Sitemap
A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
Future Blog Post
Published:
This post will show up by default. To disable scheduling of future posts, edit config.yml and set future: false.
Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
cats
Coco
Coco is a young mitted Ragdoll cat with fluffy white gloves and gentle blue eyes.
Putao
Putao is Coco’s dad. He is a gentle and affectionate seal bicolor Ragdoll who loves human company and behaves obediently.
experiences
Disease-Specific TCR Identification from Bulk TCR Sequencing Data
- Processed and analyzed multi-disease bulk TCR datasets comprising 465.8M human TCR entries, including 330.3M from 59 NCBI projects and 135.5M from 66 immuneACCESS projects, enabling comprehensive TCR repertoire analysis.
- Developed a disease-specific recognition framework utilizing unsupervised learning methodologies with the GIANA tool, enhancing TCR classification accuracy.
HDSTdb: High-definition Spatial Transcriptomics Database
- Analyzed 246 healthy and diseased samples from three subcellular-level spatial transcriptomic sequencing platforms: Visium HD, Stereo-seq, and Xenium.
- Developed an interactive, multi-resolution visualization tool (e.g., 8µm, 16µm bins for Visium HD) with adjustable leiden clustering and differential gene expression (DEG) analysis.
- Enabled visualization of cell segmentation with advanced analyses, including cell shape characterization, spatial distribution, and cell-cell interactions.
EasyLAMP: Advanced LAMP Primer Design Model
- Developed a LAMP primer design tool based on comprehensive threshold screening of primer characteristics.
- Built a predictive model using extensive LAMP experimental data to evaluate primer performance and forecast amplification success under various conditions.
SpatialMETA: A Novel Framework for Integrating Spatial Transcriptomics and Metabolomics Data
- Conducted large-scale benchmarking of 7 integration methods (spaVAE, scVI, scPoli, …) across 6 multi-batch spatial transcriptomic-metabolomic datasets.
- Developed quantitative batch integration assessment system:
- Basic ST assessment (Continuity (CHAOS, PAS, …), Marker score (Moran’s, Geary’s, …), Specificity score (Specificity, Logistic regression, …)
- Biological conservation (ASW, Cell-type LISI (cLISI), …)
- Batch correction (Batch ASW, Integration LISI (iLISI), …)
- Reconstruction fidelity (Cosine Similarity, Pearson Correlation)
SpatialTCR: An integrated platform for high-resolution spatial sequencing of T cell receptor repertoires
- Developed a high-resolution spatial TCR profiling method leveraging Stereo-seq, enabling accurate reconstruction of TCR alpha and beta chains directly from tissue sections.
- Created a dedicated computational pipeline for reliable chain pairing, clonotype mapping, and integration with spatial transcriptomic data.
- Applied the platform to human tissues, revealing spatial T cell clonotype distributions and immune microenvironments with high confidence.
portfolio
Portfolio item number 1
Short description of portfolio item number 1
Portfolio item number 2
Short description of portfolio item number 2
publications
Paper Title Number 1
Published in Journal 1, 2009
This paper is about the number 1. The number 2 is left for future work.
Recommended citation: Your Name, You. (2009). "Paper Title Number 1." Journal 1. 1(1).
Download Paper | Download Slides | Download Bibtex
Paper Title Number 2
Published in Journal 1, 2010
This paper is about the number 2. The number 3 is left for future work.
Recommended citation: Your Name, You. (2010). "Paper Title Number 2." Journal 1. 1(2).
Download Paper | Download Slides
Paper Title Number 3
Published in Journal 1, 2015
This paper is about the number 3. The number 4 is left for future work.
Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3).
Download Paper | Download Slides
Paper Title Number 4
Published in GitHub Journal of Bugs, 2024
This paper is about fixing template issue #693.
Recommended citation: Your Name, You. (2024). "Paper Title Number 3." GitHub Journal of Bugs. 1(3).
Download Paper
Paper Title Number 5, with math \(E=mc^2\)
Published in GitHub Journal of Bugs, 2024
This paper is about a famous math equation, \(E=mc^2\)
Recommended citation: Your Name, You. (2024). "Paper Title Number 3." GitHub Journal of Bugs. 1(3).
Download Paper
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.