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Annotation of the Protein Coding Regions of the Equine Genome.
Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN. Hestand MS, et al. Among authors: liu j. PLoS One. 2015 Jun 24;10(6):e0124375. doi: 10.1371/journal.pone.0124375. eCollection 2015. PLoS One. 2015. PMID: 26107351 Free PMC article.
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. Wang K, et al. Among authors: liu j. Nucleic Acids Res. 2010 Oct;38(18):e178. doi: 10.1093/nar/gkq622. Epub 2010 Aug 27. Nucleic Acids Res. 2010. PMID: 20802226 Free PMC article.
A robust method for transcript quantification with RNA-seq data.
Huang Y, Hu Y, Jones CD, MacLeod JN, Chiang DY, Liu Y, Prins JF, Liu J. Huang Y, et al. Among authors: liu j, liu y. J Comput Biol. 2013 Mar;20(3):167-87. doi: 10.1089/cmb.2012.0230. J Comput Biol. 2013. PMID: 23461570 Free PMC article.
Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.
Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML, Jaromczyk JW, Roe BA, O'Sullivan DM, Scott B, Tudzynski P, An Z, Arnaoudova EG, Bullock CT, Charlton ND, Chen L, Cox M, Dinkins RD, Florea S, Glenn AE, Gordon A, Güldener U, Harris DR, Hollin W, Jaromczyk J, Johnson RD, Khan AK, Leistner E, Leuchtmann A, Li C, Liu J, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach JE, Tanaka E, Webb JS, Wilson EV, Wiseman JL, Yoshida R, Zeng Z. Schardl CL, et al. Among authors: liu j, liu m. PLoS Genet. 2013;9(2):e1003323. doi: 10.1371/journal.pgen.1003323. Epub 2013 Feb 28. PLoS Genet. 2013. PMID: 23468653 Free PMC article.
A probabilistic framework for aligning paired-end RNA-seq data.
Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu J. Hu Y, et al. Among authors: liu j. Bioinformatics. 2010 Aug 15;26(16):1950-7. doi: 10.1093/bioinformatics/btq336. Epub 2010 Jun 23. Bioinformatics. 2010. PMID: 20576625 Free PMC article.
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J. Hu Y, et al. Among authors: liu j, liu y. Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15. Nucleic Acids Res. 2013. PMID: 23155066 Free PMC article.
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