Rebrand site visuals from Duke to NYU

_config.yml

@@ -1,6 +1,6 @@
-title: "Pearson Lab at Duke University"
+title: "Pearson Lab at NYU"
 description: >-
-  Computational neuroscience at Duke University. We build statistical and
+  Computational neuroscience at NYU. We build statistical and
   machine-learning tools to understand how brains generate behavior.
 url: "https://pearsonlab.github.io"
 author: "Pearson Lab"

_data/people.yml

@@ -43,14 +43,11 @@ pi:
     of Kentucky and his PhD in physics from Princeton. He became a neuroscientist
     at Duke, where he did his postdoctoral training with Michael Platt, working
     on the neurobiology of reward and decision-making. From 2015 to 2018, he was
-    an Assistant Research Professor in the Duke Institute for Brain Sciences. In
-    2018, he moved back to the School of Medicine as an Assistant Professor in
-    the Department of Biostatistics & Bioinformatics, and in 2022, he moved
-    to the Department of Neurobiology, where he was promoted to Associate
-    Professor in 2025. In addition, he maintains secondary appointments in the
-    departments of Biostatics & Bioinformatics, Psychology &
-    Neuroscience, and Electrical and Computer Engineering.
-    (<a href="https://www.dropbox.com/scl/fi/o05n1v0skl5el9w938oca/john_pearson_cv.pdf?rlkey=wickra8h33u8hfsr40l0jdhxf&amp;st=8buq1yz2&amp;dl=0">cv</a>)
+    an Assistant Research Professor in the Duke Institute for Brain Sciences, and
+    from 2018-2025, he was an Assistant Professor in Biostatistics & Bioinformatics
+    and Neurobiology. Since 2026, he has been an Associate Professor in the <a href="https://as.nyu.edu/departments/cns/people/CoreFaculty.html">Center for Neural
+    Science</a> at NYU, with an affiliation at the <a href="https://www.simonsfoundation.org/flatiron/center-for-computational-neuroscience/">Center for Computational Neuroscience</a>
+    at the Flatiron Institute. (<a href="https://www.dropbox.com/scl/fi/o05n1v0skl5el9w938oca/john_pearson_cv.pdf?rlkey=wickra8h33u8hfsr40l0jdhxf&amp;st=8buq1yz2&amp;dl=0">cv</a>)
 
 postdocs:
   - name: Ganchao Wei
@@ -115,23 +112,24 @@ graduate_students:
     github: https://github.com/DavidStA95
     email: david.st-amand@duke.edu
     desc: >-
-      David is a third-year graduate student in Neurobiology. He graduated
+      David is a third-year graduate student in Neurobiology at Duke. He graduated
       from McGill University, where he received his BS in Psychology and
       his MS in Neuroscience. His research investigates how efficient
       coding models can help us understand how information is computed in
       the retina. Outside the lab, he likes to work out and play games.
 
   - name: Shiyang Pan
-    title: Electrical and Computer Engineering PhD Student
+    title: Center for Data Science PhD Student
     image: /images/shiyang.jpg
     site: https://waaaaaterfall.github.io
     github: https://github.com/WaAaaAterfall
     email: shiyang.pan@duke.edu
     linkedin: https://www.linkedin.com/in/shiyangpan
     desc: >-
-      Shiyang is a graduate student in Electrical &amp; Computer Engineering
-      at Duke. She received her Bsc in Applied Mathematics from University
-      of Liverpool and Xi'an Jiaotong-Liverpool University. Her research
+      Shiyang is a graduate student in the Center for Data Science at NYU.
+      She received her Bsc in Applied Mathematics from University
+      of Liverpool and Xi'an Jiaotong-Liverpool University and her master's
+      in electrical and computer engineering from Duke. Her research
       focuses on developing computational models and real-time methods to
       understand the activity of large-scale neural populations. When not
       doing research she enjoys music, reading, and creative writing.
@@ -143,7 +141,7 @@ graduate_students:
     email: caitlin.lewis@duke.edu
     linkedin: https://www.linkedin.com/in/caitlinllewis/
     desc: >-
-      Caitlin is a second-year graduate student in Electrical &amp; Computer
+      Caitlin is a graduate student in Electrical &amp; Computer
       Engineering at Duke. She received her B.S. in Computer Science and
       Statistics from the University of North Carolina at Chapel Hill. Her
       research focuses on developing computational models and open-source
@@ -168,6 +166,7 @@ graduate_students:
     current: false
     url: https://achintzeus1994.github.io
     years: 2021-2022
+    outcome: Deep Learning Researcher, Shell
 
