Next Generation Single-Molecule Biophysics

CHIRLMIN JOO LAB

Using next-generation single-molecule techniques and machine learning, we investigate fundamental biological processes, focusing on the early stages of molecular interactions that are undetectable with conventional biochemistry. Our research spans from small regulatory RNA in gene silencing (RNA interference) and anti-viral defense (CRISPR immunity) to the dynamics of immune recognition, such as MHC-TCR interactions. A key tool in our work is SPARXS (Single-molecule Parallel Analysis for Rapid eXploration of Sequence space), a novel multiplexing single-molecule technique that allows us to probe interactions on a large scale with unprecedented resolution. We also develop single-molecule protein sequencing techniques for advanced proteomics analysis. We have organized conferences in 2017, 2019, and 2022. A new series is in 2025.

KEY PUBLICATIONS

Severins, Bastiaanssen, Kim, et al, C. Joo "Single-molecule structural and kinetic studies across sequence space" Science (2024)

Bastiaanssen, Kim et al "RNA-guided RNA silencing by an Asgard archaeal Argonaute" Nature Communications (2024)

Filius et al, "Full-length single-molecule protein fingerprinting" Nature Nanotechnology (2024)

Alfaro et al, "The emerging landscape of single-molecule protein sequencing technologies" Nature Methods (2021)

Kim, Loeff et al "Selective loading and processing of prespacers for precise CRISPR adaptation" Nature (2020) (animation)

Joo lab in Ewha

LAB NEWS

Aug 2025 João starts his PhD project

Aug 2025 KyungLim visits the Delft lab for training

Aug 2025 Jacob joins the lab as a technician

Jul 2025 Sohyun visits the Delft lab for training

Jun 2025 Yuna joins the Ewha lab for internship

Jun 2025 Our work highlighted by ERC in 8 different languages

Jun 2025 Ziming starts his project in our lab

Jun 2025 Dong Hoon•Sung Hyun's paper published in ACS Nano

Jun 2025 Carolien•Ivo's paper published in Nature Protocols

Apr 2025 Ewha lab receives NRF funding on epigenetic editors (Next-Gen Bio)

Apr 2025 Chirlmin gives a talk in Cambridge

Apr 2025 Merel starts her bachelor thesis project

Mar 2025 Sonja starts her bachelor thesis project

Mar 2025 We received funding from ZonMW Open Competition

Mar 2025 Eugene starts his bachelor thesis project

Feb 2025 Mike•Raman's paper published in Science Advances

Feb 2025 We received funding from NWO Open Competition (ENW-M)

Feb 2025 Marianne starts her master thesis project

Feb 2025 Hema starts her bachelor thesis project

Jan 2025 Chirlmin has achieved 10,000 citations with h index 40

Jan 2025 Chirlmin gives a talk in Single-Molecule Protein Sequencing conference

Jan 2025 Chirlmin organizes Single-Molecule Protein Sequencing conference in Bolzano, Italy

Jan 2025 KyungLim visits the Delft lab for training

Jan 2025 Chirlmin gives a talk in KAIST, Korea