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Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent.
PLoS One. 2024 Mar 21;19(3):e0298834. doi: 10.1371/journal.pone.0298834. eCollection 2024.
PLoS One. 2024.
PMID: 38512939
Free PMC article.
Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes.
Prusokiene A, Prusokas A, Retkute R.
Prusokiene A, et al.
NAR Genom Bioinform. 2023 Aug 21;5(3):lqad077. doi: 10.1093/nargab/lqad077. eCollection 2023 Sep.
NAR Genom Bioinform. 2023.
PMID: 37608801
Free PMC article.
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Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees.
Gong W, Granados AA, Hu J, Jones MG, Raz O, Salvador-Martínez I, Zhang H, Chow KK, Kwak IY, Retkute R, Prusokiene A, Prusokas A, Khodaverdian A, Zhang R, Rao S, Wang R, Rennert P, Saipradeep VG, Sivadasan N, Rao A, Joseph T, Srinivasan R, Peng J, Han L, Shang X, Garry DJ, Yu T, Chung V, Mason M, Liu Z, Guan Y, Yosef N, Shendure J, Telford MJ, Shapiro E, Elowitz MB, Meyer P.
Gong W, et al. Among authors: prusokiene a.
Cell Syst. 2021 Aug 18;12(8):810-826.e4. doi: 10.1016/j.cels.2021.05.008. Epub 2021 Jun 18.
Cell Syst. 2021.
PMID: 34146472
Free article.
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