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Julio Saez-Rodriguez - Publications

Affiliations: 
2002-2007 Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Sachsen-Anhalt, Germany 
 2007-2010 Harvard Medical School 
 2010-2015 EMBL-European Bioinformatics Institute 
 2015-2018 University Hospital RWTH Aachen, Aachen, Nordrhein-Westfalen, Germany 
 2018- Heidelberg Universität 
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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  0.725
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  0.414
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  0.737
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  0.306
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  0.782
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  0.342
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  0.335
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  0.807
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  0.792
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  0.81
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  0.308
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  0.32
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  0.386
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  0.426
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  0.302
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  0.324
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  0.805
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  0.425
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  0.789
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  0.315
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  0.421
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  0.306
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  0.509
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  0.527
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  0.349
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  0.329
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  0.409
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  0.343
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  0.389
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  0.428
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  0.472
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  0.376
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  0.422
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  0.354
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  0.492
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  0.423
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  0.461
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  0.464
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  0.693
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  0.438
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  0.505
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  0.401
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  0.489
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  0.467
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  0.443
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  0.402
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  0.464
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  0.407
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  0.406
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  0.686
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  0.423
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  0.429
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  0.693
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  0.388
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  0.473
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  0.515
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  0.666
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  0.418
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  0.527
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  0.444
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  0.526
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  0.455
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  0.408
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  0.472
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  0.521
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  0.321
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  0.503
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  0.452
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  0.471
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  0.518
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  0.433
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  0.346
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  0.451
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  0.513
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  0.726
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  0.681
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  0.712
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  0.449
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  0.643
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  0.595
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  0.727
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  0.765
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  0.76
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  0.632
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  0.775
