{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T12:49:56Z","timestamp":1792586996275,"version":"4.5.0"},"reference-count":139,"publisher":"American Association for the Advancement of Science (AAAS)","issue":"6704","content-domain":{"domain":["www.science.org"],"crossmark-restriction":true},"short-container-title":["Science"],"published-print":{"date-parts":[[2024,7,5]]},"abstract":"<jats:p>\n                    Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5\u2032 single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of coding and noncoding RNAs in human CD4\n                    <jats:sup>+<\/jats:sup>\n                    T cells, revealing cellular heterogeneity and differentiation trajectories. Integration of these datasets with single-cell chromatin profiles showed that active enhancers with bidirectional RNA transcription are highly cell type\u2013specific and that disease heritability is strongly enriched in these enhancers. The resulting cell type\u2013resolved multimodal atlas of bidirectionally transcribed enhancers, which we linked with promoters using fine-scale chromatin contact maps, enabled us to systematically interpret genetic variants associated with a range of immune-mediated diseases.\n                  <\/jats:p>","DOI":"10.1126\/science.add8394","type":"journal-article","created":{"date-parts":[[2024,7,4]],"date-time":"2024-07-04T13:59:47Z","timestamp":1720101587000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":37,"title":["An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases"],"prefix":"10.1126","volume":"385","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9948-6295","authenticated-orcid":true,"given":"Akiko","family":"Oguchi","sequence":"first","affiliation":[{"name":"RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."},{"name":"Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5343-3681","authenticated-orcid":true,"given":"Akari","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8082-6301","authenticated-orcid":true,"given":"Shuichiro","family":"Komatsu","sequence":"additional","affiliation":[{"name":"RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7339-9030","authenticated-orcid":true,"given":"Hiroyuki","family":"Yoshitomi","sequence":"additional","affiliation":[{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."},{"name":"Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shruti","family":"Bhagat","sequence":"additional","affiliation":[{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9250-9474","authenticated-orcid":true,"given":"Raku","family":"Son","sequence":"additional","affiliation":[{"name":"RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."},{"name":"Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2123-6536","authenticated-orcid":true,"given":"Raoul Jean Pierre","family":"Bonnal","sequence":"additional","affiliation":[{"name":"IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6764-4818","authenticated-orcid":true,"given":"Shohei","family":"Kojima","sequence":"additional","affiliation":[{"name":"Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0348-0666","authenticated-orcid":true,"given":"Masaru","family":"Koido","sequence":"additional","affiliation":[{"name":"Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan."},{"name":"Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan."},{"name":"Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1646-9167","authenticated-orcid":true,"given":"Kazuhiro","family":"Takeuchi","sequence":"additional","affiliation":[{"name":"RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."},{"name":"Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keiko","family":"Myouzen","sequence":"additional","affiliation":[{"name":"Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gyo","family":"Inoue","sequence":"additional","affiliation":[{"name":"Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomoya","family":"Hirai","sequence":"additional","affiliation":[{"name":"RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiromi","family":"Sano","sequence":"additional","affiliation":[{"name":"RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujiro","family":"Takegami","sequence":"additional","affiliation":[{"name":"K.K. DNAFORM, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ai","family":"Kanemaru","sequence":"additional","affiliation":[{"name":"K.K. DNAFORM, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Itaru","family":"Yamaguchi","sequence":"additional","affiliation":[{"name":"K.K. DNAFORM, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6514-8239","authenticated-orcid":true,"given":"Yuki","family":"Ishikawa","sequence":"additional","affiliation":[{"name":"Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2085-4682","authenticated-orcid":true,"given":"Nao","family":"Tanaka","sequence":"additional","affiliation":[{"name":"Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6684-9432","authenticated-orcid":true,"given":"Shigeki","family":"Hirabayashi","sequence":"additional","affiliation":[{"name":"RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan."},{"name":"Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2457-5824","authenticated-orcid":true,"given":"Riyo","family":"Konishi","sequence":"additional","affiliation":[{"name":"Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7918-2403","authenticated-orcid":true,"given":"Sho","family":"Sekito","sequence":"additional","affiliation":[{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."},{"name":"Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8586-784X","authenticated-orcid":true,"given":"Takahiro","family":"Inoue","sequence":"additional","affiliation":[{"name":"Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1974-0271","authenticated-orcid":true,"given":"Juha","family":"Kere","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden."},{"name":"Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland."},{"name":"Folkhalsan Research Center, Helsinki, Finland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shunichi","family":"Takeda","sequence":"additional","affiliation":[{"name":"Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan."},{"name":"Shenzhen University School of Medicine, Shenzhen, Guangdong, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7678-4284","authenticated-orcid":true,"given":"Akifumi","family":"Takaori-Kondo","sequence":"additional","affiliation":[{"name":"Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5520-8114","authenticated-orcid":true,"given":"Itaru","family":"Endo","sequence":"additional","affiliation":[{"name":"Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4064-6781","authenticated-orcid":true,"given":"Shinpei","family":"Kawaoka","sequence":"additional","affiliation":[{"name":"Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan."},{"name":"Department of Integrative Bioanalytics, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0575-0308","authenticated-orcid":true,"given":"Hideya","family":"Kawaji","sequence":"additional","affiliation":[{"name":"Research Center for Genome &amp; Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan."},{"name":"Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Science, Yokohama, Japan."},{"name":"RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2881-0657","authenticated-orcid":true,"given":"Kazuyoshi","family":"Ishigaki","sequence":"additional","affiliation":[{"name":"Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7747-0738","authenticated-orcid":true,"given":"Hideki","family":"Ueno","sequence":"additional","affiliation":[{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."},{"name":"Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0561-2802","authenticated-orcid":true,"given":"Yoshihide","family":"Hayashizaki","sequence":"additional","affiliation":[{"name":"K.K. DNAFORM, Yokohama, Japan."},{"name":"RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7017-9304","authenticated-orcid":true,"given":"Massimiliano","family":"Pagani","sequence":"additional","affiliation":[{"name":"IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy."},{"name":"Department of Medical Biotechnology and Translational Medicine, Universit\u00e0 degli Studi, Milan, Italy."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7202-7243","authenticated-orcid":true,"given":"Piero","family":"Carninci","sequence":"additional","affiliation":[{"name":"Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"Human Technopole, Milan, Italy."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0339-9008","authenticated-orcid":true,"given":"Motoko","family":"Yanagita","sequence":"additional","affiliation":[{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."},{"name":"Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"ITEC Consortium\u2021","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6971-8016","authenticated-orcid":true,"given":"Nicholas","family":"Parrish","sequence":"additional","affiliation":[{"name":"Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6452-4095","authenticated-orcid":true,"given":"Chikashi","family":"Terao","sequence":"additional","affiliation":[{"name":"Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan."},{"name":"Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9037-3625","authenticated-orcid":true,"given":"Kazuhiko","family":"Yamamoto","sequence":"additional","affiliation":[{"name":"Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5415-1352","authenticated-orcid":true,"given":"Yasuhiro","family":"Murakawa","sequence":"additional","affiliation":[{"name":"RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan."},{"name":"Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan."},{"name":"IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy."},{"name":"Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matteo","family":"Guerrini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroaki","family":"Hatano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuyoshi","family":"Ishigaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuki","family":"Ishikawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuichiro","family":"Komatsu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michihiro","family":"Kono","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasuhiro","family":"Murakawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiro","family":"Nakano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akiko","family":"Oguchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raku","family":"Son","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akari","family":"Suzuki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiro","family":"Takeuchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nao","family":"Tanaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chikashi","family":"Terao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kohei","family":"Tomizuka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiko","family":"Yamamoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soichiro","family":"Yoshino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature14248"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2493-4"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2015.11.004"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11232"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03604-1"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.10.024"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.adf7044"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1016071107"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1229386"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0485-9"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature12787"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1259418"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature09033"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-020-0446-0"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3329"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.225755.117"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-017-0447-5"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0234-5"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1101\/gad.308619.117"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-020-0686-2"},{"key":"e_1_3_3_22_2","doi-asserted-by":"crossref","unstructured":"S. C. Biddie G. Weykopf E. F. Hird E. T. Friman W. A. Bickmore DNA-binding factor footprints and enhancer RNAs identify functional non- coding genetic variants bioRxiv 2023.11.20.567860 [Preprint] (2023); https:\/\/doi.org\/10.1101\/2023.11.20.567860.10.1101\/2023.11.20.567860","DOI":"10.1101\/2023.11.20.567860"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2018.01.007"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1207-1"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/nri3158"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aan6828"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2019.01.001"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-022-01066-3"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abo0510"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12464-3"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15543-y"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aay3224"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-021-00933-1"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abe6474"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl5197"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.abm2508"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature20810"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-03145-z"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2020.00424"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature09906"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1222794"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature13835"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03766-z"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aay0793"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2559-3"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4380"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac644"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-42636-1"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad049"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1128"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0014-2"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1093\/dnares\/11.4.305"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01815-7"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature13182"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng1789"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.6831208"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-1670-6"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv054"},{"key":"e_1_3_3_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.03.056"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0414-6"},{"key":"e_1_3_3_61_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