Bussemaker HJ - Search Results

1

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.

Jansen R, Bussemaker HJ, Gerstein M. Jansen R, et al. Among authors: bussemaker hj. Nucleic Acids Res. 2003 Apr 15;31(8):2242-51. doi: 10.1093/nar/gkg306. Nucleic Acids Res. 2003. PMID: 12682375 Free PMC article.

2

REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data.

Roven C, Bussemaker HJ. Roven C, et al. Among authors: bussemaker hj. Nucleic Acids Res. 2003 Jul 1;31(13):3487-90. doi: 10.1093/nar/gkg630. Nucleic Acids Res. 2003. PMID: 12824350 Free PMC article.

3

A gene expression map for the euchromatic genome of Drosophila melanogaster.

Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP. Stolc V, et al. Among authors: bussemaker hj. Science. 2004 Oct 22;306(5696):655-60. doi: 10.1126/science.1101312. Science. 2004. PMID: 15499012

4

T-profiler: scoring the activity of predefined groups of genes using gene expression data.

Boorsma A, Foat BC, Vis D, Klis F, Bussemaker HJ. Boorsma A, et al. Among authors: bussemaker hj. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W592-5. doi: 10.1093/nar/gki484. Nucleic Acids Res. 2005. PMID: 15980543 Free PMC article.

5

Dissecting complex transcriptional responses using pathway-level scores based on prior information.

Bussemaker HJ, Ward LD, Boorsma A. Bussemaker HJ, et al. BMC Bioinformatics. 2007 Sep 27;8 Suppl 6(Suppl 6):S6. doi: 10.1186/1471-2105-8-S6-S6. BMC Bioinformatics. 2007. PMID: 17903287 Free PMC article. Review.

6

TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors.

Foat BC, Tepper RG, Bussemaker HJ. Foat BC, et al. Among authors: bussemaker hj. Nucleic Acids Res. 2008 Jan;36(Database issue):D125-31. doi: 10.1093/nar/gkm828. Epub 2007 Oct 18. Nucleic Acids Res. 2008. PMID: 17947326 Free PMC article.

7

Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis.

Bussemaker HJ, Li H, Siggia ED. Bussemaker HJ, et al. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10096-100. doi: 10.1073/pnas.180265397. Proc Natl Acad Sci U S A. 2000. PMID: 10944202 Free PMC article.

8

Dissection of transient oxidative stress response in Saccharomyces cerevisiae by using DNA microarrays.

Koerkamp MG, Rep M, Bussemaker HJ, Hardy GP, Mul A, Piekarska K, Szigyarto CA, De Mattos JM, Tabak HF. Koerkamp MG, et al. Among authors: bussemaker hj. Mol Biol Cell. 2002 Aug;13(8):2783-94. doi: 10.1091/mbc.e02-02-0075. Mol Biol Cell. 2002. PMID: 12181346 Free PMC article.

9

The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes.

Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AH. Versteeg R, et al. Among authors: bussemaker hj. Genome Res. 2003 Sep;13(9):1998-2004. doi: 10.1101/gr.1649303. Epub 2003 Aug 12. Genome Res. 2003. PMID: 12915492 Free PMC article.

10

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ. Gao F, et al. Among authors: bussemaker hj. BMC Bioinformatics. 2004 Mar 18;5:31. doi: 10.1186/1471-2105-5-31. BMC Bioinformatics. 2004. PMID: 15113405 Free PMC article.

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