Dae Kwan Ko

Dae Kwan Ko, Ph.D.

I am a Fixed-Term Assistant Professor in the Plant Research Laboratory, the Department of Plant Biology, and the Great Lakes Bioenergy Research Center (GLBRC) at Michigan State University (MSU). My research aims to understand how plants dynamically reprogram gene expression in response to environmental stress, with a particular emphasis on gene regulatory networks and their application to crop resilience.

During my Ph.D. training in the Department of Molecular Biosciences at the University of Texas at Austin, I investigated the molecular mechanisms of heterosis in maize using an integrative approach that combined experimental biology and genomics. After a short but intensive period of bioinformatics training with C. Robin Buell, I joined the lab of Federica Brandizzi at MSU as a postdoctoral researcher, where I studied gene regulatory mechanisms underlying plant responses to endoplasmic reticulum stress through systems-level approaches. This work led to the development of coexpression network-based gene discovery pipelines that enabled the identification of regulatory hub genes for functional characterization.

In my current role, I focus on how gene regulatory networks and multi-omics data can be used to uncover mechanisms of plant adaptation to climate-related stresses. While I am affiliated with the Brandizzi Lab, I also lead independent research directions. My research is supported through GLBRC within the Brandizzi Lab, as well as by independent projects, including the MSU GREEEN project and multiple JGI-funded projects for which I serve as PI.

Portrait of Dae Kwan Ko

Research Interests

I am a plant biologist driven by a passion for addressing critical biological questions at the systems level through a hypothesis-driven approach, harnessing the power of genomics. Just as individuals in society interact, so too do genes and proteins within cells. But what are the functional consequences of these molecular interactions in regulating biological pathways? These interactions, known as “biological networks,” are essential for maintaining cellular homeostasis in all living organisms. My long-term research goal is to unravel these gene networks and apply the insights to advance translational research. Representative papers are highlighted in yellow below.

Publications

Figure preview for Plant Journal 2026 paper on abiotic stress responses in sorghum

A tissue-resolved, network-based transcriptomic framework for abiotic stress responses in sorghum

Ko DK, Brandizzi F
Plant J. 2026 Apr;126(1):e70834.
GitHub page for scripts
Description: Understanding how crops coordinate gene expression across tissues and time under environmental stress is a major challenge for improving climate resilience. This study provides a comprehensive, network-based transcriptomic resource that reveals tissue specificity as the dominant driver of abiotic stress responses in sorghum, offering a valuable framework and prioritized regulatory candidates for future crop improvement.
Figure preview for JBC 2025 review on ER stress and viral defense in plants

ER stress and viral defense: Advances and future perspectives on plant unfolded protein response in pathogenesis

Adhikari B, Verchot J*, Brandizzi F, Ko DK*
*Co-corresponding authors
J Biol Chem. 2025 Feb 25;301(4):108354.
Description: Over the past decade, our understanding of how the plant UPR machinery engages with pathogen infections, especially viral infection, and the functional consequences has greatly advanced because of genetic, genomic, and technological innovations as well as the accumulation of new knowledge of plant UPR. In this review, we provide a comprehensive overview of plant UPR signaling highlighting recent advances that reveal how it is tuned to orchestrate interconnected signaling pathways, thus operating as a moderator to control cell fate.
Figure preview for Cell Reports Methods 2025 NEEDLE paper

A network-enabled pipeline for gene discovery and validation in non-model plant species

Ko DK, Brandizzi F
Cell Rep Methods. 2025 Jan 27;5(1):100963.
Highlighted in MSU-PRL bulletin Highlighted in GLBRC bulletin GitHub page for scripts
Description: Meeting the energy and food demands of a growing global population demands the swift development of climate-resilient crops, achievable through targeted gene reprogramming for growth, development, and stress responses. Accurate prediction of transcription regulators is crucial for accelerating crop improvement via targeted engineering and breeding approaches. However, this is constrained by the scarcity of multi-omics datasets for most non-model species. To address this challenge, we present a robust network-based gene discovery pipeline that identifies transcription factors upstream of genes of interest by leveraging transcriptomic dynamics in non-model plants followed by rapid in planta experimental validation.
Figure preview for Nature Reviews Genetics 2024 review on ER stress-induced gene regulation in plants