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  0.753
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  0.714
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  0.578
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  0.777
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  0.742
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  0.742
Low-probability matches (unlikely to be authored by this person)
2020 Lanzer JD, Leuschner F, Kramann R, Levinson RT, Saez-Rodriguez J. Big Data Approaches in Heart Failure Research. Current Heart Failure Reports. PMID 32783147 DOI: 10.1007/S11897-020-00469-9  0.3
2018 César-Razquin A, Girardi E, Yang M, Brehme M, Saez-Rodriguez J, Superti-Furga G. Prioritization of Transporter-Drug Relationships From Drug Sensitivity Screens. Frontiers in Pharmacology. 9: 1011. PMID 30245630 DOI: 10.3389/Fphar.2018.01011  0.3
2019 Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, ... ... Saez-Rodriguez J, et al. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology. PMID 30778230 DOI: 10.1038/S41587-019-0037-Y  0.299
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.7118.2  0.298
2018 Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O. The germline genetic component of drug sensitivity in cancer cell lines. Nature Communications. 9: 3385. PMID 30139972 DOI: 10.1038/S41467-018-05811-3  0.295
2020 Gleitz H, Dugourd AJF, Leimkühler NB, Snoeren IAM, Fuchs SNR, Menzel S, Ziegler S, Kroeger N, Triviai I, Büsche G, Kreipe H, Banjanin B, Pritchard J, Hoogenboezem R, Bindels E, ... ... Saez-Rodriguez J, et al. Increased CXCL4 expression in hematopoietic cells links inflammation and progression of bone marrow fibrosis in MPN. Blood. PMID 32726410 DOI: 10.1182/Blood.2019004095  0.294
2018 Pellegrinelli V, Peirce VJ, Howard L, Virtue S, Türei D, Senzacqua M, Frontini A, Dalley JW, Horton AR, Bidault G, Severi I, Whittle A, Rahmouni K, Saez-Rodriguez J, Cinti S, et al. Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue. Nature Communications. 9: 4974. PMID 30478315 DOI: 10.1038/S41467-018-07453-X  0.29
2023 Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J. Gene regulatory network inference in the era of single-cell multi-omics. Nature Reviews. Genetics. PMID 37365273 DOI: 10.1038/s41576-023-00618-5  0.287
2016 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, ... ... Saez-Rodriguez J, et al. A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia. Cell Reports. 17: 1193-1205. PMID 27760321 DOI: 10.1016/J.Celrep.2016.09.079  0.287
2021 Türei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O, Ölbei M, Gábor A, Theis F, Módos D, Korcsmáros T, Saez-Rodriguez J. Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Molecular Systems Biology. 17: e9923. PMID 33749993 DOI: 10.15252/msb.20209923  0.287
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  0.286
2016 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, ... ... Saez-Rodriguez J, et al. Corrigendum: Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition. Nature. PMID 27760119 DOI: 10.1038/Nature20144  0.285
2017 Brammeld J, 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, ... ... Saez-Rodriguez J, et al. Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations. Genome Research. PMID 28179366 DOI: 10.1101/Gr.213546.116  0.282
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  0.282
2019 Ghallab A, Myllys M, Holland CH, Zaza A, Murad W, Hassan R, Ahmed YA, Abbas T, Abdelrahim EA, Schneider KM, Matz-Soja M, Reinders J, Gebhardt R, Berres ML, Hatting M, ... ... Saez-Rodriguez J, et al. Influence of Liver Fibrosis on Lobular Zonation. Cells. 8. PMID 31810365 DOI: 10.3390/Cells8121556  0.281
2018 Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, et al. Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting. Bmc Genomics. 19: 604. PMID 30103702 DOI: 10.1186/S12864-018-4989-Y  0.28
2016 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, ... ... Saez-Rodriguez J, et al. Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition. Nature. PMID 27580029 DOI: 10.1038/Nature19353  0.278
2023 Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, ... ... Saez-Rodriguez J, et al. Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing. Arxiv. PMID 37332567  0.278
2016 Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R. System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects. Journal of Proteome Research. PMID 27936760 DOI: 10.1021/Acs.Jproteome.6B00815  0.278
2017 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, et al. Gli1(+) Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target. Cell Stem Cell. PMID 28457748 DOI: 10.1016/J.Stem.2017.03.008  0.277
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  0.277
2018 Dry JR, Menden MP, Bulusu K, Guinney J, Saez-Rodriguez J. Abstract 3886: A large cancer pharmacogenomics combination screen powering crowd-sourced advancement of computational drug synergy predictions Cancer Research. 78: 3886-3886. DOI: 10.1158/1538-7445.Am2018-3886  0.276
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  0.274
2022 Montagud A, Béal J, Tobalina L, Traynard P, Subramanian V, Szalai B, Alföldi R, Puskás L, Valencia A, Barillot E, Saez-Rodriguez J, Calzone L. Patient-specific Boolean models of signalling networks guide personalised treatments. Elife. 11. PMID 35164900 DOI: 10.7554/eLife.72626  0.274
2020 Saez-Rodriguez J, Blüthgen N. Personalized signaling models for personalized treatments. Molecular Systems Biology. 16: e9042. PMID 32129942 DOI: 10.15252/msb.20199042  0.271
