Herawati Sudoyo

A Global Atlas of Immune Alleles Reveals Health-Relevant Variation Across Groups

The paper presents GAIA, a global atlas of immune alleles, showing that underrepresented groups have more diverse alleles needed for vaccine design than Northwest European groups.

Rapid convergence toward an agriculturalist regulatory landscape following lifestyle transition in Bornean hunter-gatherers

This study shows that a recent lifestyle shift to agriculture in Bornean Punan people rapidly alters their transcriptome and DNA methylation, resembling agriculturalists more than their foraging relatives.

Ancestral and environmental diversity shape the immune landscape in Indonesia

This study identifies eQTLs and environmental influences on immune cell diversity in Indonesian populations, highlighting the role of ancestry and environment in shaping immunity.

From sporulation to village differentiation: the shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia

The paper presents a gut microbiome dataset from Indonesia, revealing novel species and subspecies linked to rural-to-urban lifestyle transitions and showing that community-level diet differences drive microbiome divergence.

Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context

This study benchmarks GLIMPSE imputation on low coverage genomes from underrepresented populations, showing improved performance when using target population genetic information.

The genetic origins and impacts of historical Papuan migrations into Wallacea

This study uses genome data to show that most Papuan-related ancestry in Wallacea comes from New Guinea migrations, not from ancient human settlers.

Profiling genetically driven alternative splicing across the Indonesian Archipelago

The paper analyzes alternative splicing variation across 115 Indonesian samples to identify genetic variants influencing splicing, finding over 1,000 differential splicing events and 6,000 sQTLs with some ancestry-specific effects.

The whole blood microbiome of Indonesians reveals translocated and pathogenic microbiota

The paper analyzes RNA-seq data from whole blood of Indonesians to identify pathogens, finding Flaviviridae and Plasmodium as predominant, with distinct microbiome profiles compared to Mali and UK cohorts.

Transcriptomic profiles of Plasmodium falciparum and Plasmodium vivax-infected individuals in Indonesia

This study compares transcriptomic responses to Plasmodium falciparum and P. vivax infections in Indonesian patients to African and South American studies, finding shared and unique pathways.

Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with local ancestry and archaic introgression

The paper identifies Indonesia-specific eQTLs and methylQTLs linked to local ancestry and archaic introgression, showing their impact on gene regulation and hematological traits.

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

The paper analyzes DNA methylation and gene expression in Indonesian populations to show genetic ancestry, environmental influences, and immune-related differences across regions.