowdsourced Assessment of the of Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Systems. PMID 32710834 DOI: 10.1016/J.Cels.2020.06.013 |
0.352 |
|
| 2020 |
Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, ... ... Saez-Rodriguez J, et al. The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics (Oxford, England). PMID 32637990 DOI: 10.1093/Bioinformatics/Btaa622 |
0.331 |
|
| 2020 |
Gjerga E, Trairatphisan P, Gabor A, Koch H, Chevalier C, Ceccarelli F, Dugourd A, Mitsos A, Saez-Rodriguez J. Converting networks to predictive logic models from perturbation signalling data with CellNOpt. Bioinformatics (Oxford, England). PMID 32516357 DOI: 10.1093/Bioinformatics/Btaa561 |
0.806 |
|
| 2020 |
Najgebauer H, Yang M, Francies HE, Pacini C, Stronach EA, Garnett MJ, Saez-Rodriguez J, Iorio F. CELLector: Genomics-Guided Selection of Cancer In Vitro Models. Cell Systems. 10: 424-432.e6. PMID 32437684 DOI: 10.1016/J.Cels.2020.04.007 |
0.319 |
|
| 2020 |
Niarakis A, Kuiper M, Ostaszewski M, Malik Sheriff RS, Casals-Casas C, Thieffry D, Freeman TC, Thomas P, Touré V, Noël V, Stoll G, Saez-Rodriguez J, Naldi A, Oshurko E, Xenarios I, et al. 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. Briefings in Bioinformatics. PMID 32313939 DOI: 10.1093/Bib/Bbaa046 |
0.413 |
|
| 2020 |
Eduati F, Jaaks P, Wappler J, Cramer T, Merten CA, Garnett MJ, Saez-Rodriguez J. Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies. Molecular Systems Biology. 16: e8664. PMID 32073727 DOI: 10.15252/msb.20188664 |
0.307 |
|
| 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 |
0.322 |
|
| 2020 |
Ferreira S, Fisher C, Furlong LI, Laplanche L, Park BK, Pin C, Saez-Rodriguez J, Trairatphisan P. Quantitative Systems Toxicology Modeling To Address Key Safety Questions in Drug Development: A Focus of the TransQST Consortium. Chemical Research in Toxicology. PMID 31909603 DOI: 10.1021/Acs.Chemrestox.9B00499 |
0.328 |
|
| 2020 |
Saez-Rodriguez J, Gabor A, Tognett M, Tanevski J, Yu T, Chung V, Bletz J, Picotti P, Bodenmiller B. Single cell signaling in breast cancer DREAM Challenge 2019 F1000research. 8. DOI: 10.7490/F1000Research.1117781.1 |
0.319 |
|
| 2019 |
Dugourd A, Saez-Rodriguez J. Footprint-based functional analysis of multiomic data. Current Opinion in Systems Biology. 15: 82-90. PMID 32685770 DOI: 10.1016/J.Coisb.2019.04.002 |
0.385 |
|
| 2019 |
Ceccarelli F, Turei D, Gabor A, Saez-Rodriguez J. Bringing data from curated pathway resources to Cytoscape with OmniPath. Bioinformatics (Oxford, England). PMID 31886476 DOI: 10.1093/Bioinformatics/Btz968 |
0.425 |
|
| 2019 |
Rinschen MM, Palygin O, Guijas C, Palermo A, Palacio-Escat N, Domingo-Almenara X, Montenegro-Burke R, Saez-Rodriguez J, Staruschenko A, Siuzdak G. Metabolic rewiring of the hypertensive kidney. Science Signaling. 12. PMID 31822592 DOI: 10.1126/Scisignal.Aax9760 |
0.301 |
|
| 2019 |
Berndt N, Egners A, Mastrobuoni G, Vvedenskaya O, Fragoulis A, Dugourd A, Bulik S, Pietzke M, Bielow C, van Gassel R, Damink SWO, Erdem M, Saez-Rodriguez J, Holzhütter HG, Kempa S, et al. Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer. British Journal of Cancer. PMID 31819186 DOI: 10.1038/S41416-019-0659-3 |
0.323 |
|
| 2019 |
Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, ... ... Saez-Rodriguez J, et al. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. Iscience. 21: 664-680. PMID 31733513 DOI: 10.1016/J.Isci.2019.10.059 |
0.36 |
|
| 2019 |
Liu A, Trairatphisan P, Gjerga E, Didangelos A, Barratt J, Saez-Rodriguez J. From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL. Npj Systems Biology and Applications. 5: 40. PMID 31728204 DOI: 10.1038/s41540-019-0118-z |
0.801 |
|
| 2019 |
