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Results: 1 to 20 of 61

1.

Gene network inference using continuous time Bayesian networks: a comparative study and application to Th17 cell differentiation.

Acerbi E, Zelante T, Narang V, Stella F.

BMC Bioinformatics. 2014 Dec 11;15:387. doi: 10.1186/s12859-014-0387-x.

PMID:
25495206
[PubMed - in process]
Free PMC Article
2.

A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets.

Liu LZ, Wu FX, Zhang WJ.

BMC Syst Biol. 2014;8 Suppl 3:S1. doi: 10.1186/1752-0509-8-S3-S1. Epub 2014 Oct 22.

PMID:
25350697
[PubMed - in process]
Free PMC Article
3.

Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis.

van Dam JC, Schaap PJ, Martins Dos Santos VA, Suárez-Diez M.

BMC Syst Biol. 2014 Sep 26;8(1):111. [Epub ahead of print]

PMID:
25279447
[PubMed - as supplied by publisher]
Free PMC Article
4.

Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data.

Kiani NA, Kaderali L.

BMC Bioinformatics. 2014 Jul 22;15:250. doi: 10.1186/1471-2105-15-250.

PMID:
25047753
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

In-vivo real-time control of protein expression from endogenous and synthetic gene networks.

Menolascina F, Fiore G, Orabona E, De Stefano L, Ferry M, Hasty J, di Bernardo M, di Bernardo D.

PLoS Comput Biol. 2014 May 15;10(5):e1003625. doi: 10.1371/journal.pcbi.1003625. eCollection 2014 May.

PMID:
24831205
[PubMed - in process]
Free PMC Article
6.

MIDER: network inference with mutual information distance and entropy reduction.

Villaverde AF, Ross J, Morán F, Banga JR.

PLoS One. 2014 May 7;9(5):e96732. doi: 10.1371/journal.pone.0096732. eCollection 2014.

PMID:
24806471
[PubMed - in process]
Free PMC Article
7.

An algebra-based method for inferring gene regulatory networks.

Vera-Licona P, Jarrah A, Garcia-Puente LD, McGee J, Laubenbacher R.

BMC Syst Biol. 2014 Mar 26;8:37. doi: 10.1186/1752-0509-8-37.

PMID:
24669835
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Inferring gene dependency network specific to phenotypic alteration based on gene expression data and clinical information of breast cancer.

Zhou X, Liu J.

PLoS One. 2014 Mar 17;9(3):e92023. doi: 10.1371/journal.pone.0092023. eCollection 2014.

PMID:
24637666
[PubMed - in process]
Free PMC Article
9.

CaSPIAN: a causal compressive sensing algorithm for discovering directed interactions in gene networks.

Emad A, Milenkovic O.

PLoS One. 2014 Mar 12;9(3):e90781. doi: 10.1371/journal.pone.0090781. eCollection 2014.

PMID:
24622336
[PubMed - in process]
Free PMC Article
10.

Interactive exploration of integrated biological datasets using context-sensitive workflows.

Horn F, Rittweger M, Taubert J, Lysenko A, Rawlings C, Guthke R.

Front Genet. 2014 Feb 20;5:21. doi: 10.3389/fgene.2014.00021. eCollection 2014.

PMID:
24600467
[PubMed]
Free PMC Article
11.

Synthetic biology in mammalian cells: next generation research tools and therapeutics.

Lienert F, Lohmueller JJ, Garg A, Silver PA.

Nat Rev Mol Cell Biol. 2014 Feb;15(2):95-107. doi: 10.1038/nrm3738. Epub 2014 Jan 17. Review.

PMID:
24434884
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

Villaverde AF, Banga JR.

J R Soc Interface. 2013 Dec 4;11(91):20130505. doi: 10.1098/rsif.2013.0505. Print 2014 Feb 6. Review.

PMID:
24307566
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster.

Becker K, Balsa-Canto E, Cicin-Sain D, Hoermann A, Janssens H, Banga JR, Jaeger J.

PLoS Comput Biol. 2013 Oct;9(10):e1003281. doi: 10.1371/journal.pcbi.1003281. Epub 2013 Oct 31.

PMID:
24204230
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Incorporating time-delays in S-System model for reverse engineering genetic networks.

Chowdhury AR, Chetty M, Vinh NX.

BMC Bioinformatics. 2013 Jun 18;14:196. doi: 10.1186/1471-2105-14-196.

PMID:
23777625
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Reverse engineering sparse gene regulatory networks using cubature kalman filter and compressed sensing.

Noor A, Serpedin E, Nounou M, Nounou H.

Adv Bioinformatics. 2013;2013:205763. doi: 10.1155/2013/205763. Epub 2013 May 8.

PMID:
23737768
[PubMed]
Free PMC Article
16.

Supervised, semi-supervised and unsupervised inference of gene regulatory networks.

Maetschke SR, Madhamshettiwar PB, Davis MJ, Ragan MA.

Brief Bioinform. 2014 Mar;15(2):195-211. doi: 10.1093/bib/bbt034. Epub 2013 May 21.

PMID:
23698722
[PubMed - in process]
Free PMC Article
17.

Reverse engineering validation using a benchmark synthetic gene circuit in human cells.

Kang T, White JT, Xie Z, Benenson Y, Sontag E, Bleris L.

ACS Synth Biol. 2013 May 17;2(5):255-62. doi: 10.1021/sb300093y. Epub 2013 Mar 28.

PMID:
23654266
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks.

Lim N, Senbabaoglu Y, Michailidis G, d'Alché-Buc F.

Bioinformatics. 2013 Jun 1;29(11):1416-23. doi: 10.1093/bioinformatics/btt167. Epub 2013 Apr 10.

PMID:
23574736
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

An overview of the statistical methods used for inferring gene regulatory networks and protein-protein interaction networks.

Noor A, Serpedin E, Nounou M, Nounou H, Mohamed N, Chouchane L.

Adv Bioinformatics. 2013;2013:953814. doi: 10.1155/2013/953814. Epub 2013 Feb 21.

PMID:
23509452
[PubMed]
Free PMC Article
20.

Reverse engineering: a key component of systems biology to unravel global abiotic stress cross-talk.

Friedel S, Usadel B, von Wirén N, Sreenivasulu N.

Front Plant Sci. 2012 Dec 31;3:294. doi: 10.3389/fpls.2012.00294. eCollection 2012.

PMID:
23293646
[PubMed]
Free PMC Article

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