Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 86

1.

Crowdsourcing network inference: the DREAM predictive signaling network challenge.

Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.

Sci Signal. 2011 Aug 30;4(189):mr7. doi: 10.1126/scisignal.2002212.

2.

Computational phosphorylation network reconstruction: methods and resources.

Duan G, Walther D.

Methods Mol Biol. 2015;1306:177-94. doi: 10.1007/978-1-4939-2648-0_14.

PMID:
25930703
3.

A crowd-sourcing approach for the construction of species-specific cell signaling networks.

Bilal E, Sakellaropoulos T, Melas IN, Messinis DE, Belcastro V, Rhrissorrakrai K, Meyer P, Norel R, Iskandar A, Blaese E, Rice JJ, Peitsch MC, Hoeng J, Stolovitzky G, Alexopoulos LG, Poussin C; Challenge Participants.

Bioinformatics. 2015 Feb 15;31(4):484-91. doi: 10.1093/bioinformatics/btu659. Epub 2014 Oct 7.

4.

GSGS: a computational approach to reconstruct signaling pathway structures from gene sets.

Acharya L, Judeh T, Duan Z, Rabbat M, Zhu D.

IEEE/ACM Trans Comput Biol Bioinform. 2012;9(2):438-50. doi: 10.1109/TCBB.2011.143. Epub 2011 Oct 17.

PMID:
22025758
5.

A directed protein interaction network for investigating intracellular signal transduction.

Vinayagam A, Stelzl U, Foulle R, Plassmann S, Zenkner M, Timm J, Assmus HE, Andrade-Navarro MA, Wanker EE.

Sci Signal. 2011 Sep 6;4(189):rs8. doi: 10.1126/scisignal.2001699.

6.

Phosphoproteomics-based network medicine.

Liu Z, Wang Y, Xue Y.

FEBS J. 2013 Nov;280(22):5696-704. doi: 10.1111/febs.12380. Epub 2013 Jun 28. Review.

7.

Network reconstruction based on proteomic data and prior knowledge of protein connectivity using graph theory.

Stavrakas V, Melas IN, Sakellaropoulos T, Alexopoulos LG.

PLoS One. 2015 May 28;10(5):e0128411. doi: 10.1371/journal.pone.0128411. eCollection 2015.

8.

Towards a rigorous assessment of systems biology models: the DREAM3 challenges.

Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.

PLoS One. 2010 Feb 23;5(2):e9202. doi: 10.1371/journal.pone.0009202. Erratum in: PLoS One. 2010;5(3). doi: 10.1371/annotation/f633213a-dc4f-4bee-b6c5-72d50e7073b8.

9.

Computational analysis of phosphoproteomics: progresses and perspectives.

Ren J, Gao X, Liu Z, Cao J, Ma Q, Xue Y.

Curr Protein Pept Sci. 2011 Nov;12(7):591-601. Review.

PMID:
21827424
10.

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
11.

P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations.

Young-Rae Cho, Yanan Xin, Speegle G.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Mar-Apr;12(2):309-21. doi: 10.1109/TCBB.2014.2355216.

PMID:
26357219
12.

Revealing strengths and weaknesses of methods for gene network inference.

Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.

Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6286-91. doi: 10.1073/pnas.0913357107. Epub 2010 Mar 22.

13.

Identifying the topology of signaling networks from partial RNAi data.

Ren Y, Wang Q, Hasan MM, Ay A, Kahveci T.

BMC Syst Biol. 2016 Aug 1;10 Suppl 2:53. doi: 10.1186/s12918-016-0301-4.

14.

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.

15.

A Sparse Reconstruction Approach for Identifying Gene Regulatory Networks Using Steady-State Experiment Data.

Zhang W, Zhou T.

PLoS One. 2015 Jul 24;10(7):e0130979. doi: 10.1371/journal.pone.0130979. eCollection 2015.

16.

A Boolean approach to linear prediction for signaling network modeling.

Eduati F, Corradin A, Di Camillo B, Toffolo G.

PLoS One. 2010 Sep 16;5(9). pii: e12789. doi: 10.1371/journal.pone.0012789.

17.

An integrative C. elegans protein-protein interaction network with reliability assessment based on a probabilistic graphical model.

Huang XT, Zhu Y, Chan LL, Zhao Z, Yan H.

Mol Biosyst. 2016 Jan;12(1):85-92. doi: 10.1039/c5mb00417a.

PMID:
26555698
18.

Constructing the angiome: a global angiogenesis protein interaction network.

Chu LH, Rivera CG, Popel AS, Bader JS.

Physiol Genomics. 2012 Oct 2;44(19):915-24. doi: 10.1152/physiolgenomics.00181.2011. Epub 2012 Aug 21.

19.

Gene expression complex networks: synthesis, identification, and analysis.

Lopes FM, Cesar RM, Costa Lda F.

J Comput Biol. 2011 Oct;18(10):1353-67. doi: 10.1089/cmb.2010.0118. Epub 2011 May 6.

PMID:
21548810
20.

Reverse-phase protein lysate microarray (RPA) for the experimental validation of quantitative protein network models.

Nishizuka SS.

Methods Mol Biol. 2011;785:65-77. doi: 10.1007/978-1-61779-286-1_6.

PMID:
21901594

Supplemental Content

Support Center