misc updates

_includes/footer.html

@@ -24,6 +24,8 @@
 		</a>
 	    </div>
 	</div></div>
+
+	<!--- 
 	<div class="row"><div align="center"> 
 	    <div class="col-xs-4 col-sm-4" align="center">
 		<a href="https://www.cis.jhu.edu/" target="_blank">
@@ -41,6 +43,8 @@
 		</a>
 	    </div>
 	</div></div>
+	--->
+
 	<hr style="height:1px;border-width:0;background-color:#fff;">
 	<div class="row"><div align="center">
 	    <p>Our work is made possible thanks to the following publicly funded programs</p>

_layouts/post.html

@@ -42,7 +42,7 @@ <h4>RECENT POSTS</h4>
 		    </a> on {{post.date | date_to_long_string }}</li>
                     {% endfor %}
                 </ul>
-                <a href="{{ "/allposts" | prepend: site.baseurl }}">All posts ...</a>
+                <a href="{{ "/blog" | prepend: site.baseurl }}">All posts ...</a>
             </div>
 	    <div class="well">
 		<h4>TAGS</h4>
@@ -88,7 +88,8 @@ <h4>RELATED POSTS</h4>
 	    <div class="well">
 		<h4>EXPLORE MORE POSTS</h4>
                 <a href="{{ "/tags" | prepend: site.baseurl }}">by Tags</a> | 
-                <a href="{{ "/archive" | prepend: site.baseurl }}">by Date</a>		
+                <a href="{{ "/archive" | prepend: site.baseurl }}">by Date</a> |		
+                <a href="{{ "/blog" | prepend: site.baseurl }}">View All</a>		
 	    </div>
         </div>
 

_news/2024-11-08-csa-single-cell-genomics.md

@@ -0,0 +1,4 @@
+---
+layout: news
+title: Lyla presents a poster at the Cold Spring Harbor Asia conference on Frontiers in Single Cell Genomics.
+---

_news/2024-11-12-duke-upgg.md

@@ -0,0 +1,6 @@
+---
+layout: news
+title: Dr. Fan gives an invited talk as part of the Distinguished Lecture Series for the Duke University Genetics & Genomics Program.
+---
+
+Special thanks to Odmaa Bayaraa, Emma Hatchell, Natalie Dzikowski, Anvita Kulshrestha, Ratchanon RP Pornmongkolsuk, and the rest of the UPGG graduate students for inviting and hosting. 

_team/deevelazquez.md

@@ -1,8 +1,8 @@
 ---
 layout: team
 name: Dee Velazquez
-title: Undergraduate Student
-description: I am a undergraduate student majoring in computer science and chemical & biomolecular engineering at Johns Hopkins. I have had previous lab and research experience in cellular biology, computational chemistry, and deep learning. I am currently interested in using my technical background to anaylyze data and solve biomedical problems. Outside the lab, I enjoy working out, listening to music, cooking, and watching movies/anime.
+title: Post-Bacc Student
+description: I majored in computer science and chemical & biomolecular engineering at Johns Hopkins. I have had previous lab and research experience in cellular biology, computational chemistry, and deep learning. I am currently interested in using my technical background to anaylyze data and solve biomedical problems. Outside the lab, I enjoy working out, listening to music, cooking, and watching movies/anime.
 profile: /img/deeprofile.jpg
 github: https://github.com/dvelazq
 linkedin: https://www.linkedin.com/in/deevelazquez/

_team/srujansingh.md

@@ -1,6 +1,6 @@
 ---
 layout: team
-name: Srujan Singh (Sami)
+name: Srujan (Sami) Singh 
 title: Postdoctoral Fellow
 description: I am a recent PhD from the Chemical and Biomolecular Engineering program at Johns Hopkins University. My expertise lies in the field of bone tissue engineering and regenerative medicine. As a postdoctoral fellow, I want to work at the intersection of advanced imaging and computational biology, and understand how cell-cell/cell-material interactions and spatio-temporal gene regulation play a role in the context of diseases and tissue regeneration. Outside of lab, I like to run, hike, explore new places and cuisines.
 LinkedIn: www.linkedin.com/in/srujan-singh-jhu

assets/docs/transparency.md

@@ -4,13 +4,15 @@ layout: default
 
 # JEFworks Lab Transparency in Resource Allocation
 
-Prof. Fan seeks to provide greater transparency in allocation of lab resources in order to [mitigate gender and race-specific disparities and help ensure that all lab members are treated fairly](https://science.sciencemag.org/content/366/6466/692). This is a living document and subject to modifications. Please feel [free to fork, modify, and make pull requests](https://github.com/JEFworks/JEFworks.github.io/blob/master/assets/docs/transparency.md) to introduce new policies or modify old ones. This document was last modified July 2022.
+Prof. Fan seeks to provide greater transparency in allocation of lab resources in order to [mitigate gender and race-specific disparities and help ensure that all lab members are treated fairly](https://science.sciencemag.org/content/366/6466/692). This is a living document and subject to modifications. Please feel [free to fork, modify, and make pull requests](https://github.com/JEFworks/JEFworks.github.io/blob/master/assets/docs/transparency.md) to introduce new policies or modify old ones.
+
+This document was last modified Nov 2024.
 
