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Items: 1 to 50 of 119

1.

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. 2018 Jun 22;9(1):2434. doi: 10.1038/s41467-018-04919-w.

2.

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. 2018 May 29;8(1):8322. doi: 10.1038/s41598-018-25947-y.

3.

Alternative models for sharing confidential biomedical data.

Guinney J, Saez-Rodriguez J.

Nat Biotechnol. 2018 May 9;36(5):391-392. doi: 10.1038/nbt.4128. No abstract available.

PMID:
29734317
4.

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. 2018 Apr 30;8(1):6713. doi: 10.1038/s41598-018-25076-6.

5.

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. 2018 Mar 2;50(3):e453. doi: 10.1038/emm.2017.290. Review.

6.

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. 2018 Feb 15;69(4):581-593.e7. doi: 10.1016/j.molcel.2018.01.034.

7.

Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.

Wirbel J, Cutillas P, Saez-Rodriguez J.

Methods Mol Biol. 2018;1711:103-132. doi: 10.1007/978-1-4939-7493-1_6.

PMID:
29344887
8.

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. 2018 Jan 2;9(1):20. doi: 10.1038/s41467-017-02391-6.

9.

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. 2018 Jan 2;14(1):e1005890. doi: 10.1371/journal.pcbi.1005890. eCollection 2018 Jan.

10.

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. 2018 Feb 1;78(3):769-780. doi: 10.1158/0008-5472.CAN-17-1679. Epub 2017 Dec 11.

PMID:
29229604
11.

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.

Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R.

Cell Syst. 2017 Dec 27;5(6):604-619.e7. doi: 10.1016/j.cels.2017.11.002. Epub 2017 Dec 6.

12.

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. 2018 Jan;45:149-157. doi: 10.1016/j.ymben.2017.11.011. Epub 2017 Nov 27.

13.

GDSCTools for mining pharmacogenomic interactions in cancer.

Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ.

Bioinformatics. 2018 Apr 1;34(7):1226-1228. doi: 10.1093/bioinformatics/btx744.

14.

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.

Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P.

Cell Syst. 2017 Oct 25;5(4):386-398.e4. doi: 10.1016/j.cels.2017.08.013. Epub 2017 Oct 11.

15.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.

Cell Rep. 2017 Aug 29;20(9):2201-2214. doi: 10.1016/j.celrep.2017.08.010.

16.

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.

Penas DR, Henriques D, González P, Doallo R, Saez-Rodriguez J, Banga JR.

PLoS One. 2017 Aug 15;12(8):e0182186. doi: 10.1371/journal.pone.0182186. eCollection 2017.

17.

Logic Modeling in Quantitative Systems Pharmacology.

Traynard P, Tobalina L, Eduati F, Calzone L, Saez-Rodriguez J.

CPT Pharmacometrics Syst Pharmacol. 2017 Aug;6(8):499-511. doi: 10.1002/psp4.12225. Epub 2017 Jul 29.

18.

Mechanism-based biomarker discovery.

Antoranz A, Sakellaropoulos T, Saez-Rodriguez J, Alexopoulos LG.

Drug Discov Today. 2017 Aug;22(8):1209-1215. doi: 10.1016/j.drudis.2017.04.013. Epub 2017 Apr 27. Review.

PMID:
28458042
19.

Gli1+ Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target.

Schneider RK, Mullally A, Dugourd A, Peisker F, Hoogenboezem R, Van Strien PMH, Bindels EM, Heckl D, Büsche G, Fleck D, Müller-Newen G, Wongboonsin J, Ventura Ferreira M, Puelles VG, Saez-Rodriguez J, Ebert BL, Humphreys BD, Kramann R.

Cell Stem Cell. 2017 Jun 1;20(6):785-800.e8. doi: 10.1016/j.stem.2017.03.008. Epub 2017 Apr 27.

20.

Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.

Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J.

Cancer Res. 2017 Jun 15;77(12):3364-3375. doi: 10.1158/0008-5472.CAN-17-0078. Epub 2017 Apr 5.

21.

