bib-monitor: 1 publication update 2026-09-30

[antagomir]

Automated bibliography scan (email + PubMed). No brand-new entries, but one existing preprint entry needed updating to reflect its acceptance.

• EscobarZepeda2025 — updated in place, not duplicated
  • Genome Biology sent a "Decision" email accepting the manuscript, now retitled "BioSIFTR: functional inference from shallow shotgun sequencing using biome-specific genome catalogues benchmarked in gut microbiomes" (was recorded as the bioRxiv preprint "Biome-specific genome catalogues reveal functional potential of shallow sequencing", DOI 10.1101/2025.06.16.659887)
  • Found in: Leo's own "BIB:" forward (email thread, 2026-09-29); the bioRxiv link tying the new title to the existing preprint entry came from an earlier Google Docs comment thread where Leo referenced the same bioRxiv URL as "our own BioSIFTR"
  • pubclass = {A1} (was B) — now an accepted original research article, no longer a preprint
  • keywords = {bioscience} — unchanged, matches the rest of the microbiome-methods entries
  • pubstate = {inpress} (was preprint) — accepted but not yet formally published; no DOI, volume or pages have been issued yet, so those fields were left out rather than guessed
  • Author list and key (EscobarZepeda2025) left unchanged from the preprint entry

Also checked and found nothing new:

• The two publisher/journal-office searches from email-scan.md (14-day window) turned up only this Genome Biology decision and the already-processed Elsevier CLNESP thread (already recorded as Zhang2026)
• PubMed, author "Lahti L[Author]", last 60 days: 7 hits, all 7 already present in lahti.bib (Yeo2026 iScience-obesity, Zhang2026, Karikka2026, Vargas2026 Joint-RPCA, Manzoor2026, Lindgren2026 enterosignatures, Koistinen2026)
• No open bib-candidates issue from the "Find new publications" GitHub Action
• DOI 10.64898/2026.07.03.26357002 (Lindgren2026allergic) is already proposed in open PR bib-monitor: 1 new publication(s) 2026-09-27 #331 from a bib-monitor/ branch, so it was not re-proposed here

This sandbox's network egress policy blocks ORCID, Crossref, the DOI resolver, bioRxiv and arXiv directly, so PubMed and email were the only sources checked here as intended; the daily GitHub Action covers ORCID/Crossref/arXiv separately.

After merging, run publication-list.sh locally to refresh the Seafile list.

🤖 Generated with Claude Code

https://claude.ai/code/session_01KGZ3au9N8Cut6so2heA8pK

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