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scDOT: optimal transport for mapping senescent cells in spatial transcriptomics.
Nguyen ND, Rosas L, Khaliullin T, Jiang P, Hasanaj E, Ovando-Ricardez JA, Bueno M, Rahman I, Pryhuber GS, Li D, Ma Q, Finkel T, Königshoff M, Eickelberg O, Rojas M, Mora AL, Lugo-Martinez J, Bar-Joseph Z. Nguyen ND, et al. Among authors: lugo martinez j. Genome Biol. 2024 Nov 8;25(1):288. doi: 10.1186/s13059-024-03426-0. Genome Biol. 2024. PMID: 39516853 Free PMC article.
Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A.
Jain S, Trinidad M, Nguyen TB, Jones K, Neto SD, Ge F, Glagovsky A, Jones C, Moran G, Wang B, Rahimi K, Çalıcı SZ, Cedillo LR, Berardelli S, Özden B, Chen K, Katsonis P, Williams A, Lichtarge O, Rana S, Pradhan S, Srinivasan R, Sajeed R, Joshi D, Faraggi E, Jernigan R, Kloczkowski A, Xu J, Song Z, Özkan S, Padilla N, de la Cruz X, Acuna-Hidalgo R, Grafmüller A, Jiménez Barrón LT, Manfredi M, Savojardo C, Babbi G, Martelli PL, Casadio R, Sun Y, Zhu S, Shen Y, Pucci F, Rooman M, Cia G, Raimondi D, Hermans P, Kwee S, Chen E, Astore C, Kamandula A, Pejaver V, Ramola R, Velyunskiy M, Zeiberg D, Mishra R, Sterling T, Goldstein JL, Lugo-Martinez J, Kazi S, Li S, Long K, Brenner SE, Bakolitsa C, Radivojac P, Suhr D, Suhr T, Clark WT. Jain S, et al. Among authors: lugo martinez j. bioRxiv [Preprint]. 2024 Jun 17:2024.05.16.594558. doi: 10.1101/2024.05.16.594558. bioRxiv. 2024. PMID: 38798479 Free PMC article. Preprint.
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics.
Chen H, Lee YJ, Ovando JA, Rosas L, Rojas M, Mora AL, Bar-Joseph Z, Lugo-Martinez J. Chen H, et al. Among authors: lugo martinez j. bioRxiv [Preprint]. 2023 Dec 19:2023.12.18.572269. doi: 10.1101/2023.12.18.572269. bioRxiv. 2023. Update in: Cell Rep Methods. 2024 Oct 21;4(10):100864. doi: 10.1016/j.crmeth.2024.100864. PMID: 38187629 Free PMC article. Updated. Preprint.
Inferring the molecular and phenotypic impact of amino acid variants with MutPred2.
Pejaver V, Urresti J, Lugo-Martinez J, Pagel KA, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. Pejaver V, et al. Among authors: lugo martinez j. Nat Commun. 2020 Nov 20;11(1):5918. doi: 10.1038/s41467-020-19669-x. Nat Commun. 2020. PMID: 33219223 Free PMC article.
17 results