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  0.268
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  0.266
2020 Maier-Hein L, Reinke A, Kozubek M, Martel AL, Arbel T, Eisenmann M, Hanbury A, Jannin P, Müller H, Onogur S, Saez-Rodriguez J, van Ginneken B, Kopp-Schneider A, Landman BA. BIAS: Transparent reporting of biomedical image analysis challenges. Medical Image Analysis. 66: 101796. PMID 32911207 DOI: 10.1016/J.Media.2020.101796  0.266
2020 Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, ... ... Saez-Rodriguez J, et al. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. PMID 32645325 DOI: 10.1016/J.Cell.2020.06.034  0.265
2017 Penas DR, Henriques D, González P, Doallo R, Saez-Rodriguez J, Banga JR. A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology. Plos One. 12: e0182186. PMID 28813442 DOI: 10.1371/Journal.Pone.0182186  0.262
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  0.261
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.V2  0.259
2015 Terfve CDA, 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. DOI: 10.1038/ncomms9033  0.259
2019 Yang M, Simm J, Lam CC, Zakeri P, van Westen GJP, Moreau Y, Saez-Rodriguez J. Author Correction: Linking drug target and pathway activation for effective therapy using multi-task learning. Scientific Reports. 9: 7106. PMID 31053760 DOI: 10.1038/S41598-019-43503-0  0.258
2016 Chiapparino A, Maeda K, Turei D, Saez-Rodriguez J, Gavin AC. The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling. Progress in Lipid Research. 61: 30-9. PMID 26658141 DOI: 10.1016/J.Plipres.2015.10.004  0.257
2019 Gajjala PR, Bruck H, Noels H, Heinze G, Ceccarelli F, Kribben A, Saez-Rodriguez J, Marx N, Zidek W, Jankowski J, Jankowski V. Novel plasma peptide markers involved in the pathology of CKD identified using mass spectrometric approach. Journal of Molecular Medicine (Berlin, Germany). PMID 31385015 DOI: 10.1007/S00109-019-01823-8  0.256
2021 Callegaro G, Kunnen SJ, Trairatphisan P, Grosdidier S, Niemeijer M, den Hollander W, Guney E, Piñero Gonzalez J, Furlong L, Webster YW, Saez-Rodriguez J, Sutherland JJ, Mollon J, Stevens JL, van de Water B. The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment. Archives of Toxicology. PMID 34626214 DOI: 10.1007/s00204-021-03141-w  0.254
2024 Kennedy KE, Kerlero de Rosbo N, Uccelli A, Cellerino M, Ivaldi F, Contini P, De Palma R, Harbo HF, Berge T, Bos SD, Høgestøl EA, Brune-Ingebretsen S, de Rodez Benavent SA, Paul F, Brandt AU, ... ... Saez-Rodriguez J, et al. Multiscale networks in multiple sclerosis. Plos Computational Biology. 20: e1010980. PMID 38329927 DOI: 10.1371/journal.pcbi.1010980  0.249
2021 Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, ... ... Saez-Rodriguez J, et al. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology. 17: e10387. PMID 34664389 DOI: 10.15252/msb.202110387  0.248
2018 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, et al. Gli1 Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target. Cell Stem Cell. 23: 308-309. PMID 30075132 DOI: 10.1016/J.Stem.2018.07.006  0.246
2023 Sousa A, Dugourd A, Memon D, Petursson B, Petsalaki E, Saez-Rodriguez J, Beltrao P. Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival. Molecular Systems Biology. e10631. PMID 36688815 DOI: 10.15252/msb.202110631  0.241
2019 Tajti F, Kuppe C, Antoranz A, Ibrahim M, Kim H, Ceccarelli F, Holland C, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. Sp321Dissecting The Molecular Differences Between Chronic Kidney Disease Subtypes From Transcriptomics Data Nephrology Dialysis Transplantation. 34. DOI: 10.1093/Ndt/Gfz103.Sp321  0.241
2018 Gaude E, Schmidt C, Gammage PA, Dugourd A, Blacker T, Chew SP, Saez-Rodriguez J, O'Neill JS, Szabadkai G, Minczuk M, Frezza C. NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction. Molecular Cell. 69: 581-593.e7. PMID 29452638 DOI: 10.1016/J.Molcel.2018.01.034  0.238
2019 Sun Q, Baues M, Klinkhammer BM, Ehling J, Djudjaj S, Drude NI, Daniel C, Amann K, Kramann R, Kim H, Saez-Rodriguez J, Weiskirchen R, Onthank DC, Botnar RM, Kiessling F, et al. Elastin imaging enables noninvasive staging and treatment monitoring of kidney fibrosis. Science Translational Medicine. 11. PMID 30944168 DOI: 10.1126/Scitranslmed.Aat4865  0.234
2019 Köhncke J, Wirtz T, Holland C, Brandt E, Ritz T, Heinrichs D, Fischer P, Trautwein C, Longerich T, Saez-Rodriguez J, Berres M. Novel short-termed mouse model of intrahepatic cholangiocarcinoma (ICC) by orthotopic transplantation of ICC cell line in C57/B6 mice Zeitschrift Fur Gastroenterologie. 57. DOI: 10.1055/S-0038-1677211  0.233
2023 Sun R, Ge W, Zhu Y, Sayad A, Luna A, Lyu M, Liang S, Tobalina L, Rajapakse VN, Yu C, Zhang H, Fang J, Wu F, Xie H, Saez-Rodriguez J, et al. Proteomic Dynamics of Breast Cancer Cell Lines Identifies Potential Therapeutic Protein Targets. Molecular & Cellular Proteomics : McP. 100602. PMID 37343696 DOI: 10.1016/j.mcpro.2023.100602  0.231
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: e9690. PMID 33438807 DOI: 10.15252/msb.209690  0.229
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  0.229
2022 Emdal KB, Palacio-Escat N, Wigerup C, Eguchi A, Nilsson H, Bekker-Jensen DB, Rönnstrand L, Kazi JU, Puissant A, Itzykson R, Saez-Rodriguez J, Masson K, Blume-Jensen P, Olsen JV. Phosphoproteomics of primary AML patient samples reveals rationale for AKT combination therapy and p53 context to overcome selinexor resistance. Cell Reports. 40: 111177. PMID 35947955 DOI: 10.1016/j.celrep.2022.111177  0.229
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  0.225