   - name: Na Young Jun
     current: false

_data/publications.yaml

@@ -264,9 +264,10 @@
     given: Tobias
   issued:
   - year: 2024
-  title: 'Optimal decision-making under task uncertainty: a computational basis for cognitive'
-  container-title: Proceedings of the Annual Meeting of the Cognitive Science Society, 46 (0)
-  URL: https://escholarship.org/content/qt2d40418r/qt2d40418r.pdf?v=lg
+  title: 'Optimal decision-making under task uncertainty: a computational basis for cognitive stability versus flexibility'
+  container-title: Proceedings of the Annual Meeting of the Cognitive Science Society
+  URL: https://escholarship.org/uc/item/2d40418r
+  volume: '46'
 - id: oneill2024modeling
   type: article-journal
   author:
@@ -675,6 +676,7 @@
   issue: '39'
   URL: https://www.pnas.org/doi/abs/10.1073/pnas.2105115118
 - id: martinez2021reproducible
+  badge: workshop
   type: article-journal
   author:
   - family: Martinez
@@ -788,8 +790,9 @@
   issued:
   - year: 2020
   title: Online neural connectivity estimation with ensemble stimulation
-  container-title: arXiv preprint arXiv:2007.13911
+  container-title: Advances in Neural Information Processing Systems
   URL: https://arxiv.org/abs/2007.13911
+  volume: '33'
 - id: mcdonald2020dorsolateral
   type: article-journal
   author:
@@ -1070,6 +1073,7 @@
   issue: '4'
   URL: https://link.springer.com/article/10.3758/s13423-016-1204-5
 - id: iqbal2017goal
+  badge: workshop
   type: article-journal
   author:
   - family: Iqbal
@@ -1794,38 +1798,22 @@
   volume: '82'
   issue: '2'
   URL: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.82.255
-- id: bejjani0towards
-  type: article-journal
-  author:
-  - family: Bejjani
-    given: Christina
-  - family: Egner
-    given: Tobias
-  - family: Pearson
-    given: John
-  - family: Moffitt
-    given: Terrie E
-  - family: Caspi
-    given: Avshalom
-  - family: Adcock
-    given: Alison
-  issued: []
-  title: TOWARDS A COMPUTATIONAL PSYCHIATRY OF TRANSDIAGNOSTIC DEFICITS IN COGNITIVE CONTROL
-  URL: https://scholar.google.com/scholar?cluster=478861155140086647&hl=en&oi=scholarr
-- id: mcdonald0bayesian
-  type: article-journal
+- id: mcdonald2019bayesianb
+  type: paper-conference
   author:
   - family: McDonald
     given: Kelsey
   - family: Huettel
     given: Scott
   - family: Pearson
     given: John
-  issued: []
+  issued:
+  - year: 2019
   title: Bayesian nonparametric models characterize social sensitivity in a competitive dynamic game
+  container-title: Conference on Cognitive Computational Neuroscience
   URL: https://2019.ccneuro.org/proceedings/0000705.pdf
-- id: mcdonald0gaussian
-  type: article-journal
+- id: mcdonald2018gaussian
+  type: paper-conference
   author:
   - family: McDonald
     given: Kelsey
@@ -1835,6 +1823,8 @@
     given: Scott
   - family: Pearson
     given: John
-  issued: []
+  issued:
+  - year: 2018
   title: Gaussian Process Models Characterize Other-Regarding Strategies Over Multiple Timescales in a Dynamic Social Game
+  container-title: Conference on Cognitive Computational Neuroscience
   URL: https://2018.ccneuro.org/proceedings/1126.pdf

_data/research.yml

@@ -12,6 +12,15 @@
 #                                 full description revealed via the
 #                                 "Read more" disclosure; supports
 #                                 inline links and <figure>/<img> tags)
+#   hidden: true                 (optional, defaults to showing. Set to
+#                                 true to keep the entry here but leave
+#                                 it off the Research page — use this
+#                                 instead of deleting or commenting out
+#                                 a project you may want back later.
+#                                 Use the bare YAML boolean true, not
+#                                 "true" in quotes: any non-empty string
+#                                 is truthy in Liquid, so "false" would
+#                                 hide the entry too.)
 
