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nhmmer: DNA homology search with profile HMMs.
Wheeler TJ, Eddy SR. Wheeler TJ, et al. Bioinformatics. 2013 Oct 1;29(19):2487-9. doi: 10.1093/bioinformatics/btt403. Epub 2013 Jul 9. Bioinformatics. 2013. PMID: 23842809 Free PMC article.
Multiple alignment by aligning alignments.
Wheeler TJ, Kececioglu JD. Wheeler TJ, et al. Bioinformatics. 2007 Jul 1;23(13):i559-68. doi: 10.1093/bioinformatics/btm226. Bioinformatics. 2007. PMID: 17646343
The Dfam database of repetitive DNA families.
Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ. Hubley R, et al. Among authors: wheeler tj. Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9. doi: 10.1093/nar/gkv1272. Epub 2015 Nov 26. Nucleic Acids Res. 2016. PMID: 26612867 Free PMC article.
HMMER web server: 2015 update.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR. Finn RD, et al. Among authors: wheeler tj. Nucleic Acids Res. 2015 Jul 1;43(W1):W30-8. doi: 10.1093/nar/gkv397. Epub 2015 May 5. Nucleic Acids Res. 2015. PMID: 25943547 Free PMC article.
Evaluating and improving cDNA sequence quality with cQC.
Hayden CA, Wheeler TJ, Jorgensen RA. Hayden CA, et al. Among authors: wheeler tj. Bioinformatics. 2005 Dec 15;21(24):4414-5. doi: 10.1093/bioinformatics/bti709. Epub 2005 Oct 18. Bioinformatics. 2005. PMID: 16234324
Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections.
Secor PR, Burgener EB, Kinnersley M, Jennings LK, Roman-Cruz V, Popescu M, Van Belleghem JD, Haddock N, Copeland C, Michaels LA, de Vries CR, Chen Q, Pourtois J, Wheeler TJ, Milla CE, Bollyky PL. Secor PR, et al. Among authors: wheeler tj. Front Immunol. 2020 Feb 21;11:244. doi: 10.3389/fimmu.2020.00244. eCollection 2020. Front Immunol. 2020. PMID: 32153575 Free PMC article. Review.
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