Manica M, Oskooei A, Born J, Subramanian V, Saez-Rodriguez J, Rodríguez Martínez M. Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders. Molecular Pharmaceutics. PMID 31618586 DOI: 10.1021/Acs.Molpharmaceut.9B00520 |
0.352 |
|
| 2019 |
Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O. Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis. Cell Reports. 29: 202-211.e6. PMID 31577949 DOI: 10.1016/J.Celrep.2019.08.077 |
0.323 |
|
| 2019 |
Szalai B, Subramanian V, Holland CH, Alföldi R, Puskás LG, Saez-Rodriguez J. Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction. Nucleic Acids Research. PMID 31552418 DOI: 10.1093/Nar/Gkz805 |
0.342 |
|
| 2019 |
Holland CH, Szalai B, Saez-Rodriguez J. Transfer of regulatory knowledge from human to mouse for functional genomic analysis. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 194431. PMID 31525460 DOI: 10.1016/J.Bbagrm.2019.194431 |
0.355 |
|
| 2019 |
Ellrott K, Buchanan A, Creason A, Mason M, Schaffter T, Hoff B, Eddy J, Chilton JM, Yu T, Stuart JM, Saez-Rodriguez J, Stolovitzky G, Boutros PC, Guinney J. Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges. Genome Biology. 20: 195. PMID 31506093 DOI: 10.1186/S13059-019-1794-0 |
0.332 |
|
| 2019 |
Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, Subramanian A, Zhang JD, ... ... Saez-Rodriguez J, et al. Assessment of network module identification across complex diseases. Nature Methods. 16: 843-852. PMID 31471613 DOI: 10.1038/S41592-019-0509-5 |
0.424 |
|
| 2019 |
Schäfer A, Gjerga E, Welford RW, Renz I, Lehembre F, Groenen PM, Saez-Rodriguez J, Aebersold R, Gstaiger M. Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data. Molecular Systems Biology. 15: e8828. PMID 31464372 DOI: 10.15252/Msb.20198828 |
0.785 |
|
| 2019 |
Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Research. PMID 31340985 DOI: 10.1101/Gr.240663.118 |
0.329 |
|
| 2019 |
Tang J, Gautam P, Gupta A, He L, Timonen S, Akimov Y, Wang W, Szwajda A, Jaiswal A, Turei D, Yadav B, Kankainen M, Saarela J, Saez-Rodriguez J, Wennerberg K, et al. Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer. Npj Systems Biology and Applications. 5: 20. PMID 31312514 DOI: 10.1038/s41540-019-0098-z |
0.314 |
|
| 2019 |
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang IS, Ghazoui Z, ... ... Saez-Rodriguez J, et al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. 10: 2674. PMID 31209238 DOI: 10.1038/S41467-019-09799-2 |
0.335 |
|
| 2019 |
Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B. Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling. Molecular Cell. PMID 31101498 DOI: 10.1016/J.Molcel.2019.04.021 |
0.42 |
|
| 2019 |
Picco G, Chen ED, Alonso LG, Behan FM, Gonçalves E, Bignell G, Matchan A, Fu B, Banerjee R, Anderson E, Butler A, Benes CH, McDermott U, Dow D, Iorio F, ... ... Saez-Rodriguez J, et al. Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening. Nature Communications. 10: 2198. PMID 31097696 DOI: 10.1038/S41467-019-09940-1 |
0.339 |
|
| 2019 |
Sale MJ, Balmanno K, Saxena J, Ozono E, Wojdyla K, McIntyre RE, Gilley R, Woroniuk A, Howarth KD, Hughes G, Dry JR, Arends MJ, Caro P, Oxley D, Ashton S, ... ... Saez-Rodriguez J, et al. MEK1/2 inhibitor withdrawal reverses acquired resistance driven by BRAF amplification whereas KRAS amplification promotes EMT-chemoresistance. Nature Communications. 10: 2030. PMID 31048689 DOI: 10.1038/S41467-019-09438-W |
0.303 |
|
| 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 |
0.305 |
|
| 2019 |
Saez-Rodriguez J, Rinschen MM, Floege J, Kramann R. Big science and big data in nephrology. Kidney International. PMID 30982672 DOI: 10.1016/J.Kint.2018.11.048 |
0.307 |
|
| 2019 |
Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, Santos R, Rao Y, Sassi F, Pinnelli M, Ansari R, Harper S, Jackson DA, McRae R, Pooley R, ... ... Saez-Rodriguez J, et al. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature. PMID 30971826 DOI: 10.1038/S41586-019-1103-9 |
0.32 |
|
| 2019 |
Gjerga E, Trairatphisan P, Gabor A, Saez-Rodriguez J. Literature and data-driven based inference of signalling interactions using time-course data Ifac-Papersonline. 52: 52-57. DOI: 10.1016/J.Ifacol.2019.12.235 |
0.508 |
|
| 2019 |
González P, Argüeso-Alejandro P, Penas DR, Pardo XC, Saez-Rodriguez J, Banga JR, Doallo R. Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology The Journal of Supercomputing. 75: 3471-3498. DOI: 10.1007/S11227-019-02871-0 |
0.301 |
|
| 2018 |
Kalamara A, Tobalina L, Saez-Rodriguez J. How to find the right drug for each patient? Advances and challenges in pharmacogenomics. Current Opinion in Systems Biology. 10: 53-62. PMID 31763498 DOI: 10.1016/J.Coisb.2018.07.001 |
0.355 |
|
| 2018 |
Späth MR, Bartram MP, Palacio-Escat N, Hoyer KJR, Debes C, Demir F, Schroeter CB, Mandel AM, Grundmann F, Ciarimboli G, Beyer A, Kizhakkedathu JN, Brodesser S, Göbel H, Becker JU, ... ... Saez-Rodriguez J, et al. The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury. Kidney International. PMID 30522767 DOI: 10.1016/J.Kint.2018.08.037 |
0.3 |
|
| 2018 |
Souza T, Trairatphisan P, Piñero J, Furlong LI, Saez-Rodriguez J, Kleinjans J, Jennen D. Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. Frontiers in Genetics. 9: 527. PMID 30515189 DOI: 10.3389/Fgene.2018.00527 |
0.334 |
|
| 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 |
0.526 |
|
| 2018 |
Eduati F, Utharala R, Madhavan D, Neumann UP, Longerich T, Cramer T, Saez-Rodriguez J, Merten CA. A microfluidics platform for combinatorial drug screening on cancer biopsies. Nature Communications. 9: 2434. PMID 29934552 DOI: 10.1038/S41467-018-04919-W |
0.31 |
|
| 2018 |
Yang M, Simm J, Lam CC, Zakeri P, van Westen GJP, Moreau Y, Saez-Rodriguez J. Linking drug target and pathway activation for effective therapy using multi-task learning. Scientific Reports. 8: 8322. PMID 29844324 DOI: 10.1038/S41598-018-25947-Y |
0.35 |
|
| 2018 |
Guinney J, Saez-Rodriguez J. Alternative models for sharing confidential biomedical data. Nature Biotechnology. 36: 391-392. PMID 29734317 DOI: 10.1038/Nbt.4128 |
0.331 |
|
| 2018 |
Iorio F, Garcia-Alonso L, Brammeld JS, Martincorena I, Wille DR, McDermott U, Saez-Rodriguez J. Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich. Scientific Reports. 8: 6713. PMID 29713020 DOI: 10.1038/S41598-018-25076-6 |
0.348 |
|
| 2018 |
Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, ... ... Saez-Rodriguez J, et al. Whither systems medicine? Experimental & Molecular Medicine. 50: e453. PMID 29497170 DOI: 10.1038/Emm.2017.290 |
0.317 |
|
| 2018 |
Wirbel J, Cutillas P, Saez-Rodriguez J. Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells. Methods in Molecular Biology (Clifton, N.J.). 1711: 103-132. PMID 29344887 DOI: 10.1007/978-1-4939-7493-1_6 |
0.328 |
|
| 2018 |
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nature Communications. 9: 20. PMID 29295995 DOI: 10.1038/S41467-017-02391-6 |
0.384 |
|
| 2018 |
Hadizadeh Esfahani A, Sverchkova A, Saez-Rodriguez J, Schuppert AA, Brehme M. A systematic atlas of chaperome deregulation topologies across the human cancer landscape. Plos Computational Biology. 14: e1005890. PMID 29293508 DOI: 10.1371/Journal.Pcbi.1005890 |
0.408 |
|
| 2017 |
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. Transcription factor activities enhance markers of drug sensitivity in cancer. Cancer Research. PMID 29229604 DOI: 10.1158/0008-5472.Can-17-1679 |
0.329 |
|
| 2017 |
Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R. Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines. Cell Systems. PMID 29226804 DOI: 10.1016/J.Cels.2017.11.002 |