2021 Rodrigues D, de Souza T, Coyle L, Di Piazza M, Herpers B, Ferreira S, Zhang M, Vappiani J, Sévin DC, Gabor A, Lynch A, Chung SW, Saez-Rodriguez J, Jennen DGJ, Kleinjans JCS, et al. New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids. Archives of Toxicology. PMID 34151400 DOI: 10.1007/s00204-021-03092-2  0.225
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  0.223
2020 Szalai B, Saez-Rodriguez J. Why do pathway methods work better than they should? Febs Letters. PMID 33270910 DOI: 10.1002/1873-3468.14011  0.221
2021 Reusch B, Bartram MP, Dafinger C, Palacio-Escat N, Wenzel A, Fenton RA, Saez-Rodriguez J, Schermer B, Benzing T, Altmüller J, Beck BB, Rinschen MM. MAGED2 controls vasopressin-induced aquaporin-2 expression in collecting duct cells. Journal of Proteomics. 104424. PMID 34775100 DOI: 10.1016/j.jprot.2021.104424  0.218
2015 Menden MP, Wang D, Chaibub-Neto E, Sock JI, Ghazoui Z, Yu T, Veroli GD, Stolovitzky G, Guinney J, Dry J, Saez-Rodriguez J. The AstraZeneca-Sanger DREAM synergy prediction challenge F1000research. 4. DOI: 10.7490/F1000Research.1111086.1  0.217
2021 Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Rodríguez Martínez M, Saez-Rodriguez J, Thakar J. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics (Oxford, England). PMID 34179955 DOI: 10.1093/bioinformatics/btab229  0.216
2021 Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Rodríguez Martínez M, Saez-Rodriguez J, Thakar J. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics (Oxford, England). PMID 34179955 DOI: 10.1093/bioinformatics/btab229  0.216
2022 Douglass EF, Allaway RJ, Szalai B, Wang W, Tian T, Fernández-Torras A, Realubit R, Karan C, Zheng S, Pessia A, Tanoli Z, Jafari M, Wan F, Li S, Xiong Y, ... ... Saez-Rodriguez J, et al. A community challenge for a pancancer drug mechanism of action inference from perturbational profile data. Cell Reports. Medicine. 3: 100492. PMID 35106508 DOI: 10.1016/j.xcrm.2021.100492  0.215
2019 Koehncke J, Wirtz TH, Holland C, Brandt EF, Ritz TP, Heinrichs D, Fischer P, Trautwein C, Longerich T, Saez-Rodriguez J, Berres M. THU-471-Establishment of a short-termed orthotopic transplantation model in C57/B6 mice that recapitulates characteristic features of human intrahepatic cholangiocarcinoma Journal of Hepatology. 70. DOI: 10.1016/S0618-8278(19)30718-2  0.214
2021 Surya Wijaya L, Trairatphisan P, Gabor A, Niemeijer M, Keet J, Alcalà Morera A, Snijders KE, Wink S, Yang H, Schildknecht S, Stevens JL, Bouwman P, Kamp H, Hengstler J, Beltman J, ... ... Saez-Rodriguez J, et al. Integration of temporal single cell cellular stress response activity with Logic-ODE modeling reveals activation of ATF4-CHOP axis as a critical predictor of drug-induced liver injury. Biochemical Pharmacology. 114591. PMID 33957093 DOI: 10.1016/j.bcp.2021.114591  0.21
2015 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, ... ... Saez-Rodriguez J, et al. Erratum: Prediction of human population responses to toxic compounds by a collaborative competition. Nature Biotechnology. 33: 1109. PMID 26448092 DOI: 10.1038/Nbt1015-1109A  0.209
2020 Sellmayr M, Hernandez Petzsche MR, Ma Q, Krüger N, Liapis H, Brink A, Lenz B, Angelotti ML, Gnemmi V, Kuppe C, Kim H, Bindels EMJ, Tajti F, Saez-Rodriguez J, Lech M, et al. Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease. Journal of the American Society of Nephrology : Jasn. PMID 32938648 DOI: 10.1681/Asn.2020040523  0.208
2010 Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G. Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges Plos One. 5. DOI: 10.1371/Annotation/F633213A-Dc4F-4Bee-B6C5-72D50E7073B8  0.207
2020 Rinschen MM, Saez-Rodriguez J. The tissue proteome in the multi-omic landscape of kidney disease. Nature Reviews. Nephrology. PMID 33028957 DOI: 10.1038/s41581-020-00348-5  0.204
2023 Salovska B, Gao E, Müller-Dott S, Li W, Cordon CC, Wang S, Dugourd A, Rosenberger G, Saez-Rodriguez J, Liu Y. Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities. Clinical and Translational Medicine. 13: e1179. PMID 36781298 DOI: 10.1002/ctm2.1179  0.202
2022 Utharala R, Grab A, Vafaizadeh V, Peschke N, Ballinger M, Turei D, Tuechler N, Ma W, Ivanova O, Ortiz AG, Saez-Rodriguez J, Merten CA. A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets. Nature Protocols. PMID 36261631 DOI: 10.1038/s41596-022-00740-4  0.199
2023 Müller-Dott S, Tsirvouli E, Vazquez M, Ramirez Flores RO, Badia-I-Mompel P, Fallegger R, Türei D, Lægreid A, Saez-Rodriguez J. Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities. Nucleic Acids Research. 51: 10934-10949. PMID 37843125 DOI: 10.1093/nar/gkad841  0.199
2020 Yang M, Jaaks P, Dry J, Garnett M, Menden MP, Saez-Rodriguez J. Stratification and prediction of drug synergy based on target functional similarity. Npj Systems Biology and Applications. 6: 16. PMID 32487991 DOI: 10.1038/s41540-020-0136-x  0.195
2023 Ramirez Flores RO, Lanzer JD, Dimitrov D, Velten B, Saez-Rodriguez J. Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease. Elife. 12. PMID 37991480 DOI: 10.7554/eLife.93161  0.192
2022 Badia-I-Mompel P, Vélez Santiago J, Braunger J, Geiss C, Dimitrov D, Müller-Dott S, Taus P, Dugourd A, Holland CH, Ramirez Flores RO, Saez-Rodriguez J. decoupleR: ensemble of computational methods to infer biological activities from omics data. Bioinformatics Advances. 2: vbac016. PMID 36699385 DOI: 10.1093/bioadv/vbac016  0.188
2020 Cappelletti V, Hauser T, Piazza I, Pepelnjak M, Malinovska L, Fuhrer T, Li Y, Dörig C, Boersema P, Gillet L, Grossbach J, Dugourd A, Saez-Rodriguez J, Beyer A, Zamboni N, et al. Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell. PMID 33357446 DOI: 10.1016/j.cell.2020.12.021  0.187
