Genomics 🧬

Inspirational Works

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference

Baele, Ji, Hassler, et al.

Nat Methods, 22, 1653–1656 (2025)

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Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

Dellicour, Lequime, Vrancken, et al.

Nat Commun, 11, 5620 (2020)

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Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

Ianiro, Punčochář, Karcher, et al.

Nat Med, 28, 1913–1923 (2022)

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Learning the fitness dynamics of pathogens from phylogenies

Lefrancq, Duret, Bouchez, et al.

Nature, 637, 683–690 (2025)

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Analysis of metagenomic data

Liu, Rodriguez, Munteanu, et al.

Nat Rev Methods Primers, 5, 5 (2025)

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The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia

Schluter, Djukovic, Taylor, et al.

Cell Host Microbe, 31, 1126–1139 (2023)

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Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Scholz, Ward, Pasolli, et al.

Nat Methods, 13, 435–438 (2016)

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Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences

Tran-Kiem, Paredes, Perofsky, et al.

Nature, 640, 176–185 (2025)

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Long-read metagenomics reveals phage dynamics in the human gut microbiome

Wirbel, Hickey, Chang, et al.

Nature (2025)

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Using clusterProfiler to characterize multiomics data

Xu, Hu, Cai, et al.

Nat Protoc, 19, 3292–3320 (2024)

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High-resolution landscape of an antibiotic binding site

Yang, Cameranesi, Gowder, et al.

Nature, 622, 180–187 (2023)

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Lab Publications