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We are interested in revealing the biological basis and evolutionary histories of various unique and interesting species by using genomics, bioinformatics and biostatistics.
We are interested in revealing the biological basis and evolutionary histories of various unique and interesting species by using genomics, bioinformatics and biostatistics.
Call for Master’s Interns/Visiting Researchers:
Evolutionary Genomics and Comparative Transcriptomics in Mammals
We are seeking motivated master’s students for internships in evolutionary genomics and transcriptomics. The project focuses on the origin and diversification of mammary glands, using public genomic and transcriptomic datasets.
Please note that we are not able to provide financial support. Interested candidates are expected to secure their own funding (e.g. travel, living expenses, or scholarships) through their home institution or external sources. If you are interested, please send a brief CV and a short statement of your research interests to the PI.
Potential Projects
Potential Projects
Project 1. Comparative Transcriptomic Architecture of Mammary and Other Exocrine Glands in Humans and Mice
This project investigates the evolutionary origin of the mammary gland by analyzing its molecular similarity to other exocrine tissues such as salivary, sweat, and sebaceous glands. Despite being considered a mammalian innovation, the mammary gland may have evolved by repurposing existing gene regulatory modules shared with ancestral glandular systems.
To test this hypothesis, we will perform a meta-analysis of public single-cell and bulk transcriptomic datasets (e.g., PanglaoDB, Tabula Muris, GTEx) from human and mouse mammary and non-mammary tissues. We will identify tissue-specific and shared gene expression modules using network-based approaches (WGCNA, scMTNI), reconstruct developmental trajectories, and assess transcriptomic similarities across tissues and stages. Functional relevance of candidate genes will be evaluated through integration with gene-phenotype databases such as MGI and GWAS Atlas. This computational analysis will yield a high-resolution map of mammary gland–specific and shared regulatory modules, clarifying whether the mammary gland represents a unique innovation or a composite derivative of ancestral exocrine systems. The results will provide a molecular framework for understanding the evolutionary assembly of complex glandular traits in mammals.
Project 2. The Genomic Basis of Mammalian Diversity in Milk Composition and Teat Number
Mammalian species exhibit remarkable diversity in milk composition and teat number, reflecting adaptations to ecological conditions such as temperature, aquatic environment, and reproductive strategy. While phenotypic variation has been linked to environmental variables, the genetic basis underlying these traits remains largely unresolved.
This project aims to identify the evolutionary mechanisms driving mammary trait diversification by analyzing genomic data from non-model mammals including goat, sheep, pig, rabbit, dog, and seal. Using published phenotypic datasets and high-quality genomes, we will identify gene family expansions and contractions with CAFE, detect signatures of positive selection using PAML, and assess the role of transposable elements in regulatory evolution near core mammary genes. Functional interpretation will draw on livestock GWAS and transcriptomic datasets to connect genetic variation with trait expression.
The project will produce a comparative genomic framework for understanding how mammary traits evolved across lineages and elucidate the role of adaptive and regulatory genomic changes, including transposon-mediated innovation, in shaping the biology of milk production. These insights are central to understanding the genetic architecture of complex, ecologically responsive traits in mammals.
1. Genomic Diversity and Evolution
1. Genomic Diversity and Evolution
We are interested in investigating the evolutionary history of species and populations such as adaptation and demographic history by comparing population-scale genomes.
key words: population genetics, comparative genomics, natural selection, demographic history.
2. Connect Genome to Phenotype
2. Connect Genome to Phenotype
We are interested in investigating how the genetic variants contributes to the phenotypic diversity in the view of evolution. We use functional genomics toolsets, such as RNA-sequencing and genome-wide association study to investigate this question.
key words: functional genomics, transcriptome, eQTL, polygenic score, genome-wide association study.
Funded Project: SalmoSV (8M NOK, 2021-2024, Researcher Project for Young Talents (FRIPRO) grant from the Research Council of Norway)
We are investigating how the genomic variants of salmonids contribute to their evolution and diversity. Salmonids are particularly interesting in the view of evolutionary genomics because of their recent “whole-genome duplication” event. Specifically, we are investigating genomic variants in wild and farmed populations and trying to identify adaptive and/or function-altering genetic variants by developing bioinformatics methods through collaboration with laboratory-based researchers.
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