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Items: 1 to 20 of 79

1.

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 Feb 8. doi: 10.18632/oncotarget.7255. [Epub ahead of print]

PMID:
26871292
2.

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. 2015 Dec 29. doi: 10.18632/oncotarget.6793. [Epub ahead of print]

3.

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.

4.

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.

5.

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.

6.

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
7.

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.

8.

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.

9.

Modeling Signaling Networks to Advance New Cancer Therapies.

Saez-Rodriguez J, MacNamara A, Cook S.

Annu Rev Biomed Eng. 2015 Dec 7;17:143-63. doi: 10.1146/annurev-bioeng-071813-104927. Epub 2015 Aug 14.

PMID:
26274601
10.

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].

PMID:
26258538
11.

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
12.

Empirical inference of circuitry and plasticity in a kinase signaling network.

Wilkes EH, Terfve C, Gribben JG, Saez-Rodriguez J, Cutillas PR.

Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):7719-24. doi: 10.1073/pnas.1423344112. Epub 2015 Jun 9.

13.

A single-cell model of PIP3 dynamics using chemical dimerization.

MacNamara A, Stein F, Feng S, Schultz C, Saez-Rodriguez J.

Bioorg Med Chem. 2015 Jun 15;23(12):2868-76. doi: 10.1016/j.bmc.2015.04.074. Epub 2015 May 7.

14.

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

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

Bioinformatics. 2015 Sep 15;31(18):2999-3007. doi: 10.1093/bioinformatics/btv314. Epub 2015 May 21.

15.

Prospective derivation of a living organoid biobank of colorectal cancer patients.

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, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H.

Cell. 2015 May 7;161(4):933-45. doi: 10.1016/j.cell.2015.03.053.

PMID:
25957691
16.

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.

Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP.

Integr Biol (Camb). 2015 Aug;7(8):904-20. doi: 10.1039/c4ib00294f.

PMID:
25932872
17.

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.

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.

BMC Syst Biol. 2015 Feb 20;9:8. doi: 10.1186/s12918-015-0144-4.

18.

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Naldi A, Monteiro PT, Müssel C; Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C.

Bioinformatics. 2015 Apr 1;31(7):1154-9. doi: 10.1093/bioinformatics/btv013. Epub 2015 Jan 25.

PMID:
25619997
19.

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.

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.

Mol Syst Biol. 2014 Dec 9;10:767. doi: 10.15252/msb.20145112.

20.

A community computational challenge to predict the activity of pairs of compounds.

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, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A; NCI-DREAM Community.

Nat Biotechnol. 2014 Dec;32(12):1213-22. doi: 10.1038/nbt.3052. Epub 2014 Nov 17.

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