Genomics 🧬

Inspirational Works

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data
Andrews, Kiselev, McCarthy, et al.
Nat Protoc, 16, 1–9 (2021)

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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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Super-resolved spatial transcriptomics by deep data fusion

Super-resolved spatial transcriptomics by deep data fusion
BergenstrĂĄhle, He, et al.
Nat Biotechnol, 40, 476–479 (2022)

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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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The druggable genome

The druggable genome
Hopkins, Groom
Nat Rev Drug Discov, 1, 727–730 (2002)

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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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Method of the Year: spatially resolved transcriptomics

Method of the Year: spatially resolved transcriptomics
Marx
Nat Methods, 18, 9–14 (2021)

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High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer

High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer
Oliveira, Romero, Chung, et al.
Nat Genet, 57, 1512–1523 (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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Spatially resolved mapping of cells associated with human complex traits

Spatially resolved mapping of cells associated with human complex traits
Song, Chen, Hou, et al.
Nature, 641, 932–941 (2025)

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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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Predicting drug responses of unseen cell types through transfer learning with foundation models

Predicting drug responses of unseen cell types through transfer learning with foundation models
Wang, Liu, Fan, et al.
Nat Comput Sci, 6, 39–52 (2026)

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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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