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Non-linear dimensionality reduction of signaling networks.

Ivakhno S, Armstrong JD.

BMC Syst Biol. 2007 Jun 8;1:27.PMID: 17559646 [PubMed - indexed for MEDLINE]Related articlesFree article

A compendium of signals and responses triggered by prodeath and prosurvival cytokines.

Gaudet S, Janes KA, Albeck JG, Pace EA, Lauffenburger DA, Sorger PK.

Mol Cell Proteomics. 2005 Oct;4(10):1569-90. Epub 2005 Jul 18.PMID: 16030008 [PubMed - indexed for MEDLINE]Related articlesFree article

Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data.

Janes KA, Kelly JR, Gaudet S, Albeck JG, Sorger PK, Lauffenburger DA.

J Comput Biol. 2004;11(4):544-61.PMID: 15579231 [PubMed - indexed for MEDLINE]Related articles

A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis.

Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA, Yaffe MB.

Science. 2005 Dec 9;310(5754):1646-53.PMID: 16339439 [PubMed - indexed for MEDLINE]Related articlesFree article

Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data.

Kumar N, Wolf-Yadlin A, White FM, Lauffenburger DA.

PLoS Comput Biol. 2007 Jan 5;3(1):e4. Epub 2006 Nov 21.PMID: 17206861 [PubMed - indexed for MEDLINE]Related articlesFree article

Modularization of biochemical networks based on classification of Petri net t-invariants.

Grafahrend-Belau E, Schreiber F, Heiner M, Sackmann A, Junker BH, Grunwald S, Speer A, Winder K, Koch I.

BMC Bioinformatics. 2008 Feb 8;9:90.PMID: 18257938 [PubMed - indexed for MEDLINE]Related articlesFree article

Supervised nonlinear dimensionality reduction for visualization and classification.

Geng X, Zhan DC, Zhou ZH.

IEEE Trans Syst Man Cybern B Cybern. 2005 Dec;35(6):1098-107.PMID: 16366237 [PubMed - indexed for MEDLINE]Related articles

Adenoviral vector saturates Akt pro-survival signaling and blocks insulin-mediated rescue of tumor necrosis-factor-induced apoptosis.

Miller-Jensen K, Janes KA, Wong YL, Griffith LG, Lauffenburger DA.

J Cell Sci. 2006 Sep 15;119(Pt 18):3788-98. Epub 2006 Aug 29.PMID: 16940353 [PubMed - indexed for MEDLINE]Related articlesFree article

A structural approach for finding functional modules from large biological networks.

Mete M, Tang F, Xu X, Yuruk N.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S19.PMID: 18793464 [PubMed - indexed for MEDLINE]Related articlesFree article

In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells.

Naamane N, van Helden J, Eizirik DL.

BMC Bioinformatics. 2007 Feb 15;8:55.PMID: 17302974 [PubMed - indexed for MEDLINE]Related articlesFree article

Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm.

Dawson K, Rodriguez RL, Malyj W.

BMC Bioinformatics. 2005 Aug 2;6:195.PMID: 16076401 [PubMed - indexed for MEDLINE]Related articlesFree article

Effects of HER2 overexpression on cell signaling networks governing proliferation and migration.

Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova V, Lauffenburger DA, White FM.

Mol Syst Biol. 2006;2:54. Epub 2006 Oct 3.PMID: 17016520 [PubMed - indexed for MEDLINE]Related articlesFree article

Spectral embedding finds meaningful (relevant) structure in image and microarray data.

Higgs BW, Weller J, Solka JL.

BMC Bioinformatics. 2006 Feb 16;7:74.PMID: 16483359 [PubMed - indexed for MEDLINE]Related articlesFree article

Multivariate analysis of neuronal interactions in the generalized partial least squares framework: simulations and empirical studies.

Lin FH, McIntosh AR, Agnew JA, Eden GF, Zeffiro TA, Belliveau JW.

Neuroimage. 2003 Oct;20(2):625-42.PMID: 14568440 [PubMed - indexed for MEDLINE]Related articles

Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling.

Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA.

PLoS Comput Biol. 2009 Apr;5(4):e1000340. Epub 2009 Apr 3.PMID: 19343194 [PubMed - indexed for MEDLINE]Related articlesFree article

caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data.

Zhu Y, Li H, Miller DJ, Wang Z, Xuan J, Clarke R, Hoffman EP, Wang Y.

BMC Bioinformatics. 2008 Sep 18;9:383.PMID: 18801195 [PubMed - indexed for MEDLINE]Related articlesFree article

A high-throughput quantitative multiplex kinase assay for monitoring information flow in signaling networks: application to sepsis-apoptosis.

Janes KA, Albeck JG, Peng LX, Sorger PK, Lauffenburger DA, Yaffe MB.

Mol Cell Proteomics. 2003 Jul;2(7):463-73. Epub 2003 Jun 26.PMID: 12832460 [PubMed - indexed for MEDLINE]Related articlesFree article

Understanding complex signaling networks through models and metaphors.

Bhalla US.

Prog Biophys Mol Biol. 2003 Jan;81(1):45-65. Review.PMID: 12475569 [PubMed - indexed for MEDLINE]Related articles

A methodology for the structural and functional analysis of signaling and regulatory networks.

Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED.

BMC Bioinformatics. 2006 Feb 7;7:56.PMID: 16464248 [PubMed - indexed for MEDLINE]Related articlesFree article

Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility.

Kharait S, Hautaniemi S, Wu S, Iwabu A, Lauffenburger DA, Wells A.

BMC Syst Biol. 2007 Jan 29;1:9.PMID: 17408516 [PubMed - indexed for MEDLINE]Related articlesFree article