{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T15:59:30Z","timestamp":1785340770059,"version":"3.55.0"},"publisher-location":"New York, NY, USA","reference-count":27,"publisher":"ACM","license":[{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2026,6,30]]},"DOI":"10.1145\/3807503.3819485","type":"proceedings-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T02:55:27Z","timestamp":1785293727000},"page":"1-10","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Cross-batch concordant clustering for comprehensive single-cell transcriptomic stratification"],"prefix":"10.1145","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-3707-1965","authenticated-orcid":false,"given":"Jiayu","family":"Zhao","sequence":"first","affiliation":[{"name":"Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6379-9759","authenticated-orcid":false,"given":"Xinzhu","family":"Jiang","sequence":"additional","affiliation":[{"name":"Global College, Shanghai Jiao Tong University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7294-7160","authenticated-orcid":false,"given":"Chongxiao","family":"Mao","sequence":"additional","affiliation":[{"name":"Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2864-7386","authenticated-orcid":false,"given":"Hongyi","family":"Xin","sequence":"additional","affiliation":[{"name":"Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"320","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"e_1_3_3_2_2_2","doi-asserted-by":"publisher","unstructured":"David\u00a0J. Ahern Zhichao Ai Mark Ainsworth Chris Allan Alice Allcock Zixi Angus Rebecca\u00a0K. Young Jonathan Youngs Ping Zhang and Yasemin-Xiomara Zurke. 2022. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell 185 5 (March 2022) 916\u2013938.e58. 10.1016\/j.cell.2022.01.012","DOI":"10.1016\/j.cell.2022.01.012"},{"key":"e_1_3_3_2_3_2","doi-asserted-by":"publisher","unstructured":"Vincent\u00a0D Blondel Jean-Loup Guillaume Renaud Lambiotte and Etienne Lefebvre. 2008. Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment 2008 10 (Oct. 2008) P10008. 10.1088\/1742-5468\/2008\/10\/p10008","DOI":"10.1088\/1742-5468\/2008\/10\/p10008"},{"key":"e_1_3_3_2_4_2","doi-asserted-by":"publisher","unstructured":"Andrew Butler Paul Hoffman Peter Smibert Efthymia Papalexi and Rahul Satija. 2018. Integrating single-cell transcriptomic data across different conditions technologies and species. Nature Biotechnology 36 5 (April 2018) 411\u2013420. 10.1038\/nbt.4096","DOI":"10.1038\/nbt.4096"},{"key":"e_1_3_3_2_5_2","unstructured":"Cmu G.\u00a0Ayorkor Mills-Tettey Anthony Stentz M.\u00a0Bernardine Dias G. Ayorkor Mills-Tettey Anthony and Stentz M.\u00a0Bernardine Dias. 2007. The Dynamic Hungarian Algorithm for the Assignment Problem with Changing Costs. https:\/\/api.semanticscholar.org\/CorpusID:10791376"},{"key":"e_1_3_3_2_6_2","doi-asserted-by":"publisher","unstructured":"Yuhan Hao Stephanie Hao Erica Andersen-Nissen William\u00a0M. Mauck Shiwei Zheng Andrew Butler Maddie\u00a0J. Lee Aaron\u00a0J. Wilk Charlotte Darby Michael Zager Paul Hoffman Marlon Stoeckius Efthymia Papalexi Eleni\u00a0P. Mimitou Jaison Jain Avi Srivastava Tim Stuart Lamar\u00a0M. Fleming Bertrand Yeung Angela\u00a0J. Rogers Juliana\u00a0M. McElrath Catherine\u00a0A. Blish Raphael Gottardo Peter Smibert and Rahul Satija. 2021. Integrated analysis of multimodal single-cell data. Cell 184 13 (June 2021) 3573\u20133587.e29. 10.1016\/j.cell.2021.04.048","DOI":"10.1016\/j.cell.2021.04.048"},{"key":"e_1_3_3_2_7_2","doi-asserted-by":"crossref","unstructured":"Lawrence Hubert and Phipps Arabie. 1985. Comparing partitions. Journal of Classification 2 1 (1985) 193\u2013218.","DOI":"10.1007\/BF01908075"},{"key":"e_1_3_3_2_8_2","doi-asserted-by":"publisher","unstructured":"Bridget\u00a0P. Keenan Elizabeth\u00a0E. McCarthy Arielle Ilano Hai Yang Li Zhang Kathryn Allaire Zenghua Fan Tony Li David\u00a0S. Lee Yang Sun Alexander Cheung Diamond Luong Hewitt Chang Brandon Chen Jaqueline Marquez Brenna Sheldon Robin\u00a0K. Kelley Chun\u00a0Jimmie Ye and Lawrence Fong. 2022. Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis. Cell Reports 40 12 (Sept. 2022) 111384. 10.1016\/j.celrep.2022.111384","DOI":"10.1016\/j.celrep.2022.111384"},{"key":"e_1_3_3_2_9_2","doi-asserted-by":"crossref","unstructured":"Ilya Korsunsky Nghia Millard Jean Fan Kamil Slowikowski Fan Zhang Kevin Wei Yuriy Baglaenko Michael Brenner Po-ru Loh and Soumya Raychaudhuri. 2019. Fast sensitive and accurate integration of single-cell data with Harmony. Nature methods 16 12 (2019) 1289\u20131296.","DOI":"10.1038\/s41592-019-0619-0"},{"key":"e_1_3_3_2_10_2","doi-asserted-by":"publisher","unstructured":"Gang Li Yuchen Yang Eric Van\u00a0Buren and Yun Li. 2019. Dropout imputation and batch effect correction for single-cell RNA sequencing data. Journal of Bio-X Research 02 04 (Dec. 2019) 169\u2013177. 10.1097\/jbr.0000000000000053","DOI":"10.1097\/jbr.0000000000000053"},{"key":"e_1_3_3_2_11_2","doi-asserted-by":"crossref","unstructured":"Romain Lopez Jeffrey Regier Michael\u00a0B Cole Michael\u00a0I Jordan and Nir Yosef. 2018. Deep generative modeling for single-cell transcriptomics. Nature methods 15 12 (2018) 1053\u20131058.","DOI":"10.1038\/s41592-018-0229-2"},{"key":"e_1_3_3_2_12_2","doi-asserted-by":"publisher","unstructured":"Malte\u00a0D. Luecken M. B\u00fcttner K. Chaichoompu A. Danese M. Interlandi M.\u00a0F. Mueller D.\u00a0C. Strobl L. Zappia M. Dugas M. Colom\u00e9-Tatch\u00e9 and Fabian\u00a0J. Theis. 2021. Benchmarking atlas-level data integration in single-cell genomics. Nature Methods 19 1 (Dec. 2021) 41\u201350. 10.1038\/s41592-021-01336-8","DOI":"10.1038\/s41592-021-01336-8"},{"key":"e_1_3_3_2_13_2","doi-asserted-by":"publisher","unstructured":"Malte\u00a0D Luecken and Fabian\u00a0J Theis. 2019. Current best practices in single\u2010cell RNA\u2010seq analysis: a tutorial. Molecular Systems Biology 15 6 (June 2019). 10.15252\/msb.20188746","DOI":"10.15252\/msb.20188746"},{"key":"e_1_3_3_2_14_2","doi-asserted-by":"publisher","unstructured":"Lieke Michielsen Mohammad Lotfollahi Daniel Strobl Lisa Sikkema Marcel J\u00a0T Reinders Fabian\u00a0J Theis and Ahmed Mahfouz. 2023. Single-cell reference mapping to construct and extend cell-type hierarchies. NAR Genomics and Bioinformatics 5 3 (July 2023). 10.1093\/nargab\/lqad070","DOI":"10.1093\/nargab\/lqad070"},{"key":"e_1_3_3_2_15_2","doi-asserted-by":"publisher","unstructured":"Lieke Michielsen Marcel J.\u00a0T. Reinders and Ahmed Mahfouz. 2021. Hierarchical progressive learning of cell identities in single-cell data. Nature Communications 12 1 (May 2021). 10.1038\/s41467-021-23196-8","DOI":"10.1038\/s41467-021-23196-8"},{"key":"e_1_3_3_2_16_2","doi-asserted-by":"crossref","unstructured":"Krzysztof Pola\u0144ski Matthew\u00a0D Young Zhichao Miao Kerstin\u00a0B Meyer Sarah\u00a0A Teichmann and Jong-Eun Park. 2020. BBKNN: fast batch alignment of single cell transcriptomes. Bioinformatics 36 3 (2020) 964\u2013965.","DOI":"10.1093\/bioinformatics\/btz625"},{"key":"e_1_3_3_2_17_2","doi-asserted-by":"publisher","unstructured":"Aviv Regev Sarah\u00a0A Teichmann Eric\u00a0S Lander Ido Amit Christophe Benoist Ewan Birney Bernd Bodenmiller Peter Campbell Piero Carninci Menna Clatworthy Michael Clevers Michael J\u00a0T Stubbington Fabian\u00a0J Theis Matthias Uhlen Alexander van Oudenaarden Allon Wagner Fiona Watt Jonathan Weissman Barbara Wold Ramnik Xavier and Nir Yosef. 2017. The Human Cell Atlas. eLife 6 (Dec. 2017). 10.7554\/elife.27041","DOI":"10.7554\/elife.27041"},{"key":"e_1_3_3_2_18_2","doi-asserted-by":"publisher","unstructured":"Orit Rozenblatt-Rosen Michael J.\u00a0T. Stubbington Aviv Regev and Sarah\u00a0A. Teichmann. 2017. The Human Cell Atlas: from vision to reality. Nature 550 7677 (Oct. 2017) 451\u2013453. 10.1038\/550451a","DOI":"10.1038\/550451a"},{"key":"e_1_3_3_2_19_2","doi-asserted-by":"publisher","unstructured":"Rahul Satija Jeffrey\u00a0A Farrell David Gennert Alexander\u00a0F Schier and Aviv Regev. 2015. Spatial reconstruction of single-cell gene expression data. Nature Biotechnology 33 5 (April 2015) 495\u2013502. 