Benchmarking substrate-based kinase activity inference using phosphoproteomic data.

Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P.

Bioinformatics. 2017 Jun 15;33(12):1845-1851. doi: 10.1093/bioinformatics/btx082.

22.

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.

Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S, Tarpey P, Alifrangis C, Bignell G, Vidal J, Young J, Stebbings L, Beal K, Stratton MR, Saez-Rodriguez J, Garnett M, Montagut C, Iorio F, McDermott U.

Genome Res. 2017 Apr;27(4):613-625. doi: 10.1101/gr.213546.116. Epub 2017 Feb 8.

23.

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.

Henriques D, Villaverde AF, Rocha M, Saez-Rodriguez J, Banga JR.

PLoS Comput Biol. 2017 Feb 6;13(2):e1005379. doi: 10.1371/journal.pcbi.1005379. eCollection 2017 Feb.

24.

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J.

PLoS Comput Biol. 2017 Jan 10;13(1):e1005297. doi: 10.1371/journal.pcbi.1005297. eCollection 2017 Jan.

25.

caspo: a toolbox for automated reasoning on the response of logical signaling networks families.

Videla S, Saez-Rodriguez J, Guziolowski C, Siegel A.

Bioinformatics. 2017 Mar 15;33(6):947-950. doi: 10.1093/bioinformatics/btw738.

26.

Efficient randomization of biological networks while preserving functional characterization of individual nodes.

Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J.

BMC Bioinformatics. 2016 Dec 20;17(1):542. doi: 10.1186/s12859-016-1402-1.

27.

Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.

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

Oncogene. 2017 May 11;36(19):2737-2749. doi: 10.1038/onc.2016.427. Epub 2016 Dec 19.

28.

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R.

J Proteome Res. 2017 Feb 3;16(2):831-841. doi: 10.1021/acs.jproteome.6b00815. Epub 2017 Jan 10.

PMID:
27936760
29.

OmniPath: guidelines and gateway for literature-curated signaling pathway resources.

Türei D, Korcsmáros T, Saez-Rodriguez J.

Nat Methods. 2016 Nov 29;13(12):966-967. doi: 10.1038/nmeth.4077. No abstract available.

PMID:
27898060
30.

Looking beyond the cancer cell for effective drug combinations.

Dry JR, Yang M, Saez-Rodriguez J.

Genome Med. 2016 Nov 25;8(1):125.

31.

Corrigendum: Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.

Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa AS, Gaude E, Drubbel AV, Theobald SJ, Abbo SR, Tran MG, Rajeeve V, Cardaci S, Foster S, Yun H, Cutillas P, Warren A, Gnanapragasam V, Gottlieb E, Franze K, Huntly B, Maher ER, Maxwell PH, Saez-Rodriguez J, Frezza C.

Nature. 2016 Dec 1;540(7631):150. doi: 10.1038/nature20144. Epub 2016 Oct 19. No abstract available.

PMID:
27760119
32.

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.

Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Ohnishi S, Cooper J, Patel M, McKerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, McDermott U, Saez-Rodriguez J, Huntly BJP, Iorio F, Pina C, Vassiliou GS, Yusa K.

Cell Rep. 2016 Oct 18;17(4):1193-1205. doi: 10.1016/j.celrep.2016.09.079.

33.

Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.

Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa AS, Gaude E, Drubbel AV, Theobald SJ, Abbo SR, Tran MG, Rajeeve V, Cardaci S, Foster S, Yun H, Cutillas P, Warren A, Gnanapragasam V, Gottlieb E, Franze K, Huntly B, Maher ER, Maxwell PH, Saez-Rodriguez J, Frezza C.

Nature. 2016 Aug 31;537(7621):544-547. doi: 10.1038/nature19353. Erratum in: Nature. 2016 Dec 1;540(7631):150.

34.

Crowdsourcing biomedical research: leveraging communities as innovation engines.

Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G.

Nat Rev Genet. 2016 Jul 15;17(8):470-86. doi: 10.1038/nrg.2016.69. Review.

35.

A Landscape of Pharmacogenomic Interactions in Cancer.

