update font size and collections format

aristoteleo · Jan 31, 2024 · c4053ac · c4053ac
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commit c4053ac
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Showing 19 changed files with 51 additions and 34 deletions.
diff --git a/_layouts/paper.html b/_layouts/paper.html
@@ -11,11 +11,14 @@
             <img class="pad-right media-object" src="{{ page.image_url }}" style="max-width: 160px; max-height: 200px;">
 
             <div class="media-body">
-                <h3><strong>{{ page.paper_title }}</strong></h3>
+                <h3>{{ page.paper_title }}</h3>
+                {% if page.paper_subtitle %}
+                <div class="smallhead" style="text-align: right; margin-right: 60px;">{{ page.paper_subtitle }}</div>
+                {% endif %}
                 <p></p>
-                <div class="smallhead">{{ page.author_list }}</div>
+                <div class="smallsubhead">{{ page.author_list }}</div>
                 <div class="bigspacer"></div>
-                <div class="smallhead">
+                <div class="smallsubhead">
                     {{ page.journal }}
                     ({{ page.year }})
                 </div>
@@ -56,7 +59,7 @@ <h3><strong>{{ page.paper_title }}</strong></h3>
     </div>
     <div class="col-lg-5">
         <div class="post">
-            <h1 id="abstract">Abstract</h1>
+            <h3 id="abstract">Abstract</h3>
         </div>
         <div class="justified-paragraph">
             {{ content }}

diff --git a/_layouts/people.html b/_layouts/people.html
@@ -9,9 +9,9 @@
                 <div class="media">
                     <img class="pull-left pad-right media-object" width="160" src="{{ site.baseurl }}/assets/images/headshots/{% if page.headshot %}{{ page.headshot }}{% else %}placeholder-headshot.png{% endif %}">
                     <div class="media-body">
-                        <div class="bigtitle media-heading">
+                        <h2>
                             {{ page.name }}
-                        </div>
+                        </h2>
                         <p>
                             <div class="smallhead">
                                 {{ page.position }}
@@ -35,17 +35,6 @@
                 </div>
                 <div class="bigspacer"></div>
                 {% endif %}
-                {% if page.twitter %}
-                <div class="smallhead">
-                    Twitter
-                </div>
-                <div class="pad-left note">
-                    <div class="smallspacer"></div>
-                    <i class="fab fa-twitter"></i>
-                    <a class="off" href={{ page.twitter }}>{{ page.name }}</a>
-                </div>
-                <div class="bigspacer"></div>
-                {% endif %}
                 {% if page.GitHub %}
                 <div class="smallhead">
                     GitHub
@@ -68,31 +57,31 @@
                 </div>
                 <div class="bigspacer"></div>
                 {% endif %}
-                {% if page.email %}
+                {% if page.twitter %}
                 <div class="smallhead">
-                    Email
+                    Twitter
                 </div>
                 <div class="pad-left note">
                     <div class="smallspacer"></div>
-                    <i class="fa fa-inbox fa-fw"></i>
-                    {{ page.email }}
+                    <i class="fab fa-twitter"></i>
+                    <a class="off" href={{ page.twitter }}>{{ page.name }}</a>
                 </div>
                 <div class="bigspacer"></div>
                 {% endif %}
-                {% if page.website %}
+                {% if page.email %}
                 <div class="smallhead">
-                    Personal Website
+                    Email
                 </div>
                 <div class="pad-left note">
                     <div class="smallspacer"></div>
-                    <i class="fa fa-globe fa-fw"></i>
-                    <a class="off" href="{{ page.website }}">{{ page.name }}</a>
+                    <i class="fa fa-inbox fa-fw"></i>
+                    {{ page.email }}
                 </div>
                 <div class="bigspacer"></div>
                 {% endif %}
             </div>
             <div class="col-lg-8">
-                <div class="head">Bio</div>
+                <h3>Bio</h3>
                 <div class="justified-paragraph">
                   {{ page.bio }}
                 </div>