 ---
 
 ## Compensation (Wages/Stipends/Benefits)
 
-For **Post-doc Associates and Fellows**, compensation levels start at $68,500 and is commensurate with years of post-doctoral experience at rates consistent with University Guidelines. A one-time relocation package of up to $1,500 will be provided to assist with reasonable moving costs per IRS guidelines. In addition, post-docs will be provided with health and dental insurance benefits through University Health Services. 
+For **Post-doc Associates and Fellows**, compensation levels start at $70,000 and is commensurate with years of post-doctoral experience at rates consistent with University Guidelines. A one-time relocation package of up to $1,500 will be provided to assist with reasonable moving costs per IRS guidelines. In addition, post-docs will be provided with health and dental insurance benefits through University Health Services. 
 
 Post-docs are strongly encouraged to apply for fellowships as a part of their career development. If the fellowship’s compensation level falls below those provided in the lab and/or does not include comparable benefits, additional compensation and benefits will be provided to ensure that final compensation and benefit levels are matched to those of other post-docs in the lab. No additional compensation or benefit will be provided on the basis of fellowships alone in order to maintain fairness, particularly among US and international students. Likewise, in order to mitigate gender and race-specific disparities, compensation levels are non-negotiable with the following exception: negotiations to increase compensation by one post-doc will be considered on the basis that commensurate increases in compensation will be provided for all post-docs in the lab to maintain fairness. 
 
@@ -34,6 +36,6 @@ Increases in travel allowances will be considered on a case-by-case basis to bes
 
 ## Lab Outings
 
-Expenses associated with formal lab outings such as lab dinners and retreats, including reasonable associated child-care expenses for attending lab members, will be covered in full.
+Expenses associated with formal lab outings such as lab dinners and retreats, including cost of transportation and reasonable associated child-care expenses for attending lab members, will be covered in full.
 
 Expenses associated with informal lab outings organized by other lab members can be reimbursed up to $20 per lab member without approval and increased with approval from Prof. Fan. 

contact.html

@@ -22,11 +22,11 @@ <h3>Contact Email</h3>
     <h3>Lab Address</h3>
     <i>
 	Johns Hopkins University<br>
-	Center for Computational Biology<br>
 	Department of Biomedical Engineering<br>
+	Center for Computational Biology<br>
 	Wyman Park S253<br>
-	3400 N. Charles Street<br>
-	Baltimore, MD 21218-2681<br>	
+	3100 Wyman Park Dr<br>
+	Baltimore, MD 21211<br>
     </i><br>
 
     <div class="mapouter"><div class="gmap_canvas"><iframe width="100%" height="500" id="gmap_canvas" src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d3086.3716646870334!2d-76.62495218379901!3d39.32516412921923!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x89c804dea8e61d47%3A0x1bb613bf91cd5296!2sWyman%20Park%20Building%2C%20Baltimore%2C%20MD%2021218!5e0!3m2!1sen!2sus!4v1631545663419!5m2!1sen!2sus" frameborder="0" scrolling="no" marginheight="0" marginwidth="0"></iframe>Google Maps Generator by <a href="https://www.embedgooglemap.net">embedgooglemap.net</a></div><style>.mapouter{position:relative;text-align:right;height:500px;width:100%;}.gmap_canvas {overflow:hidden;background:none!important;height:500px;width:100%;}</style></div>

index.html

@@ -2,13 +2,12 @@
 layout: default
 image: /img/bg.jpg
 sectionid: home
-desc: Welcome to the JEFworks Lab,<br> where Prof. Jean Fan and team work on computational software and statistical approaches to address questions in developmental and cancer biology. <br><br> <a href="join"><button type="button" class="btn btn-warning btn-lg">Recruiting at all levels! Join us!</button></a>
+desc: Welcome to the JEFworks Lab,<br> where Prof. Jean Fan and team work on statistical analysis approaches and machine learning tools for analyzing big spatially resolved omics data to better understand the molecular and spatial-contextual factors shaping cellular identity and heterogeneity in the context of human health and disease. <!--- <br><br> <a href="join"><button type="button" class="btn btn-warning btn-lg">Recruiting at all levels! Join us!</button></a> --->
 ---
 
