Genomics 🧬

Inspirational Works

Advancing regulatory variant effect prediction with AlphaGenome

Advancing regulatory variant effect prediction with AlphaGenome
Avsec, Latysheva, Cheng, Novati, Taylor, Ward, Bycroft, Nicolaisen, Arvaniti, Pan, Thomas, Dutordoir, Perino, De, Karollus, Gayoso, Sargeant, Mottram, Wong, Drotár, Kosiorek, Senior, Tanburn, Applebaum, Basu, Hassabis, Kohli
Nature, 649, 1206-1218 (2026)

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BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference

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

Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework
Dellicour, Lequime, Vrancken, et al.
Nat Commun, 11, 5620 (2020)

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Web-based multi-omics integration using the Analyst software suite

Web-based multi-omics integration using the Analyst software suite
Ewald, Zhou, Lu, et al.
Nat Protoc, 19, 1467–1497 (2024)

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

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

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

Analysis of metagenomic data
Liu, Rodriguez, Munteanu, et al.
Nat Rev Methods Primers, 5, 5 (2025)

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The Nagoya Protocol and its implications for microbiology

The Nagoya Protocol and its implications for microbiology
Salem, Kaltenpoth
Nat Microbiol, 8, 2234–2237 (2023)

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

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

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

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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Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery

Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery
Wan, Torres, Guan, de la Fuente-Nunez
Nat Protoc, 20, 2685–2697 (2025)

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

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

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

High-resolution landscape of an antibiotic binding site
Yang, Cameranesi, Gowder, et al.
Nature, 622, 180–187 (2023)

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