Publications

For a full list of individuals’ references, please visit their profile page.

2018

  • Benchmark and integration of resources for the estimation of human transcription factor activities
    Garcia-Alonso L, Ibrahim MM, Turei D, Saez-Rodriguez J.
    (2018)
  • Signatures of cell death and proliferation in perturbation transcriptomics data - from confounding factor to effective prediction
    Szalai B, Subramanian V, Saez-Rodriguez J.
    (2018)
  • Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
    Eduati F, Jaaks P, Merten CA, Garnett MJ, Saez-Rodriguez J.
    (2018)
  • In silico prioritization of transporter-drug relationships from drug sensitivity screens
    Cesar-Razquin A, Girardi E, Yang M, Brehme M, Saez-Rodriguez J, Superti-Furga G.
    (2018)
  • A functional landscape of chronic kidney disease entities from public transcriptomic data
    Tajti F, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Kuppe C, Alexopoulos LG, Kramann R, Saez-Rodriguez J.
    (2018)
  • Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases
    Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, Subramanian A, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D, The DREAM Module Identification Challenge Consortium.
    (2018)
  • Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells
    Guo T, Luna A, Koh CC, Rajapakse V, Wu Z, Menden MP, Cheng Y, Calzone L, Martignetti L, Ori A, Iskar M, Gillet L, Zhong Q, Varma S, Schmitt U, Qiu P, Sun Y, zhu Y, Wild P, Mathew G, Bork P, Beck M, Saez-Rodriguez J, Reinhold W, Sander C, Pommier Y, Aebersold R.
    (2018)
  • Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer
    Berndt N, Egners A, Mastrobuoni G, Vvedenskaya O, Fragoulis A, Dugourd A, Bulik S, Pietzke M, Bielow C, van Gassel R, Olde Damink S, Erdem M, Saez-Rodriguez J, Holzhuetter H, Kempa S, Cramer T.
    (2018)
  • Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis
    Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O.
    (2018)
  • CELLector: Genomics Guided Selection of Cancer in vitro Models
    Najgebauer H, Yang M, Francies H, Stronach EA, Garnett MJ, Saez-Rodriguez J, Iorio F.
    (2018)
  • Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results
    Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Germain P, Frank M, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt W, Aebersold R.
    (2018)
  • Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression
    Lun X, Szklarczyk D, Gabor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B.
    (2018)
  • In silico Prioritization of Transporter–Drug Relationships From Drug Sensitivity Screens.
    César-Razquin A, Girardi E, Yang M, Brehme M, Saez-Rodriguez J, Superti-Furga G.
    Front Pharmacol   Volume 9 (2018)
  • The germline genetic component of drug sensitivity in cancer cell lines.
    Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O.
    Nat Commun   Volume 9 (2018) p. 3385
  • Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.
    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, Garnett MJ.
    BMC Genomics   Volume 19 (2018) p. 604
  • A microfluidics platform for combinatorial drug screening on cancer biopsies.
    Eduati F, Utharala R, Madhavan D, Neumann UP, Longerich T, Cramer T, Saez-Rodriguez J, Merten CA.
    Nat Commun   Volume 9 (2018) p. 2434
  • Linking drug target and pathway activation for effective therapy using multi-task learning.
    Yang M, Simm J, Lam CC, Zakeri P, van Westen GJP, Moreau Y, Saez-Rodriguez J.
    Sci Rep   Volume 8 (2018) p. 8322
  • Alternative models for sharing confidential biomedical data.
    Guinney J, Saez-Rodriguez J.
    Nat Biotechnol   Volume 36 (2018) p. 391-392
  • Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.
    Iorio F, Garcia-Alonso L, Brammeld JS, Martincorena I, Wille DR, McDermott U, Saez-Rodriguez J.
    Sci Rep   Volume 8 (2018) p. 6713
  • Whither systems medicine?
    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, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O.
    Exp Mol Med   Volume 50 (2018) p. e453
  • NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction.
    Gaude E, Schmidt C, Gammage PA, Dugourd A, Blacker T, Chew SP, Saez-Rodriguez J, O'Neill JS, Szabadkai G, Minczuk M, Frezza C.
    Mol Cell   Volume 69 (2018) p. 581-593.e7
  • Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.
    Wirbel J, Cutillas P, Saez-Rodriguez J.
    Methods Mol Biol   Volume 1711 (2018) p. 103-132
  • Perturbation-response genes reveal signaling footprints in cancer gene expression.
    Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J.
    Nat Commun   Volume 9 (2018) p. 20
  • A systematic atlas of chaperome deregulation topologies across the human cancer landscape.
    Hadizadeh Esfahani A, Sverchkova A, Saez-Rodriguez J, Schuppert AA, Brehme M.
    PLoS Comput Biol   Volume 14 (2018) p. e1005890
  • Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
    Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J.
    Cancer Res   Volume 78 (2018) p. 769-780
  • Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.
    Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J.
    Metab Eng   Volume 45 (2018) p. 149-157
  • GDSCTools for mining pharmacogenomic interactions in cancer.
    Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ.
    Bioinformatics   Volume 34 (2018) p. 1226-1228

2017

2016

2015

2014

2013

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