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Results: 1 to 20 of 88

1.

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.

Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V.

Genome Biol. 2006;7(5):R36. Epub 2006 May 10.

PMID:
16686963
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.

Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L.

Genome Biol. 2004;5(8):R52. Epub 2004 Jul 12.

PMID:
15287974
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.

Reiss DJ, Baliga NS, Bonneau R.

BMC Bioinformatics. 2006 Jun 2;7:280.

PMID:
16749936
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Learning global models of transcriptional regulatory networks from data.

Madar A, Bonneau R.

Methods Mol Biol. 2009;541:181. doi: 10.1007/978-1-59745-243-4_9. Review.

PMID:
19381524
[PubMed - indexed for MEDLINE]
5.

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J.

Genome Res. 2004 Jun;14(6):1025-35. Epub 2004 May 12.

PMID:
15140832
[PubMed - indexed for MEDLINE]
Free PMC Article
6.
7.

The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum.

Brune I, Werner H, Hüser AT, Kalinowski J, Pühler A, Tauch A.

BMC Genomics. 2006 Feb 9;7:21.

PMID:
16469103
[PubMed - indexed for MEDLINE]
Free PMC Article
8.
9.

Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach.

Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L.

Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14913-8. Epub 2002 Oct 28.

PMID:
12403819
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Prediction and integration of regulatory and protein-protein interactions.

Wichadakul D, McDermott J, Samudrala R.

Methods Mol Biol. 2009;541:101-43. doi: 10.1007/978-1-59745-243-4_6. Review.

PMID:
19381527
[PubMed - indexed for MEDLINE]
11.

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon.

Sharma K, Gillum N, Boyd JL, Schmid A.

BMC Genomics. 2012 Jul 30;13:351. doi: 10.1186/1471-2164-13-351.

PMID:
22846541
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Model-based redesign of global transcription regulation.

Carrera J, Rodrigo G, Jaramillo A.

Nucleic Acids Res. 2009 Apr;37(5):e38. doi: 10.1093/nar/gkp022. Epub 2009 Feb 2.

PMID:
19188257
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

A predictive model for transcriptional control of physiology in a free living cell.

Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS.

Cell. 2007 Dec 28;131(7):1354-65.

PMID:
18160043
[PubMed - indexed for MEDLINE]
Free Article
14.

IRIS: a method for reverse engineering of regulatory relations in gene networks.

Morganella S, Zoppoli P, Ceccarelli M.

BMC Bioinformatics. 2009 Dec 23;10:444. doi: 10.1186/1471-2105-10-444.

PMID:
20030818
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Re-annotation is an essential step in systems biology modeling of functional genomics data.

van den Berg BH, McCarthy FM, Lamont SJ, Burgess SC.

PLoS One. 2010 May 14;5(5):e10642. doi: 10.1371/journal.pone.0010642.

PMID:
20498845
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations.

Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A.

BMC Syst Biol. 2009 Apr 14;3:39. doi: 10.1186/1752-0509-3-39.

PMID:
19366454
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator.

Madar A, Greenfield A, Vanden-Eijnden E, Bonneau R.

PLoS One. 2010 Mar 22;5(3):e9803. doi: 10.1371/journal.pone.0009803.

PMID:
20339551
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ.

BMC Bioinformatics. 2004 Mar 18;5:31.

PMID:
15113405
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Genome-wide responses of the model archaeon Halobacterium sp. strain NRC-1 to oxygen limitation.

DasSarma P, Zamora RC, Müller JA, DasSarma S.

J Bacteriol. 2012 Oct;194(20):5530-7. Epub 2012 Aug 3.

PMID:
22865851
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Combining sequence and time series expression data to learn transcriptional modules.

Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):194-202.

PMID:
17044183
[PubMed - indexed for MEDLINE]

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