10.1038\/nbt.3192","DOI":"10.1038\/nbt.3192"},{"key":"e_1_3_3_2_20_2","unstructured":"Alexander Strehl and Joydeep Ghosh. 2002. Cluster ensembles\u2014a knowledge reuse framework for combining multiple partitions. Journal of Machine Learning Research 3 Dec (2002) 583\u2013617."},{"key":"e_1_3_3_2_21_2","doi-asserted-by":"publisher","unstructured":"Tim Stuart Andrew Butler Paul Hoffman Christoph Hafemeister Efthymia Papalexi William\u00a0M. Mauck Yuhan Hao Marlon Stoeckius Peter Smibert and Rahul Satija. 2019. Comprehensive Integration of Single-Cell Data. Cell 177 7 (June 2019) 1888\u20131902.e21. 10.1016\/j.cell.2019.05.031","DOI":"10.1016\/j.cell.2019.05.031"},{"key":"e_1_3_3_2_22_2","doi-asserted-by":"publisher","unstructured":"V.\u00a0A. Traag L. Waltman and N.\u00a0J. van Eck. 2019. From Louvain to Leiden: guaranteeing well-connected communities. Scientific Reports 9 1 (March 2019). 10.1038\/s41598-019-41695-z","DOI":"10.1038\/s41598-019-41695-z"},{"key":"e_1_3_3_2_23_2","doi-asserted-by":"publisher","unstructured":"Alexandra-Chlo\u00e9 Villani Rahul Satija Gary Reynolds Siranush Sarkizova Karthik Shekhar James Fletcher Morgane Griesbeck Andrew Butler Shiwei Zheng Suzan Lazo Laura Jardine David Dixon Emily Stephenson Emil Nilsson Ida Grundberg David McDonald Andrew Filby Weibo Li Philip\u00a0L. De\u00a0Jager Orit Rozenblatt-Rosen Andrew\u00a0A. Lane Muzlifah Haniffa Aviv Regev and Nir Hacohen. 2017. Single-cell RNA-seq reveals new types of human blood dendritic cells monocytes and progenitors. Science 356 6335 (April 2017). 10.1126\/science.aah4573","DOI":"10.1126\/science.aah4573"},{"key":"e_1_3_3_2_24_2","unstructured":"Nguyen\u00a0Xuan Vinh Julien Epps and James Bailey. 2010. Information theoretic measures for clusterings comparison: Variants properties normalization and correction for chance. Journal of Machine Learning Research 11 Oct (2010) 2837\u20132854."},{"key":"e_1_3_3_2_25_2","doi-asserted-by":"publisher","unstructured":"Allon Wagner Aviv Regev and Nir Yosef. 2016. Revealing the vectors of cellular identity with single-cell genomics. Nature Biotechnology 34 11 (Nov. 2016) 1145\u20131160. 10.1038\/nbt.3711","DOI":"10.1038\/nbt.3711"},{"key":"e_1_3_3_2_26_2","doi-asserted-by":"publisher","unstructured":"Chuan Xu Martin Prete Simone Webb Laura Jardine Benjamin\u00a0J. Stewart Regina Hoo Peng He Kerstin\u00a0B. Meyer and Sarah\u00a0A. Teichmann. 2023. Automatic cell-type harmonization and integration across Human Cell Atlas datasets. Cell 186 26 (Dec. 2023) 5876\u20135891.e20. 10.1016\/j.cell.2023.11.026","DOI":"10.1016\/j.cell.2023.11.026"},{"key":"e_1_3_3_2_27_2","doi-asserted-by":"publisher","unstructured":"Yun Zhang Brian\u00a0D Aevermann Trygve\u00a0E Bakken Jeremy\u00a0A Miller Rebecca\u00a0D Hodge Ed\u00a0S Lein and Richard\u00a0H Scheuermann. 2020. FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman\u2013Rafsky non-parametric test. Briefings in Bioinformatics 22 4 (Nov. 2020). 10.1093\/bib\/bbaa339","DOI":"10.1093\/bib\/bbaa339"},{"key":"e_1_3_3_2_28_2","doi-asserted-by":"publisher","unstructured":"Yiliang Zhang Kexuan Liang Molei Liu Yue Li Hao Ge and Hongyu Zhao. 2019. SCRIBE: a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data. (Oct. 2019). 10.1101\/793463","DOI":"10.1101\/793463"}],"event":{"name":"BCB '26: 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","location":"Rende (CS) Italy","acronym":"BCB '26","sponsor":["SIGBio ACM Special Interest Group on Bioinformatics"]},"container-title":["Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3807503.3819485","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T15:14:53Z","timestamp":1785338093000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3807503.3819485"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,30]]},"references-count":27,"alternative-id":["10.1145\/3807503.3819485","10.1145\/3807503"],"URL":"https:\/\/doi.org\/10.1145\/3807503.3819485","relation":{},"subject":[],"published":{"date-parts":[[2026,6,30]]},"assertion":[{"value":"2026-07-28","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}