0.342 |
|
| 2017 |
Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J. Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells. Metabolic Engineering. PMID 29191787 DOI: 10.1016/J.Ymben.2017.11.011 |
0.342 |
|
| 2017 |
Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ. GDSCTools for Mining Pharmacogenomic Interactions in Cancer. Bioinformatics (Oxford, England). PMID 29186349 DOI: 10.1093/Bioinformatics/Btx744 |
0.322 |
|
| 2017 |
Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P. Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer. Cell Systems. PMID 29032074 DOI: 10.1016/J.Cels.2017.08.013 |
0.317 |
|
| 2017 |
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, ... ... Saez-Rodriguez J, et al. Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. Cell Reports. 20: 2201-2214. PMID 28854368 DOI: 10.1016/J.Celrep.2017.08.010 |
0.388 |
|
| 2017 |
Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models. Cancer Research. 77: 3364-3375. PMID 28381545 DOI: 10.1158/0008-5472.Can-17-0078 |
0.427 |
|
| 2017 |
Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P. Benchmarking substrate-based kinase activity inference using phosphoproteomic data. Bioinformatics (Oxford, England). PMID 28200105 DOI: 10.1093/Bioinformatics/Btx082 |
0.33 |
|
| 2017 |
Henriques D, Villaverde AF, Rocha M, Saez-Rodriguez J, Banga JR. Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. Plos Computational Biology. 13: e1005379. PMID 28166222 DOI: 10.1371/Journal.Pcbi.1005379 |
0.471 |
|
| 2017 |
Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J. Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. Plos Computational Biology. 13: e1005297. PMID 28072816 DOI: 10.1371/Journal.Pcbi.1005297 |
0.363 |
|
| 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 |
0.375 |
|
| 2017 |
Iorio F, Knijnenburg T, vis D, Bignell G, Menden M, Wessels L, Saez-Rodriguez J, McDermott U, Garnett M. Abstract A44: A landscape of pharmacogenomic interactions in cancer Clinical Cancer Research. 23. DOI: 10.1158/1557-3265.Pmccavuln16-A44 |
0.337 |
|
| 2016 |
Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J. Efficient randomization of biological networks while preserving functional characterization of individual nodes. Bmc Bioinformatics. 17: 542. PMID 27998275 DOI: 10.1186/S12859-016-1402-1 |
0.421 |
|
| 2016 |
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, ... ... Saez-Rodriguez J, et al. Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition. Oncogene. PMID 27991928 DOI: 10.1038/Onc.2016.427 |
0.32 |
|
| 2016 |
Türei D, Korcsmáros T, Saez-Rodriguez J. OmniPath: guidelines and gateway for literature-curated signaling pathway resources. Nature Methods. 13: 966-967. PMID 27898060 DOI: 10.1038/Nmeth.4077 |
0.353 |
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| 2016 |
Dry JR, Yang M, Saez-Rodriguez J. Looking beyond the cancer cell for effective drug combinations. Genome Medicine. 8: 125. PMID 27887656 DOI: 10.1186/S13073-016-0379-8 |
0.352 |
|
| 2016 |
Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G. Crowdsourcing biomedical research: leveraging communities as innovation engines. Nature Reviews. Genetics. 17: 470-86. PMID 27418159 DOI: 10.1038/Nrg.2016.69 |
0.305 |
|
| 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 |
0.344 |
|
| 2016 |
Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C. Logical Modeling and Dynamical Analysis of Cellular Networks. Frontiers in Genetics. 7: 94. PMID 27303434 DOI: 10.3389/Fgene.2016.00094 |
0.491 |
|
| 2016 |
Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T. Transcriptional response networks for elucidating mechanisms of action of multitargeted agents. Drug Discovery Today. PMID 26979547 DOI: 10.1016/J.Drudis.2016.03.001 |