 - title: Real-time analysis of neural data
   image: /images/colorFish.png
@@ -66,6 +75,7 @@
 
 - title: Autoencoding whole-brain dynamics
   image: /images/website_VAEGAM_fig.png
+  hidden: true
   caption: >-
     A) VAE-GAM Model Schematic: brain volumes with signal of interest are
     compressed to a lower dimensional representation using encoder

_includes/footer.html

@@ -7,4 +7,16 @@
             document.write(year)
         </script>
     </p>
+    <!-- The header photo is CC BY 2.0, which requires visible credit, a
+         link to the licence, and a note of any changes. This include is
+         used by the same layouts that render the banner, so the credit
+         appears on exactly the pages that show the photo. Remove this if
+         the banner image is ever replaced. -->
+    <p class="photo-credit">
+        Header photo:
+        <a href="https://commons.wikimedia.org/wiki/File:Greenwich_Village_(27483343909).jpg">Greenwich Village</a>
+        by Felix Stahlberg,
+        <a href="https://creativecommons.org/licenses/by/2.0/">CC BY 2.0</a>
+        &mdash; cropped and colour-tinted.
+    </p>
 </footer>

_includes/jumbotron.html

@@ -2,6 +2,8 @@
   <div class="container">
     <br>
     <h1>{{ page.title }}</h1>
-    <h5 style="color: #B5B5B5">{{ page.desc }}</h5>
+    <!-- No colour override: inherits white from .jumbotron. The old grey
+         (#B5B5B5) washed out once the flat violet header became a photo. -->
+    <h5>{{ page.desc }}</h5>
   </div>
 </div>

_includes/pubs.html

@@ -23,16 +23,40 @@
   tighter than last-name-only — keeps Amanda Li from being bolded just
   because Thomas Li is a former undergrad.
 {%- endcomment -%}
+{%- comment -%}
+  Drop parenthesised nicknames before picking the surname. people.yml
+  carries entries like "Lun (Sam) Yin" and "Chaichontat Sriworarat
+  (Richard)"; a trailing one would otherwise be taken as the surname,
+  giving the key "C|(Richard)", which matches no author and silently
+  leaves that person unbolded.
+{%- endcomment -%}
 {%- assign lab_keys = "" | split: "" -%}
 {%- for full_name in all_lab_people -%}
-  {%- assign parts = full_name | split: " " -%}
+  {%- assign tokens = full_name | split: " " -%}
+  {%- assign parts = "" | split: "" -%}
+  {%- for token in tokens -%}
+    {%- unless token contains "(" -%}
+      {%- assign parts = parts | push: token -%}
+    {%- endunless -%}
+  {%- endfor -%}
   {%- assign first = parts | first -%}
   {%- assign last = parts | last -%}
   {%- assign initial = first | slice: 0, 1 -%}
   {%- assign key = initial | append: "|" | append: last -%}
   {%- assign lab_keys = lab_keys | push: key -%}
 {%- endfor -%}
 
+{%- comment -%}
+  Display-name overrides, for people who publish under a name they don't
+  go by. Scholar supplies the published name and the scraper rewrites
+  author fields on every run, so this can't live in publications.yaml.
+  Parallel arrays, comma-separated: "PublishedGiven|Family" -> preferred
+  given name. Bolding still matches on the published name, so an entry
+  here doesn't affect lab-member detection.
+{%- endcomment -%}
+{%- assign alias_keys = "Chaichontat|Sriworarat" | split: "," -%}
+{%- assign alias_given = "Richard" | split: "," -%}
+
 <p>This list is not guaranteed to be up to date, but the lab's complete publications can be found <a href="https://scholar.google.com/citations?user=4whjDosAAAAJ&hl=en">here</a>.</p>
 
