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Models for transcript quantification from RNA-Seq. (2011)cite arxiv:1104.3889.Parametric Alignment of Drosophila Genomes., , , , and . PLoS Comput. Biol., (2006)Multiple-sequence functional annotation and the generalized hidden Markov phylogeny., , and . Bioinform., 20 (12): 1850-1860 (2004)Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures., , , , , , , , , and 36 other author(s). Nature, 450 (7167): 219--232 (November 2007)Reconstructing trees from subtree weights., and . Appl. Math. Lett., 17 (6): 615-621 (2004)Applications of generalized pair hidden Markov models to alignment and gene finding problems., , and . RECOMB, page 241-248. ACM, (2001)Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, , , , , , , , , and . Nat. Protocols, 7 (3): 562--578 (March 2012)TopHat: discovering splice junctions with RNA-Seq., , and . Bioinformatics, 25 (9): 1105--1111 (May 2009)Interpretable factor models of single-cell RNA-seq via variational autoencoders., , , and . Bioinform., 36 (11): 3418-3421 (2020)Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems., , and . J. Comput. Biol., 9 (2): 389-399 (2002)