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Items: 20

1.

Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube.

Balaskas N, Ribeiro A, Panovska J, Dessaud E, Sasai N, Page KM, Briscoe J, Ribes V.

Cell. 2012 Jan 20;148(1-2):273-84. doi: 10.1016/j.cell.2011.10.047.

2.

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters.

Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, Keren L, Yakhini Z, Weinberger A, Segal E.

Nat Biotechnol. 2012 May 20;30(6):521-30. doi: 10.1038/nbt.2205.

3.

Gene regulatory logic of dopamine neuron differentiation.

Flames N, Hobert O.

Nature. 2009 Apr 16;458(7240):885-9. doi: 10.1038/nature07929. Epub 2009 Mar 15.

4.

Logic and extent of miRNA-mediated control of autoimmune gene expression.

Vinuesa CG, Rigby RJ, Yu D.

Int Rev Immunol. 2009;28(3-4):112-38. doi: 10.1080/08830180902934909. Review.

PMID:
19811318
5.

Gene expression biomarkers in the brain of a mouse model for Alzheimer's disease: mining of microarray data by logic classification and feature selection.

Arisi I, D'Onofrio M, Brandi R, Felsani A, Capsoni S, Drovandi G, Felici G, Weitschek E, Bertolazzi P, Cattaneo A.

J Alzheimers Dis. 2011;24(4):721-38. doi: 10.3233/JAD-2011-101881.

PMID:
21321390
6.

Fundamentally different logic of gene regulation in eukaryotes and prokaryotes.

Struhl K.

Cell. 1999 Jul 9;98(1):1-4. Review. No abstract available.

7.

Gene regulation logic in retinal ganglion cell development: Isl1 defines a critical branch distinct from but overlapping with Pou4f2.

Mu X, Fu X, Beremand PD, Thomas TL, Klein WH.

Proc Natl Acad Sci U S A. 2008 May 13;105(19):6942-7. doi: 10.1073/pnas.0802627105. Epub 2008 May 6.

8.

Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene.

Yuh CH, Bolouri H, Davidson EH.

Science. 1998 Mar 20;279(5358):1896-902.

9.

Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach.

Sternberg MJ, Tamaddoni-Nezhad A, Lesk VI, Kay E, Hitchen PG, Cootes A, van Alphen LB, Lamoureux MP, Jarrell HC, Rawlings CJ, Soo EC, Szymanski CM, Dell A, Wren BW, Muggleton SH.

J Mol Biol. 2013 Jan 9;425(1):186-97. doi: 10.1016/j.jmb.2012.10.014. Epub 2012 Oct 24.

10.

The gene regulatory logic of transcription factor evolution.

Wagner GP, Lynch VJ.

Trends Ecol Evol. 2008 Jul;23(7):377-85. doi: 10.1016/j.tree.2008.03.006. Epub 2008 May 22. Review.

PMID:
18501470
11.

Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states.

Crespo I, Krishna A, Le Béchec A, del Sol A.

Nucleic Acids Res. 2013 Jan 7;41(1):e8. doi: 10.1093/nar/gks785. Epub 2012 Aug 31.

12.

The influence of assortativity on the robustness of signal-integration logic in gene regulatory networks.

Pechenick DA, Payne JL, Moore JH.

J Theor Biol. 2012 Mar 7;296:21-32. doi: 10.1016/j.jtbi.2011.11.029. Epub 2011 Dec 8.

13.

Stochastic modeling of the relationship between copy number and gene expression based on transcriptional logic.

Hsu FH, Serpedin E, Chen Y, Dougherty ER.

IEEE Trans Biomed Eng. 2012 Jan;59(1):272-80. doi: 10.1109/TBME.2011.2173341. Epub 2011 Oct 24.

PMID:
22042124
14.

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.

Mørk S, Holmes I.

Bioinformatics. 2012 Mar 1;28(5):636-42. doi: 10.1093/bioinformatics/btr698. Epub 2012 Jan 3.

15.

Logic regression analysis of association of gene polymorphisms with low HDL: Tehran Lipid and Glucose Study.

Sarbakhsh P, Mehrabi Y, Daneshpour MS, Zayeri F, Zarkesh M.

Gene. 2013 Jan 25;513(2):278-81. doi: 10.1016/j.gene.2012.10.084. Epub 2012 Nov 10.

PMID:
23147266
16.

Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.

Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M.

BMC Syst Biol. 2009 Dec 14;3:115. doi: 10.1186/1752-0509-3-115.

17.

Plasticity of the mitoproteome to nitrogen sources (nitrate and ammonium) in Chlamydomonas reinhardtii: the logic of Aox1 gene localization.

Gérin S, Mathy G, Blomme A, Franck F, Sluse FE.

Biochim Biophys Acta. 2010 Jun-Jul;1797(6-7):994-1003. doi: 10.1016/j.bbabio.2010.02.034. Epub 2010 Mar 6.

18.

Pursuing gene regulation 'logic' via RNA interference and chromatin immunoprecipitation.

Li CC, Ramirez-Carrozzi VR, Smale ST.

Nat Immunol. 2006 Jul;7(7):692-7.

PMID:
16785883
19.
20.

Logic of gene regulatory networks.

Materna SC, Davidson EH.

Curr Opin Biotechnol. 2007 Aug;18(4):351-4. Epub 2007 Aug 6. Review.

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