Zio Kim

EDUCATION

College / University

Heinrich Heine University Düsseldorf

Highest Degree

Bachelor of Science

Major Subjects

Quantitative Biology

Country

Republic of Korea

Lab Experience

Molecular & Synthetic biology: Restriction enzyme cloning, Gibson Assembly, Golden Gate cloning, plasmid design (SnapGene/Benchling), bacterial transformation, colony PCR, Sanger sequencing prep, optogenetic gene expression control
Protein & biochemical techniques: Bradford assay, SDS-PAGE, Western blot, high-performance anion-exchange chromatography (HPAEC), single worm proteomics, liposome-based drug formulation
Model organisms: Escherichia coli cultivation, Komagataeibacter xylinus cultivation, Angomonas deanei cultivation and transfection, Caenorhabditis elegans husbandry, lifespan assays, drug screening
Imaging & phenotyping: DIC & fluorescence microscopy, nucleolar imaging, image analysis with FIJI/ImageJ
Computational biology: Deterministic ODE simulations of gene circuits, Linear Stability Analysis (LSA), transcriptomics & proteomics data analysis (volcano plots, clustering, pathway enrichment, proteomic clocks for biological age estimation), flux balance analysis and enzyme-constrained metabolic modelling, programming in R, Python, Julia, Unix/Linux

Projects / Research

2025: Bachelor thesis, “Comparison of drug-delivery and proteomics responses of geroprotectors in C. elegans”, Molecular Genetics of Ageing Department, Max Planck Institute for Biology of Ageing, Cologne, Germany
2024 – 2025: Teaching Assistant, “Cell Bioenergetics and Deterministic Processes in Biology”, Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
2024: Student Intern, “Transcriptomic analysis of age-associated gene-regulation changes across human tissues”, Cellular Networks and Systems Biology Group, CECAD, Cologne, Germany
2023 – 2024: Team Leader, “KlothY: metabolic engineering, production, and characterisation of bacterial cellulose as a sustainable textile alternative in K. xylinus”, iGEM Düsseldorf Team, Düsseldorf, Germany
2023 – 2024: Student Researcher, “Blue-light optogenetic control of endosymbiont-targeted protein expression in A. deanei”, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
2016 – 2017: Student Researcher, “Biomarkers for bloodstream infection in paediatric intestinal failure patients with central venous lines”, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan, USA

Publications

Kröninger, L., Kim, Z., et al. T7 RNA polymerase-based gene expression from a transcriptionally silent rDNA spacer in the endosymbiont-harboring trypanosomatid Angomonas deanei. PLOS ONE 20(5): e0322611 (2025). DOI: 10.1371/journal.pone.0322611
Fischer, J. B., Kim, Z., et al. Clinical features and biomarkers suggestive of bloodstream infection in pediatric patients with intestinal failure and central venous lines for parenteral nutrition: a retrospective pilot study. Pediatric Emergency Care 37(10): e585–e588 (2021). DOI: 10.1097/PEC.0000000000001731

Scholarships / Awards

2025 – 2026:	Stipend by the International Max Planck Research School
2024 – 2025:	Wübben Stiftung Wissenschaft Student Grant
2024:	Gold Medal in the iGEM Competition
2023 – 2025:	Deutschlandstipendium

SCIENTIFIC INTERESTS AND GOALS

What draws me to molecular biology is the challenge of making the invisible visible. We work with molecules and pathways that we cannot see, yet we reveal their effects through experiments that produce measurable changes at the cellular and organismal level. Advances in high-throughput and multi-omics methods now capture these changes in unprecedented detail, opening new possibilities to understand complex biological questions. Yet this flood of data raises an important question: how do we make sense of it? Systems biology, by combining computational models, quantitative methods, and emerging AI tools, offers ways to interpret complexity and test predictions. In my research so far, I have conducted drug screening and single worm proteomics, applying a proteomic clock in C. elegans to test whether pharmacological interventions can lower biological age; analysed gene expression correlations in human tissues to find potential ageing biomarkers; and used flux balance and enzyme-constrained models to simulate how gene modifications can rewire bacterial metabolism to optimise bacterial cellulose production. I hope to keep bridging experiments with models in this way to tackle fundamental questions about how cells and organisms adapt, age, and develop disease, so we can improve prevention and promote healthier lives.