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Results: 1 to 20 of 58

1.

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-i623. doi: 10.1093/bioinformatics/btu474.

PMID:
25161255
[PubMed - in process]
Free PMC Article
2.

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. 2014 Aug 11. pii: 1352458514543339. [Epub ahead of print]

PMID:
25112814
[PubMed - as supplied by publisher]
3.

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 Jul 23;124C:26-38. doi: 10.1016/j.biosystems.2014.07.002. [Epub ahead of print]

PMID:
25063553
[PubMed - as supplied by publisher]
4.

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
5.

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; NCI DREAM Community.

Nat Biotechnol. 2014 Jun 1. doi: 10.1038/nbt.2877. [Epub ahead of print]

PMID:
24880487
[PubMed - as supplied by publisher]
6.

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]
7.

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, Sauro HM, Stolovitzky G, Saez-Rodriguez J.

BMC Syst Biol. 2014 Feb 7;8(1):13. [Epub ahead of print]

PMID:
24507381
[PubMed - as supplied by publisher]
Free PMC Article
8.

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]
9.

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
10.

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
11.

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 Article
12.

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
13.

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
14.

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]
15.

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
16.

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
17.

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.

Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J.

Mol Biosyst. 2013 Jul;9(7):1576-83. doi: 10.1039/c3mb25489e. Epub 2013 Mar 25. Review.

PMID:
23525368
[PubMed - indexed for MEDLINE]
18.

Evaluation of methods for modeling transcription factor sequence specificity.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.

Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27.

PMID:
23354101
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

CySBGN: a Cytoscape plug-in to integrate SBGN maps.

Gonçalves E, van Iersel M, Saez-Rodriguez J.

BMC Bioinformatics. 2013 Jan 16;14:17. doi: 10.1186/1471-2105-14-17.

PMID:
23324051
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

Gonçalves E, Saez-Rodriguez J.

F1000Res. 2013 Sep 19;2:192. doi: 10.12688/f1000research.2-192.v1. eCollection 2013.

PMID:
24715956
[PubMed]
Free PMC Article

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