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De novo assembly of bacterial transcriptomes from RNA-seq data.
Tjaden B. Tjaden B. Genome Biol. 2015 Jan 13;16(1):1. doi: 10.1186/s13059-014-0572-2. Genome Biol. 2015. PMID: 25583448 Free PMC article.
Computational identification of sRNA targets.
Tjaden B. Tjaden B. Methods Mol Biol. 2012;905:227-34. doi: 10.1007/978-1-61779-949-5_14. Methods Mol Biol. 2012. PMID: 22736007
Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response.
Gerrick ER, Barbier T, Chase MR, Xu R, Fran├žois J, Lin VH, Szucs MJ, Rock JM, Ahmad R, Tjaden B, Livny J, Fortune SM. Gerrick ER, et al. Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6464-6469. doi: 10.1073/pnas.1718003115. Epub 2018 Jun 5. Proc Natl Acad Sci U S A. 2018. PMID: 29871950 Free PMC article.
Computational analysis of bacterial RNA-Seq data.
McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B. McClure R, et al. Nucleic Acids Res. 2013 Aug;41(14):e140. doi: 10.1093/nar/gkt444. Epub 2013 May 28. Nucleic Acids Res. 2013. PMID: 23716638 Free PMC article.
TargetRNA2: identifying targets of small regulatory RNAs in bacteria.
Kery MB, Feldman M, Livny J, Tjaden B. Kery MB, et al. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W124-9. doi: 10.1093/nar/gku317. Epub 2014 Apr 21. Nucleic Acids Res. 2014. PMID: 24753424 Free PMC article.
TargetRNA: a tool for predicting targets of small RNA action in bacteria.
Tjaden B. Tjaden B. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W109-13. doi: 10.1093/nar/gkn264. Epub 2008 May 13. Nucleic Acids Res. 2008. PMID: 18477632 Free PMC article.
Prediction of small, noncoding RNAs in bacteria using heterogeneous data.
Tjaden B. Tjaden B. J Math Biol. 2008 Jan;56(1-2):183-200. doi: 10.1007/s00285-007-0079-5. Epub 2007 Mar 13. J Math Biol. 2008. PMID: 17354017
Target prediction for small, noncoding RNAs in bacteria.
Tjaden B, Goodwin SS, Opdyke JA, Guillier M, Fu DX, Gottesman S, Storz G. Tjaden B, et al. Nucleic Acids Res. 2006 May 22;34(9):2791-802. doi: 10.1093/nar/gkl356. Print 2006. Nucleic Acids Res. 2006. PMID: 16717284 Free PMC article.
An approach for clustering gene expression data with error information.
Tjaden B. Tjaden B. BMC Bioinformatics. 2006 Jan 12;7:17. doi: 10.1186/1471-2105-7-17. BMC Bioinformatics. 2006. PMID: 16409635 Free PMC article.
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