Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 101

1.

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, Alexopoulos LG.

PLoS One. 2012;7(11):e50085. doi: 10.1371/journal.pone.0050085. Epub 2012 Nov 30.

PMID:
23226239
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Construction of cell type-specific logic models of signaling networks using CellNOpt.

Morris MK, Melas I, Saez-Rodriguez J.

Methods Mol Biol. 2013;930:179-214. doi: 10.1007/978-1-62703-059-5_8.

PMID:
23086842
[PubMed - indexed for MEDLINE]
3.

Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA.

PLoS Comput Biol. 2011 Mar;7(3):e1001099. doi: 10.1371/journal.pcbi.1001099. Epub 2011 Mar 3.

PMID:
21408212
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

Mitsos A, Melas IN, Siminelakis P, Chairakaki AD, Saez-Rodriguez J, Alexopoulos LG.

PLoS Comput Biol. 2009 Dec;5(12):e1000591. doi: 10.1371/journal.pcbi.1000591. Epub 2009 Dec 4.

PMID:
19997482
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach.

Chen BS, Wu CC.

Bioinformatics. 2012 Jun 15;28(12):1604-11. doi: 10.1093/bioinformatics/bts159. Epub 2012 Apr 6.

PMID:
22492637
[PubMed - indexed for MEDLINE]
Free Article
6.

State-time spectrum of signal transduction logic models.

MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J.

Phys Biol. 2012 Aug;9(4):045003. doi: 10.1088/1478-3975/9/4/045003. Epub 2012 Aug 7. Review.

PMID:
22871648
[PubMed - indexed for MEDLINE]
7.

Automatic modeling of signaling pathways by network flow model.

Zhao XM, Wang RS, Chen L, Aihara K.

J Bioinform Comput Biol. 2009 Apr;7(2):309-22.

PMID:
19340917
[PubMed - indexed for MEDLINE]
8.

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data.

Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S.

PLoS Comput Biol. 2009 Aug;5(8):e1000438. doi: 10.1371/journal.pcbi.1000438. Epub 2009 Aug 7.

PMID:
19662154
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions.

Morris MK, Shriver Z, Sasisekharan R, Lauffenburger DA.

Biotechnol J. 2012 Mar;7(3):374-86. doi: 10.1002/biot.201100222. Epub 2012 Jan 10.

PMID:
22125256
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Deterministic global optimization algorithm based on outer approximation for the parameter estimation of nonlinear dynamic biological systems.

Miró A, Pozo C, Guillén-Gosálbez G, Egea JA, Jiménez L.

BMC Bioinformatics. 2012 May 10;13:90. doi: 10.1186/1471-2105-13-90.

PMID:
22574924
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Combined logical and data-driven models for linking signalling pathways to cellular response.

Melas IN, Mitsos A, Messinis DE, Weiss TS, Alexopoulos LG.

BMC Syst Biol. 2011 Jul 5;5:107. doi: 10.1186/1752-0509-5-107.

PMID:
21729292
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways.

Alves R, Vilaprinyo E, Hernádez-Bermejo B, Sorribas A.

Biotechnol Genet Eng Rev. 2008;25:1-40. Review.

PMID:
21412348
[PubMed - indexed for MEDLINE]
13.

Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs.

Melas IN, Samaga R, Alexopoulos LG, Klamt S.

PLoS Comput Biol. 2013;9(9):e1003204. doi: 10.1371/journal.pcbi.1003204. Epub 2013 Sep 5.

PMID:
24039561
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.

Melas IN, Mitsos A, Messinis DE, Weiss TS, Rodriguez JS, Alexopoulos LG.

Mol Biosyst. 2012 Apr;8(5):1571-84. doi: 10.1039/c2mb05482e. Epub 2012 Mar 23.

PMID:
22446821
[PubMed - indexed for MEDLINE]
15.

Linear time-varying models can reveal non-linear interactions of biomolecular regulatory networks using multiple time-series data.

Kim J, Bates DG, Postlethwaite I, Heslop-Harrison P, Cho KH.

Bioinformatics. 2008 May 15;24(10):1286-92. doi: 10.1093/bioinformatics/btn107. Epub 2008 Mar 26.

PMID:
18367478
[PubMed - indexed for MEDLINE]
Free Article
16.

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.

BMC Syst Biol. 2012 May 1;6:29. doi: 10.1186/1752-0509-6-29.

PMID:
22548703
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Discrete dynamic modeling of cellular signaling networks.

Albert R, Wang RS.

Methods Enzymol. 2009;467:281-306. doi: 10.1016/S0076-6879(09)67011-7.

PMID:
19897097
[PubMed - indexed for MEDLINE]
18.

Soft constraints-based multiobjective framework for flux balance analysis.

Nagrath D, Avila-Elchiver M, Berthiaume F, Tilles AW, Messac A, Yarmush ML.

Metab Eng. 2010 Sep;12(5):429-45. doi: 10.1016/j.ymben.2010.05.003. Epub 2010 May 27.

PMID:
20553945
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

OR/AND neurons and the development of interpretable logic models.

Pedrycz W, Reformat M, Li K.

IEEE Trans Neural Netw. 2006 May;17(3):636-58.

PMID:
16722169
[PubMed - indexed for MEDLINE]
20.

Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways.

Hardy S, Robillard PN.

Bioinformatics. 2008 Jan 15;24(2):209-17. Epub 2007 Nov 22.

PMID:
18033796
[PubMed - indexed for MEDLINE]
Free Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk