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Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach.
Scherf M, Klingenhoff A, Werner T. Scherf M, et al. Among authors: klingenhoff a. J Mol Biol. 2000 Mar 31;297(3):599-606. doi: 10.1006/jmbi.2000.3589. J Mol Biol. 2000. PMID: 10731414
We present a new algorithm called PromoterInspector to locate eukaryotic polymase II promoter regions in large genomic sequences with a high degree of specificity. ...Application of PromoterInspector can serve as a crucial pre-processing step for other method …
We present a new algorithm called PromoterInspector to locate eukaryotic polymase II promoter regions in large genomic sequences with …
MatInspector and beyond: promoter analysis based on transcription factor binding sites.
Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T. Cartharius K, et al. Among authors: klingenhoff a. Bioinformatics. 2005 Jul 1;21(13):2933-42. doi: 10.1093/bioinformatics/bti473. Epub 2005 Apr 28. Bioinformatics. 2005. PMID: 15860560
Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach.
Klingenhoff A, Frech K, Werner T. Klingenhoff A, et al. In Silico Biol. 2002;2(1):S17-26. In Silico Biol. 2002. PMID: 11808874
First pass annotation of promoters on human chromosome 22.
Scherf M, Klingenhoff A, Frech K, Quandt K, Schneider R, Grote K, Frisch M, Gailus-Durner V, Seidel A, Brack-Werner R, Werner T. Scherf M, et al. Among authors: klingenhoff a. Genome Res. 2001 Mar;11(3):333-40. doi: 10.1101/gr.154601. Genome Res. 2001. PMID: 11230158 Free PMC article.
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity.
Klingenhoff A, Frech K, Quandt K, Werner T. Klingenhoff A, et al. Bioinformatics. 1999 Mar;15(3):180-6. doi: 10.1093/bioinformatics/15.3.180. Bioinformatics. 1999. PMID: 10222404
RESULTS: We developed a new method (FastM) which combines a search algorithm for individual transcription factor binding sites (MatInspector) with a distance correlation function. FastM allows fast definition of a model of correlated binding sites deri …
RESULTS: We developed a new method (FastM) which combines a search algorithm for individual transcription factor binding sites …
Linking disease-associated genes to regulatory networks via promoter organization.
Döhr S, Klingenhoff A, Maier H, Hrabé de Angelis M, Werner T, Schneider R. Döhr S, et al. Among authors: klingenhoff a. Nucleic Acids Res. 2005 Feb 8;33(3):864-72. doi: 10.1093/nar/gki230. Print 2005. Nucleic Acids Res. 2005. PMID: 15701758 Free PMC article.
In silico prediction of scaffold/matrix attachment regions in large genomic sequences.
Frisch M, Frech K, Klingenhoff A, Cartharius K, Liebich I, Werner T. Frisch M, et al. Among authors: klingenhoff a. Genome Res. 2002 Feb;12(2):349-54. doi: 10.1101/gr.206602. Genome Res. 2002. PMID: 11827955 Free PMC article.
Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.
Hestand MS, Klingenhoff A, Scherf M, Ariyurek Y, Ramos Y, van Workum W, Suzuki M, Werner T, van Ommen GJ, den Dunnen JT, Harbers M, 't Hoen PA. Hestand MS, et al. Among authors: klingenhoff a. Nucleic Acids Res. 2010 Sep;38(16):e165. doi: 10.1093/nar/gkq602. Epub 2010 Jul 7. Nucleic Acids Res. 2010. PMID: 20615900 Free PMC article.
Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins.
Cohen CD, Klingenhoff A, Boucherot A, Nitsche A, Henger A, Brunner B, Schmid H, Merkle M, Saleem MA, Koller KP, Werner T, Gröne HJ, Nelson PJ, Kretzler M. Cohen CD, et al. Among authors: klingenhoff a. Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5682-7. doi: 10.1073/pnas.0511257103. Epub 2006 Mar 31. Proc Natl Acad Sci U S A. 2006. PMID: 16581909 Free PMC article.
Stat3 is involved in control of MASP2 gene expression.
Unterberger C, Hanson S, Klingenhoff A, Oesterle D, Frankenberger M, Endo Y, Matsushita M, Fujita T, Schwaeble W, Weiss EH, Ziegler-Heitbrock L, Stover C. Unterberger C, et al. Among authors: klingenhoff a. Biochem Biophys Res Commun. 2007 Dec 28;364(4):1022-5. doi: 10.1016/j.bbrc.2007.10.114. Epub 2007 Oct 29. Biochem Biophys Res Commun. 2007. PMID: 17971300
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