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Page 1
Metadata retrieval from sequence databases with ffq.
Gálvez-Merchán Á, Min KHJ, Pachter L, Booeshaghi AS. Gálvez-Merchán Á, et al. Among authors: min khj. Bioinformatics. 2023 Jan 1;39(1):btac667. doi: 10.1093/bioinformatics/btac667. Bioinformatics. 2023. PMID: 36610997 Free PMC article.
Modular, efficient and constant-memory single-cell RNA-seq preprocessing.
Melsted P, Booeshaghi AS, Liu L, Gao F, Lu L, Min KHJ, da Veiga Beltrame E, Hjörleifsson KE, Gehring J, Pachter L. Melsted P, et al. Among authors: min khj. Nat Biotechnol. 2021 Jul;39(7):813-818. doi: 10.1038/s41587-021-00870-2. Epub 2021 Apr 1. Nat Biotechnol. 2021. PMID: 33795888
kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.
Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. Sullivan DK, et al. Among authors: min khj. bioRxiv [Preprint]. 2024 Jan 23:2023.11.21.568164. doi: 10.1101/2023.11.21.568164. bioRxiv. 2024. Update in: Nat Protoc. 2024 Oct 10. doi: 10.1038/s41596-024-01057-0 PMID: 38045414 Free PMC article. Updated. Preprint.
Quantifying orthogonal barcodes for sequence census assays.
Booeshaghi AS, Min KHJ, Gehring J, Pachter L. Booeshaghi AS, et al. Among authors: min khj. Bioinform Adv. 2023 Dec 20;4(1):vbad181. doi: 10.1093/bioadv/vbad181. eCollection 2024. Bioinform Adv. 2023. PMID: 38213823 Free PMC article.
Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.
Yang D, Jones MG, Naranjo S, Rideout WM 3rd, Min KHJ, Ho R, Wu W, Replogle JM, Page JL, Quinn JJ, Horns F, Qiu X, Chen MZ, Freed-Pastor WA, McGinnis CS, Patterson DM, Gartner ZJ, Chow ED, Bivona TG, Chan MM, Yosef N, Jacks T, Weissman JS. Yang D, et al. Among authors: min khj. Cell. 2022 May 26;185(11):1905-1923.e25. doi: 10.1016/j.cell.2022.04.015. Epub 2022 May 5. Cell. 2022. PMID: 35523183 Free PMC article.
Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis.
Jones MG, Sun D, Min KHJ, Colgan WN, Tian L, Weir JA, Chen VZ, Koblan LW, Yost KE, Mathey-Andrews N, Russell AJC, Stickels RR, Balderrama KS, Rideout WM 3rd, Chang HY, Jacks T, Chen F, Weissman JS, Yosef N, Yang D. Jones MG, et al. Among authors: min khj. bioRxiv [Preprint]. 2024 Oct 24:2024.10.21.619529. doi: 10.1101/2024.10.21.619529. bioRxiv. 2024. PMID: 39484491 Free PMC article. Preprint.