Publications Data Notes

Publication pages live under _publications/. They are rendered by the publications Jekyll collection configured in _config.yml and listed by _pages/publications.html.

Filename and permalink conventions

The filename prefix encodes the publication type and is used to split the listing on _pages/publications.html.

• Active preprint
  • Filename: _publications/preprint-<yyyy-mm-dd>-<slug>.md
  • Permalink: /publication/preprint-<yyyy-mm-dd>-<slug>
  • Listed under “Preprints” on the publications page
• Peer-reviewed paper
  • Filename: _publications/<yyyy-mm-dd>-<slug>.md
  • Permalink: /publication/<yyyy-mm-dd>-<slug>
  • Listed under “Peer-reviewed publications” on the publications page
• Preprint that has since been published
  • Filename: _publications/published-preprint-<yyyy-mm-dd>-<slug>.md
  • Permalink: keep the original /publication/preprint-<yyyy-mm-dd>-<slug>
  • Front matter: add ispublishedpreprint: "True"
  • The publications page hides these from the active “Preprints” list while keeping the preprint URL alive as a redirect to the published page

The date in the filename and permalink should be the original posting date for preprints, and the publication date for peer-reviewed papers.

Required front matter

Each publication page should define these fields in front matter:

• title
  • For preprints, prefix the title with [Preprint] so the listing visually flags it
• collection: publications
• permalink
  • Must match the filename pattern above
• excerpt
  • One- or two-sentence summary shown on the publications page
• date
  • yyyy-mm-dd posting or publication date
• venue
  • Preprint server such as bioRxiv or medRxiv, or the journal name
• paperurl
  • DOI link, journal link, or preprint server link
• citation
  • Full citation string used on the publication page

Recommended front matter

• excerpt_image
  • Path under /files/<year>/... to a small graphical abstract or figure used as the listing thumbnail
• highlight: true
  • Marks the entry as a select publication; select publications appear at the top of _pages/publications.html
• ispublishedpreprint: "True"
  • Only on published-preprint-* files; hides them from the active preprint list

File assets

Store publication figures, graphical abstracts, and any locally hosted PDFs under files/<year>/.

When a paper has its own image-rich summary on the publication page, store the figures under files/<year>/ and reference them with /files/<year>/<filename> in the Markdown body.

When the publisher provides a stable PDF link or a DOI, prefer linking out via paperurl rather than mirroring the PDF in this repository. Mirror the PDF only when the external link is unstable or when the publisher’s terms allow and the file is small.

Example

---
title: "[Preprint] Example Title"
collection: publications
permalink: /publication/preprint-2025-11-19-example
excerpt: "One- or two-sentence summary of the contribution."
excerpt_image: '/files/2025/example_thumb.jpg'
date: 2025-11-19
venue: 'bioRxiv'
paperurl: 'https://doi.org/10.1101/2025.11.19.689166'
citation: "Author A, Author B, Y. Tanigawa. Example Title. bioRxiv, 2025.11.19.689166 (2025)."
---

Moving a preprint to a paper

When a preprint is accepted and published as a peer-reviewed paper:

1. Rename the existing preprint file from _publications/preprint-<yyyy-mm-dd>-<slug>.md to _publications/published-preprint-<yyyy-mm-dd>-<slug>.md.
2. Keep the existing permalink value pointing at /publication/preprint-<yyyy-mm-dd>-<slug> so the original preprint URL keeps working.
3. Add ispublishedpreprint: "True" to the renamed file’s front matter.

4. Replace the body of the renamed file with a short note that links to the new published page, for example:

   This preprint is [now published in <Journal>](/publication/<yyyy-mm-dd>-<slug>)!
   

5. Create a new _publications/<yyyy-mm-dd>-<slug>.md file for the published version, with permalink: /publication/<yyyy-mm-dd>-<slug>, the journal as venue, the journal DOI as paperurl, and a fresh citation string.
6. Verify both pages render locally with bundle exec jekyll serve and that the old preprint URL still resolves and points readers to the published version.

Updating the home page News list

When adding a new preprint or paper, add a corresponding entry near the top of the News section in _pages/about.md. The entry should follow the existing format: date, a bold label such as **New Preprint** or **New Publication**, the linked title, and a one-sentence summary.