Dynamics of ER stress-induced gene regulation in plants

Ko DK, Brandizzi F
Nat Rev Genet. 2024 Jul;25(7):513-525.
Description: Plants have uniquely adapted to manage endoplasmic reticulum stress triggered by protein misfolding. We review the dynamics of gene expression regulation underlying the unfolded protein response in plants, highlighting recent insights provided by systems-level approaches and omics data.
Figure preview for Nature Plants 2023 paper on IRE1-proteasome signaling in unresolved ER stress

An IRE1-proteasome system signaling cohort controls cell fate determination in unresolved proteotoxic stress of the plant ER

Ko DK, Kim JY, Thibault ET, Brandizzi F
Nat Plants. 2023 9:1333-1346.
Spotlight by Varshney et al. Trends Plant Sci GitHub page for scripts Media highlight
Description: In this study, we performed a forward genetic screening and discovered a new regulator that helps cells determine life or death under unresolved ER stress. Using an interdisciplinary approach of omics, biochemistry, and genetics, we identified its working mechanism and functional relationship with existing regulators.
Figure preview for Nature Communications 2023 paper on TGNap1 and defense

Defense against phytopathogens relies on efficient antimicrobial protein secretion mediated by the microtubule-binding protein TGNap1

Bhandari BD, Ko DK, Kim SJ, Nomura K, He SY, Brandizzi F
Nat Commun. 2023 14,6357.
Description: Defining plant defense machinery against pathogens is significant in cell biology and crop yield. This paper shows that TGNap1, a TGN and microtubule-binding protein, is required for defense and efficient anti-microbial protein secretion, linking secretion and cytoskeleton. I performed the RNA-seq analysis as a co-author.
Figure preview for Plant Journal 2020 review on network-based approaches in plants

Network-based approaches for understanding gene regulation and function in plants

Ko DK, Brandizzi F
Plant J. 2020 Oct;104(2):302-317.
Highlighted in the Society for Experimental Biology's Spring Bulletin
Description: Understanding gene function is a critical requirement to advance knowledge of the principles underpinning fundamental and applied plant biology. In this review, we describe predictive analyses, their strengths and pitfalls that are fast-forwarding our understanding of gene regulation and function in plants.
Figure preview for Trends in Biochemical Sciences 2020 review on ER stress responses in Arabidopsis

Functional diversification of ER stress responses in Arabidopsis

Pastor-Cantizano N, Ko DK, Angelos E, Pu Y, Brandizzi F.
Trends Biochem Sci. 2020 Feb;45(2):123-136.
On The Cover
Description: In recent years, the field of plant UPR has substantially advanced, revealing new regulators and mechanisms. My colleagues and I provide recent updates on the new development in the plant UPR to the research community.
Figure preview for PLOS One 2018 paper on transcriptome profiling of transgenic potato

Transcriptome profiling of transgenic potato plants provides insights into variability caused by plant transformation

Ko DK, Nadakuduti SS, Douches DS, Buell CR.
PLoS One. 2018 Nov 8;13(11):e0206055.
Description: We describe the impact of Agrobacterium-mediated transformation of a mutated acetolactate synthase gene on the transcriptome of potato, highlight the extent of positional effect of transgene insertion and that one component of somaclonal variation is due to altered expression of transcription factors and their downstream targets.

Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids

Ko DK*, Rohozinski D*, Song Q, Taylor SH, Juenger TE, Harmon FG, *Chen ZJ.
*These authors contributed equally to this work
PLoS Genet. 2016 Jul 28;12(7):e1006197.
Description: Heterosis, or hybrid vigor, has been widely used in agriculture for more than a century. Despite extensive investigation and various models proposed, the molecular basis for heterosis remains largely elusive. I led this collaborative project to identify and characterize the molecular link of growth heterosis and the circadian clock. We report that higher carbon fixation and starch accumulation in maize hybrids than in the parents are associated with differences in the diurnal regulation of gene expression.