2022 Dimitrov D, Türei D, Garrido-Rodriguez M, Burmedi PL, Nagai JS, Boys C, Ramirez Flores RO, Kim H, Szalai B, Costa IG, Valdeolivas A, Dugourd A, Saez-Rodriguez J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nature Communications. 13: 3224. PMID 35680885 DOI: 10.1038/s41467-022-30755-0  0.187
2020 Wang D, Hensman J, Kutkaite G, Toh TS, Galhoz ACP, Dry JR, Saez-Rodriguez J, Garnett MJ, Menden MP, Dondelinger F. A statistical framework for assessing pharmacological response and biomarkers using uncertainty estimates. Elife. 9. PMID 33274713 DOI: 10.7554/eLife.60352  0.186
2024 Valdeolivas A, Amberg B, Giroud N, Richardson M, Gálvez EJC, Badillo S, Julien-Laferrière A, Túrós D, Voith von Voithenberg L, Wells I, Pesti B, Lo AA, Yángüez E, Das Thakur M, Bscheider M, ... ... Saez-Rodriguez J, et al. Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics. Npj Precision Oncology. 8: 10. PMID 38200223 DOI: 10.1038/s41698-023-00488-4  0.186
2021 Bernardo-Faura M, Rinas M, Wirbel J, Pertsovskaya I, Pliaka V, Messinis DE, Vila G, Sakellaropoulos T, Faigle W, Stridh P, Behrens JR, Olsson T, Martin R, Paul F, Alexopoulos LG, ... ... Saez-Rodriguez J, et al. Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis. Genome Medicine. 13: 117. PMID 34271980 DOI: 10.1186/s13073-021-00925-8  0.184
2022 Poletti M, Treveil A, Csabai L, Gul L, Modos D, Madgwick M, Olbei M, Bohar B, Valdeolivas A, Turei D, Verstockt B, Triana S, Alexandrov T, Saez-Rodriguez J, Stanifer ML, et al. Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways. Npj Systems Biology and Applications. 8: 15. PMID 35501398 DOI: 10.1038/s41540-022-00224-x  0.181
2021 Bülow RD, Dimitrov D, Boor P, Saez-Rodriguez J. How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade? Seminars in Immunopathology. PMID 33835214 DOI: 10.1007/s00281-021-00847-y  0.18
2024 Schäfer PSL, Dimitrov D, Villablanca EJ, Saez-Rodriguez J. Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system. Nature Immunology. 25: 405-417. PMID 38413722 DOI: 10.1038/s41590-024-01768-2  0.177
2021 Holland CH, Ramirez Flores RO, Myllys M, Hassan R, Edlund K, Hofmann U, Marchan R, Cadenas C, Reinders J, Hoehme S, Seddek AL, Dooley S, Keitel V, Godoy P, Begher-Tibbe B, ... ... Saez-Rodriguez J, et al. Transcriptomic Cross-Species Analysis of Chronic Liver Disease Reveals Consistent Regulation Between Humans and Mice. Hepatology Communications. PMID 34558834 DOI: 10.1002/hep4.1797  0.177
2020 Kuppe C, Perales-Patón J, Saez-Rodriguez J, Kramann R. Experimental and computational technologies to dissect the kidney at the single-cell level. Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association. PMID 33332571 DOI: 10.1093/ndt/gfaa233  0.176
2020 Kuppe C, Perales-Patón J, Saez-Rodriguez J, Kramann R. Experimental and computational technologies to dissect the kidney at the single-cell level. Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association. PMID 33332571 DOI: 10.1093/ndt/gfaa233  0.176
2021 Ramirez Flores RO, Lanzer JD, Holland CH, Leuschner F, Most P, Schultz JH, Levinson RT, Saez-Rodriguez J. Consensus Transcriptional Landscape of Human End-Stage Heart Failure. Journal of the American Heart Association. 10: e019667. PMID 33787284 DOI: 10.1161/JAHA.120.019667  0.175
2024 Ramirez Flores RO, Schäfer PSL, Küchenhoff L, Saez-Rodriguez J. Complementing cell taxonomies with a multicellular analysis of tissues. Physiology (Bethesda, Md.). PMID 38319138 DOI: 10.1152/physiol.00001.2024  0.175
2023 Baghdassarian H, Dimitrov D, Armingol E, Saez-Rodriguez J, Lewis NE. Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. Biorxiv : the Preprint Server For Biology. PMID 37162916 DOI: 10.1101/2023.04.28.538731  0.174
2022 Parigi SM, Larsson L, Das S, Ramirez Flores RO, Frede A, Tripathi KP, Diaz OE, Selin K, Morales RA, Luo X, Monasterio G, Engblom C, Gagliani N, Saez-Rodriguez J, Lundeberg J, et al. The spatial transcriptomic landscape of the healing mouse intestine following damage. Nature Communications. 13: 828. PMID 35149721 DOI: 10.1038/s41467-022-28497-0  0.174
2017 Traynard P, Tobalina L, Eduati F, Calzone L, Saez-Rodriguez J. Logic modeling in quantitative systems pharmacology. Cpt: Pharmacometrics & Systems Pharmacology. PMID 28681552 DOI: 10.1002/psp4.12225  0.173
2023 Erawijantari PP, Kartal E, Liñares-Blanco J, Laajala TD, Feldman LE, Carmona-Saez P, Shigdel R, Claesson MJ, Bertelsen RJ, Gomez-Cabrero D, Minot S, Albrecht J, Chung V, Inouye M, Jousilahti P, ... ... Saez-Rodriguez J, et al. Microbiome-based risk prediction in incident heart failure: a community challenge. Medrxiv : the Preprint Server For Health Sciences. PMID 37873403 DOI: 10.1101/2023.10.12.23296829  0.167
2022 Sciacovelli M, Dugourd A, Jimenez LV, Yang M, Nikitopoulou E, Costa ASH, Tronci L, Caraffini V, Rodrigues P, Schmidt C, Ryan DG, Young T, Zecchini VR, Rossi SH, Massie C, ... ... Saez-Rodriguez J, et al. Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature Communications. 13: 7830. PMID 36539415 DOI: 10.1038/s41467-022-35036-4  0.165
2021 Bidault G, Virtue S, Petkevicius K, Jolin HE, Dugourd A, Guénantin AC, Leggat J, Mahler-Araujo B, Lam BYH, Ma MK, Dale M, Carobbio S, Kaser A, Fallon PG, Saez-Rodriguez J, et al. SREBP1-induced fatty acid synthesis depletes macrophages antioxidant defences to promote their alternative activation. Nature Metabolism. PMID 34531575 DOI: 10.1038/s42255-021-00440-5  0.163
