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BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences.
Bao E, Jiang T, Girke T. Bao E, et al. Among authors: girke t. Bioinformatics. 2013 May 15;29(10):1250-9. doi: 10.1093/bioinformatics/btt127. Epub 2013 Mar 14. Bioinformatics. 2013. PMID: 23493323
Genome cluster database. A sequence family analysis platform for Arabidopsis and rice.
Horan K, Lauricha J, Bailey-Serres J, Raikhel N, Girke T. Horan K, et al. Among authors: girke t. Plant Physiol. 2005 May;138(1):47-54. doi: 10.1104/pp.104.059048. Plant Physiol. 2005. PMID: 15888677 Free PMC article.
ChemMine. A compound mining database for chemical genomics.
Girke T, Cheng LC, Raikhel N. Girke T, et al. Plant Physiol. 2005 Jun;138(2):573-7. doi: 10.1104/pp.105.062687. Plant Physiol. 2005. PMID: 15955920 Free PMC article. No abstract available.
Annotating genes of known and unknown function by large-scale coexpression analysis.
Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JC, Gollery M, Girke T. Horan K, et al. Among authors: girke t. Plant Physiol. 2008 May;147(1):41-57. doi: 10.1104/pp.108.117366. Epub 2008 Mar 19. Plant Physiol. 2008. PMID: 18354039 Free PMC article.
A maximum common substructure-based algorithm for searching and predicting drug-like compounds.
Cao Y, Jiang T, Girke T. Cao Y, et al. Among authors: girke t. Bioinformatics. 2008 Jul 1;24(13):i366-74. doi: 10.1093/bioinformatics/btn186. Bioinformatics. 2008. PMID: 18586736 Free PMC article.
ChemmineR: a compound mining framework for R.
Cao Y, Charisi A, Cheng LC, Jiang T, Girke T. Cao Y, et al. Among authors: girke t. Bioinformatics. 2008 Aug 1;24(15):1733-4. doi: 10.1093/bioinformatics/btn307. Epub 2008 Jul 2. Bioinformatics. 2008. PMID: 18596077 Free PMC article.
Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing.
Cao Y, Jiang T, Girke T. Cao Y, et al. Among authors: girke t. Bioinformatics. 2010 Apr 1;26(7):953-9. doi: 10.1093/bioinformatics/btq067. Epub 2010 Feb 23. Bioinformatics. 2010. PMID: 20179075 Free PMC article.
Predicting conserved protein motifs with Sub-HMMs.
Horan K, Shelton CR, Girke T. Horan K, et al. Among authors: girke t. BMC Bioinformatics. 2010 Apr 26;11:205. doi: 10.1186/1471-2105-11-205. BMC Bioinformatics. 2010. PMID: 20420695 Free PMC article.
Single feature polymorphism detection using recombinant inbred line microarray expression data.
Cui X, You N, Girke T, Michelmore R, Van Deynze A. Cui X, et al. Among authors: girke t. Bioinformatics. 2010 Aug 15;26(16):1983-9. doi: 10.1093/bioinformatics/btq316. Epub 2010 Jun 23. Bioinformatics. 2010. PMID: 20576626
ChemMine tools: an online service for analyzing and clustering small molecules.
Backman TW, Cao Y, Girke T. Backman TW, et al. Among authors: girke t. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W486-91. doi: 10.1093/nar/gkr320. Epub 2011 May 16. Nucleic Acids Res. 2011. PMID: 21576229 Free PMC article.
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