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Results: 1 to 20 of 62

1.

Cooperative development of logical modelling standards and tools with CoLoMoTo.

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

Bioinformatics. 2015 Jan 25. pii: btv013. [Epub ahead of print]

PMID:
25619997
[PubMed - as supplied by publisher]
2.

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.

PMID:
25492886
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
25419740
[PubMed - in process]
4.

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
[PubMed - in process]
5.

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.

PMID:
25161255
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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
[PubMed - in process]
7.

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
[PubMed - in process]
8.

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.

PMID:
24885957
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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
[PubMed - in process]
10.

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
[PubMed - in process]
11.

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.

PMID:
24507381
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
[PubMed - indexed for MEDLINE]
13.

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.

PMID:
24330611
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
24321545
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
24180668
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
24064416
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
23853063
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
[PubMed - indexed for MEDLINE]
19.

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.

Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J.

PLoS One. 2013 Apr 30;8(4):e61318. doi: 10.1371/journal.pone.0061318. Print 2013.

PMID:
23646105
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors.

Casado P, Alcolea MP, Iorio F, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR.

Genome Biol. 2013 Apr 29;14(4):R37. doi: 10.1186/gb-2013-14-4-r37.

PMID:
23628362
[PubMed - in process]
Free PMC Article
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