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Computational Detection of Stage-Specific Transcription Factor Clusters during Heart Development.

Zeidler S, Meckbach C, Tacke R, Raad FS, Roa A, Uchida S, Zimmermann WH, Wingender E, Gültas M.

Front Genet. 2016 Mar 23;7:33. doi: 10.3389/fgene.2016.00033.


PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information.

Meckbach C, Tacke R, Hua X, Waack S, Wingender E, Gültas M.

BMC Bioinformatics. 2015 Dec 1;16:400. doi: 10.1186/s12859-015-0827-2.


MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters.

Deyneko IV, Kel AE, Kel-Margoulis OV, Deineko EV, Wingender E, Weiss S.

BMC Bioinformatics. 2013 Aug 8;14:241. doi: 10.1186/1471-2105-14-241.


TFClass: an expandable hierarchical classification of human transcription factors.

Wingender E, Schoeps T, Dönitz J.

Nucleic Acids Res. 2013 Jan;41(Database issue):D165-70. doi: 10.1093/nar/gks1123.


CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

Nikulova AA, Favorov AV, Sutormin RA, Makeev VJ, Mironov AA.

Nucleic Acids Res. 2012 Jul;40(12):e93. doi: 10.1093/nar/gks235.


The porcine circovirus type 1 capsid gene promoter improves antigen expression and immunogenicity in a HIV-1 plasmid vaccine.

Tanzer FL, Shephard EG, Palmer KE, Burger M, Williamson AL, Rybicki EP.

Virol J. 2011 Feb 7;8:51. doi: 10.1186/1743-422X-8-51.


Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems.

Dabrowski M, Dojer N, Zawadzka M, Mieczkowski J, Kaminska B.

BMC Syst Biol. 2010 Jun 17;4:86. doi: 10.1186/1752-0509-4-86.


Functional NPY variation as a factor in stress resilience and alcohol consumption in rhesus macaques.

Lindell SG, Schwandt ML, Sun H, Sparenborg JD, Björk K, Kasckow JW, Sommer WH, Goldman D, Higley JD, Suomi SJ, Heilig M, Barr CS.

Arch Gen Psychiatry. 2010 Apr;67(4):423-31. doi: 10.1001/archgenpsychiatry.2010.23.


Short Promoters in Viral Vectors Drive Selective Expression in Mammalian Inhibitory Neurons, but do not Restrict Activity to Specific Inhibitory Cell-Types.

Nathanson JL, Jappelli R, Scheeff ED, Manning G, Obata K, Brenner S, Callaway EM.

Front Neural Circuits. 2009 Nov 9;3:19. doi: 10.3389/neuro.04.019.2009.


D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.

Sen N, Mishra M, Khan F, Meena A, Sharma A.

Bioinformation. 2009 Jul 27;3(10):415-8.


Strategies for performing genotype-phenotype association studies in nonhuman primates.

Barr CS.

Methods. 2009 Sep;49(1):56-62. doi: 10.1016/j.ymeth.2009.05.014. Review.


Network integration and graph analysis in mammalian molecular systems biology.

Ma'ayan A.

IET Syst Biol. 2008 Sep;2(5):206-21. doi: 10.1049/iet-syb:20070075. Review.


CRH haplotype as a factor influencing cerebrospinal fluid levels of corticotropin-releasing hormone, hypothalamic-pituitary-adrenal axis activity, temperament, and alcohol consumption in rhesus macaques.

Barr CS, Dvoskin RL, Yuan Q, Lipsky RH, Gupte M, Hu X, Zhou Z, Schwandt ML, Lindell SG, McKee M, Becker ML, Kling MA, Gold PW, Higley D, Heilig M, Suomi SJ, Goldman D.

Arch Gen Psychiatry. 2008 Aug;65(8):934-44. doi: 10.1001/archpsyc.65.8.934.


Recent computational approaches to understand gene regulation: mining gene regulation in silico.

Abnizova I, Subhankulova T, Gilks W.

Curr Genomics. 2007 Apr;8(2):79-91.


TRANSPATH--a high quality database focused on signal transduction.

Choi C, Krull M, Kel A, Kel-Margoulis O, Pistor S, Potapov A, Voss N, Wingender E.

Comp Funct Genomics. 2004;5(2):163-8. doi: 10.1002/cfg.386.


MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs.

Hu J, Hu H, Li X.

Nucleic Acids Res. 2008 Aug;36(13):4488-97. doi: 10.1093/nar/gkn407.


Probabilistic inference of transcription factor binding from multiple data sources.

Lähdesmäki H, Rust AG, Shmulevich I.

PLoS One. 2008 Mar 26;3(3):e1820. doi: 10.1371/journal.pone.0001820.


Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions.

Murakami K, Imanishi T, Gojobori T, Nakai K.

BMC Genomics. 2008 Mar 1;9:112. doi: 10.1186/1471-2164-9-112.


Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context.

Kel AE, Niehof M, Matys V, Zemlin R, Borlak J.

Genome Biol. 2008;9(2):R36. doi: 10.1186/gb-2008-9-2-r36.

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