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Results: 1 to 20 of 43


A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis.

Turkarslan S, Peterson EJ, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S, Price ND, Sherman DR, Baliga NS.

Sci Data. 2015 Mar 31;2:150010. doi: 10.1038/sdata.2015.10. eCollection 2015.


Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.

Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS.

BMC Syst Biol. 2015;9 Suppl 2:S1. doi: 10.1186/1752-0509-9-S2-S1. Epub 2015 Apr 15.


cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.

Reiss DJ, Plaisier CL, Wu WJ, Baliga NS.

Nucleic Acids Res. 2015 Jul 27;43(13):e87. doi: 10.1093/nar/gkv300. Epub 2015 Apr 14.


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.


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;8:122. doi: 10.1186/s12918-014-0122-2.


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. Erratum in: PLoS One. 2014;9(11):e114450.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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