tweaks and cleanup

Author: clauswilke

_config.yml

@@ -8,9 +8,7 @@ description: > # this means to ignore newlines until "baseurl:"
   Room: MBB 3.232
 baseurl: "" # the subpath of your site, e.g. /blog
 #url: "" # the base hostname & protocol for your site, e.g. http://example.com
-twitter_username: ClausWilke
 github_username:  wilkelab
-instagram_username: wilkelab
 
 # Build settings
 markdown: kramdown

_data/current_members.yml

@@ -10,6 +10,10 @@
   joined: 2022
   pubs: "https://scholar.google.com/citations?hl=en&user=FSW5GvMAAAAJ"
 
+- name: Bahar Kasgari
+  role: Graduate Student (EEB)
+  joined: 2024
+
 - name: Aaron L. Feller
   role: Graduate Student (BCH)
   joined: 2022

_data/menu.yml

@@ -4,9 +4,6 @@
 - title: People
   link: "people"
 
-- title: Software
-  link: "software"
-
 - title: Joining the lab
   link: "positions"
 

_data/publications.yml

@@ -4,18 +4,6 @@
   ref: bioRxiv 611278
   doi: 10.1101/2024.09.04.611278
 
-- author: A. L. Feller, C. O. Wilke
-  year: preprint
-  title: Peptide-specific chemical language model successfully predicts membrane diffusion of cyclic peptides.
-  ref: "bioRxiv 607221"
-  doi: 10.1101/2024.08.09.607221
-
-- author: A. M. Hill, T. A. Ingle, C. O. Wilke
-  year: preprint
-  title: A computational model for bacteriophage ϕX174 gene expression.
-  ref: "bioRxiv 586356"
-  doi: 10.1101/2024.03.22.586356
-
 - author: M. M. Johnson, C. O. Wilke
   year: preprint
   title: Recombination rate inference via deep learning is limited by sequence diversity.
@@ -34,12 +22,32 @@
   ref: "bioRxiv 411025"
   doi: 10.1101/411025
 
+- author: A. L. Feller, C. O. Wilke
+  year: 2025
+  title: Peptide-specific chemical language model successfully predicts membrane diffusion of cyclic peptides.
+  ref: "J. Chem. Inf. Model 65:571–579"
+  doi: 10.1021/acs.jcim.4c01441
+
+- author: W. Liu, C. O. Wilke, J. J. Arnold, M. S. Sotoudegan, C. E. Cameron
+  year: 2024
+  title: "Single-cell virology: On-chip, quantitative characterization of the dynamics of virus spread from one single cell to another"
+  ref: "Viruses 16:1659"
+  doi: 10.3390/v16111659
+  pmcid: PMC11598947
+
+- author: A. M. Hill, T. A. Ingle, C. O. Wilke
+  year: 2024
+  title: A computational model for bacteriophage ϕX174 gene expression.
+  ref: "PLoS One 19:e0313039"
+  doi: 10.1371/journal.pone.0313039
+  pmcid: PMC11527146
+
 - author: A. V. Kulikova, J. K. Parker, B. W. Davies, C. O. Wilke
   year: 2024
   title: Semantic search using protein large language models detects class II microcins in bacterial genomes.
-  ref: "mSystems, in press"
-  doi: 10.1101/2023.11.15.567263
-  comment: doi not final
+  ref: "mSystems 9:e01044-24"
+  doi: 10.1128/msystems.01044-24
+  pmcid: PMC11494933
 
 - author: K. Hu, C.-W. Chou, C. O. Wilke, I. J. Finkelstein
   year: 2024

_includes/footer.html

@@ -10,8 +10,6 @@ <h2>
       </div>
       <div class="footer-links">
         <a href="https://github.com/{{ site.github_username }}"><span class="mdi mdi-github"> </span> GitHub</a> <br />
-        <a href="https://instagram.com/{{ site.instagram_username }}"><span class="mdi mdi-instagram"> </span> Instagram</a> <br />
-        <a href="https://twitter.com/{{ site.twitter_username}}"><span class="mdi mdi-twitter"> </span> Twitter</a>
       </div>
       <div class="footer-description">
         {{ site.description }}