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Items: 1 to 20 of 45


Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.

Plaisier CL, O'Brien S, Bernard B, Reynolds S, Simon Z, Toledo CM, Ding Y, Reiss DJ, Paddison PJ, Baliga NS.

Cell Syst. 2016 Aug;3(2):172-86. doi: 10.1016/j.cels.2016.06.006.


Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.

López García de Lomana A, Schäuble S, Valenzuela J, Imam S, Carter W, Bilgin DD, Yohn CB, Turkarslan S, Reiss DJ, Orellana MV, Price ND, Baliga NS.

Biotechnol Biofuels. 2015 Dec 2;8:207. doi: 10.1186/s13068-015-0391-z.


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.


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.


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.


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. 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.


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.


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.


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.


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.


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.


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.


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.


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.

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