Project:

• We introduced spatially-resolved transcript amplicon readout mapping with protein localization and unlimited sequencing (termed STARmap PLUS), a high-resolution spatial transcriptomics concomitantly with specific protein localization in the same tissue section and also expand the gene-coding capacity to 10^6, to draw the single-cell resolution spatial cell atlas in the context of Aβ plaques and tau tangles from Alzheimer Disease(AD) and control samples .
• The cell atlas revealed a core-shell structure near Aβ plaques composed of disease-associated microglia (DAM), disease-associated astrocytes (DAA), oligodendrocyte precursor cell (OPC), and oligodendrocytes subtypes.
• We also found infiltration of oligodendrocyte subtypes in hippocampal alveus near the tau tangles from CA1 excitatory neurons.

Contribution:

• Performed differential expression analysis and Gene set enrichment analysis to find out disease associated genes and pathways in each cell cluster.
• Developed pipeline to integrate the spatial and expression profile to reveal the cell distribution pattern around plaque/p-Tau and cluster the genes based on spatial expression pattern.
• Conducted pseudo-time analysis with clustering result and potential pathologic evolution pathways of disease-associated cells (DAM/DAA/OPC) were obtained.

Ongoing Project:

Developing a novel model to decipher mRNA dynamics (Synthesis, degradation etc.) at sub-cellular resolution from in situ sequencing data.

Project:

Development of an unsupervised and annotation-free framework, termed ClusterMap, which incorporates physical proximity and gene identity of RNAs and thus defines biologically meaningful structures and groups

Contribution:

Benchmarked and validated ClusterMap by performing the leave-one-out benchmark, which calculates the goodness of fit after integrating the ClusterMap-generated expression matrix with scRNA-seq data.

Project:

• Development of in situ electro-sequencing (electro-seq), combining soft bioelectronics with in situ RNA sequencing to stably map millisecond-timescale cellular electrophysiology and simultaneously profile a large number of genes at single-cell level across 3D tissues.
• In this project, electro-seq was applied to 3D human induced pluripotent stem cell-derived cardiomyocyte patches to study cardiac tissue maturation.

Contribution:

• Performed pseudo-time analysis and differential expression analysis to find out variable genes during maturation process.
• Conducted pathway enrichment analysis (Using g:Profiler) using both reduced-rank regression model and differential expression analysis to reveal related process during cardiac tissue maturation.

Project:

Development of a easy-to-use tool based on computer vision for tracking and analyze multi-animal behavior

Contribution:

• Build the web interface for end-user to view and manipulate the tracking results based on Javascript and utilized frameworks like Bootstrap and jQuery.
• Using PyIodine to enable end-user call python curation function inside web browser without opening another terminal window.

Project:

Differential Analysis of the immune response of human macrophages infected by HIV/bacteria/fungi using RNA-seq

Contribution:

• Obtained differentially expressed genes among macrophage samples from HIV/bacteria/fungi patients and control group using DEseq and other statistic tools.
• Developed a new algorithm based on p-value calculation across multiple ways of comparison to tackle the problem of insufficient samples when evaluating the differentially expressed genes.
• Analyzed gene circuits influenced by infection using WGCNA(Finding interesting gene modules) and gProfiler(Enrichment analysis).
• Implemented network and GO analysis to verify the result of our new algorithm.

Project:

• A Biological Storage Method with CRISPR and Off-target Detection in Gene Editing with LURE sequences
• Awarded Gold Medal & Best New Application Project Nominee (Percentage: 1.38%)
• Details can be found at our team wiki

Contribution:

• Applied Reed–Solomon code applied in the two-dimensional code to solve the possible storage error caused by off-target effects.
• Constructed the Wiki system of our team project using HTML, CSS and JavaScript.

Interdisciplinarity:

• Computational Biology, Biological Big Data Analysis, Introduction to Functional Genomics, Biostatistics, Introduction to Cardiovascular Mechanobiology,

Biology & Chemistry:

• Biology (Micro/Macro),Genetics, Biochemistry, Cell Biology
• Chemical Principles, Organic Chemistry,

Math, Physics, Statistics & Computer Science:

• Mathematics Analysis, Linear Algebra, Probability and Statistics, Generalized Linear Model
• Introduction to physics
• Introduction to Computing, Thinking and Approach of Programming, Algorithm and Data Structure, Machine Learning, Principle and Technology of Database

Laboratory & Seminar:

• Introductory Biology Seminar, Cell Biology Seminar, Genetics Seminar
• Laboratory of Chemical Principles, Physics Laboratory, Organic Chemistry Laboratory, Biology Laboratory