2024 Ghasemi DR, Okonechnikov K, Rademacher A, Tirier S, Maass KK, Schumacher H, Joshi P, Gold MP, Sundheimer J, Statz B, Rifaioglu AS, Bauer K, Schumacher S, Bortolomeazzi M, Giangaspero F, ... ... Saez-Rodriguez J, et al. Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage. Nature Communications. 15: 269. PMID 38191550 DOI: 10.1038/s41467-023-44117-x  0.162
2020 Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, ... ... Saez-Rodriguez J, et al. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Life Science Alliance. 3. PMID 32972997 DOI: 10.26508/lsa.202000867  0.16
2024 Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, ... ... Saez-Rodriguez J, et al. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology. 14: 1282859. PMID 38414974 DOI: 10.3389/fimmu.2023.1282859  0.152
2023 Reinke A, Tizabi MD, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Kavur AE, Rädsch T, Sudre CH, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Blaschko M, Büttner F, ... ... Saez-Rodriguez J, et al. Understanding metric-related pitfalls in image analysis validation. Arxiv. PMID 36945687  0.145
2022 Barsi S, Papp H, Valdeolivas A, Tóth DJ, Kuczmog A, Madai M, Hunyady L, Várnai P, Saez-Rodriguez J, Jakab F, Szalai B. Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity. Plos Computational Biology. 18: e1010021. PMID 35404937 DOI: 10.1371/journal.pcbi.1010021  0.138
2022 Xu Y, Kuppe C, Perales-Patón J, Hayat S, Kranz J, Abdallah AT, Nagai J, Li Z, Peisker F, Saritas T, Halder M, Menzel S, Hoeft K, Kenter A, Kim H, ... ... Saez-Rodriguez J, et al. Adult human kidney organoids originate from CD24 cells and represent an advanced model for adult polycystic kidney disease. Nature Genetics. 54: 1690-1701. PMID 36303074 DOI: 10.1038/s41588-022-01202-z  0.138
2021 Martorell-Marugán J, López-Domínguez R, García-Moreno A, Toro-Domínguez D, Villatoro-García JA, Barturen G, Martín-Gómez A, Troule K, Gómez-López G, Al-Shahrour F, González-Rumayor V, Peña-Chilet M, Dopazo J, Sáez-Rodríguez J, Alarcón-Riquelme ME, et al. A comprehensive database for integrated analysis of omics data in autoimmune diseases. Bmc Bioinformatics. 22: 343. PMID 34167460 DOI: 10.1186/s12859-021-04268-4  0.135
2024 Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J. Corrigendum to "Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells" [Metabol. Eng. 45 (2018) 149-157]. Metabolic Engineering. PMID 38245482 DOI: 10.1016/j.ymben.2024.01.002  0.132
2023 Lanzer JD, Valdeolivas A, Pepin M, Hund H, Backs J, Frey N, Friederich HC, Schultz JH, Saez-Rodriguez J, Levinson RT. A network medicine approach to study comorbidities in heart failure with preserved ejection fraction. Bmc Medicine. 21: 267. PMID 37488529 DOI: 10.1186/s12916-023-02922-7  0.132
2024 Reinke A, Tizabi MD, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Kavur AE, Rädsch T, Sudre CH, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Buettner F, Cardoso MJ, ... ... Saez-Rodriguez J, et al. Understanding metric-related pitfalls in image analysis validation. Nature Methods. 21: 182-194. PMID 38347140 DOI: 10.1038/s41592-023-02150-0  0.132
2022 Gegner HM, Naake T, Dugourd A, Müller T, Czernilofsky F, Kliewer G, Jäger E, Helm B, Kunze-Rohrbach N, Klingmüller U, Hopf C, Müller-Tidow C, Dietrich S, Saez-Rodriguez J, Huber W, et al. Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis. Frontiers in Molecular Biosciences. 9: 961448. PMID 36605986 DOI: 10.3389/fmolb.2022.961448  0.13
2020 Kuppe C, Ibrahim MM, Kranz J, Zhang X, Ziegler S, Perales-Patón J, Jansen J, Reimer KC, Smith JR, Dobie R, Wilson-Kanamari JR, Halder M, Xu Y, Kabgani N, Kaesler N, ... ... Saez-Rodriguez J, et al. Decoding myofibroblast origins in human kidney fibrosis. Nature. PMID 33176333 DOI: 10.1038/s41586-020-2941-1  0.128
2023 Polychronidou M, Hou J, Babu MM, Liberali P, Amit I, Deplancke B, Lahav G, Itzkovitz S, Mann M, Saez-Rodriguez J, Theis F, Eils R. Single-cell biology: what does the future hold? Molecular Systems Biology. e11799. PMID 37318792 DOI: 10.15252/msb.202311799  0.127
2023 Solé P, Yamanouchi J, Garnica J, Uddin MM, Clarke R, Moro J, Garabatos N, Thiessen S, Ortega M, Singha S, Mondal D, Fandos C, Saez-Rodriguez J, Yang Y, Serra P, et al. A T follicular helper cell origin for T regulatory type 1 cells. Cellular & Molecular Immunology. PMID 36973489 DOI: 10.1038/s41423-023-00989-z  0.126
2022 Kuppe C, Ramirez Flores RO, Li Z, Hayat S, Levinson RT, Liao X, Hannani MT, Tanevski J, Wünnemann F, Nagai JS, Halder M, Schumacher D, Menzel S, Schäfer G, Hoeft K, ... ... Saez-Rodriguez J, et al. Spatial multi-omic map of human myocardial infarction. Nature. PMID 35948637 DOI: 10.1038/s41586-022-05060-x  0.125
2021 van Kuijk K, Demandt JAF, Perales-Patón J, Theelen TL, Kuppe C, Marsch E, de Bruijn J, Jin H, Gijbels MJ, Matic L, Mees BME, Reutelingsperger CPM, Hedin U, Biessen EAL, Carmeliet P, ... ... Saez-Rodriguez J, et al. DEFICIENCY OF MYELOID PHD PROTEINS AGGRAVATES ATHEROGENESIS VIA MACROPHAGE APOPTOSIS AND PARACRINE FIBROTIC SIGNALING: Atherogenic effects of myeloid PHD knockdown. Cardiovascular Research. PMID 33913468 DOI: 10.1093/cvr/cvab152  0.125
2022 Frede A, Czarnewski P, Monasterio G, Tripathi KP, Bejarano DA, Ramirez Flores RO, Sorini C, Larsson L, Luo X, Geerlings L, Novella-Rausell C, Zagami C, Kuiper R, Morales RA, Castillo F, ... ... Saez-Rodriguez J, et al. B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing. Immunity. PMID 36462502 DOI: 10.1016/j.immuni.2022.11.002  0.123
2021 Lopez-Dominguez R, Toro-Dominguez D, Martorell-Marugan J, Garcia-Moreno A, Holland CH, Saez-Rodriguez J, Goldman D, Petri MA, Alarcon-Riquelme ME, Carmona-Saez P. Transcription Factor Activity Inference in Systemic Lupus Erythematosus. Life (Basel, Switzerland). 11. PMID 33915751 DOI: 10.3390/life11040299  0.123
