{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T15:33:45Z","timestamp":1770219225124,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T00:00:00Z","timestamp":1767744000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Albert L Williams Professorship funds and the National Institutes of Health","award":["R01DA063148"],"award-info":[{"award-number":["R01DA063148"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Despite significant advances in spatial transcriptomics, the analysis of formalin-fixed paraffin-embedded (FFPE) tissues, which constitute most clinically available samples, remains challenging. Additionally, capturing both coding and non-coding RNAs in a spatial context poses significant challenges. We recently introduced Patho-DBiT, a technology designed to address these unmet needs. However, the marked differences between Patho-DBiT and existing spatial transcriptomics protocols necessitate specialized computational tools for comprehensive whole-transcriptome analysis in FFPE samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present ASTRO, an automated pipeline developed to process spatial transcriptomics data. In addition to supporting standard datasets, ASTRO is optimized for whole-transcriptome analyses of FFPE samples, enabling the detection of various RNA species, including non-coding RNAs such as miRNAs. To compensate for the reduced RNA quality in FFPE tissues, ASTRO incorporates a specialized filtering step and optimizes spatial barcode calling, increasing the mapping rate. These optimizations allow ASTRO to spatially quantify coding and non-coding RNA species in the entire transcriptome and achieve robust performance in FFPE samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Codes are available at GitHub (https:\/\/github.com\/gersteinlab\/ASTRO) and Zenodo (doi: 10.5281\/zenodo.17913760).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf688","type":"journal-article","created":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T12:30:15Z","timestamp":1767357015000},"source":"Crossref","is-referenced-by-count":0,"title":["ASTRO: Automated Spatial-Transcriptome whole RNA Output"],"prefix":"10.1093","volume":"42","author":[{"given":"Dingyao","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Genetics, Yale School of Medicine , New Haven, CT 06520,","place":["United 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, New Haven, CT 06520,","place":["United States"]},{"name":"Yale Stem Cell Center, Yale School of Medicine , New Haven, CT 06520,","place":["United States"]},{"name":"Yale Cancer Center and Yale Center for RNA Science and Medicine, Yale School of Medicine , New Haven, CT 06520,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2726-7613","authenticated-orcid":false,"given":"Jun","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Genetics, Yale School of Medicine , New Haven, CT 06520,","place":["United States"]},{"name":"Yale Stem Cell Center, Yale School of Medicine , New Haven, CT 06520,","place":["United States"]},{"name":"Yale Cooperative Center of Excellence in Hematology, Yale School of Medicine , New Haven, CT 06520,","place":["United States"]},{"name":"Yale Cancer Center and Yale Center for RNA Science and Medicine, Yale School of Medicine , New Haven, CT 06520,","place":["United 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