diff --git a/_papers/stereo_seq.md b/_papers/stereo_seq.md
@@ -2,7 +2,8 @@
 layout: paper
 title: "Read our work"
 type: selected work
-paper_title: Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays published in Cell and selected as cover story
+paper_title: Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
+paper_subtitle: -published in Cell and selected as cover story
 author_list: Ao Chen*, Sha Liao*, Mengnan Cheng*, Kailong Ma*, Liang Wu*, Yiwei Lai*, Xiaojie Qiu*, Jin Yang, 
     Jiangshan Xu, Shijie Hao, Xin Wang, Huifang Lu, Xi Chen, Xing Liu, Xin Huang, Zhao Li, Yan Hong, Yujia Jiang, 
     Jian Peng, Shuai Liu, Mengzhe Shen, Chuanyu Liu, Quanshui Li, Yue Yuan, Xiaoyu Wei, Huiwen Zheng, Weimin Feng, 

diff --git a/_people/cinlong.md b/_people/cinlong.md
@@ -6,5 +6,5 @@ name: "Cinlong Huang"
 position: "Research Assistant"
 current: true
 headshot: "placeholder-headshot.png"
-website: ""
+twitter: ""
 ---
diff --git a/_people/hadley.md b/_people/hadley.md
@@ -6,5 +6,5 @@ name: "Hadley Bickford"
 position: "Administrative Associate"
 current: true
 headshot: "hadley.png"
-website: ""
+twitter: ""
 ---
diff --git a/_people/jiayuan.md b/_people/jiayuan.md
@@ -7,4 +7,5 @@ position: "Visiting PhD Student"
 current: true
 headshot: "jiayuan.png"
 google_scholar: "https://scholar.google.com/citations?user=7lwkXGEAAAAJ&hl=en"
+twitter: ""
 ---
diff --git a/_people/mengchen.md b/_people/mengchen.md
@@ -9,4 +9,5 @@ headshot: "mengchen.png"
 bio: "I am a Computer Science undergrad at Tsinghua University, captivated by the synergy of artificial intelligence and biological exploration. My academic journey 
     has exposed me to the intricate tapestry of artificial intelligence, genomics, and computational biology. Outside the lab, I am interested in reading books and playing 
     badminton."
+twitter: ""
 ---
diff --git a/_people/michelle.md b/_people/michelle.md
@@ -6,5 +6,5 @@ name: "Michelle Ameri"
 position: "Operations Manager"
 current: true
 headshot: "michelle.png"
-website: ""
+twitter: ""
 ---
diff --git a/_people/oriane.md b/_people/oriane.md
@@ -6,5 +6,5 @@ name: "Oriane Rubio"
 position: "Research Project Manager"
 current: true
 headshot: "oriane.jpeg"
-website: ""
+twitter: ""
 ---
diff --git a/_people/qiaolin.md b/_people/qiaolin.md
@@ -10,4 +10,5 @@ bio: "I’m a Computer Science master student in Jilin University. Before that,
     Computer Science and Technology, Jilin University. During my undergraduate years, I delved into  total synthesis in natural organic molecules which help me deepen my 
     understanding of biochemical mechanisms. In my current academic pursuit, I am particularly captivated by the intersection of deep learning, single-cell technologies, and 
     drug discovery. I am eager to leverage my computational skills to contribute to advancements in these fields. Outside the lab, I enjoy playing guitar and cooking.”"
+twitter: ""
 ---
diff --git a/_people/samuel.md b/_people/samuel.md
@@ -11,4 +11,5 @@ bio: "I’m a Bioengineering Ph.D. student rotating in the Qiu lab. My interests
     synthetic biology, machine learning, and omics approaches. I earned my B.Sc. Hon. in Biology at the University of British Columbia, where I performed research primarily in 
     the Yachie lab creating technologies to study mammalian morphogenesis and viral evolution. When I’m not in the lab, I greatly enjoy spending time exploring my surroundings, 
     riding my motorcycle, and working on graphic design projects."
+twitter: ""
 ---
diff --git a/_people/sichao.md b/_people/sichao.md
@@ -7,4 +7,5 @@ position: "Remote Software Engineer"
 current: true
 headshot: "sichao.jpg"
 website: ""
+twitter: ""
 ---
diff --git a/_people/sijie.md b/_people/sijie.md
@@ -12,4 +12,5 @@ bio: "I'm an incoming postdoctoral researcher at the Qiu lab in Stanford. I rece
     state transitions and exploring how cells give rise to tissues. In particular, I am interested in developing analysis methods for spatiotemporal cell dynamics and building 
     self-organizing models that perceive internal molecular signals and external interactions, with applications in <i>in-silico</> modeling for mimicking and perturbing organogenesis. 
     Outside the lab, I enjoy cooking and aquascaping."
+twitter: ""
 ---
diff --git a/_people/xiaojie.md b/_people/xiaojie.md
@@ -7,7 +7,6 @@ position: "Principal Investigator"
 current: true
 headshot: "xiaojie.jpg"
 google_scholar: "https://scholar.google.com/citations?user=XlMd8TAAAAAJ&hl=en"
-website: ""
 GitHub: "https://github.com/Xiaojieqiu"
 cv_url: "assets/PDFs/xiaojie-cv.pdf"
 email: "[email protected]"
@@ -17,16 +16,17 @@ bio: "I’m an Assistant Professor at the Department of Genetics, the BASE progr
     to reconstruct RNA velocity vector field and make reprogramming and in silico perturbation predictions with metabolic labeling enabled single-cell RNA-seq. I recently also
     lead the development of <a href='https://github.com/aristoteleo/spateo-release'>Spateo</a>, for advanced spatiotemporal modeling of single cells. My lab is currently focused 
     mostly on predictive modeling of single cells through a uniuqe synthesis of genomics and machine learning. Outside the lab, I like going to the gym, run and read all kinds of books."
+twitter: ""
 ---
 