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

Cell. 2016 Jul 28;166(3):740-754. doi: 10.1016/j.cell.2016.06.017. Epub 2016 Jul 7.

36.

Logical Modeling and Dynamical Analysis of Cellular Networks.

Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.

Front Genet. 2016 May 31;7:94. doi: 10.3389/fgene.2016.00094. eCollection 2016. Review.

37.

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.

Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C.

BMC Bioinformatics. 2016 Apr 8;17:155. doi: 10.1186/s12859-016-1008-7.

38.

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.

Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T.

Drug Discov Today. 2016 Jul;21(7):1063-75. doi: 10.1016/j.drudis.2016.03.001. Epub 2016 Mar 12. Review.

PMID:
26979547
39.

Inferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.

Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22.

40.

Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.

Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D, Braicu I, Sehouli J, Saez-Rodriguez J, Cutillas PR, Balkwill FR.

Oncotarget. 2016 Mar 29;7(13):15648-61. doi: 10.18632/oncotarget.7255.

41.

Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A.

Rohwer N, Bindel F, Grimm C, Lin SJ, Wappler J, Klinger B, Blüthgen N, Du Bois I, Schmeck B, Lehrach H, de Graauw M, Goncalves E, Saez-Rodriguez J, Tan P, Grabsch HI, Prigione A, Kempa S, Cramer T.

Oncotarget. 2016 Feb 9;7(6):6693-710. doi: 10.18632/oncotarget.6793.

42.

The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling.

Chiapparino A, Maeda K, Turei D, Saez-Rodriguez J, Gavin AC.

Prog Lipid Res. 2016 Jan;61:30-9. doi: 10.1016/j.plipres.2015.10.004. Epub 2015 Dec 1. Review.

43.

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.

Thiele S, Cerone L, Saez-Rodriguez J, Siegel A, Guziołowski C, Klamt S.

BMC Bioinformatics. 2015 Oct 28;16:345. doi: 10.1186/s12859-015-0733-7.

44.

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.

Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J, Draviam VM.

PLoS One. 2015 Oct 9;10(10):e0139446. doi: 10.1371/journal.pone.0139446. eCollection 2015.

45.

Erratum: Prediction of human population responses to toxic compounds by a collaborative competition.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.

Nat Biotechnol. 2015 Oct;33(10):1109. doi: 10.1038/nbt1015-1109a. No abstract available.

PMID:
26448092
46.

Designing Experiments to Discriminate Families of Logic Models.

Videla S, Konokotina I, Alexopoulos LG, Saez-Rodriguez J, Schaub T, Siegel A, Guziolowski C.

Front Bioeng Biotechnol. 2015 Sep 4;3:131. doi: 10.3389/fbioe.2015.00131. eCollection 2015.

47.

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.

Terfve CD, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J.

Nat Commun. 2015 Sep 10;6:8033. doi: 10.1038/ncomms9033.

48.

Modeling Signaling Networks to Advance New Cancer Therapies.

Saez-Rodriguez J, MacNamara A, Cook S.

Annu Rev Biomed Eng. 2015;17:143-63. doi: 10.1146/annurev-bioeng-071813-104927. Epub 2015 Aug 14. Review.

PMID:
26274601
49.

Prediction of human population responses to toxic compounds by a collaborative competition.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.

Nat Biotechnol. 2015 Sep;33(9):933-40. doi: 10.1038/nbt.3299. Epub 2015 Aug 10. Erratum in: Nat Biotechnol. 2015 Oct;33(10):1109. Friend, Stephen; Dearry, Allen; Simeonov, Anton; Tice, Raymond R; Rusyn, Ivan; Wright, Fred A; Stolovitzky, Gustavo; Xie, Yang; and Saez-Rodriguez, Julio [Added].

50.

Integrative approaches for signalling and metabolic networks.

Hatzimanikatis V, Saez-Rodriguez J.

Integr Biol (Camb). 2015 Aug;7(8):844-5. doi: 10.1039/c5ib90030a. No abstract available.

PMID:
26198436

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