Jaehee Kim

A multi-omic, spatial, and whole-slide image dataset of lung neuroendocrine tumours from the lungNENomics cohort

The paper presents a large multi-omic dataset of lung neuroendocrine tumours, including genomics, transcriptomics, methylation, spatial proteomics, and histopathology, enabling comprehensive molecular and morphological analysis.

Gene drive dynamics in plants: the role of seedbanks

This study develops a modeling framework for gene drives in plants that includes soil seedbanks, showing how seedbanks can slow spread but reduce genetic load and provide biosafety.

e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology

The paper introduces e3SIM, a simulator that models epidemiological, ecological, and evolutionary processes in pathogens, demonstrating its use with SARS-CoV-2 and Mycobacterium tuberculosis.

Network-based genetic monitoring of landscape fragmentation

This paper develops a network-based framework to study genetic consequences of habitat fragmentation, showing distinct genetic measure trajectories and early warning signals for rapid transitions.

Bayesian phylodynamic inference of population dynamics with dormancy

This paper develops a Bayesian framework to infer population dynamics with dormancy using molecular sequence data under the strong seedbank coalescent model.

Admixed populations in the neighbor-joining algorithm: a geometric analysis with five taxa

This paper analyzes the Neighbor-Joining algorithm's behavior under admixture using geometric methods, showing clustering order is always satisfied while other properties depend on admixture fraction.

Record-matching of STR profiles with fragmentary genomic SNP data

The paper evaluates using SNP data from poor-quality DNA to match STR profiles, showing similar accuracy to full-genome data with 5-10% coverage.

Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

Bayesian Inference of Dependent Population Dynamics in Coalescent Models

This paper introduces a Bayesian model for inferring dependent population dynamics using Markov random fields and applies it to study SARS-CoV-2 variants.

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

This paper develops a high-throughput method to generate host and pathogen genomic data from single nasopharyngeal swabs of COVID-19 patients.

Human-Genetic Ancestry Inference and False Positives in Forensic Familial Searching

This paper demonstrates that using ancestry inference on query profiles can reduce false-positive rates in familial searching by avoiding extreme allele-frequency misspecifications.

Linkage disequilibrium connects genetic records of relatives typed with disjoint genomic marker sets

The paper shows linkage disequilibrium can identify relatives using nonoverlapping genetic markers, with 30-36% accuracy for parent-offspring and sib pairs.