2021 Tillie RJHA, De Bruijn J, Perales-Patón J, Temmerman L, Ghosheh Y, Van Kuijk K, Gijbels MJ, Carmeliet P, Ley K, Saez-Rodriguez J, Sluimer JC. Partial Inhibition of the 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase-3 (PFKFB3) Enzyme in Myeloid Cells Does Not Affect Atherosclerosis. Frontiers in Cell and Developmental Biology. 9: 695684. PMID 34458258 DOI: 10.3389/fcell.2021.695684  0.121
2024 Baghdassarian HM, Dimitrov D, Armingol E, Saez-Rodriguez J, Lewis NE. Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. Cell Reports Methods. 100758. PMID 38631346 DOI: 10.1016/j.crmeth.2024.100758  0.12
2024 Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P, Bergamini G, Bantscheff M, Fälth-Savitski M, Saez-Rodriguez J. Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition. Molecular Systems Biology. 20: 458-474. PMID 38454145 DOI: 10.1038/s44320-024-00025-w  0.12
2021 Schwabenland M, Salié H, Tanevski J, Killmer S, Lago MS, Schlaak AE, Mayer L, Matschke J, Püschel K, Fitzek A, Ondruschka B, Mei HE, Boettler T, Neumann-Haefelin C, Hofmann M, ... ... Saez-Rodriguez J, et al. Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions. Immunity. PMID 34174183 DOI: 10.1016/j.immuni.2021.06.002  0.12
2023 Fuchs SNR, Stalmann USA, Snoeren IAM, Bindels E, Schmitz S, Banjanin B, Hoogenboezem R, van Herk S, Saad M, Walter W, Haferlach T, Seillier L, Saez-Rodriguez J, Dugourd AJF, Lehmann KV, et al. Collaborative effect of Csnk1a1 haploinsufficiency and mutant p53 in Myc induction can promote leukemic transformation. Blood Advances. PMID 38147624 DOI: 10.1182/bloodadvances.2022008926  0.119
2022 Tanevski J, Flores ROR, Gabor A, Schapiro D, Saez-Rodriguez J. Explainable multiview framework for dissecting spatial relationships from highly multiplexed data. Genome Biology. 23: 97. PMID 35422018 DOI: 10.1186/s13059-022-02663-5  0.118
2021 Petkevicius K, Bidault G, Virtue S, Newland SA, Dale M, Dugourd A, Saez-Rodriguez J, Mallat Z, Vidal-Puig A. Macrophage beta2-adrenergic receptor is dispensable for the adipose tissue inflammation and function. Molecular Metabolism. 101220. PMID 33774223 DOI: 10.1016/j.molmet.2021.101220  0.117
2021 Petkevicius K, Bidault G, Virtue S, Newland SA, Dale M, Dugourd A, Saez-Rodriguez J, Mallat Z, Vidal-Puig A. Macrophage beta2-adrenergic receptor is dispensable for the adipose tissue inflammation and function. Molecular Metabolism. 101220. PMID 33774223 DOI: 10.1016/j.molmet.2021.101220  0.117
2024 Maier-Hein L, Reinke A, Godau P, Tizabi MD, Buettner F, Christodoulou E, Glocker B, Isensee F, Kleesiek J, Kozubek M, Reyes M, Riegler MA, Wiesenfarth M, Kavur AE, Sudre CH, ... ... Saez-Rodriguez J, et al. Metrics reloaded: recommendations for image analysis validation. Nature Methods. 21: 195-212. PMID 38347141 DOI: 10.1038/s41592-023-02151-z  0.117
2022 Schneider KM, Mohs A, Gui W, Galvez EJC, Candels LS, Hoenicke L, Muthukumarasamy U, Holland CH, Elfers C, Kilic K, Schneider CV, Schierwagen R, Strnad P, Wirtz TH, Marschall HU, ... ... Saez-Rodriguez J, et al. Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment. Nature Communications. 13: 3964. PMID 35803930 DOI: 10.1038/s41467-022-31312-5  0.116
2023 Kaesler N, Cheng M, Nagai J, O'Sullivan J, Peisker F, Bindels EMJ, Babler A, Moellmann J, Droste P, Franciosa G, Dugourd A, Saez-Rodriguez J, Neuss S, Lehrke M, Boor P, et al. Mapping cardiac remodeling in chronic kidney disease. Science Advances. 9: eadj4846. PMID 38000021 DOI: 10.1126/sciadv.adj4846  0.115
2023 Engblom C, Thrane K, Lin Q, Andersson A, Toosi H, Chen X, Steiner E, Lu C, Mantovani G, Hagemann-Jensen M, Saarenpää S, Jangard M, Saez-Rodriguez J, Michaëlsson J, Hartman J, et al. Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics. Science (New York, N.Y.). 382: eadf8486. PMID 38060664 DOI: 10.1126/science.adf8486  0.111
2021 Lanzer P, Hannan FM, Lanzer JD, Janzen J, Raggi P, Furniss D, Schuchardt M, Thakker R, Fok PW, Saez-Rodriguez J, Millan A, Sato Y, Ferraresi R, Virmani R, St Hilaire C. Medial Arterial Calcification: JACC State-of-the-Art Review. Journal of the American College of Cardiology. 78: 1145-1165. PMID 34503684 DOI: 10.1016/j.jacc.2021.06.049  0.109
2020 Manica M, Kim HR, Mathis R, Chouvarine P, Rutishauser D, De Vargas Roditi L, Szalai B, Wagner U, Oehl K, Saba K, Pati A, Saez-Rodriguez J, Roy A, Parsons DW, Wild PJ, et al. Inferring clonal composition from multiple tumor biopsies. Npj Systems Biology and Applications. 6: 27. PMID 32843649 DOI: 10.1038/s41540-020-00147-5  0.105
2020 Buhl EM, Djudjaj S, Klinkhammer BM, Ermert K, Puelles VG, Lindenmeyer MT, Cohen CD, He C, Borkham-Kamphorst E, Weiskirchen R, Denecke B, Trairatphisan P, Saez-Rodriguez J, Huber TB, Olson LE, et al. Dysregulated mesenchymal PDGFR-β drives kidney fibrosis. Embo Molecular Medicine. e11021. PMID 31943786 DOI: 10.15252/emmm.201911021  0.103
2022 Trobisch T, Zulji A, Stevens NA, Schwarz S, Wischnewski S, Öztürk M, Perales-Patón J, Haeussler M, Saez-Rodriguez J, Velmeshev D, Schirmer L. Cross-regional homeostatic and reactive glial signatures in multiple sclerosis. Acta Neuropathologica. PMID 36112223 DOI: 10.1007/s00401-022-02497-2  0.1
2021 Bülow RD, Dimitrov D, Boor P, Saez-Rodriguez J. Correction to: How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade? Seminars in Immunopathology. PMID 33963429 DOI: 10.1007/s00281-021-00858-9  0.094
