240621: add project details

Xieeeee · Jun 21, 2024 · 5f404e0 · 5f404e0
1 parent 9e9fba1
commit 5f404e0
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Showing 22 changed files with 24 additions and 16 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.__config.yml b/.__config.yml
diff --git a/.__includes b/.__includes
diff --git a/_config.yml b/_config.yml
@@ -48,8 +48,8 @@ rss_icon: false
 
 navbar_fixed: true
 footer_fixed: true
-search_enabled: true
-socials_in_search: true
+search_enabled: false
+socials_in_search: false
 
 # Dimensions
 max_width: 930px

diff --git a/_includes/._figure.liquid b/_includes/._figure.liquid
diff --git a/_includes/._projects.liquid b/_includes/._projects.liquid
diff --git a/_includes/projects.liquid b/_includes/projects.liquid
@@ -6,7 +6,7 @@
           include figure.liquid
           loading="eager"
           path=project.img
-          sizes = "250px"
+          sizes = "20px"
           alt="project thumbnail"
           class="card-img-top"
         %}

diff --git a/_layouts/._about.liquid b/_layouts/._about.liquid
diff --git a/_layouts/about.liquid b/_layouts/about.liquid
@@ -65,14 +65,15 @@ layout: default
     {% endif %}
 
     <!-- Projects -->
-    <a href="{{ '/projects/' }}" style="color: inherit">projects</a>
+    <a href="{{ '/projects/' | relative_url }}" style="color: inherit">projects</a>
     {% include projects.liquid %}
 
     <!-- Social -->
     {% if page.social %}
       <div class="social">
+        {% comment %}
         <div class="contact-icons">{% include social.liquid %}</div>
-
+        {% endcomment %}
         <div class="contact-note">{{ site.contact_note }}</div>
       </div>
     {% endif %}

diff --git a/_pages/._about.md b/_pages/._about.md
diff --git a/_pages/._projects.md b/_pages/._projects.md
diff --git a/_pages/about.md b/_pages/about.md
@@ -15,12 +15,10 @@ selected_papers: false # includes a list of papers marked as "selected={true}"
 social: true # includes social icons at the bottom of the page
 ---
 
-Hi there! My name is Yang Xie (谢旸). I am currently a Ph.D. candidate in [Ren lab](https://renlab.sdsc.edu/renlab_website/) at UC San Diego.
+My name is Yang Xie (谢旸). I am currently a Ph.D. candidate in [Ren lab](https://renlab.sdsc.edu/renlab_website/) at UC San Diego. My primary research interests include gene regulation, chromatin organization, and epigenomics.
 
-Our body is a complex system. Each cell in our body can have different roles and developmental trajetories, even though they usually have the same genes. The diversity is mainly driven by the way genes are turned on and off in specific places and times. This precious regulation process is controlled by different elements in our genome, through various chemical modifications and conformation changes in DNA or associated proteins, all of which make up what we call the epigenome.
+During my graduate studies, I focused on developing high-throughput, multi-modal single-cell sequencing methods to capture the epigenomic diversity in mammalian brains, aiming to link epigenome with transcription to better understand how non-coding sequences control gene expression. Check out the [project](https://xieeeee.github.io/projects/) section to know more about my work. 
 
-During my graduate studies, I focused on developing high-throughput, multi-modal single-cell sequencing techniques to capture the epigenomic diversity in mammalian brains, and study how does the dysregulation contribute to diseases including glioblastoma, a type of malignant brain tumor.
+I grew up in Shantou, a charming coastal city known for its delicious food. I completed my BSc in Biological Sciences from Fudan University, Shanghai. Before joing Ren lab, I worked in [O'Shea lab](https://www.salk.edu/scientist/clodagh-oshea/) at Salk Institute, where I studied how DNA folds using electron microscope and live-cell imaging.
 