0.422 |
|
| 2016 |
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, ... ... Saez-Rodriguez J, et al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods. PMID 26901648 DOI: 10.1038/Nmeth.3773 |
0.46 |
|
| 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 |
0.463 |
|
| 2015 |
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, et al. Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. Oncotarget. PMID 26760764 DOI: 10.18632/Oncotarget.6793 |
0.31 |
|
| 2015 |
Stransky N, Ghandi M, Kryukov GV, Garraway LA, Lehár J, Liu M, Sonkin D, Kauffmann A, Venkatesan K, Edelman EJ, Riester M, Barretina J, Caponigro G, Schlegel R, Sellers WR, ... ... Saez-Rodriguez J, et al. Pharmacogenomic agreement between two cancer cell line data sets Nature. 528: 84-87. PMID 26570998 DOI: 10.1038/Nature15736 |
0.309 |
|
| 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 |
0.689 |
|
| 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 |
0.337 |
|
| 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 |
0.409 |
|
| 2015 |
Terfve CD, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J. Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data. Nature Communications. 6: 8033. PMID 26354681 DOI: 10.1038/Ncomms9033 |
0.437 |
|
| 2015 |
Saez-Rodriguez J, MacNamara A, Cook S. Modeling Signaling Networks to Advance New Cancer Therapies. Annual Review of Biomedical Engineering. PMID 26274601 DOI: 10.1146/Annurev-Bioeng-071813-104927 |
0.504 |
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| 2015 |
Hatzimanikatis V, Saez-Rodriguez J. Integrative approaches for signalling and metabolic networks. Integrative Biology : Quantitative Biosciences From Nano to Macro. 7: 844-5. PMID 26198436 DOI: 10.1039/C5Ib90030A |
0.4 |
|
| 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 |
0.488 |
|
| 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 |
0.41 |
|
| 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 |
0.354 |
|
| 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 |
0.301 |
|
| 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 |
0.466 |
|
| 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 |
0.367 |
|
| 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 |
0.442 |
|
| 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 |
0.401 |
|
| 2015 |
Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Mazan MM, Gozdecka M, Cooper JL, Patel M, McKerrell TDH, Chen B, Ponstingl H, ... ... Saez-Rodriguez J, et al. A Crispr/Cas9 Drop-out Screen Identifies Genome-Wide Genetic Valnerubilities in Acute Myeloid Leukaemia Blood. 126: 554-554. DOI: 10.1182/Blood.V126.23.554.554 |
0.315 |
|
| 2015 |
Videla S, Guziolowski C, Eduati F, Thiele S, Gebser M, Nicolas J, Saez-Rodriguez J, Schaub T, Siegel A. Learning Boolean logic models of signaling networks with ASP Theoretical Computer Science. 599: 79-101. DOI: 10.1016/J.Tcs.2014.06.022 |
0.463 |
|
| 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 |
0.406 |
|
| 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 |
0.38 |
|
| 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 |
0.405 |
|
| 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 |
0.683 |
|
| 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 |
0.317 |
|
| 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 |
0.422 |
|
| 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 |
0.428 |
|
| 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 |
0.689 |
|
| 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 |
0.387 |
|
| 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 |
0.471 |
|
| 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 |
0.514 |
|
| 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 |
0.329 |
|
| 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 |