 <div class="container">
     <div class="row">
-
-	<h2>We are a bioinformatics research lab in the <a href="https://ccb.jhu.edu/">Center for Computational Biology</a> and the <a href="https://www.bme.jhu.edu/">Department of Biomedical Engineering</a> at Johns Hopkins University. We are also affiliated with the <a href="https://www.cs.jhu.edu/">Department of Computer Science</a>, the <a href="https://www.cis.jhu.edu/">Center for Imaging Science</a>, the <a href="https://kavlijhu.org/">Kavli Neuroscience Discovery Institute</a>, and more.</h2>
+      <h2>We are a bioinformatics research lab in the <a href="https://ccb.jhu.edu/">Center for Computational Biology</a> and the <a href="https://www.bme.jhu.edu/">Department of Biomedical Engineering</a> at Johns Hopkins University. <a href="team">Meet our team!</a></h2>
 	<div class="row" style="padding: 15px;">
 	    <!--- <a href="team"><img src="img/team.jpg" width="100%"></a> --->
 	    <div class="col-xs-4 col-md-2">
@@ -24,9 +23,11 @@ <h2>We are a bioinformatics research lab in the <a href="https://ccb.jhu.edu/">C
 		</div>
 		{% endif %}
 		{% endfor %}
-	    </div>
-
+	    </div>	    
 	</div>
+
+	<hr>
+
 	<h2>We develop methods for analyzing spatially resolved transcriptomic sequencing and imaging data.</h2>
 	<div class="row">
 	    <div class="col-md-7">
@@ -58,12 +59,12 @@ <h2>We develop methods for analyzing spatially resolved transcriptomic sequencin
 	</div>
 
 	<div class="row">
-	    <h2>We apply these methods to better understand the impact of cellular heterogeneity on cancer pathogenesis and prognosis.</h2>
+	    <h2>We apply these methods to better understand the impact of cellular heterogeneity on disease progression and prognosis.</h2>
 	    <div class="col-md-6">
 		<img src="img/main1.jpg" width="100%">
 	    </div>
 	    <div class="col-md-6">
-		<p>Advancements in high-throughput sequencing and imaging technologies have uncovered tremendous genetic, epigenetic, transcriptional, and spatial heterogeneity in various cancers but their impact on clinical outcomes is not well understood. We establish close collaborations with clinical collaborators to develop and apply bioinformatics methods that contribute to a more complete understanding of how cellular heterogeneity impacts tumor progression, therapeutic resistance, and ultimately clinical prognosis. We are particularly interested in pediatric gliomas.</p>
+		<p>Advancements in high-throughput sequencing and imaging technologies have uncovered tremendous genetic, epigenetic, transcriptional, and spatial heterogeneity in various diseases but their impact on clinical outcomes is not well understood. We establish close collaborations with clinical collaborators to develop and apply bioinformatics methods that contribute to a more complete understanding of how cellular heterogeneity impacts disease progression, therapeutic resistance, and ultimately clinical prognosis.</p>
 		<ul>
 		    <li>
 			<a href="/publications#/papers/2020/09/15/natureemm101038/"><u>Jean Fan^</u>, Kamil Slowikowski, Fan Zhang. Single-cell transcriptomics in cancer - computational challenges and opportunities. Nature Experimental and Molecular Medicine. 2020, doi.org:10.1038/s12276-020-0422-0</a>
@@ -108,7 +109,7 @@ <h2 class="text-center">Latest News</h2>
 		<li><a href="{{ post.url | prepend: site.baseurl }}">{{ post.title }}</a> on {{ post.date | date_to_long_string}}</li>
 		{% endfor %}
 	    </ul>	    
-	    <a href="{{ site.baseurl }}/allnews">
+	    <a href="{{ site.baseurl }}/news">
 		<button type="button" class="btn btn-primary btn-block">
 		    More News
 		</button>
@@ -122,7 +123,7 @@ <h2 class="text-center">Latest Blog Posts</h2>
 		<li><a href="{{ post.url | prepend: site.baseurl }}">{{ post.title }}</a> on {{ post.date | date_to_long_string }}</li>
 		{% endfor %}
 	    </ul>
-	    <a href="{{ site.baseurl }}/allposts"> 
+	    <a href="{{ site.baseurl }}/blog"> 
 		<button type="button" class="btn btn-primary btn-block">
 		    More Blog Posts
 		</button>