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Results: 1 to 20 of 64

1.

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 May 1. [Epub ahead of print]

PMID:
25932872
2.

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(1):8. doi: 10.1186/s12918-015-0144-4.

3.

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
4.

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.

5.

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.

6.

Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy.

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.

Integr Biol (Camb). 2014 Dec;6(12):1170-82. doi: 10.1039/c4ib00086b.

PMID:
25303361
7.

Fast randomization of large genomic datasets while preserving alteration counts.

Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G, Saez-Rodriguez J.

Bioinformatics. 2014 Sep 1;30(17):i617-23. doi: 10.1093/bioinformatics/btu474.

8.

Signaling networks in MS: a systems-based approach to developing new pharmacological therapies.

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, Zamora A, Paul F, Saez-Rodriguez J, Villoslada P.

Mult Scler. 2015 Feb;21(2):138-46. doi: 10.1177/1352458514543339. Epub 2014 Aug 11.

PMID:
25112814
9.

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.

Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S.

Biosystems. 2014 Oct;124:26-38. doi: 10.1016/j.biosystems.2014.07.002. Epub 2014 Jul 23.

PMID:
25063553
10.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J.

BMC Bioinformatics. 2014 May 10;15:136. doi: 10.1186/1471-2105-15-136.

11.

A community effort to assess and improve drug sensitivity prediction algorithms.

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; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.

Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1.

PMID:
24880487
12.

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.

Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C.

Angew Chem Int Ed Engl. 2014 Jun 23;53(26):6720-3. doi: 10.1002/anie.201402294. Epub 2014 May 19.

PMID:
24841150
13.

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.

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, Stolovitzky G, Saez-Rodriguez J.

BMC Syst Biol. 2014 Feb 7;8:13. doi: 10.1186/1752-0509-8-13.

14.

PIP₃ induces the recycling of receptor tyrosine kinases.

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.

Sci Signal. 2014 Jan 14;7(308):ra5. doi: 10.1126/scisignal.2004532.

PMID:
24425787
15.

Network based elucidation of drug response: from modulators to targets.

Iorio F, Saez-Rodriguez J, di Bernardo D.

BMC Syst Biol. 2013 Dec 13;7:139. doi: 10.1186/1752-0509-7-139. Review.

16.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

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, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.

BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135.

17.

Path2Models: large-scale generation of computational models from biochemical pathway maps.

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, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

18.

BioServices: a common Python package to access biological Web Services programmatically.

Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J.

Bioinformatics. 2013 Dec 15;29(24):3241-2. doi: 10.1093/bioinformatics/btt547. Epub 2013 Sep 23.

19.

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.

Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J.

Bioinformatics. 2013 Sep 15;29(18):2320-6. doi: 10.1093/bioinformatics/btt393. Epub 2013 Jul 12. Erratum in: Bioinformatics. 2014 Jul 1;30(13):1942.

20.

Modeling signaling networks with different formalisms: a preview.

MacNamara A, Henriques D, Saez-Rodriguez J.

Methods Mol Biol. 2013;1021:89-105. doi: 10.1007/978-1-62703-450-0_5.

PMID:
23715981
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