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Results: 1 to 20 of 40

1.

The DNA-binding network of Mycobacterium tuberculosis.

Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, Hickey M, Brabant W, Morrison B, Turkarslan S, Mawhinney C, Galagan JE, Price ND, Baliga NS, Sherman DR.

Nat Commun. 2015 Jan 12;6:5829. doi: 10.1038/ncomms6829.

PMID:
25581030
[PubMed - in process]
2.

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.

Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS.

BMC Syst Biol. 2014 Nov 14;8(1):122. [Epub ahead of print]

PMID:
25394904
[PubMed - as supplied by publisher]
Free PMC Article
3.

Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.

Ashworth J, Plaisier CL, Lo FY, Reiss DJ, Baliga NS.

PLoS One. 2014 Sep 25;9(9):e107863. doi: 10.1371/journal.pone.0107863. eCollection 2014.

PMID:
25255272
[PubMed - in process]
Free PMC Article
4.

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.

Peterson EJ, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJ, Sherman DR, Baliga NS.

Nucleic Acids Res. 2014 Oct;42(18):11291-303. doi: 10.1093/nar/gku777. Epub 2014 Sep 17.

PMID:
25232098
[PubMed - indexed for MEDLINE]
Free Article
5.

A system-level model for the microbial regulatory genome.

Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS.

Mol Syst Biol. 2014 Jul 15;10:740. doi: 10.15252/msb.20145160.

PMID:
25028489
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Network portal: a database for storage, analysis and visualization of biological networks.

Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS.

Nucleic Acids Res. 2014 Jan;42(Database issue):D184-90. doi: 10.1093/nar/gkt1190. Epub 2013 Nov 23.

PMID:
24271392
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Molecular mechanisms of system responses to novel stimuli are predictable from public data.

Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD.

Nucleic Acids Res. 2014 Feb;42(3):1442-60. doi: 10.1093/nar/gkt938. Epub 2013 Oct 31.

PMID:
24185701
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.

Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie TJ, Slagel J, Moritz RL, Hackett M, Leigh JA, Baliga NS.

Genome Res. 2013 Nov;23(11):1839-51. doi: 10.1101/gr.153916.112. Epub 2013 Oct 2.

PMID:
24089473
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Global analysis of mRNA stability in Mycobacterium tuberculosis.

Rustad TR, Minch KJ, Brabant W, Winkler JK, Reiss DJ, Baliga NS, Sherman DR.

Nucleic Acids Res. 2013 Jan 7;41(1):509-17. doi: 10.1093/nar/gks1019. Epub 2012 Nov 3.

PMID:
23125364
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A novel approach for transcription factor analysis using SELEX with high-throughput sequencing (TFAST).

Reiss DJ, Howard FM, Mobley HL.

PLoS One. 2012;7(8):e42761. doi: 10.1371/journal.pone.0042761. Epub 2012 Aug 3.

PMID:
22956994
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Niche adaptation by expansion and reprogramming of general transcription factors.

Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS.

Mol Syst Biol. 2011 Nov 22;7:554. doi: 10.1038/msb.2011.87.

PMID:
22108796
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Determination of target sequence bound by PapX, repressor of bacterial motility, in flhD promoter using systematic evolution of ligands by exponential enrichment (SELEX) and high throughput sequencing.

Reiss DJ, Mobley HL.

J Biol Chem. 2011 Dec 30;286(52):44726-38. doi: 10.1074/jbc.M111.290684. Epub 2011 Oct 28.

PMID:
22039053
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The broadly conserved regulator PhoP links pathogen virulence and membrane potential in Escherichia coli.

Alteri CJ, Lindner JR, Reiss DJ, Smith SN, Mobley HL.

Mol Microbiol. 2011 Oct;82(1):145-63. doi: 10.1111/j.1365-2958.2011.07804.x. Epub 2011 Sep 2.

PMID:
21854465
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Parallel evolution of transcriptome architecture during genome reorganization.

Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL, Adams MW, Barnebey A, Yannone SM, Leigh JA, Baliga NS.

Genome Res. 2011 Nov;21(11):1892-904. doi: 10.1101/gr.122218.111. Epub 2011 Jul 12.

PMID:
21750103
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Multi-species integrative biclustering.

Waltman P, Kacmarczyk T, Bate AR, Kearns DB, Reiss DJ, Eichenberger P, Bonneau R.

Genome Biol. 2010;11(9):R96. doi: 10.1186/gb-2010-11-9-r96. Epub 2010 Sep 29.

PMID:
20920250
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Coordination of frontline defense mechanisms under severe oxidative stress.

Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss DJ, DiRuggiero J, Baliga NS.

Mol Syst Biol. 2010 Jul;6:393. doi: 10.1038/msb.2010.50.

PMID:
20664639
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Integration and visualization of systems biology data in context of the genome.

Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS.

BMC Bioinformatics. 2010 Jul 19;11:382. doi: 10.1186/1471-2105-11-382.

PMID:
20642854
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model.

Youn A, Reiss DJ, Stuetzle W.

Bioinformatics. 2010 Aug 1;26(15):1879-86. doi: 10.1093/bioinformatics/btq289. Epub 2010 Jun 4.

PMID:
20525821
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis.

Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ, Hoang L, Kalisiak E, Northen T, Trauger SA, Siuzdak G, Baliga NS.

BMC Syst Biol. 2010 May 14;4:64. doi: 10.1186/1752-0509-4-64.

PMID:
20470417
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Prevalence of transcription promoters within archaeal operons and coding sequences.

Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS.

Mol Syst Biol. 2009;5:285. doi: 10.1038/msb.2009.42. Epub 2009 Jun 16.

PMID:
19536208
[PubMed - indexed for MEDLINE]
Free PMC Article
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