2022 Robrahn L, Dupont A, Jumpertz S, Zhang K, Holland CH, Guillaume J, Rappold S, Roth J, Cerovic V, Saez-Rodriguez J, Hornef MW, Cramer T. Stabilization but no functional influence of HIF-1α expression in the intestinal epithelium during Typhimurium infection. Infection and Immunity. iai0022221. PMID 34978927 DOI: 10.1128/iai.00222-21  0.093
2023 Alexandrov T, Saez-Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Molecular Systems Biology. 19: e10571. PMID 37842805 DOI: 10.15252/msb.202110571  0.092
2021 Petkevicius K, Bidault G, Virtue S, Jenkins B, van Dierendonck XAMH, Dugourd A, Saez-Rodriguez J, Stienstra R, Koulman A, Vidal-Puig A. Norepinephrine promotes triglyceride storage in macrophages via beta2-adrenergic receptor activation. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 35: e21266. PMID 33484195 DOI: 10.1096/fj.202001101R  0.09
2021 Petkevicius K, Bidault G, Virtue S, Jenkins B, van Dierendonck XAMH, Dugourd A, Saez-Rodriguez J, Stienstra R, Koulman A, Vidal-Puig A. Norepinephrine promotes triglyceride storage in macrophages via beta2-adrenergic receptor activation. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 35: e21266. PMID 33484195 DOI: 10.1096/fj.202001101R  0.09
2022 Wanner N, Andrieux G, Badia-I-Mompel P, Edler C, Pfefferle S, Lindenmeyer MT, Schmidt-Lauber C, Czogalla J, Wong MN, Okabayashi Y, Braun F, Lütgehetmann M, Meister E, Lu S, Noriega MLM, ... ... Saez-Rodriguez J, et al. Molecular consequences of SARS-CoV-2 liver tropism. Nature Metabolism. 4: 310-319. PMID 35347318 DOI: 10.1038/s42255-022-00552-6  0.081
2021 Pawluczyk IZ, Didangelos A, Barbour SJ, Er L, Becker JU, Martin R, Taylor S, Bhachu JS, Lyons EG, Jenkins R, Fraser D, Molyneux K, Perales-Patón J, Saez-Rodriguez J, Barratt J. Differential expression of microRNA miR-150-5p in IgA nephropathy as a potential mediator and marker of disease progression. Kidney International. PMID 33417998 DOI: 10.1016/j.kint.2020.12.028  0.079
2021 Pawluczyk IZ, Didangelos A, Barbour SJ, Er L, Becker JU, Martin R, Taylor S, Bhachu JS, Lyons EG, Jenkins R, Fraser D, Molyneux K, Perales-Patón J, Saez-Rodriguez J, Barratt J. Differential expression of microRNA miR-150-5p in IgA nephropathy as a potential mediator and marker of disease progression. Kidney International. PMID 33417998 DOI: 10.1016/j.kint.2020.12.028  0.079
2021 Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, ... ... Saez-Rodriguez J, et al. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology. 17: e10851. PMID 34939300 DOI: 10.15252/msb.202110851  0.078
2023 Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, ... ... Saez-Rodriguez J, et al. Democratizing knowledge representation with BioCypher. Nature Biotechnology. PMID 37337100 DOI: 10.1038/s41587-023-01848-y  0.075
2022 Schreibing F, Hannani MT, Kim H, Nagai JS, Ticconi F, Fewings E, Bleckwehl T, Begemann M, Torow N, Kuppe C, Kurth I, Kranz J, Frank D, Anslinger TM, Ziegler P, ... ... Saez-Rodriguez J, et al. Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling. Frontiers in Immunology. 13: 1066176. PMID 36591270 DOI: 10.3389/fimmu.2022.1066176  0.075
2020 Mohs A, Otto T, Schneider KM, Peltzer M, Boekschoten M, Holland CH, Hudert CA, Kalveram L, Wiegand S, Saez-Rodriguez J, Longerich T, Hengstler JG, Trautwein C. Hepatocyte-specific NRF2 activation controls fibrogenesis and carcinogenesis in steatohepatitis. Journal of Hepatology. PMID 33342543 DOI: 10.1016/j.jhep.2020.09.037  0.074
2021 Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Research. 31: 745. PMID 33795376 DOI: 10.1101/gr.275408.121  0.074
2023 Andorra M, Freire A, Zubizarreta I, de Rosbo NK, Bos SD, Rinas M, Høgestøl EA, de Rodez Benavent SA, Berge T, Brune-Ingebretse S, Ivaldi F, Cellerino M, Pardini M, Vila G, Pulido-Valdeolivas I, ... ... Saez-Rodriguez J, et al. Predicting disease severity in multiple sclerosis using multimodal data and machine learning. Journal of Neurology. PMID 38133801 DOI: 10.1007/s00415-023-12132-z  0.067
2014 Sáez-Rodríguez J, Rocha MP, Fdez-Riverola F, De Paz Santana JF. 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014) Advances in Intelligent Systems and Computing. 294. DOI: 10.1007/978-3-319-07581-5  0.067
2022 Pérez-Martí A, Ramakrishnan S, Li J, Dugourd A, Molenaar MR, De La Motte LR, Grand K, Mansouri A, Parisot M, Lienkamp SS, Saez-Rodriguez J, Simons M. Reducing lipid bilayer stress by monounsaturated fatty acids protects renal proximal tubules in diabetes. Elife. 11. PMID 35550039 DOI: 10.7554/eLife.74391  0.062
2023 Billing AM, Kim YC, Gullaksen S, Schrage B, Raabe J, Hutzfeldt A, Demir F, Kovalenko E, Lassé M, Dugourd A, Fallegger R, Klampe B, Jaegers J, Li Q, Kravtsova O, ... ... Saez-Rodriguez J, et al. Metabolic Communication by SGLT2 Inhibition. Circulation. PMID 38152989 DOI: 10.1161/CIRCULATIONAHA.123.065517  0.056
2023 Wolf SD, Ehlting C, Müller-Dott S, Poschmann G, Petzsch P, Lautwein T, Wang S, Helm B, Schilling M, Saez-Rodriguez J, Vucur M, Stühler K, Köhrer K, Tacke F, Dooley S, et al. Hepatocytes reprogram liver macrophages involving control of TGF-β activation, influencing liver regeneration and injury. Hepatology Communications. 7. PMID 37486964 DOI: 10.1097/HC9.0000000000000208  0.056
2021 Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Santa Pau EC, D'Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, ... ... Saez-Rodriguez J, et al. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology. 12: 635781. PMID 33692771 DOI: 10.3389/fmicb.2021.635781  0.035
2019 Saez-Rodriguez J, Rinschen MM, Floege J, Kramann R. The authors reply. Kidney International. 96: 1422-1423. PMID 31759488 DOI: 10.1016/j.kint.2019.09.011  0.019
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