-I grew up in Shantou, a charming coastal city known for its delicious food. I completed my BSc in Biological Sciences from Fudan University, Shanghai, with Guodong Ren as my undergraduate thesis advisor. Before joing Ren lab, I worked in [O'Shea lab](https://www.salk.edu/scientist/clodagh-oshea/) at Salk Institute, where I studied how DNA folds using electron microscope and live-cell imaging.
-
-Besides research, I enjoy listening to music, exploring different food and cooking. The best part of my weekend is (currently) composed of: Fuji Kaze, Yakiniku, Negori, and Hazy IPA.
+Besides research, I enjoy listening to music, exploring different cuisines and cooking. The best part of my weekend is (currently) composed of: Fuji Kaze, Yakiniku, and Hazy IPA.
diff --git a/_pages/projects.md b/_pages/projects.md
@@ -1,14 +1,21 @@
 ---
 layout: page
-title: projects
+title: Projects
 permalink: /projects/
 description: 
 nav: true
 nav_order: 3
 display_categories: 
-horizontal: true
+horizontal: false
 ---
 
+Our body is a complex system. Each cell in our body can have different roles and developmental trajetories, even though they usually have the same genes. The diversity is mainly driven by the way genes are turned on and off in specific places and times. This precious regulation process is controlled by different elements in our genome, through various chemical modifications and conformation changes in DNA or associated proteins, all of which make up what we call the epigenome.
+
+Being able to probe the dynamics of the epigenome in individual cells can provide insights into a cell's history, and in some cases, predict its future. This knowledge is crucial for mapping the complex landscapes of biological processes, and designing more precise and effective therapies for diseases. 
+
+My current research focuses on developing a toolkit to measure various types of epigenetic changes at the single-cell level. This will enable us to capture a comprehensive picture of how these changes influence cell function and disease progression.
+
+
 <!-- pages/projects.md -->
 <div class="projects">
 {% if site.enable_project_categories and page.display_categories %}

diff --git a/_projects/1_project.md b/_projects/1_project.md
@@ -16,7 +16,8 @@ Understanding the types of modifications present on genes or regulatory elements
 
 Compared with previous methods, Droplet Paired-Tag has higher signal specificty and is way easier to do. In our manuscript, we have used this method to resolve the repressive elements in adult mouse brain, which is difficult to do before. [Other study](https://www.nature.com/articles/s41586-023-06819-6) has utilized Droplet Paired-Tag to characrize enhancers in human brain, and concluded that epi-conserved regulatory elements across multiple species are more likely to be active enhancers.
 
-For more details, please refer to our [manuscript](https://www.nature.com/articles/s41594-023-01060-1)
+For more details, please refer to our [manuscript](https://www.nature.com/articles/s41594-023-01060-1).
+
 
 <div class="row">
     <div class="col-sm mt-3 mt-md-0">

diff --git a/_projects/2_project.md b/_projects/2_project.md
@@ -14,7 +14,8 @@ It is unclear how the very long DNA strand (around 2 meters) from a human cell i
 
 We combined Hi-C with commercial microfluidics to allow efficient measurement of chromatin conformation in individual cells, which we named Droplet Hi-C. This technique not only enables the analysis of cell type-specific chromatin structures in heterogeneous tissues, such as the mouse brain, but also has been pivotal in detecting copy number or structural variations, including extrachromosomal DNA (ecDNA), in brain cancer cells or glioblastoma. Furthermore, we extended Droplet Hi-C to a multiomics approach (Paired Hi-C), facilitating the simultaneous analysis of gene expression and chromatin conformation in the same cell, thereby linking ecDNA copy number with gene expression variations in brain cancer cells under drug treatment.
 
-For more details, please refer to our [manuscript](https://www.biorxiv.org/content/10.1101/2024.04.18.590148v1)
+For more details, please refer to our [manuscript](https://www.biorxiv.org/content/10.1101/2024.04.18.590148v1).
+
 
 <div class="row">
     <div class="col-sm mt-3 mt-md-0">

diff --git a/_sass/.DS_Store b/_sass/.DS_Store
diff --git a/_sass/._.DS_Store b/_sass/._.DS_Store
diff --git a/_sass/.__base.scss b/_sass/.__base.scss
diff --git a/_sass/.__layout.scss b/_sass/.__layout.scss
diff --git a/_sass/_base.scss b/_sass/_base.scss
@@ -373,7 +373,7 @@ ul.task-list input[type="checkbox"] {
   text-align: center;
 
   .contact-icons {
-    font-size: 4rem;
+    font-size: 2rem;
 
     a {
       i::before {

diff --git a/assets/.DS_Store b/assets/.DS_Store
diff --git a/assets/css/._main.scss b/assets/css/._main.scss