 {% assign sorted_pubs = site.data.publications | group_by_exp:'item', 'item.issued.first.year' | sort: 'name' | reverse %}
@@ -43,9 +67,30 @@
   <h3>{{ year.name }}</h3>
   <ol>
   {% for pub in year.items %}
+    {%- comment -%}
+      Type badge. An explicit `badge:` on the entry in publications.yaml
+      wins; otherwise it is derived from the venue string.
+
+      The override exists because some venues can't be inferred from
+      Scholar's metadata — a workshop paper often looks like a bare arXiv
+      preprint, or carries no venue at all. Set `badge: workshop` (or any
+      of journal / preprint / conference) by hand on those entries. The
+      scraper preserves keys it doesn't produce, so the override survives
+      the weekly refresh; add a matching .pub-badge-<name> rule in
+      css/publications.css for any new value.
+
+      Derivation order matters: a few journals are named "Proceedings
+      of ..." (PNAS, Proc. R. Soc.) and would otherwise be caught by the
+      generic "proceedings" rule and badged as conference papers, so they
+      are matched first.
+    {%- endcomment -%}
     {%- assign venue_lc = pub.container-title | downcase -%}
-    {%- if venue_lc contains "biorxiv" or venue_lc contains "arxiv" or venue_lc contains "medrxiv" or venue_lc contains "chemrxiv" or venue_lc contains "psyarxiv" or venue_lc contains "osf preprints" -%}
+    {%- if pub.badge and pub.badge != "" -%}
+      {%- assign pub_type = pub.badge -%}
+    {%- elsif venue_lc contains "biorxiv" or venue_lc contains "arxiv" or venue_lc contains "medrxiv" or venue_lc contains "chemrxiv" or venue_lc contains "psyarxiv" or venue_lc contains "osf preprints" -%}
       {%- assign pub_type = "preprint" -%}
+    {%- elsif venue_lc contains "national academy of sciences" or venue_lc contains "proceedings of the royal society" -%}
+      {%- assign pub_type = "journal" -%}
     {%- elsif venue_lc contains "proceedings" or venue_lc contains "advances in neural" or venue_lc contains "neurips" or venue_lc contains "cosyne" or venue_lc contains "conference" -%}
       {%- assign pub_type = "conference" -%}
     {%- else -%}
@@ -55,12 +100,24 @@ <h3>{{ year.name }}</h3>
       <span class="pub-badge pub-badge-{{ pub_type }}">{{ pub_type }}</span>
       {% if pub.URL and pub.URL != "" %}<a href="{{ pub.URL }}"><b>{{ pub.title }}</b></a>{% else %}<b>{{ pub.title }}</b>{% endif %}
       <br>
+      {%- comment -%}
+        Separator between authors: two-author papers read "A and B" with no
+        comma, three or more take the serial comma, "A, B, and C". The
+        trailing "and " is added by the loop below.
+      {%- endcomment -%}
+      {%- assign author_sep = ", " -%}
+      {%- if pub.author.size == 2 %}{% assign author_sep = " " %}{% endif -%}
       {% for aa in pub.author -%}
         {%- if forloop.last and forloop.first == false %}and {% endif -%}
         {%- assign author_initial = aa.given | slice: 0, 1 -%}
         {%- assign author_key = author_initial | append: "|" | append: aa.family -%}
-        {%- if lab_keys contains author_key -%}<b>{{ aa.given }} {{ aa.family }}</b>{%- else -%}{{ aa.given }} {{ aa.family }}{%- endif -%}
-        {%- if forloop.last == false %}, {% endif -%}
+        {%- assign shown_given = aa.given -%}
+        {%- assign alias_lookup = aa.given | append: "|" | append: aa.family -%}
+        {%- for ak in alias_keys -%}
+          {%- if ak == alias_lookup -%}{%- assign shown_given = alias_given[forloop.index0] -%}{%- endif -%}
+        {%- endfor -%}
+        {%- if lab_keys contains author_key -%}<b>{{ shown_given }} {{ aa.family }}</b>{%- else -%}{{ shown_given }} {{ aa.family }}{%- endif -%}
+        {%- if forloop.last == false %}{{ author_sep }}{% endif -%}
       {%- endfor %}
        ({{ year.name }}).
       <br>

_layouts/home.html

@@ -3,13 +3,22 @@
   {% include head.html %}
 
   <body>
-  <!-- Viewport-locked background so the [λ] logo always centers in the
-       visible area, regardless of how tall/wide body grows. Inset from
-       the viewport edges so the SVG doesn't push flush against the
-       window frame. -->
-  <div style="position: fixed; top: 80px; right: 80px; bottom: 80px; left: 80px; z-index: -1; background: url('/images/plab_logo_dark.svg') no-repeat center center; background-size: contain;"></div>
+  <!-- Viewport-locked splash so the [λ] logo always centers in the visible
+       area, regardless of how tall/wide body grows. Inset from the viewport
+       edges so the SVG doesn't push flush against the window frame. The
+       moving announcement stacks directly above the logo.
+
+       MOVING ANNOUNCEMENT: delete the <p class="move-note"> line below (and
+       the matching .move-note rule in css/custom.css) once the move is
+       complete (after 2026-09-01). -->
+  <div class="splash">
+    <p class="move-note" role="status">
+      The Pearson Lab is moving to the <b>Center for Neural Science at NYU</b>
+    </p>
+    <img class="splash-logo" src="/images/plab_logo_dark.svg" alt="Pearson Lab">
+  </div>
   {% include navbar.html %}
-  <img src="/images/DUSOM_Dept_Neurobio_stack.jpg" alt="Duke School of Medicine, Department of Neurobiology" style="width: 25%; float: right; padding-top: 50px"/>
+
   <footer>
       <div style="display: block; position: fixed; bottom: 20px; left: 30px">
           <h3 style="color: #9d9d9d">{{ page.desc }}</h3>