{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T18:41:13Z","timestamp":1774550473856,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T00:00:00Z","timestamp":1749427200000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["OT2 OD032742"],"award-info":[{"award-number":["OT2 OD032742"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Cells are organized as a hierarchy of macromolecular assemblies, ranging from small protein complexes to entire organelles. Various technologies have been developed to elucidate subcellular architecture at different scales, such as mass spectrometry approaches for mapping protein biophysical interactions and immunofluorescence imaging for mapping protein localization. We present the Cell Mapping Toolkit, which is designed to systematically integrate data from different modalities into unified hierarchical maps of subcellular organization. The toolkit facilitates an end-to-end pipeline including processing datasets, integrating modalities, and visualizing the final cell map with rich metadata including provenance documentation at each step. The Cell Mapping Toolkit provides researchers with tools for analyzing, integrating, and visualizing diverse protein datasets in a robust and reproducible framework.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code is freely available and is hosted on GitHub at https:\/\/github.com\/idekerlab\/cellmaps_pipeline. Comprehensive documentation and practical examples are provided at https:\/\/cellmaps-pipeline.readthedocs.io\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf205","type":"journal-article","created":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T19:09:46Z","timestamp":1749496186000},"source":"Crossref","is-referenced-by-count":1,"title":["Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization"],"prefix":"10.1093","volume":"41","author":[{"given":"Joanna","family":"Lenkiewicz","sequence":"first","affiliation":[{"name":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","place":["United States"]}]},{"given":"Christopher","family":"Churas","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","place":["United 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Charlottesville, VA, 22903,","place":["United States"]},{"name":"Center for Advanced Medical Analytics, University of Virginia School of Medicine , Charlottesville, VA, 22903,","place":["United States"]},{"name":"University of Virginia School of Data Science , Charlottesville, VA, 22903,","place":["United States"]}]},{"given":"Trey","family":"Ideker","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","place":["United States"]},{"name":"Department of Computer Science and Engineering, University of California San Diego , La Jolla, CA, 92037,","place":["United States"]},{"name":"Department of Bioengineering, University of California San Diego , La Jolla, CA, 92037,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6339-9141","authenticated-orcid":false,"given":"Leah V","family":"Schaffer","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San 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