 <div class="bigspacer"></div>
-<div class="head">Research</div>
+<h3>Research</h3>
 <div class="post">
     <p>Dr. Xiaojie Qiu is currently an assistant professor at the Department of Genetics, the BASE program, and the Department of Computer Science at Stanford. Xiaojie’s Ph.D. work at University of Washington with Dr. Cole Trapnell made critical contributions to the field of single-cell genomics, exemplified by the development of Monocle ⅔ (monocle 2 & monocle 3) for pseudotemporal trajectory analysis of scRNA-seq data. In his post-doc at Whitehead Institute and MIT with Dr. Jonathan Weissman, Xiaojie developed Dynamo (aristoteleo/dynamo-release) to reconstruct RNA velocity vector field and make reprogramming and in silico perturbation predictions with metabolic labeling enabled single-cell RNA-seq. Recently he also leaded the development of a powerful toolkit, Spateo (aristoteleo/spateo-release), for advanced multi-dimensional spatiotemporal modeling of high definition spatial transcriptomics. </p>
     <p>The Qiu lab at Stanford started on Dec. 16, 2023. Xiaojie will continue leveraging his unique background in single-cell genomics, mathematical modeling, and machine learning to lead a research team that bridges the gap between the “big data” from single-cell and spatial genomics and quantitative/predictive modeling in order to address fundamental questions in mammalian cell fate transitions, especially those of heart evolution, development and disease. His research has been supported by the National Human Genome Research Institute, Chan Zuckerberg Institute, Impetus longevity grant, Arc institute and others.</p>
 </div>
 <div class="bigspacer"></div>
-<div class="head">Papers</div>
+<h3>Papers</h3>
 <div class="spacer"></div>
 <ul>
     {% assign sorted_array = site.papers | sort: "rank" %}

