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The Mathematics of Phylogenomics., and . SIAM Rev., 49 (1): 3-31 (2007)Efficient querying of genomic reference databases with gget., and . Bioinform., (January 2023)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)Constructing Status Injective Graphs.. Discret. Appl. Math., 80 (1): 107-113 (1997)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)Near-optimal RNA-Seq quantification., , , and . CoRR, (2015)Interpretable factor models of single-cell RNA-seq via variational autoencoders., , , and . Bioinform., 36 (11): 3418-3421 (2020)Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x)., and . Bioinform., 37 (15): 2223-2224 (2021)