0591-3"},{"key":"e_1_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.1038\/nri3790"},{"key":"e_1_3_3_63_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2667"},{"key":"e_1_3_3_64_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1907883116"},{"key":"e_1_3_3_65_2","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abe3348"},{"key":"e_1_3_3_66_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.10.001"},{"key":"e_1_3_3_67_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-022-01056-5"},{"key":"e_1_3_3_68_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41551-022-00961-8"},{"key":"e_1_3_3_69_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.05.048"},{"key":"e_1_3_3_70_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.03.003"},{"key":"e_1_3_3_71_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.03.002"},{"key":"e_1_3_3_72_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-023-01442-7"},{"key":"e_1_3_3_73_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03639-4"},{"key":"e_1_3_3_74_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-023-01391-1"},{"key":"e_1_3_3_75_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3211"},{"key":"e_1_3_3_76_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3404"},{"key":"e_1_3_3_77_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03767-x"},{"key":"e_1_3_3_78_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0538-0"},{"key":"e_1_3_3_79_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03446-x"},{"key":"e_1_3_3_80_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.adh7699"},{"key":"e_1_3_3_81_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.11.029"},{"key":"e_1_3_3_82_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1933104"},{"key":"e_1_3_3_83_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10525-1"},{"key":"e_1_3_3_84_2","doi-asserted-by":"publisher","DOI":"10.1002\/med.21601"},{"key":"e_1_3_3_85_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2296-7"},{"key":"e_1_3_3_86_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14049"},{"key":"e_1_3_3_87_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01767-y"},{"key":"e_1_3_3_88_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01282-5"},{"key":"e_1_3_3_89_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"e_1_3_3_90_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"e_1_3_3_91_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.11.021"},{"key":"e_1_3_3_92_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02167-0"},{"key":"e_1_3_3_93_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv201"},{"key":"e_1_3_3_94_2","unstructured":"MurakawaLab \/ ReapTEC First release of ReapTEC pipeline (2024); 10.5281\/zenodo.10972341"},{"key":"e_1_3_3_95_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-1597-3"},{"key":"e_1_3_3_96_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-0805-9_7"},{"key":"e_1_3_3_97_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2021.04.019"},{"key":"e_1_3_3_98_2","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.73600.2"},{"key":"e_1_3_3_99_2","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa151"},{"key":"e_1_3_3_100_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0619-0"},{"key":"e_1_3_3_101_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.135350.111"},{"key":"e_1_3_3_102_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_3_103_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.209601.116"},{"key":"e_1_3_3_104_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq351"},{"key":"e_1_3_3_105_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1910-1"},{"key":"e_1_3_3_106_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_3_107_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp616"},{"key":"e_1_3_3_108_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11247"},{"key":"e_1_3_3_109_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku365"},{"key":"e_1_3_3_110_2","unstructured":"H. Li Aligning sequence reads clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio.GN] (2013)."},{"key":"e_1_3_3_111_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-021-04408-w"},{"key":"e_1_3_3_112_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0992-2"},{"key":"e_1_3_3_113_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0160-6"},{"key":"e_1_3_3_114_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1808850115"},{"key":"e_1_3_3_115_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature15393"},{"key":"e_1_3_3_116_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0121-0"},{"key":"e_1_3_3_117_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15649-3"},{"key":"e_1_3_3_118_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3359"},{"key":"e_1_3_3_119_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12760-y"},{"key":"e_1_3_3_120_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03552-w"},{"key":"e_1_3_3_121_2","doi-asserted-by":"publisher","DOI":"10.15252\/embr.201846255"},{"key":"e_1_3_3_122_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac199"},{"key":"e_1_3_3_123_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr064"},{"key":"e_1_3_3_124_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1113"},{"key":"e_1_3_3_125_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv416"},{"key":"e_1_3_3_126_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.3715005"},{"key":"e_1_3_3_127_2","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0410s25"},{"key":"e_1_3_3_128_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1272"},{"key":"e_1_3_3_129_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2021.100081"},{"key":"e_1_3_3_130_2","doi-asserted-by":"publisher","DOI":"10.1006\/geno.1996.0567"},{"key":"e_1_3_3_131_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00281-021-00886-5"},{"key":"e_1_3_3_132_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(94)90802-8"},{"key":"e_1_3_3_133_2","doi-asserted-by":"publisher","DOI":"10.2144\/01304pf02"},{"key":"e_1_3_3_134_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1470"},{"key":"e_1_3_3_135_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-08126-5"},{"key":"e_1_3_3_136_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.05.002"},{"key":"e_1_3_3_137_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.04.044"},{"key":"e_1_3_3_138_2","doi-asserted-by":"publisher","DOI":"10.1038\/266235a0"},{"key":"e_1_3_3_139_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3947"},{"key":"e_1_3_3_140_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-020-0844-1"}],"container-title":["Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.science.org\/doi\/pdf\/10.1126\/science.add8394","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,4]],"date-time":"2024-07-04T14:01:24Z","timestamp":1720101684000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.science.org\/doi\/10.1126\/science.add8394"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,5]]},"references-count":139,"journal-issue":{"issue":"6704","published-print":{"date-parts":[[2024,7,5]]}},"alternative-id":["10.1126\/science.add8394"],"URL":"https:\/\/doi.org\/10.1126\/science.add8394","relation":{},"ISSN":["0036-8075","1095-9203"],"issn-type":[{"value":"0036-8075","type":"print"},{"value":"1095-9203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,5]]},"assertion":[{"value":"2022-07-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-01","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-07-05","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"eadd8394"}}