diff --git a/_people/yifan.md b/_people/yifan.md
@@ -10,4 +10,5 @@ bio: "I am currently an incoming visiting Ph.D. student at Wuhan University, spe
     focused on computer vision and pattern recognition, particularly in 3D vision and feature matching. Intrigued by computational biology, I've shifted my interests towards the 
     integration of spatial transcriptomics and RNA velocity in single cells, and actively expanding my knowledge in biology. Beyond academics, I enjoy activities like ping pong 
     and exploring new places through travel."
+twitter: ""
 ---
diff --git a/_people/yimeng.md b/_people/yimeng.md
@@ -9,4 +9,5 @@ headshot: "yimeng.jpg"
 bio: "I got my master's degree and bachelor's degree from Fudan University and Shandong University in 2023 and 2020, respectively. Both of them were awarded in Software 
     Engineering. My future research interest is the application of deep learning in life science, especially in cancer genomics. Outside the lab, I enjoy reading and making 
     handicrafts. I am interested in learning some new and different things."
+twitter: ""
 ---
diff --git a/_people/yuzhen.md b/_people/yuzhen.md
@@ -10,4 +10,5 @@ google_scholar: "https://scholar.google.com/citations?user=9wKn1A0AAAAJ&hl=en"
 bio: "I'm now a visting Computing Science M.Sc. student of Simon Fraser University, Canada. I am interested in leveraging my background in machine learning, 
     particularly transformer-based models, to reveal the regulatory mechanism of biological processes and disease progression. I earned a B.E. in Computer Science 
     and Technology from Zhejiang University and a B.S. in Computing Science from Simon Fraser University. When I am not in the lab, I love to explore nature."
+twitter: ""
 ---
diff --git a/_sass/2-layouts/index.sass b/_sass/2-layouts/index.sass
@@ -98,6 +98,12 @@ section
   line-height: 23px
   text-align: justify
 
+.smallsubhead
+  font-size: 16px
+  font-weight: 200
+  line-height: 23px
+  text-align: justify
+
 .note
   font-size: 15px
   font-weight: 200

diff --git a/papers.html b/papers.html
@@ -30,6 +30,9 @@ <h4>Selected work</h4>
                             <div class="smallhead mb-1">
                                 <strong><a href="{{ paper.url }}" class="off">{{ paper.paper_title }}</a></strong>
                             </div>
+                            {% if paper.paper_subtitle %}
+                                <div class="smallhead mb-1" style="text-align: right; margin-right: 60px;">{{ paper.paper_subtitle }}</div>
+                            {% endif %}
                             <p class="note" style="text-align: justify;"> {{ paper.author_list }} {{ paper.year }}</p>
                             <p class="note"><i>{{ paper.journal }}</i></p>
                             {% if paper.rank == 1 %}
@@ -79,6 +82,9 @@ <h4>Other work</h4>
                             <div class="smallhead mb-1">
                                 <strong><a href="{{ paper.url }}" class="off">{{ paper.paper_title }}</a></strong>
                             </div>
+                            {% if paper.paper_subtitle %}
+                                <div class="smallhead mb-1" style="text-align: right; margin-right: 60px;">{{ paper.paper_subtitle }}</div>
+                            {% endif %}
                             <p class="note" style="text-align: justify;"> {{ paper.author_list }} {{ paper.year }}</p>
                             <p class="note"><i>{{ paper.journal }}</i></p>
                         </div>
@@ -115,6 +121,9 @@ <h4>Other work</h4>
                             <div class="smallhead mb-1">
                                 <strong><a href="{{ paper.url }}" class="off">{{ paper.paper_title }}</a></strong>
                             </div>
+                            {% if paper.paper_subtitle %}
+                                <div class="smallhead mb-1" style="text-align: right; margin-right: 60px;">{{ paper.paper_subtitle }}</div>
+                            {% endif %}
                             <p class="note" style="text-align: justify;"> {{ paper.author_list }} {{ paper.year }}</p>
                             <p class="note"><i>{{ paper.journal }}</i></p>
                         </div>