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Gene-Centered Yeast One-Hybrid Assays.

Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ.

Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.top077669. doi: 10.1101/pdb.top077669.


A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions.

Fuxman Bass JI, Pons C, Kozlowski L, Reece-Hoyes JS, Shrestha S, Holdorf AD, Mori A, Myers CL, Walhout AJ.

Mol Syst Biol. 2016 Oct 24;12(10):884. doi: 10.15252/msb.20167131.


HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.

Guillen-Ahlers H, Rao PK, Levenstein ME, Kennedy-Darling J, Perumalla DS, Jadhav AY, Glenn JP, Ludwig-Kubinski A, Drigalenko E, Montoya MJ, Göring HH, Anderson CD, Scalf M, Gildersleeve HI, Cole R, Greene AM, Oduro AK, Lazarova K, Cesnik AJ, Barfknecht J, Cirillo LA, Gasch AP, Shortreed MR, Smith LM, Olivier M.

Genomics. 2016 Jun;107(6):267-73. doi: 10.1016/j.ygeno.2016.05.002. Epub 2016 May 13.


Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice.

Smita S, Katiyar A, Chinnusamy V, Pandey DM, Bansal KC.

Front Plant Sci. 2015 Dec 24;6:1157. doi: 10.3389/fpls.2015.01157. eCollection 2015.


Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance.

Chai C, Wang Y, Joshi T, Valliyodan B, Prince S, Michel L, Xu D, Nguyen HT.

BMC Genomics. 2015 Aug 13;16:596. doi: 10.1186/s12864-015-1743-6.


Elements of the cellular metabolic structure.

De la Fuente IM.

Front Mol Biosci. 2015 Apr 28;2:16. doi: 10.3389/fmolb.2015.00016. eCollection 2015.


Human gene-centered transcription factor networks for enhancers and disease variants.

Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJ.

Cell. 2015 Apr 23;161(3):661-73. doi: 10.1016/j.cell.2015.03.003.


Revealing shared and distinct gene network organization in Arabidopsis immune responses by integrative analysis.

Dong X, Jiang Z, Peng YL, Zhang Z.

Plant Physiol. 2015 Mar;167(3):1186-203. doi: 10.1104/pp.114.254292. Epub 2015 Jan 22.


Advanced methods for the analysis of chromatin-associated proteins.

Guillen-Ahlers H, Shortreed MR, Smith LM, Olivier M.

Physiol Genomics. 2014 Jul 1;46(13):441-7. doi: 10.1152/physiolgenomics.00041.2014. Epub 2014 May 6. Review.


The grammar of transcriptional regulation.

Weingarten-Gabbay S, Segal E.

Hum Genet. 2014 Jun;133(6):701-11. doi: 10.1007/s00439-013-1413-1. Epub 2014 Jan 5. Review.


Using networks to measure similarity between genes: association index selection.

Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ.

Nat Methods. 2013 Dec;10(12):1169-76. doi: 10.1038/nmeth.2728. Erratum in: Nat Methods. 2014 Mar;11(3):349.


Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.

Guturu H, Doxey AC, Wenger AM, Bejerano G.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130029. doi: 10.1098/rstb.2013.0029. Print 2013 Dec 19.


Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets.

Teng L, He B, Gao P, Gao L, Tan K.

Nucleic Acids Res. 2014 Feb;42(4):e24. doi: 10.1093/nar/gkt1105. Epub 2013 Nov 11.


Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters.

Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJ.

Nucleic Acids Res. 2014 Jan;42(1):153-62. doi: 10.1093/nar/gkt858. Epub 2013 Sep 24.


Navigating the transcriptional roadmap regulating plant secondary cell wall deposition.

Hussey SG, Mizrachi E, Creux NM, Myburg AA.

Front Plant Sci. 2013 Aug 29;4:325. doi: 10.3389/fpls.2013.00325. Review.


Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.

Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A.

Database (Oxford). 2013 Aug 27;2013:bat062. doi: 10.1093/database/bat062. Print 2013.


A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae.

Geistlinger L, Csaba G, Dirmeier S, Küffner R, Zimmer R.

Nucleic Acids Res. 2013 Oct;41(18):8452-63. doi: 10.1093/nar/gkt631. Epub 2013 Jul 19.


Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network.

Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR, Ribeiro PS, Weirauch MT, Hill DE, Hughes TR, Myers CL, Walhout AJ.

Mol Cell. 2013 Jul 11;51(1):116-27. doi: 10.1016/j.molcel.2013.05.018. Epub 2013 Jun 20.


Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11.

Ngondo-Mbongo RP, Myslinski E, Aster JC, Carbon P.

Nucleic Acids Res. 2013 Apr;41(7):4000-14. doi: 10.1093/nar/gkt088. Epub 2013 Feb 13.

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