0.312 |
|
| 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 |
0.662 |
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| 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 |
0.321 |
|
| 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 |
0.417 |
|
| 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 |
0.526 |
|
| 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 |
0.304 |
|
| 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 |
0.443 |
|
| 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 |
0.525 |
|
| 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 |
0.423 |
|
| 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 |
0.454 |
|
| 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 |
0.407 |
|
| 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 |
0.471 |
|
| 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 |
0.519 |
|
| 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 |
0.32 |
|
| 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 |
0.502 |
|
| 2012 |
Gherardini P, Sacco F, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G. A combined computational/experimental strategy to map phosphatases on growth pathways Embnet.Journal. 18: 28. DOI: 10.14806/Ej.18.A.395 |
0.455 |
|
| 2012 |
Kulbe H, Chakravarty P, Moore R, Iorio F, Montoya A, Saez-Rodriguez J, Cutillas P, Balkwill F. Abstract 49: Targeting the TNF network in human ovarian cancer - A systems biology approach Cancer Research. 72: 49-49. DOI: 10.1158/1538-7445.Am2012-49 |
0.451 |
|
| 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 |
0.47 |
|
| 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 |
0.517 |
|
| 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 |
0.45 |
|
| 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 |
0.432 |
|
| 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 |
0.345 |
|
| 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 |
0.45 |
|
| 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 |
0.512 |
|
| 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 |
0.41 |
|
| 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 |
0.375 |
|
| 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 |
0.723 |
|
| 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 |
0.677 |
|
| 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 |
0.709 |
|
| 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 |
0.448 |
|
| 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 |
0.642 |
|
| 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 DOI: 10.4049/Jimmunol.180.10.6703 |
0.594 |
|
| 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 |
0.724 |
|
| 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 |
0.342 |
|
| 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 |
0.763 |
|
| 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 |
0.758 |
|
| 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 |
0.631 |
|
| 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 |
0.773 |
|
| 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 |
0.751 |
|
| 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 |
0.71 |
|
| 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 |
0.577 |
|
| 2005 |
Saez-Rodriguez J, Kremling A, Gilles ED. Dissecting the puzzle of life: Modularization of signal transduction networks Computers and Chemical Engineering. 29: 619-629. DOI: 10.1016/J.Compchemeng.2004.08.035 |
0.776 |
|
| 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 |
0.739 |
|
| 2004 |
Saez-Rodriguez J, Kremling A, Conzelmann H, Bettenbrock K, Gilles ED. Modular analysis of signal transduction networks Ieee Control Systems Magazine. 24: 35-52. DOI: 10.1109/Mcs.2004.1316652 |
0.741 |
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