Selected Projects From systems inference to validation-aware design

This project focuses on recurrent communication architectures across tumor types, aiming to identify conserved regulatory axes and cancer-specific signaling niches with stronger mechanistic interpretability.

• Built standardized scRNA pipelines across 10+ cancer types to characterize tumor ecosystems.
• Used CellChat and NicheNet to identify conserved and cancer-specific ligand-receptor circuits.
• Reimplemented CoVarnet in Python to detect five modules associated with cancer development.
• Integrated spatial transcriptomics to localize signaling niches and confirm sender-receiver co-localization patterns.
• Defined cell-hub populations with topology-aware metrics and linked hub-driven pathways to phenotypic programs.

This project asks whether TP53RK function in medulloblastoma is better explained by phosphorylation activity or by KEOPS-complex-dependent logic, using controlled perturbation and rescue designs.

• Constructed phosphorylation-site mutants and KEOPS critical-site mutants of TP53RK.
• Introduced mutant constructs through lentiviral transduction and degraded endogenous TP53RK with dTAG-V1.
• Used Incucyte live-cell measurements to compare proliferation and cell-death rescue between mutant classes.

TasAnchor was designed as a modular adhesion and immobilization platform in Bacillus subtilis, combining genome editing, scaffold design, and functional material integration.

• Knocked out endogenous TasA and constructed a pHT01 vector using a SpyTag/SpyCatcher scaffold.
• Cloned expression constructs into E. coli BL21(DE3), induced protein expression with IPTG, and purified targets by Ni-NTA affinity chromatography.
• Integrated an adhesion module on polystyrene substrates to support biofilm immobilization on reactor membranes.