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Merge pull request #119 from mcphersonlab/copilot/add-genomics-inspirations
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‎inspirations/Baele_NatMethods_2025/index.qmd‎

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title: "BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference"
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author:
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- Baele
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- Ji
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- Hassler
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- et al.
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publication: "Nat Methods, **22**, 1653–1656 (2025)"
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categories:
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- external-publication
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- genomics
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url_source: https://doi.org/10.1038/s41592-025-02751-x
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url_preprint:
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journ: "Nat Methods"
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issue: 22
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page: 1653–1656
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year: 2025
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image: ""
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pub_number:
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doi: 10.1038/s41592-025-02751-x
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‎inspirations/Dellicour_NatCommun_2020/index.qmd‎

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title: "Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework"
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author:
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- Dellicour
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- Lequime
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- Vrancken
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- et al.
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publication: "Nat Commun, **11**, 5620 (2020)"
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categories:
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- external-publication
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- genomics
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url_source: https://doi.org/10.1038/s41467-020-19122-z
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url_preprint:
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journ: "Nat Commun"
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issue: 11
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page: 5620
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year: 2020
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image: ""
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pub_number:
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doi: 10.1038/s41467-020-19122-z
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‎inspirations/Ianiro_NatMed_2022/index.qmd‎

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title: "Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases"
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author:
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- Ianiro
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- Punčochář
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- Karcher
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- et al.
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publication: "Nat Med, **28**, 1913–1923 (2022)"
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categories:
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- external-publication
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- genomics
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- human-gut-microbiome
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url_source: https://doi.org/10.1038/s41591-022-01964-3
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url_preprint:
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journ: "Nat Med"
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issue: 28
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page: 1913–1923
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year: 2022
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image: ""
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pub_number:
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doi: 10.1038/s41591-022-01964-3
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‎inspirations/Lefrancq_Nature_2025/index.qmd‎

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title: "Learning the fitness dynamics of pathogens from phylogenies"
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author:
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- Lefrancq
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- Duret
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- Bouchez
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- et al.
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publication: "Nature, **637**, 683–690 (2025)"
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categories:
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- external-publication
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- genomics
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url_source: https://doi.org/10.1038/s41586-024-08309-9
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url_preprint:
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journ: "Nature"
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issue: 637
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page: 683–690
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year: 2025
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image: ""
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pub_number:
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doi: 10.1038/s41586-024-08309-9
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‎inspirations/Liu_NatRevMethodsPrimers_2025/index.qmd‎

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title: "Analysis of metagenomic data"
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author:
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- Liu
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- Rodriguez
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- Munteanu
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- et al.
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publication: "Nat Rev Methods Primers, **5**, 5 (2025)"
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categories:
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- external-publication
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- genomics
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- human-gut-microbiome
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url_source: https://doi.org/10.1038/s43586-024-00376-6
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url_preprint:
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journ: "Nat Rev Methods Primers"
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issue: 5
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page: 5
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year: 2025
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image: ""
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pub_number:
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doi: 10.1038/s43586-024-00376-6
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‎inspirations/Schluter_CellHostMicrobe_2023/index.qmd‎

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title: "The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia"
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author:
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- Schluter
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- Djukovic
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- Taylor
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- et al.
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publication: "Cell Host Microbe, **31**, 1126–1139 (2023)"
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categories:
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- external-publication
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- genomics
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- human-gut-microbiome
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url_source: https://doi.org/10.1016/j.chom.2023.05.027
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url_preprint:
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journ: "Cell Host Microbe"
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issue: 31
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page: 1126–1139
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year: 2023
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image: ""
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pub_number:
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doi: 10.1016/j.chom.2023.05.027
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‎inspirations/Scholz_NatMethods_2016/index.qmd‎

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title: "Strain-level microbial epidemiology and population genomics from shotgun metagenomics"
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author:
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- Scholz
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- Ward
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- Pasolli
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- et al.
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publication: "Nat Methods, **13**, 435–438 (2016)"
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categories:
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- external-publication
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- genomics
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- human-gut-microbiome
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url_source: https://doi.org/10.1038/nmeth.3802
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url_preprint:
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journ: "Nat Methods"
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issue: 13
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page: 435–438
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year: 2016
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image: ""
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pub_number:
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doi: 10.1038/nmeth.3802
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‎inspirations/Tran-Kiem_Nature_2025/index.qmd‎

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title: "Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences"
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author:
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- Tran-Kiem
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- Paredes
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- Perofsky
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- et al.
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publication: "Nature, **640**, 176–185 (2025)"
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categories:
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- external-publication
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- genomics
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url_source: https://doi.org/10.1038/s41586-025-08637-4
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url_preprint:
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journ: "Nature"
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issue: 640
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page: 176–185
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year: 2025
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image: ""
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pub_number:
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doi: 10.1038/s41586-025-08637-4
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‎inspirations/Wirbel_Nature_2025/index.qmd‎

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title: "Long-read metagenomics reveals phage dynamics in the human gut microbiome"
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author:
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- Wirbel
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- Hickey
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- Chang
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- et al.
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publication: "Nature (2025)"
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categories:
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- external-publication
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- genomics
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- human-gut-microbiome
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url_source: https://doi.org/10.1038/s41586-025-09786-2
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url_preprint:
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journ: "Nature"
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issue:
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page:
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year: 2025
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image: ""
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pub_number:
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doi: 10.1038/s41586-025-09786-2
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‎inspirations/Xu_NatProtoc_2024/index.qmd‎

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title: "Using clusterProfiler to characterize multiomics data"
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author:
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- Xu
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- Hu
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- Cai
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- et al.
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publication: "Nat Protoc, **19**, 3292–3320 (2024)"
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categories:
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- external-publication
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- genomics
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- human-gut-microbiome
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url_source: https://doi.org/10.1038/s41596-024-01020-z
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url_preprint:
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journ: "Nat Protoc"
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issue: 19
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page: 3292–3320
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year: 2024
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image: ""
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pub_number:
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doi: 10.1038/s41596-024-01020-z
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---

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